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Sample records for thermophilic microbial community

  1. Screening of complex thermophilic microbial community and ...

    African Journals Online (AJOL)

    Screening of complex thermophilic microbial community and application during municipal solid waste aerobic composting. ... African Journal of Biotechnology ... Complex microbial community HP83 and HC181 were applied during municipal solid waste aerobic composting that was carried out in a composting reactor under ...

  2. Rapid establishment of thermophilic anaerobic microbial community during the one-step startup of thermophilic anaerobic digestion from a mesophilic digester.

    Science.gov (United States)

    Tian, Zhe; Zhang, Yu; Li, Yuyou; Chi, Yongzhi; Yang, Min

    2015-02-01

    The purpose of this study was to explore how fast the thermophilic anaerobic microbial community could be established during the one-step startup of thermophilic anaerobic digestion from a mesophilic digester. Stable thermophilic anaerobic digestion was achieved within 20 days from a mesophilic digester treating sewage sludge by adopting the one-step startup strategy. The succession of archaeal and bacterial populations over a period of 60 days after the temperature increment was followed by using 454-pyrosequencing and quantitative PCR. After the increase of temperature, thermophilic methanogenic community was established within 11 days, which was characterized by the fast colonization of Methanosarcina thermophila and two hydrogenotrophic methanogens (Methanothermobacter spp. and Methanoculleus spp.). At the same time, the bacterial community was dominated by Fervidobacterium, whose relative abundance rapidly increased from 0 to 28.52 % in 18 days, followed by other potential thermophilic genera, such as Clostridium, Coprothermobacter, Anaerobaculum and EM3. The above result demonstrated that the one-step startup strategy could allow the rapid establishment of the thermophilic anaerobic microbial community. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. High-solids enrichment of thermophilic microbial communities and their enzymes on bioenergy feedstocks

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, A. P.; Allgaier, M.; Singer, S.W.; Hazen, T.C.; Simmons, B.A.; Hugenholtz, P.; VanderGheynst, J.S.

    2011-04-01

    Thermophilic microbial communities that are active in a high-solids environment offer great potential for the discovery of industrially relevant enzymes that efficiently deconstruct bioenergy feedstocks. In this study, finished green waste compost was used as an inoculum source to enrich microbial communities and associated enzymes that hydrolyze cellulose and hemicellulose during thermophilic high-solids fermentation of the bioenergy feedstocks switchgrass and corn stover. Methods involving the disruption of enzyme and plant cell wall polysaccharide interactions were developed to recover xylanase and endoglucanase activity from deconstructed solids. Xylanase and endoglucanase activity increased by more than a factor of 5, upon four successive enrichments on switchgrass. Overall, the changes for switchgrass were more pronounced than for corn stover; solids reduction between the first and second enrichments increased by a factor of four for switchgrass while solids reduction remained relatively constant for corn stover. Amplicon pyrosequencing analysis of small-subunit ribosomal RNA genes recovered from enriched samples indicated rapid changes in the microbial communities between the first and second enrichment with the simplified communities achieved by the third enrichment. The results demonstrate a successful approach for enrichment of unique microbial communities and enzymes active in a thermophilic high-solids environment.

  4. Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions.

    Science.gov (United States)

    Yu, Chaowei; Reddy, Amitha P; Simmons, Christopher W; Simmons, Blake A; Singer, Steven W; VanderGheynst, Jean S

    2015-01-01

    Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methods included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. A stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and

  5. Comparing mesophilic and thermophilic anaerobic digestion of chicken manure: Microbial community dynamics and process resilience

    International Nuclear Information System (INIS)

    Niu, Qigui; Takemura, Yasuyuki; Kubota, Kengo; Li, Yu-You

    2015-01-01

    Highlights: • Microbial community dynamics and process functional resilience were investigated. • The threshold of TAN in mesophilic reactor was higher than the thermophilic reactor. • The recoverable archaeal community dynamic sustained the process resilience. • Methanosarcina was more sensitive than Methanoculleus on ammonia inhibition. • TAN and FA effects the dynamic of hydrolytic and acidogenic bacteria obviously. - Abstract: While methane fermentation is considered as the most successful bioenergy treatment for chicken manure, the relationship between operational performance and the dynamic transition of archaeal and bacterial communities remains poorly understood. Two continuous stirred-tank reactors were investigated under thermophilic and mesophilic conditions feeding with 10%TS. The tolerance of thermophilic reactor on total ammonia nitrogen (TAN) was found to be 8000 mg/L with free ammonia (FA) 2000 mg/L compared to 16,000 mg/L (FA1500 mg/L) of mesophilic reactor. Biomethane production was 0.29 L/gV S in in the steady stage and decreased following TAN increase. After serious inhibition, the mesophilic reactor was recovered successfully by dilution and washing stratagem compared to the unrecoverable of thermophilic reactor. The relationship between the microbial community structure, the bioreactor performance and inhibitors such as TAN, FA, and volatile fatty acid was evaluated by canonical correspondence analysis. The performance of methanogenic activity and substrate removal efficiency were changed significantly correlating with the community evenness and phylogenetic structure. The resilient archaeal community was found even after serious inhibition in both reactors. Obvious dynamics of bacterial communities were observed in acidogenic and hydrolytic functional bacteria following TAN variation in the different stages

  6. Comparing mesophilic and thermophilic anaerobic digestion of chicken manure: Microbial community dynamics and process resilience

    Energy Technology Data Exchange (ETDEWEB)

    Niu, Qigui; Takemura, Yasuyuki; Kubota, Kengo [Department of Civil and Environmental Engineering, Graduate School of Engineering Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 (Japan); Li, Yu-You, E-mail: yyli@epl1.civil.tohoku.ac.jp [Department of Civil and Environmental Engineering, Graduate School of Engineering Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 (Japan); Key Lab of Northwest Water Resource, Environment and Ecology, MOE, Xi’an University of Architecture and Technology, Xi’an (China)

    2015-09-15

    Highlights: • Microbial community dynamics and process functional resilience were investigated. • The threshold of TAN in mesophilic reactor was higher than the thermophilic reactor. • The recoverable archaeal community dynamic sustained the process resilience. • Methanosarcina was more sensitive than Methanoculleus on ammonia inhibition. • TAN and FA effects the dynamic of hydrolytic and acidogenic bacteria obviously. - Abstract: While methane fermentation is considered as the most successful bioenergy treatment for chicken manure, the relationship between operational performance and the dynamic transition of archaeal and bacterial communities remains poorly understood. Two continuous stirred-tank reactors were investigated under thermophilic and mesophilic conditions feeding with 10%TS. The tolerance of thermophilic reactor on total ammonia nitrogen (TAN) was found to be 8000 mg/L with free ammonia (FA) 2000 mg/L compared to 16,000 mg/L (FA1500 mg/L) of mesophilic reactor. Biomethane production was 0.29 L/gV S{sub in} in the steady stage and decreased following TAN increase. After serious inhibition, the mesophilic reactor was recovered successfully by dilution and washing stratagem compared to the unrecoverable of thermophilic reactor. The relationship between the microbial community structure, the bioreactor performance and inhibitors such as TAN, FA, and volatile fatty acid was evaluated by canonical correspondence analysis. The performance of methanogenic activity and substrate removal efficiency were changed significantly correlating with the community evenness and phylogenetic structure. The resilient archaeal community was found even after serious inhibition in both reactors. Obvious dynamics of bacterial communities were observed in acidogenic and hydrolytic functional bacteria following TAN variation in the different stages.

  7. Microbial community changes in methanogenic granules during the transition from mesophilic to thermophilic conditions

    DEFF Research Database (Denmark)

    Zhu, Xinyu; Kougias, Panagiotis; Treu, Laura

    2017-01-01

    Upflow anaerobic sludge blanket (UASB) reactor is one of the most applied technologies for various high-strength wastewater treatments. The present study analysed the microbial community changes in UASB granules during the transition from mesophilic to thermophilic conditions. Dynamicity...

  8. Microbial community dynamics in thermophilic undefined milk starter cultures.

    Science.gov (United States)

    Parente, Eugenio; Guidone, Angela; Matera, Attilio; De Filippis, Francesca; Mauriello, Gianluigi; Ricciardi, Annamaria

    2016-01-18

    Model undefined thermophilic starter cultures were produced from raw milk of nine pasta-filata cheesemaking plants using a selective procedure based on pasteurization and incubation at high temperature with the objective of studying the microbial community dynamics and the variability in performances under repeated (7-13) reproduction cycles with backslopping. The traditional culture-dependent approach, based on random isolation and molecular characterization of isolates was coupled to the determination of pH and the evaluation of the ability to produce acid and fermentation metabolites. Moreover, a culture-independent approach based on amplicon-targeted next-generation sequencing was employed. The microbial diversity was evaluated by 16S rRNA gene sequencing (V1-V3 regions), while the microdiversity of Streptococcus thermophilus populations was explored by using novel approach based on sequencing of partial amplicons of the phosphoserine phosphatase gene (serB). In addition, the occurrence of bacteriophages was evaluated by qPCR and by multiplex PCR. Although it was relatively easy to select for a community dominated by thermophilic lactic acid bacteria (LAB) within a single reproduction cycle, final pH, LAB populations and acid production activity fluctuated over reproduction cycles. Both culture-dependent and -independent methods showed that the cultures were dominated by either S. thermophilus or Lactobacillus delbrueckii subsp. lactis or by both species. Nevertheless, subdominant mesophilic species, including lactococci and spoilage organisms, persisted at low levels. A limited number of serB sequence types (ST) were present in S. thermophilus populations. L. delbrueckii and Lactococcus lactis bacteriophages were below the detection limit of the method used and high titres of cos type S. thermophilus bacteriophages were detected in only two cases. In one case a high titre of bacteriophages was concurrent with a S. thermophilus biotype shift in the culture

  9. The chemical properties and microbial community characterization of the thermophilic microaerobic pretreatment process.

    Science.gov (United States)

    Fu, Shan-Fei; He, Shuai; Shi, Xiao-Shuang; Katukuri, Naveen Reddy; Dai, Meng; Guo, Rong-Bo

    2015-12-01

    Thermophilic microaerobic pretreatment (TMP) was recently reported as an efficient pretreatment method of anaerobic digestion (AD). In this study, the chemical properties and microbial community were characterized to reveal how TMP working. Compared with thermophilic treatment under anaerobic condition (TMP0), cellulase activity obviously improved under microaerobic condition (TMP1), which was 10.9-49.0% higher than that of TMP0. Reducing sugar, SCOD and VFAs concentrations of TMP1 were 2.6-8.9%, 1.8-4.8% and 13.8-24% higher than those of TMP0, respectively. TMP gave obvious rise to phylum Firmicutes, which associated with extracellular enzymes production. The proportion of class Bacilli (belongs to phylum Firmicutes and mainly acts during hydrolysis) in TMP1 was 124.89% higher than that of TMP0, which reflected the greater hydrolytic ability under microaerobic condition. The improved abundance of phylum Firmicutes (especially class Bacilli, order Bacillales) under microaerobic condition could be the fundamental reason for the improved AD performance of thermophilic microaerobic pretreated corn straw. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors.

    Science.gov (United States)

    Pervin, Hasina M; Dennis, Paul G; Lim, Hui J; Tyson, Gene W; Batstone, Damien J; Bond, Philip L

    2013-12-01

    Temperature-phased anaerobic digestion (TPAD) is an emerging technology that facilitates improved performance and pathogen destruction in anaerobic sewage sludge digestion by optimising conditions for 1) hydrolytic and acidogenic organisms in a first-stage/pre-treatment reactor and then 2) methogenic populations in a second stage reactor. Pre-treatment reactors are typically operated at 55-65 °C and as such select for thermophilic bacterial communities. However, details of key microbial populations in hydrolytic communities and links to functionality are very limited. In this study, experimental thermophilic pre-treatment (TP) and control mesophilic pre-treatment (MP) reactors were operated as first-stages of TPAD systems treating activated sludge for 340 days. The TP system was operated sequentially at 50, 60 and 65 °C, while the MP rector was held at 35 °C for the entire period. The composition of microbial communities associated with the MP and TP pre-treatment reactors was characterised weekly using terminal-restriction fragment length polymorphism (T-RFLP) supported by clone library sequencing of 16S rRNA gene amplicons. The outcomes of this approach were confirmed using 454 pyrosequencing of gene amplicons and fluorescence in-situ hybridisation (FISH). TP associated bacterial communities were dominated by populations affiliated to the Firmicutes, Thermotogae, Proteobacteria and Chloroflexi. In particular there was a progression from Thermotogae to Lutispora and Coprothermobacter and diversity decreased as temperature and hydrolysis performance increased. While change in the composition of TP associated bacterial communities was attributable to temperature, that of MP associated bacterial communities was related to the composition of the incoming feed. This study determined processes driving the dynamics of key microbial populations that are correlated with an enhanced hydrolytic functionality of the TPAD system. Copyright © 2013 Elsevier Ltd. All rights

  11. Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities

    Energy Technology Data Exchange (ETDEWEB)

    Duncan, Kathleen E.; Gieg, Lisa M.; Parisi, Victoria A.; Tanner, Ralph S.; Green Tringe, Susannah; Bristow, Jim; Suflita, Joseph M.

    2009-09-16

    Corrosion of metallic oilfield pipelines by microorganisms is a costly but poorly understood phenomenon, with standard treatment methods targeting mesophilic sulfatereducing bacteria. In assessing biocorrosion potential at an Alaskan North Slope oil field, we identified thermophilic hydrogen-using methanogens, syntrophic bacteria, peptideand amino acid-fermenting bacteria, iron reducers, sulfur/thiosulfate-reducing bacteria and sulfate-reducing archaea. These microbes can stimulate metal corrosion through production of organic acids, CO2, sulfur species, and via hydrogen oxidation and iron reduction, implicating many more types of organisms than are currently targeted. Micromolar quantities of putative anaerobic metabolites of C1-C4 n-alkanes in pipeline fluids were detected, implying that these low molecular weight hydrocarbons, routinely injected into reservoirs for oil recovery purposes, are biodegraded and provide biocorrosive microbial communities with an important source of nutrients.

  12. Characterisation of community structure of bacteria in parallel mesophilic and thermophilic pilot scale anaerobe sludge digesters.

    Science.gov (United States)

    Tauber, T; Berta, Brigitta; Székely, Anna J; Gyarmati, I; Kékesi, Katalin; Márialigeti, K; Tóth, Erika M

    2007-03-01

    The aim of the present work was to compare the microbial communities of a mesophilic and a thermophilic pilot scale anaerobe sludge digester. For studying the communities cultivation independent chemotaxonomical methods (RQ and PLFA analyses) and T-RFLP were applied. Microbial communities of the mesophilic and thermophilic pilot digesters showed considerable differences, both concerning the species present, and their abundance. A Methanosarcina sp. dominated the thermophilic, while a Methanosaeta sp. the mesophilic digester among Archaea. Species diversity of Bacteria was reduced in the thermophilic digester. Based on the quinone patterns in both digesters the dominance of sulphate reducing respiratory bacteria could be detected. The PLFA profiles of the digester communities were similar though in minor components characteristic differences were shown. Level of branched chain fatty acids is slightly lower in the thermophilic digester that reports less Gram positive bacteria. The relative ratio of fatty acids characteristic to Enterobacteriaceae, Bacteroidetes and Clostridia shows differences between the two digesters: their importance generally decreased under thermophilic conditions. The sulphate reducer marker (15:1 and 17:1) fatty acids are present in low quantity in both digesters.

  13. A comparative study of thermophilic and mesophilic anaerobic co-digestion of food waste and wheat straw: Process stability and microbial community structure shifts.

    Science.gov (United States)

    Shi, Xuchuan; Guo, Xianglin; Zuo, Jiane; Wang, Yajiao; Zhang, Mengyu

    2018-05-01

    Renewable energy recovery from organic solid waste via anaerobic digestion is a promising way to provide sustainable energy supply and eliminate environmental pollution. However, poor efficiency and operational problems hinder its wide application of anaerobic digestion. The effects of two key parameters, i.e. temperature and substrate characteristics on process stability and microbial community structure were studied using two lab-scale anaerobic reactors under thermophilic and mesophilic conditions. Both the reactors were fed with food waste (FW) and wheat straw (WS). The organic loading rates (OLRs) were maintained at a constant level of 3 kg VS/(m 3 ·d). Five different FW:WS substrate ratios were utilized in different operational phases. The synergetic effects of co-digestion improved the stability and performance of the reactors. When FW was mono-digested, both reactors were unstable. The mesophilic reactor eventually failed due to volatile fatty acid accumulation. The thermophilic reactor had better performance compared to mesophilic one. The biogas production rate of the thermophilic reactor was 4.9-14.8% higher than that of mesophilic reactor throughout the experiment. The shifts in microbial community structures throughout the experiment in both thermophilic and mesophilic reactors were investigated. With increasing FW proportions, bacteria belonging to the phylum Thermotogae became predominant in the thermophilic reactor, while the phylum Bacteroidetes was predominant in the mesophilic reactor. The genus Methanosarcina was the predominant methanogen in the thermophilic reactor, while the genus Methanothrix remained predominant in the mesophilic reactor. The methanogenesis pathway shifted from acetoclastic to hydrogenotrophic when the mesophilic reactor experienced perturbations. Moreover, the population of lignocellulose-degrading microorganisms in the thermophilic reactor was higher than those in mesophilic reactor, which explained the better

  14. Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion.

    Directory of Open Access Journals (Sweden)

    Emily B Hollister

    Full Text Available The carboxylate platform is a flexible, cost-effective means of converting lignocellulosic materials into chemicals and liquid fuels. Although the platform's chemistry and engineering are well studied, relatively little is known about the mixed microbial communities underlying its conversion processes. In this study, we examined the metagenomes of two actively fermenting platform communities incubated under contrasting temperature conditions (mesophilic 40°C; thermophilic 55 °C, but utilizing the same inoculum and lignocellulosic feedstock. Community composition segregated by temperature. The thermophilic community harbored genes affiliated with Clostridia, Bacilli, and a Thermoanaerobacterium sp, whereas the mesophilic community metagenome was composed of genes affiliated with other Clostridia and Bacilli, Bacteriodia, γ-Proteobacteria, and Actinobacteria. Although both communities were able to metabolize cellulosic materials and shared many core functions, significant differences were detected with respect to the abundances of multiple Pfams, COGs, and enzyme families. The mesophilic metagenome was enriched in genes related to the degradation of arabinose and other hemicellulose-derived oligosaccharides, and the production of valerate and caproate. In contrast, the thermophilic community was enriched in genes related to the uptake of cellobiose and the transfer of genetic material. Functions assigned to taxonomic bins indicated that multiple community members at either temperature had the potential to degrade cellulose, cellobiose, or xylose and produce acetate, ethanol, and propionate. The results of this study suggest that both metabolic flexibility and functional redundancy contribute to the platform's ability to process lignocellulosic substrates and are likely to provide a degree of stability to the platform's fermentation processes.

  15. Bacteria and archaea communities in full-scale thermophilic and mesophilic anaerobic digesters treating food wastewater: Key process parameters and microbial indicators of process instability.

    Science.gov (United States)

    Lee, Joonyeob; Shin, Seung Gu; Han, Gyuseong; Koo, Taewoan; Hwang, Seokhwan

    2017-12-01

    In this study, four different mesophilic and thermophilic full-scale anaerobic digesters treating food wastewater (FWW) were monitored for 1-2years in order to investigate: 1) microbial communities underpinning anaerobic digestion of FWW, 2) significant factors shaping microbial community structures, and 3) potential microbial indicators of process instability. Twenty-seven bacterial genera were identified as abundant bacteria underpinning the anaerobic digestion of FWW. Methanosaeta harundinacea, M. concilii, Methanoculleus bourgensis, M. thermophilus, and Methanobacterium beijingense were revealed as dominant methanogens. Bacterial community structures were clearly differentiated by digesters; archaeal community structures of each digester were dominated by one or two methanogen species. Temperature, ammonia, propionate, Na + , and acetate in the digester were significant factors shaping microbial community structures. The total microbial populations, microbial diversity, and specific bacteria genera showed potential as indicators of process instability in the anaerobic digestion of FWW. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Multiple approaches to characterize the microbial community in a thermophilic anaerobic digester running on swine manure: a case study.

    Science.gov (United States)

    Tuan, Nguyen Ngoc; Chang, Yi-Chia; Yu, Chang-Ping; Huang, Shir-Ly

    2014-01-01

    In this study, the first survey of microbial community in thermophilic anaerobic digester using swine manure as sole feedstock was performed by multiple approaches including denaturing gradient gel electrophoresis (DGGE), clone library and pyrosequencing techniques. The integrated analysis of 21 DGGE bands, 126 clones and 8506 pyrosequencing read sequences revealed that Clostridia from the phylum Firmicutes account for the most dominant Bacteria. In addition, our analysis also identified additional taxa that were missed by the previous researches, including members of the bacterial phyla Synergistetes, Planctomycetes, Armatimonadetes, Chloroflexi and Nitrospira which might also play a role in thermophilic anaerobic digester. Most archaeal 16S rRNA sequences could be assigned to the order Methanobacteriales instead of Methanomicrobiales comparing to previous studies. In addition, this study reported that the member of Methanothermobacter genus was firstly found in thermophilic anaerobic digester. Copyright © 2014 Elsevier GmbH. All rights reserved.

  17. Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics

    Science.gov (United States)

    Antunes, Luciana Principal; Martins, Layla Farage; Pereira, Roberta Verciano; Thomas, Andrew Maltez; Barbosa, Deibs; Lemos, Leandro Nascimento; Silva, Gianluca Major Machado; Moura, Livia Maria Silva; Epamino, George Willian Condomitti; Digiampietri, Luciano Antonio; Lombardi, Karen Cristina; Ramos, Patricia Locosque; Quaggio, Ronaldo Bento; de Oliveira, Julio Cezar Franco; Pascon, Renata Castiglioni; Cruz, João Batista da; da Silva, Aline Maria; Setubal, João Carlos

    2016-01-01

    Composting is a promising source of new organisms and thermostable enzymes that may be helpful in environmental management and industrial processes. Here we present results of metagenomic- and metatranscriptomic-based analyses of a large composting operation in the São Paulo Zoo Park. This composting exhibits a sustained thermophilic profile (50 °C to 75 °C), which seems to preclude fungal activity. The main novelty of our study is the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscriptome high-throughput sequencing, enabling an unprecedented detailed view of microbial community structure, dynamics, and function in this ecosystem. The time-series data showed that the turning procedure has a strong impact on the compost microbiota, restoring to a certain extent the population profile seen at the beginning of the process; and that lignocellulosic biomass deconstruction occurs synergistically and sequentially, with hemicellulose being degraded preferentially to cellulose and lignin. Moreover, our sequencing data allowed near-complete genome reconstruction of five bacterial species previously found in biomass-degrading environments and of a novel biodegrading bacterial species, likely a new genus in the order Bacillales. The data and analyses provided are a rich source for additional investigations of thermophilic composting microbiology. PMID:27941956

  18. Relationship between microbial community dynamics and process performance during thermophilic sludge bioleaching.

    Science.gov (United States)

    Chen, Shen-Yi; Chou, Li-Chieh

    2016-08-01

    Heavy metals can be removed from the sludge using bioleaching technologies at thermophilic condition, thereby providing an option for biotreatment of wasted sludge generated from wastewater treatment. The purposes of this study were to establish a molecular biology technique, real-time PCR, for the detection and enumeration of the sulfur-oxidizing bacteria during the thermophilic sludge bioleaching. The 16S rRNA gene for real-time PCR quantification targeted the bioleaching bacteria: Sulfobacillus thermosulfidooxidans, Sulfobacillus acidophilus, and Acidithiobacillus caldus. The specificity and stringency for thermophilic sulfur-oxidizing bacteria were tested before the experiments of monitoring the bacterial community, bacterial number during the thermophilic sludge bioleaching and the future application on testing various environmental samples. The results showed that S. acidophilus was identified as the dominant sulfur-oxidizing bacteria, while A. caldus and S. thermosulfidooxidans occurred in relatively low numbers. The total number of the sulfur-oxidizing bacteria increased during the thermophilic bioleaching process. Meanwhile, the decrease of pH, production of sulfate, degradation of SS/VSS, and solubilization of heavy metal were found to correlate well with the population of thermophilic sulfur-oxidizing bacteria during the bioleaching process. The real-time PCR used in this study is a suitable method to monitor numbers of thermophilic sulfur-oxidizing bacteria during the bioleaching process.

  19. Effects of seed sludge on fermentative characteristics and microbial community structures in thermophilic hydrogen fermentation of starch

    Energy Technology Data Exchange (ETDEWEB)

    Akutsu, Yohei; Tandukar, Madan; Kubota, Kengo; Harada, Hideki [Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Sendai, Miyagi 980-8579 (Japan); Li, Yu-You [Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Sendai, Miyagi 980-8579 (Japan); Department of Urban and Environmental Engineering, Tianjin Institute of Urban Construction, Jinjinggonglu 26, Tianjin, 300384 (China)

    2008-11-15

    In this work, effects of seed sludge on thermophilic hydrogen fermentation were investigated. Five different kinds of sludge were separately inoculated in completely stirred tank reactors (CSTRs), without any pretreatment. The reactors were operated in parallel with starch as substrate under thermophilic condition (55 C) at a hydraulic retention time (HRT) of 24 h for 50 days. Stable hydrogen production was achieved in all reactors. The highest hydrogen yield (2.32 mol H{sub 2}/mol glucose) was obtained from the reactor seeded with thermophilically digested activated sludge. The stoichiometric equation of hydrogen fermentation calculated using the data obtained in this study was expressed as follows: starch ([C{sub 6}H{sub 10}O{sub 5}]n) {yields} 2.32n H{sub 2} + 2.14n CO{sub 2} + 0.50n acetate + 0.63n butyrate + 0.11n cell (C{sub 5}H{sub 7}NO{sub 2}). Microbial community structure was analyzed by polymerase chain reaction-denaturing gel gradient electrophoresis (PCR-DGGE) and 16S rRNA gene cloning. Close relatives of the Thermoanaerobacterium were found to be the most predominated one in all reactors. (author)

  20. Characterization of microbial compositions in a thermophilic chemostat of mixed culture fermentation.

    Science.gov (United States)

    Zhang, Fang; Yang, Jing-Hua; Dai, Kun; Chen, Yun; Li, Qiu-Rong; Gao, Fa-Ming; Zeng, Raymond J

    2016-02-01

    The microbial community compositions of a chemostat enriched in a thermophilic (55 °C) mixed culture fermentation (MCF) for hydrogen production under different operational conditions were revealed in this work by integrating denaturing gradient gel electrophoresis (DGGE), Illumina Miseq high-throughput sequencing, and 16S rRNA clone library sequencing. The results showed that the community structure of the enriched cultures was relatively simple. Clones close to the genera of Thermoanaerobacter and/or Bacillus mainly dominated the bacteria. And homoacetogens and archaea were washed out and not detected even by Illumina Miseq high-throughput sequencing which supported the benefit for hydrogen production. On the other hand, the results revealed that the metabolic shift was clearly associated with the change of dominated bacterial groups. The effects of hydrogen partial pressure (PH2) and pH from 4.0 to 5.5 on the microbial compositions were not notable and Thermoanaerobacter was dominant, thus, the metabolites were also not changed. While Bacillus, Thermoanaerobacter and Propionispora hippei dominated the bacteria communities at neutral pH, or Bacillus and Thermoanaerobacter dominated at high influent glucose concentrations, consequently the main metabolites shifted to acetate, ethanol, propionate, or lactate. Thereby, the effect of microbial composition on the metabolite distribution and shift shall be considered when modeling thermophilic MCF in the future.

  1. Thermophilic Dry Methane Fermentation of Distillation Residue Eluted from Ethanol Fermentation of Kitchen Waste and Dynamics of Microbial Communities.

    Science.gov (United States)

    Huang, Yu-Lian; Tan, Li; Wang, Ting-Ting; Sun, Zhao-Yong; Tang, Yue-Qin; Kida, Kenji

    2017-01-01

    Thermophilic dry methane fermentation is advantageous for feedstock with high solid content. Distillation residue with 65.1 % moisture content was eluted from ethanol fermentation of kitchen waste and subjected to thermophilic dry methane fermentation, after adjusting the moisture content to 75 %. The effect of carbon to nitrogen (C/N) ratio on thermophilic dry methane fermentation was investigated. Results showed that thermophilic dry methane fermentation could not be stably performed for >10 weeks at a C/N ratio of 12.6 and a volatile total solid (VTS) loading rate of 1 g/kg sludge/d; however, it was stably performed at a C/N ratio of 19.8 and a VTS loading rate of 3 g/kg sludge/d with 83.4 % energy recovery efficiency. Quantitative PCR analysis revealed that the number of bacteria and archaea decreased by two orders of magnitude at a C/N ratio of 12.6, whereas they were not influenced at a C/N ratio of 19.8. Microbial community analysis revealed that the relative abundance of protein-degrading bacteria increased and that of organic acid-oxidizing bacteria and acetic acid-oxidizing bacteria decreased at a C/N ratio of 12.6. Therefore, there was accumulation of NH 4 + and acetic acid, which inhibited thermophilic dry methane fermentation.

  2. Long-chain fatty acids inhibition and adaptation process in anaerobic thermophilic digestion: Batch tests, microbial community structure and mathematical modelling

    DEFF Research Database (Denmark)

    Paltsi, Jordi; Illa, J.; Prenafeta-Boldu, F.X.

    2010-01-01

    Biomass samples taken during the continuous operation of thermophilic anaerobic digestors fed with manure and exposed to successive inhibitory pulses of long-chain fatty acids (LCFA) were characterized in terms of specific metabolic activities and 16S rDNA DGGE profiling of the microbial community....... Population profiles of eubacterial and archaeal 16S rDNA genes revealed that no significant shift on microbial community composition took place upon biomass exposure to LCFA. DNA sequencing of predominant DGGE bands showed close phylogenetic affinity to ribotypes characteristic from specific beta...... kinetics considering the relation between LCFA inhibitory substrate concentration and specific biomass content, as an approximation to the adsorption process, improved the model fitting and provided a better insight on the physical nature of the LCFA inhibition process. (C) 2009 Elsevier Ltd. All rights...

  3. Community dynamics and glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass

    Energy Technology Data Exchange (ETDEWEB)

    Gladden, J.M.; Allgaier, M.; Miller, C.S.; Hazen, T.C.; VanderGheynst, J.S.; Hugenholtz, P.; Simmons, B.A.; Singer, S.W.

    2011-05-01

    Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60 C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80 C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.

  4. The distribution of active β-glucosidase-producing microbial communities in composting.

    Science.gov (United States)

    Zang, Xiangyun; Liu, Meiting; Wang, Han; Fan, Yihong; Zhang, Haichang; Liu, Jiawen; Xing, Enlu; Xu, Xiuhong; Li, Hongtao

    2017-12-01

    The composting ecosystem is a suitable source for the discovery of novel microorganisms and secondary metabolites. Cellulose degradation is an important part of the global carbon cycle, and β-glucosidases complete the final step of cellulose hydrolysis by converting cellobiose to glucose. This work analyzes the succession of β-glucosidase-producing microbial communities that persist throughout cattle manure - rice straw composting, and evaluates their metabolic activities and community advantage during the various phases of composting. Fungal and bacterial β-glucosidase genes belonging to glycoside hydrolase families 1 and 3 (GH1 and GH3) amplified from DNA were classified and gene abundance levels were analyzed. The major reservoirs of β-glucosidase genes were the fungal phylum Ascomycota and the bacterial phyla Firmicutes, Actinobacteria, Proteobacteria, and Deinococcus-Thermus. This indicates that a diverse microbial community utilizes cellobiose. The succession of dominant bacteria was also detected during composting. Firmicutes was the dominant bacteria in the thermophilic phase of composting; there was a shift to Actinomycetes in the maturing stage. Proteobacteria accounted for the highest proportions during the heating and thermophilic phases of composting. By contrast, the fungal phylum Ascomycota was a minor microbial community constituent in thermophilic phase of composting. Combined with the analysis of the temperature, cellulose degradation rate and the carboxymethyl cellulase and β-glucosidase activities showed that the bacterial GH1 family β-glucosidase genes make greater contribution in cellulose degradation at the later thermophilic stage of composting. In summary, even GH1 bacteria families β-glucosidase genes showing low abundance in DNA may be functionally important in the later thermophilic phase of composting. The results indicate that a complex community of bacteria and fungi expresses β-glucosidases in compost. Several

  5. Two-Step Oxidation of Refractory Gold Concentrates with Different Microbial Communities.

    Science.gov (United States)

    Wang, Guo-Hua; Xie, Jian-Ping; Li, Shou-Peng; Guo, Yu-Jie; Pan, Ying; Wu, Haiyan; Liu, Xin-Xing

    2016-11-28

    Bio-oxidation is an effective technology for treatment of refractory gold concentrates. However, the unsatisfactory oxidation rate and long residence time, which cause a lower cyanide leaching rate and gold recovery, are key factors that restrict the application of traditional bio-oxidation technology. In this study, the oxidation rate of refractory gold concentrates and the adaption of microorganisms were analyzed to evaluate a newly developed two-step pretreatment process, which includes a high temperature chemical oxidation step and a subsequent bio-oxidation step. The oxidation rate and recovery rate of gold were improved significantly after the two-step process. The results showed that the highest oxidation rate of sulfide sulfur could reach to 99.01 % with an extreme thermophile microbial community when the pulp density was 5%. Accordingly, the recovery rate of gold was elevated to 92.51%. Meanwhile, the results revealed that moderate thermophiles performed better than acidophilic mesophiles and extreme thermophiles, whose oxidation rates declined drastically when the pulp density was increased to 10% and 15%. The oxidation rates of sulfide sulfur with moderate thermophiles were 93.94% and 65.73% when the pulp density was increased to 10% and 15%, respectively. All these results indicated that the two-step pretreatment increased the oxidation rate of refractory gold concentrates and is a potential technology to pretreat the refractory sample. Meanwhile, owing to the sensitivity of the microbial community under different pulp density levels, the optimization of microbial community in bio-oxidation is necessary in industry.

  6. Electricity production and microbial characterization of thermophilic microbial fuel cells.

    Science.gov (United States)

    Dai, Kun; Wen, Jun-Li; Zhang, Fang; Ma, Xi-Wen; Cui, Xiang-Yu; Zhang, Qi; Zhao, Ting-Jia; Zeng, Raymond J

    2017-11-01

    Thermophilic microbial fuel cell (TMFC) offers many benefits, but the investigations on the diversity of exoelectrogenic bacteria are scarce. In this study, a two-chamber TMFC was constructed using ethanol as an electron donor, and the microbial dynamics were analyzed by high-throughput sequencing and 16S rRNA clone-library sequencing. The open-circuit potential of TMFC was approximately 650mV, while the maximum voltage was around 550mV. The maximum power density was 437mW/m 2 , and the columbic efficiency in this work was 20.5±6.0%. The Firmicutes bacteria, related to the uncultured bacterium clone A55_D21_H_B_C01 with a similarity of 99%, accounted for 90.9% of all bacteria in the TMFC biofilm. This unknown bacterium has the potential to become a new thermophilic exoelectrogenic bacterium that is yet to be cultured. The development of TMFC-involved biotechnologies will be beneficial for the production of valuable chemicals and generation of energy in the future. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Effects of organic loading rates on reactor performance and microbial community changes during thermophilic aerobic digestion process of high-strength food wastewater.

    Science.gov (United States)

    Jang, Hyun Min; Lee, Jae Won; Ha, Jeong Hyub; Park, Jong Moon

    2013-11-01

    To evaluate the applicability of single-stage thermophilic aerobic digestion (TAD) process treating high-strength food wastewater (FWW), TAD process was operated at four organic loading rates (OLRs) from 9.2 to 37.2 kg COD/m(3)d. The effects of OLRs on microbial community changes were also examined. The highest volumetric removal rate (13.3 kg COD/m(3)d) and the highest thermo-stable protease activity (0.95 unit/mL) were detected at OLR=18.6 kg COD/m(3)d. Denaturing gradient gel electrophoresis (DGGE) profiles and quantitative PCR (qPCR) results showed significant microbial community shifts in response to changes in OLR. In particular, DGGE and phylogenetic analysis demonstrate that the presence of Bacillus sp. (phylum of Firmicutes) was strongly correlated with efficient removal of organic particulates from high-strength food wastewater. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Conductive iron oxides accelerate thermophilic methanogenesis from acetate and propionate.

    Science.gov (United States)

    Yamada, Chihaya; Kato, Souichiro; Ueno, Yoshiyuki; Ishii, Masaharu; Igarashi, Yasuo

    2015-06-01

    Anaerobic digester is one of the attractive technologies for treatment of organic wastes and wastewater, while continuous development and improvements on their stable operation with efficient organic removal are required. Particles of conductive iron oxides (e.g., magnetite) are known to facilitate microbial interspecies electron transfer (termed as electric syntrophy). Electric syntrophy has been reported to enhance methanogenic degradation of organic acids by mesophilic communities in soil and anaerobic digester. Here we investigated the effects of supplementation of conductive iron oxides (magnetite) on thermophilic methanogenic microbial communities derived from a thermophilic anaerobic digester. Supplementation of magnetite accelerated methanogenesis from acetate and propionate under thermophilic conditions, while supplementation of ferrihydrite also accelerated methanogenesis from propionate. Microbial community analysis revealed that supplementation of magnetite drastically changed bacterial populations in the methanogenic acetate-degrading cultures, in which Tepidoanaerobacter sp. and Coprothermobacter sp. dominated. These results suggest that supplementation of magnetite induce electric syntrophy between organic acid-oxidizing bacteria and methanogenic archaea and accelerate methanogenesis even under thermophilic conditions. Findings from this study would provide a possibility for the achievement of stably operating thermophilic anaerobic digestion systems with high efficiency for removal of organics and generation of CH4. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  9. Microbial conversion of food wastes for biofertilizer production with thermophilic lipolytic microbes

    Energy Technology Data Exchange (ETDEWEB)

    Tsai, Shu-Hsien; Yang, Shang-Shyng [Institute of Microbiology and Biochemistry, National Taiwan University, Taipei 10617, (Taiwan); Liu, Ching-Piao [Department of Biological Science and Technology, Meiho Institute of Technology, Pingtung 91201, (Taiwan)

    2007-05-15

    Food waste is approximately one quarter of the total garbage in Taiwan. To investigate the feasibility of microbial conversion of food waste to multiple functional biofertilizer, food waste was mixed with bulking materials, inoculated with thermophilic and lipolytic microbes and incubated at 50{sup o}C in a mechanical composter. Microbial inoculation enhanced the degradation of food wastes, increased the total nitrogen and the germination rate of alfalfa seed, shortened the maturity period and improved the quality of biofertilizer. In food waste inoculated with thermophilic and lipolytic Brevibacillus borstelensis SH168 for 28 days, total nitrogen increased from 2.01% to 2.10%, ash increased from 24.94% to 29.21%, crude fat decreased from 4.88% to 1.34% and the C/N ratio decreased from 18.02 to 17.65. Each gram of final product had a higher population of thermophilic microbes than mesophilic microbes. Microbial conversion of food waste to biofertilizer is a feasible and potential technology in the future to maintain the natural resources and to reduce the impact on environmental quality. (author)

  10. Comparison of the microbial communities in solid-state anaerobic digestion (SS-AD) reactors operated at mesophilic and thermophilic temperatures.

    Science.gov (United States)

    Li, Yueh-Fen; Nelson, Michael C; Chen, Po-Hsu; Graf, Joerg; Li, Yebo; Yu, Zhongtang

    2015-01-01

    The microbiomes involved in liquid anaerobic digestion process have been investigated extensively, but the microbiomes underpinning solid-state anaerobic digestion (SS-AD) are poorly understood. In this study, microbiome composition and temporal succession in batch SS-AD reactors, operated at mesophilic or thermophilic temperatures, were investigated using Illumina sequencing of 16S rRNA gene amplicons. A greater microbial richness and evenness were found in the mesophilic than in the thermophilic SS-AD reactors. Firmicutes accounted for 60 and 82 % of the total Bacteria in the mesophilic and in the thermophilic SS-AD reactors, respectively. The genus Methanothermobacter dominated the Archaea in the thermophilic SS-AD reactors, while Methanoculleus predominated in the mesophilic SS-AD reactors. Interestingly, the data suggest syntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis as an important pathway for biogas production during the thermophilic SS-AD. Canonical correspondence analysis (CCA) showed that temperature was the most influential factor in shaping the microbiomes in the SS-AD reactors. Thermotogae showed strong positive correlation with operation temperature, while Fibrobacteres, Lentisphaerae, Spirochaetes, and Tenericutes were positively correlated with daily biogas yield. This study provided new insight into the microbiome that drives SS-AD process, and the findings may help advance understanding of the microbiome in SS-AD reactors and the design and operation of SS-AD systems.

  11. Bacterial community analysis of swine manure treated with autothermal thermophilic aerobic digestion.

    Science.gov (United States)

    Han, Il; Congeevaram, Shankar; Ki, Dong-Won; Oh, Byoung-Taek; Park, Joonhong

    2011-02-01

    Due to the environmental problems associated with disposal of livestock sludge, many stabilization studies emphasizing on the sludge volume reduction were performed. However, little is known about the microbial risk present in sludge and its stabilized products. This study microbiologically explored the effects of anaerobic lagoon fermentation (ALF) and autothermal thermophilic aerobic digestion (ATAD) on pathogen-related risk of raw swine manure by using culture-independent 16S rDNA cloning and sequencing methods. In raw swine manure, clones closely related to pathogens such as Dialister pneumosintes, Erysipelothrix rhusiopathiae, Succinivibrioan dextrinosolvens, and Schineria sp. were detected. Meanwhile, in the mesophilic ALF-treated swine manure, bacterial community clones closely related to pathogens such as Schineria sp. and Succinivibrio dextrinosolvens were still detected. Interestingly, the ATAD treatment resulted in no detection of clones closely related to pathogens in the stabilized thermophilic bacterial community, with the predominance of novel Clostridia class populations. These findings support the superiority of ATAD in selectively reducing potential human and animal pathogens compared to ALF, which is a typical manure stabilization method used in livestock farms.

  12. Characterization of microbial community in the two-stage process for hydrogen and methane production from food waste

    Energy Technology Data Exchange (ETDEWEB)

    Chu, Chun-Feng [School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240 (China); Ebie, Yoshitaka [National Institute for Environmental Studies, Tsukuba 305-8506 (Japan); Xu, Kai-Qin [National Institute for Environmental Studies, Tsukuba 305-8506 (Japan); State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072 (China); Li, Yu-You [Department of Civil and Environmental Engineering, Tohoku University, Sendai 980-8579 (Japan); Inamori, Yuhei [Faculty of Symbiotic Systems Science, Fukushima University, Fukushima 960-1296 (Japan)

    2010-08-15

    The structure of a microbial community in the two-stage process for H{sub 2} and CH{sub 4} production from food waste was investigated by a molecular biological approach. The process was a continuous combined thermophilic acidogenic hydrogenesis and mesophilic (RUN1) or thermophilic (RUN2) methanogenesis with recirculation of the digested sludge. A two-phase process suggested in this study effectively separate H{sub 2}-producing bacteria from methanogenic archaea by optimization of design parameters such as pH, hydraulic retention time (HRT) and temperature. Galore microbial diversity was found in the thermophilic acidogenic hydrogenesis, Clostridium sp. strain Z6 and Thermoanaerobacterium thermosaccharolyticum were considered to be the dominant thermophilic H{sub 2}-producing bacteria. The hydrogenotrophic methanogens were inhibited in thermophilic methanogenesis, whereas archaeal rDNAs were higher in the thermophilic methanogenesis than those in mesophilic methanogenesis. The yields of H{sub 2} and CH{sub 4} were in equal range depending on the characteristics of food waste, whereas effluent water quality indicators were different obviously in RUN1 and RUN2. The results indicated that hydrolysis and removal of food waste were higher in RUN2 than RUN1. (author)

  13. New microbial resource: microbial diversity, function and dynamics in Chinese liquor starter.

    Science.gov (United States)

    Huang, Yuhong; Yi, Zhuolin; Jin, Yanling; Zhao, Yonggui; He, Kaize; Liu, Dayu; Zhao, Dong; He, Hui; Luo, Huibo; Zhang, Wenxue; Fang, Yang; Zhao, Hai

    2017-11-06

    Traditional Chinese liquor (Baijiu) solid state fermentation technology has lasted for several thousand years. The microbial communities that enrich in liquor starter are important for fermentation. However, the microbial communities are still under-characterized. In this study, 454 pyrosequencing technology was applied to comprehensively analyze the microbial diversity, function and dynamics of two most-consumed liquor starters (Jiang- and Nong-flavor) during production. In total, 315 and 83 bacterial genera and 72 and 47 fungal genera were identified in Jiang- and Nong-flavor liquor starter, respectively. The relatively high diversity was observed when the temperature increased to 70 and 62 °C for Jiang- and Nong-flavor liquor starter, respectively. Some thermophilic fungi have already been isolated. Microbial communities that might contribute to ethanol fermentation, saccharification and flavor development were identified and shown to be core communities in correlation-based network analysis. The predictively functional profile of bacterial communities showed significant difference in energy, carbohydrate and amino acid metabolism and the degradation of aromatic compounds between the two kinds of liquor starters. Here we report these liquor starters as a new functionally microbial resource, which can be used for discovering thermophilic and aerobic enzymes and for food and feed preservation.

  14. Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass.

    Science.gov (United States)

    Gladden, John M; Allgaier, Martin; Miller, Christopher S; Hazen, Terry C; VanderGheynst, Jean S; Hugenholtz, Philip; Simmons, Blake A; Singer, Steven W

    2011-08-15

    Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60°C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80°C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.

  15. Responses of microbial community to pH stress in bioleaching of low grade copper sulfide.

    Science.gov (United States)

    Wang, Yuguang; Li, Kai; Chen, Xinhua; Zhou, Hongbo

    2018-02-01

    The microbial diversity and dynamics in the leachates and on the ore surfaces of different depth of the column were analyzed during bioleaching of low grade copper sulfide at different pH, after inoculation with the same inoculum containing mesophiles and moderate thermophiles. The results indicate that low pH was beneficial to enhance copper extraction. The highest copper extraction (86%) was obtained when pH was controlled at 1.0-1.5. The microbial structures on the ore surfaces were independent of community structures in the leachate, even at the top portion of column. Microbial richness and evenness increased with decreasing pH during bioleaching. pH had significant effects on microbial community structure in the leachate and on the mineral surface of different depth of the column. Leptospirillum ferriphilum accounted for the highest proportions of the community at most times when pH was operated during bioleaching, especially at the end of run. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China.

    Science.gov (United States)

    Jiang, Zhou; Li, Ping; Jiang, Dawei; Dai, Xinyue; Zhang, Rui; Wang, Yanhong; Wang, Yanxin

    2016-01-01

    Arsenic biogeochemistry has been studied extensively in acid sulfate-chloride hot springs, but not in acid sulfate hot springs with low chloride. In this study, Zhenzhuquan in Tengchong geothermal area, a representative acid sulfate hot spring with low chloride, was chosen to study arsenic geochemistry and microbial community structure using Illumina MiSeq sequencing. Over 0.3 million 16S rRNA sequence reads were obtained from 6-paired parallel water and sediment samples along its outflow channel. Arsenic oxidation occurred in the Zhenxhuquan pool, with distinctly high ratios of arsenate to total dissolved arsenic (0.73-0.86). Coupled with iron and sulfur oxidation along the outflow channel, arsenic accumulated in downstream sediments with concentrations up to 16.44 g/kg and appeared to significantly constrain their microbial community diversity. These oxidations might be correlated with the appearance of some putative functional microbial populations, such as Aquificae and Pseudomonas (arsenic oxidation), Sulfolobus (sulfur and iron oxidation), Metallosphaera and Acidicaldus (iron oxidation). Temperature, total organic carbon and dissolved oxygen significantly shaped the microbial community structure of upstream and downstream samples. In the upstream outflow channel region, most microbial populations were microaerophilic/anaerobic thermophiles and hyperthermophiles, such as Sulfolobus, Nocardia, Fervidicoccus, Delftia, and Ralstonia. In the downstream region, aerobic heterotrophic mesophiles and thermophiles were identified, including Ktedonobacteria, Acidicaldus, Chthonomonas and Sphingobacteria. A total of 72.41-95.91% unassigned-genus sequences were derived from the downstream high arsenic sediments 16S rRNA clone libraries. This study could enable us to achieve an integrated understanding on arsenic biogeochemistry in acid hot springs.

  17. Microbial community shifts and biogas conversion computation during steady, inhibited and recovered stages of thermophilic methane fermentation on chicken manure with a wide variation of ammonia.

    Science.gov (United States)

    Niu, Qigui; Qiao, Wei; Qiang, Hong; Li, Yu-You

    2013-10-01

    The thermophilic methane fermentation of chicken manure (10% TS) was investigated within a wide range of ammonia. Microbiological analysis showed significant shifts in Archaeal and Bacterial proportions with VFA accmulation and CH4 formation before and after inhibition. VFA accumulated sharply with lower methane production, 0.29 L/g VS, than during the steady stage, 0.32 L/g VS. Biogas production almost ceased with the synergy inhibition of TAN (8000 mg/L) and VFA (25,000 mg/L). Hydrogenotrophic Methanothermobacter thermautotrophicus str. was the dominate archaea with 95% in the inhibition stage and 100% after 40 days recovery compared to 9.3% in the steady stage. Aceticlastic Methanosarcina was not encountered with coincided phenomenal of high VFA in the inhibition stage as well as recovery stage. Evaluation of the microbial diversity and functional bacteria indicated the dominate phylum of Firmicutes were 94.74% and 84.4% with and without inhibition. The microbial community shifted significantly with elevated ammonia concentration affecting the performance. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass.

    Science.gov (United States)

    Eichorst, Stephanie A; Joshua, Chijioke; Sathitsuksanoh, Noppadon; Singh, Seema; Simmons, Blake A; Singer, Steven W

    2014-12-01

    Microbial communities that deconstruct plant biomass have broad relevance in biofuel production and global carbon cycling. Biomass pretreatments reduce plant biomass recalcitrance for increased efficiency of enzymatic hydrolysis. We exploited these chemical pretreatments to study how thermophilic bacterial consortia adapt to deconstruct switchgrass (SG) biomass of various compositions. Microbial communities were adapted to untreated, ammonium fiber expansion (AFEX)-pretreated, and ionic-liquid (IL)-pretreated SG under aerobic, thermophilic conditions using green waste compost as the inoculum to study biomass deconstruction by microbial consortia. After microbial cultivation, gravimetric analysis of the residual biomass demonstrated that both AFEX and IL pretreatment enhanced the deconstruction of the SG biomass approximately 2-fold. Two-dimensional nuclear magnetic resonance (2D-NMR) experiments and acetyl bromide-reactive-lignin analysis indicated that polysaccharide hydrolysis was the dominant process occurring during microbial biomass deconstruction, and lignin remaining in the residual biomass was largely unmodified. Small-subunit (SSU) rRNA gene amplicon libraries revealed that although the dominant taxa across these chemical pretreatments were consistently represented by members of the Firmicutes, the Bacteroidetes, and Deinococcus-Thermus, the abundance of selected operational taxonomic units (OTUs) varied, suggesting adaptations to the different substrates. Combining the observations of differences in the community structure and the chemical and physical structure of the biomass, we hypothesize specific roles for individual community members in biomass deconstruction. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  19. Converting mesophilic upflow sludge blanket (UASB) reactors to thermophilic by applying axenic methanogenic culture bioaugmentation

    DEFF Research Database (Denmark)

    Zhu, Xinyu; Treu, Laura; Kougias, Panagiotis G.

    2018-01-01

    on the microbial consortium. The adaptation of microbial community to a new environment or condition can be accelerated by a process known as “bioaugmentation” or “microbial community manipulation”, during which exogenous microorganisms harbouring specific metabolic activities are introduced to the reactor....... The aim of the current study was to rapidly convert the operational temperature of up-flow anaerobic sludge blanket (UASB) reactors from mesophilic to thermophilic conditions by applying microbial community manipulation techniques. Three different bioaugmentation strategies were compared and it was proven...... that the injection of axenic methanogenic culture was the most efficient approach leading to improved biomethanation process with 40% higher methane production rate compared to the control reactor. Microbial community analyses revealed that during bioaugmentation, the exogenous hydrogenotrophic methanogen could...

  20. Impacts of shallow geothermal energy production on redox processes and microbial communities.

    Science.gov (United States)

    Bonte, Matthijs; Röling, Wilfred F M; Zaura, Egija; van der Wielen, Paul W J J; Stuyfzand, Pieter J; van Breukelen, Boris M

    2013-12-17

    Shallow geothermal systems are increasingly being used to store or harvest thermal energy for heating or cooling purposes. This technology causes temperature perturbations exceeding the natural variations in aquifers, which may impact groundwater quality. Here, we report the results of laboratory experiments on the effect of temperature variations (5-80 °C) on redox processes and associated microbial communities in anoxic unconsolidated subsurface sediments. Both hydrochemical and microbiological data showed that a temperature increase from 11 °C (in situ) to 25 °C caused a shift from iron-reducing to sulfate-reducing and methanogenic conditions. Bioenergetic calculations could explain this shift. A further temperature increase (>45 °C) resulted in the emergence of a thermophilic microbial community specialized in fermentation and sulfate reduction. Two distinct maxima in sulfate reduction rates, of similar orders of magnitude (5 × 10(-10) M s(-1)), were observed at 40 and 70 °C. Thermophilic sulfate reduction, however, had a higher activation energy (100-160 kJ mol(-1)) than mesophilic sulfate reduction (30-60 kJ mol(-1)), which might be due to a trade-off between enzyme stability and activity with thermostable enzymes being less efficient catalysts that require higher activation energies. These results reveal that while sulfate-reducing functionality can withstand a substantial temperature rise, other key biochemical processes appear more temperature sensitive.

  1. Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China.

    Directory of Open Access Journals (Sweden)

    Zhou Jiang

    Full Text Available Arsenic biogeochemistry has been studied extensively in acid sulfate-chloride hot springs, but not in acid sulfate hot springs with low chloride. In this study, Zhenzhuquan in Tengchong geothermal area, a representative acid sulfate hot spring with low chloride, was chosen to study arsenic geochemistry and microbial community structure using Illumina MiSeq sequencing. Over 0.3 million 16S rRNA sequence reads were obtained from 6-paired parallel water and sediment samples along its outflow channel. Arsenic oxidation occurred in the Zhenxhuquan pool, with distinctly high ratios of arsenate to total dissolved arsenic (0.73-0.86. Coupled with iron and sulfur oxidation along the outflow channel, arsenic accumulated in downstream sediments with concentrations up to 16.44 g/kg and appeared to significantly constrain their microbial community diversity. These oxidations might be correlated with the appearance of some putative functional microbial populations, such as Aquificae and Pseudomonas (arsenic oxidation, Sulfolobus (sulfur and iron oxidation, Metallosphaera and Acidicaldus (iron oxidation. Temperature, total organic carbon and dissolved oxygen significantly shaped the microbial community structure of upstream and downstream samples. In the upstream outflow channel region, most microbial populations were microaerophilic/anaerobic thermophiles and hyperthermophiles, such as Sulfolobus, Nocardia, Fervidicoccus, Delftia, and Ralstonia. In the downstream region, aerobic heterotrophic mesophiles and thermophiles were identified, including Ktedonobacteria, Acidicaldus, Chthonomonas and Sphingobacteria. A total of 72.41-95.91% unassigned-genus sequences were derived from the downstream high arsenic sediments 16S rRNA clone libraries. This study could enable us to achieve an integrated understanding on arsenic biogeochemistry in acid hot springs.

  2. Thermophilic anaerobic oxidation of methane by marine microbial consortia.

    Science.gov (United States)

    Holler, Thomas; Widdel, Friedrich; Knittel, Katrin; Amann, Rudolf; Kellermann, Matthias Y; Hinrichs, Kai-Uwe; Teske, Andreas; Boetius, Antje; Wegener, Gunter

    2011-12-01

    The anaerobic oxidation of methane (AOM) with sulfate controls the emission of the greenhouse gas methane from the ocean floor. AOM is performed by microbial consortia of archaea (ANME) associated with partners related to sulfate-reducing bacteria. In vitro enrichments of AOM were so far only successful at temperatures ≤25 °C; however, energy gain for growth by AOM with sulfate is in principle also possible at higher temperatures. Sequences of 16S rRNA genes and core lipids characteristic for ANME as well as hints of in situ AOM activity were indeed reported for geothermally heated marine environments, yet no direct evidence for thermophilic growth of marine ANME consortia was obtained to date. To study possible thermophilic AOM, we investigated hydrothermally influenced sediment from the Guaymas Basin. In vitro incubations showed activity of sulfate-dependent methane oxidation between 5 and 70 °C with an apparent optimum between 45 and 60 °C. AOM was absent at temperatures ≥75 °C. Long-term enrichment of AOM was fastest at 50 °C, yielding a 13-fold increase of methane-dependent sulfate reduction within 250 days, equivalent to an apparent doubling time of 68 days. The enrichments were dominated by novel ANME-1 consortia, mostly associated with bacterial partners of the deltaproteobacterial HotSeep-1 cluster, a deeply branching phylogenetic group previously found in a butane-amended 60 °C-enrichment culture of Guaymas sediments. The closest relatives (Desulfurella spp.; Hippea maritima) are moderately thermophilic sulfur reducers. Results indicate that AOM and ANME archaea could be of biogeochemical relevance not only in cold to moderate but also in hot marine habitats.

  3. Microbial Activity and Silica Degradation in Rice Straw

    Science.gov (United States)

    Kim, Esther Jin-kyung

    Abundantly available agricultural residues like rice straw have the potential to be feedstocks for bioethanol production. Developing optimized conditions for rice straw deconstruction is a key step toward utilizing the biomass to its full potential. One challenge associated with conversion of rice straw to bioenergy is its high silica content as high silica erodes machinery. Another obstacle is the availability of enzymes that hydrolyze polymers in rice straw under industrially relevant conditions. Microbial communities that colonize compost may be a source of enzymes for bioconversion of lignocellulose to products because composting systems operate under thermophilic and high solids conditions that have been shown to be commercially relevant. Compost microbial communities enriched on rice straw could provide insight into a more targeted source of enzymes for the breakdown of rice straw polysaccharides and silica. Because rice straw is low in nitrogen it is important to understand the impact of nitrogen concentrations on the production of enzyme activity by the microbial community. This study aims to address this issue by developing a method to measure microbial silica-degrading activity and measure the effect of nitrogen amendment to rice straw on microbial activity and extracted enzyme activity during a high-solids, thermophilic incubation. An assay was developed to measure silica-degrading enzyme or silicase activity. This process included identifying methods of enzyme extraction from rice straw, identifying a model substrate for the assay, and optimizing measurement techniques. Rice straw incubations were conducted with five different levels of nitrogen added to the biomass. Microbial activity was measured by respiration and enzyme activity. A microbial community analysis was performed to understand the shift in community structure with different treatments. With increased levels of nitrogen, respiration and cellulose and hemicellulose degrading activity

  4. Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: Geochemical controls on microbial community structure and function

    Directory of Open Access Journals (Sweden)

    William P. Inskeep

    2015-10-01

    Full Text Available Yellowstone Lake (Yellowstone National Park, WY, USA is a large high-altitude (2200 m, fresh-water lake, which straddles an extensive caldera and is the center of significant geothermal activity. The primary goal of this interdisciplinary study was to evaluate the microbial populations inhabiting thermal vent communities in Yellowstone Lake (Yellowstone Lake using 16S rRNA gene and random metagenome sequencing, and to determine how geochemical attributes of vent waters influence the distribution of specific microorganisms and their metabolic potential. Thermal vent waters and associated microbial biomass were sampled during two field seasons (2007 - 2008 using a remotely operated vehicle (ROV. Sublacustrine thermal vent waters (circa 50 - 90 oC contained elevated concentrations of numerous constituents associated with geothermal activity including dissolved hydrogen, sulfide, methane and carbon dioxide. Microorganisms associated with sulfur-rich filamentous ‘streamer’ communities of Inflated Plain and West Thumb (pH range 5 - 6 were dominated by bacteria from the Aquificales, but also contained thermophilic archaea from the Crenarchaeota and Euryarchaeota. Novel groups of methanogens and members of the Korarchaeota were observed in vents from West Thumb and Elliot’s Crater (pH 5 - 6. Conversely, metagenome sequence from Mary Bay vent sediments did not yield large assemblies, and contained diverse thermophilic and nonthermophilic bacterial relatives. Analysis of functional genes associated with the major vent populations indicated a direct linkage to high concentrations of carbon dioxide, reduced sulfur (sulfide and/or elemental S, hydrogen and methane in the deep thermal ecosystems. Our observations show that sublacustrine thermal vents in Yellowstone Lake support novel thermophilic communities, which contain microorganisms with functional attributes not found to date in terrestrial geothermal systems of YNP.

  5. Digestion performance and microbial community in full-scale methane fermentation of stillage from sweet potato-shochu production.

    Science.gov (United States)

    Kobayashi, Tsutomu; Tang, Yueqin; Urakami, Toyoshi; Morimura, Shigeru; Kida, Kenji

    2014-02-01

    Sweet potato shochu is a traditional Japanese spirit produced mainly in the South Kyushu area in Japan. The amount of stillage reaches approximately 8 x 10(5) tons per year. Wastewater mainly containing stillage from the production of sweet potato-shochu was treated thermophilically in a full-scale treatment plant using fixed-bed reactors (8 reactors x 283 m3). Following the addition of Ni2+ and Co2+, the reactors have been stably operated for six years at a high chemical oxygen demand (COD) loading rate of 14 kg/(m3 x day). Analysis of coenzyme content and microbial communities indicated that similar microbial communities were present in the liquid phase and on the fiber carriers installed in reactors. Bacteria in the phyla Firmicutes as well as Bacteroidetes were dominant bacteria, and Methanosarcina thermophila as well as Methanothermobacter crinale were dominant methanogens in the reactors. This study reveals that stillage from sweet potato-shochu production can be treated effectively in a full-scale fixed-bed reactor under thermophilic conditions with the help of Ni2+ and Co2+. The high diversity of bacterial community and the coexistence of both aceticlastic and hydrogenotrophic methanogens contributed to the excellent fermentation performance.

  6. Microbial community shifts in a farm-scale anaerobic digester treating swine waste: Correlations between bacteria communities associated with hydrogenotrophic methanogens and environmental conditions.

    Science.gov (United States)

    Cho, Kyungjin; Shin, Seung Gu; Kim, Woong; Lee, Joonyeob; Lee, Changsoo; Hwang, Seokhwan

    2017-12-01

    Microbial community structure in a farm-scale anaerobic digester treating swine manure was investigated during three process events: 1) prolonged starvation, and changes of 2) operating temperature (between meso- and thermophilic) and 3) hydraulic retention time (HRT). Except during the initial period, the digester was dominated by hydrogenotrophic methanogens (HMs). The bacterial community structure significantly shifted with operating temperature and HRT but not with long-term starvation. Clostridiales (26.5-54.4%) and Bacteroidales (2.5-13.7%) became dominant orders in the digester during the period of HM dominance. Abundance of diverse meso- and thermophilic bacteria increased during the same period; many of these species may be H 2 producers, and/or syntrophic acetate oxidizers. Some of these species showed positive correlations with [NH 4 + -N] (panaerobic digesters treating swine manure that contains high ammonia content. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Effects of the feeding ratio of food waste on fed-batch aerobic composting and its microbial community.

    Science.gov (United States)

    Wang, Xiaojun; Pan, Songqing; Zhang, Zhaoji; Lin, Xiangyu; Zhang, Yuzhen; Chen, Shaohua

    2017-01-01

    To determine the suitable feeding ratio for fed-batch aerobic composting, four fermenters were operated by adding 0%, 5%, 10% or 15% of food waste every day. The results showed that the 5% and 10% treatments were able to maintain continuous thermophilic conditions, while the 15% treatment performed badly in regard to composting temperature, which was probably due to the negative effects of excessive moisture on microbial activity. As composting proceeded, both the 5% and the 10% treatments reached maturity and achieved weight losses of approximately 65%. High-throughput sequencing results indicated that Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were the dominant phyla of the community structure. The communities sampled at the thermophilic phases had high similarity and relatively low diversity, while species diversity increased in the maturity phase. This study was devoted to optimizing the fed-batch composting process and assessing bacterial communities, both of which were supplied as a reference for practical application. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Biogas production and methanogenic archaeal community in mesophilic and thermophilic anaerobic co-digestion processes.

    Science.gov (United States)

    Yu, D; Kurola, J M; Lähde, K; Kymäläinen, M; Sinkkonen, A; Romantschuk, M

    2014-10-01

    Over 258 Mt of solid waste are generated annually in Europe, a large fraction of which is biowaste. Sewage sludge is another major waste fraction. In this study, biowaste and sewage sludge were co-digested in an anaerobic digestion reactor (30% and 70% of total wet weight, respectively). The purpose was to investigate the biogas production and methanogenic archaeal community composition in the anaerobic digestion reactor under meso- (35-37 °C) and thermophilic (55-57 °C) processes and an increasing organic loading rate (OLR, 1-10 kg VS m(-3) d(-1)), and also to find a feasible compromise between waste treatment capacity and biogas production without causing process instability. In summary, more biogas was produced with all OLRs by the thermophilic process. Both processes showed a limited diversity of the methanogenic archaeal community which was dominated by Methanobacteriales and Methanosarcinales (e.g. Methanosarcina) in both meso- and thermophilic processes. Methanothermobacter was detected as an additional dominant genus in the thermophilic process. In addition to operating temperatures, the OLRs, the acetate concentration, and the presence of key substrates like propionate also affected the methanogenic archaeal community composition. A bacterial cell count 6.25 times higher than archaeal cell count was observed throughout the thermophilic process, while the cell count ratio varied between 0.2 and 8.5 in the mesophilic process. This suggests that the thermophilic process is more stable, but also that the relative abundance between bacteria and archaea can vary without seriously affecting biogas production. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production

    Energy Technology Data Exchange (ETDEWEB)

    Hollister, Emily B.; Gentry, Terry J. [Texas A and M Univ., College Station, TX (United States). Dept. of Soil and Crop Sciences; Forrest, Andrea K.; Holtzapple, Mark T. [Texas A and M Univ., College Station, TX (United States). Dept. of Chemical Engineering; Wilkinson, Heather H.; Ebbole, Daniel J. [Texas A and M Univ., College Station, TX (United States). Dept. of Plant Pathology and Microbiology; Malfatti, Stephanie A.; Tringe, Susannah G. [DOE Joint Genome Institute, Walnut Creek, CA (United States)

    2010-09-15

    The carboxylate platform utilizes a mixed microbial community to convert lignocellulosic biomass into chemicals and fuels. While much of the platform is well understood, little is known about its microbiology. Mesophilic (40 C) and thermophilic (55 C) fermentations employing a sorghum feedstock and marine sediment inoculum were profiled using 16S rRNA tag-pyrosequencing over the course of a 30-day incubation. The contrasting fermentation temperatures converted similar amounts of biomass, but the mesophilic community was significantly more productive, and the two temperatures differed significantly with respect to propionic and butyric acid production. Pyrotag sequencing revealed the presence of dynamic communities that responded rapidly to temperature and changed substantially over time. Both temperatures were dominated by bacteria resembling Clostridia, but they shared few taxa in common. The species-rich mesophilic community harbored a variety of Bacteroidetes, Actinobacteria, and {gamma}-Proteobacteria, whereas the thermophilic community was composed mainly of Clostridia and Bacilli. Despite differences in composition and productivity, similar patterns of functional class dynamics were observed. Over time, organisms resembling known cellulose degraders decreased in abundance, while organisms resembling known xylose degraders increased. Improved understanding of the carboxylate platform's microbiology will help refine platform performance and contribute to our growing knowledge regarding biomass conversion and biofuel production processes. (orig.)

  10. Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production

    Energy Technology Data Exchange (ETDEWEB)

    Hollister, Emily B; Gentry, Terry J [Texas A and M Univ., College Station, TX (United States). Dept. of Soil and Crop Sciences; Forrest, Andrea K; Holtzapple, Mark T [Texas A and M Univ., College Station, TX (United States). Dept. of Chemical Engineering; Wilkinson, Heather H; Ebbole, Daniel J [Texas A and M Univ., College Station, TX (United States). Dept. of Plant Pathology and Microbiology; Malfatti, Stephanie A; Tringe, Susannah G [DOE Joint Genome Institute, Walnut Creek, CA (United States)

    2010-09-15

    The carboxylate platform utilizes a mixed microbial community to convert lignocellulosic biomass into chemicals and fuels. While much of the platform is well understood, little is known about its microbiology. Mesophilic (40 C) and thermophilic (55 C) fermentations employing a sorghum feedstock and marine sediment inoculum were profiled using 16S rRNA tag-pyrosequencing over the course of a 30-day incubation. The contrasting fermentation temperatures converted similar amounts of biomass, but the mesophilic community was significantly more productive, and the two temperatures differed significantly with respect to propionic and butyric acid production. Pyrotag sequencing revealed the presence of dynamic communities that responded rapidly to temperature and changed substantially over time. Both temperatures were dominated by bacteria resembling Clostridia, but they shared few taxa in common. The species-rich mesophilic community harbored a variety of Bacteroidetes, Actinobacteria, and {gamma}-Proteobacteria, whereas the thermophilic community was composed mainly of Clostridia and Bacilli. Despite differences in composition and productivity, similar patterns of functional class dynamics were observed. Over time, organisms resembling known cellulose degraders decreased in abundance, while organisms resembling known xylose degraders increased. Improved understanding of the carboxylate platform's microbiology will help refine platform performance and contribute to our growing knowledge regarding biomass conversion and biofuel production processes. (orig.)

  11. Enrichment of anaerobic syngas-converting bacteria from thermophilic bioreactor sludge.

    Science.gov (United States)

    Alves, Joana I; Stams, Alfons J M; Plugge, Caroline M; Alves, M Madalena; Sousa, Diana Z

    2013-12-01

    Thermophilic (55 °C) anaerobic microbial communities were enriched with a synthetic syngas mixture (composed of CO, H2 , and CO2 ) or with CO alone. Cultures T-Syn and T-CO were incubated and successively transferred with syngas (16 transfers) or CO (9 transfers), respectively, with increasing CO partial pressures from 0.09 to 0.88 bar. Culture T-Syn, after 4 successive transfers with syngas, was also incubated with CO and subsequently transferred (9 transfers) with solely this substrate - cultures T-Syn-CO. Incubation with syngas and CO caused a rapid decrease in the microbial diversity of the anaerobic consortium. T-Syn and T-Syn-CO showed identical microbial composition and were dominated by Desulfotomaculum and Caloribacterium species. Incubation initiated with CO resulted in the enrichment of bacteria from the genera Thermincola and Thermoanaerobacter. Methane was detected in the first two to three transfers of T-Syn, but production ceased afterward. Acetate was the main product formed by T-Syn and T-Syn-CO. Enriched T-CO cultures showed a two-phase conversion, in which H2 was formed first and then converted to acetate. This research provides insight into how thermophilic anaerobic communities develop using syngas/CO as sole energy and carbon source can be steered for specific end products and subsequent microbial synthesis of chemicals. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  12. Anaerobic digestion of spent mushroom substrate under thermophilic conditions: performance and microbial community analysis.

    Science.gov (United States)

    Xiao, Zheng; Lin, Manhong; Fan, Jinlin; Chen, Yixuan; Zhao, Chao; Liu, Bin

    2018-01-01

    Spent mushroom substrate (SMS) is the residue of edible mushroom production occurring in huge amounts. The SMS residue can be digested for biogas production in the mesophilic anaerobic digestion. In the present study, performance of batch thermophilic anaerobic digestion (TAD) of SMS was investigated as well as the interconnected microbial population structure changes. The analyzed batch TAD process lasted for 12 days with the cumulative methane yields of 177.69 mL/g volatile solid (VS). Hydrolytic activities of soluble sugar, crude protein, and crude fat in SMS were conducted mainly in the initial phase, accompanied by the excessive accumulation of volatile fatty acids and low methane yield. Biogas production increased dramatically from days 4 to 6. The degradation rates of cellulose and hemicellulose were 47.53 and 55.08%, respectively. The high-throughput sequencing of 16S rRNA gene amplicons revealed that Proteobacteria (56.7%-62.8%) was the dominant phylum in different fermentative stages, which was highly specific compared with other anaerobic processes of lignocellulosic materials reported in the literature. Crenarchaeota was abundant in the archaea. The most dominant genera of archaea were retrieved as Methanothermobacter and Methanobacterium, but the latter decreased sharply with time. This study shows that TAD is a feasible method to handle the waste SMS.

  13. Microbial community structure in a thermophilic aerobic digester used as a sludge pretreatment process for the mesophilic anaerobic digestion and the enhancement of methane production.

    Science.gov (United States)

    Jang, Hyun Min; Park, Sang Kyu; Ha, Jeong Hyub; Park, Jong Moon

    2013-10-01

    An effective two-stage sewage sludge digestion process, consisting of thermophilic aerobic digestion (TAD) followed by mesophilic anaerobic digestion (MAD), was developed for efficient sludge reduction and methane production. Using TAD as a biological pretreatment, the total volatile suspended solid reduction (VSSR) and methane production rate (MPR) in the MAD reactor were significantly improved. According to denaturing gradient gel electrophoresis (DGGE) analysis, the results indicated that the dominant bacteria species such as Ureibacillus thermophiles and Bacterium thermus in TAD were major routes for enhancing soluble organic matter. TAD pretreatment using a relatively short SRT of 1 day showed highly increased soluble organic products and positively affected an increment of bacteria populations which performed interrelated microbial metabolisms with methanogenic species in the MAD; consequently, a quantitative real-time PCR indicated greatly increased Methanosarcinales (acetate-utilizing methanogens) in the MAD, resulting in enhanced methane production. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Champagne Pool (New Zealand) Thermophiles Yield Insights into the Evolution of Microbial Arsenic Resistance

    Science.gov (United States)

    Hug, K.; Krikowa, F.; Morgan, X.; Maher, W. A.; Stott, M. B.; Moreau, J. W.

    2011-12-01

    detoxification mechanism. These results yield insights into potential arsenic detoxification strategies that may have fostered the evolution of thermophiles in ancient geothermal systems. Ref. : Childs A.M., Mountain B.W., O'Toole R., Stott M.B. (2008). "Relating Microbial Community and Physiochemical parameters of a Hot Spring: Champagne Pool, Wai-o-tapu, New Zealand." Geomicrobiology Journal 25 (7-8):441-453.

  15. Anaerobic digestion of nitrogen rich poultry manure: Impact of thermophilic biogas process on metal release and microbial resistances.

    Science.gov (United States)

    Anjum, Reshma; Grohmann, Elisabeth; Krakat, Niclas

    2017-02-01

    Poultry manure is a nitrogen rich fertilizer, which is usually recycled and spread on agricultural fields. Due to its high nutrient content, chicken manure is considered to be one of the most valuable animal wastes as organic fertilizer. However, when chicken litter is applied in its native form, concerns are raised as such fertilizers also include high amounts of antibiotic resistant pathogenic Bacteria and heavy metals. We studied the impact of an anaerobic thermophilic digestion process on poultry manure. Particularly, microbial antibiotic resistance profiles, mobile genetic elements promoting the resistance dissemination in the environment as well as the presence of heavy metals were focused in this study. The initiated heat treatment fostered a community shift from pathogenic to less pathogenic bacterial groups. Phenotypic and molecular studies demonstrated a clear reduction of multiple resistant pathogens and self-transmissible plasmids in the heat treated manure. That treatment also induced a higher release of metals and macroelements. Especially, Zn and Cu exceeded toxic thresholds. Although the concentrations of a few metals reached toxic levels after the anaerobic thermophilic treatment, the quality of poultry manure as organic fertilizer may raise significantly due to the elimination of antibiotic resistance genes (ARG) and self-transmissible plasmids. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing.

    Science.gov (United States)

    Rademacher, Antje; Zakrzewski, Martha; Schlüter, Andreas; Schönberg, Mandy; Szczepanowski, Rafael; Goesmann, Alexander; Pühler, Alfred; Klocke, Michael

    2012-03-01

    DNAs of two biofilms of a thermophilic two-phase leach-bed biogas reactor fed with rye silage and winter barley straw were sequenced by 454-pyrosequencing technology to assess the biofilm-based microbial community and their genetic potential for anaerobic digestion. The studied biofilms matured on the surface of the substrates in the hydrolysis reactor (HR) and on the packing in the anaerobic filter reactor (AF). The classification of metagenome reads showed Clostridium as most prevalent bacteria in the HR, indicating a predominant role for plant material digestion. Notably, insights into the genetic potential of plant-degrading bacteria were determined as well as further bacterial groups, which may assist Clostridium in carbohydrate degradation. Methanosarcina and Methanothermobacter were determined as most prevalent methanogenic archaea. In consequence, the biofilm-based methanogenesis in this system might be driven by the hydrogenotrophic pathway but also by the aceticlastic methanogenesis depending on metabolite concentrations such as the acetic acid concentration. Moreover, bacteria, which are capable of acetate oxidation in syntrophic interaction with methanogens, were also predicted. Finally, the metagenome analysis unveiled a large number of reads with unidentified microbial origin, indicating that the anaerobic degradation process may also be conducted by up to now unknown species. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  17. Performance and microbial community analysis of two-stage process with extreme thermophilic hydrogen and thermophilic methane production from hydrolysate in UASB reactors

    DEFF Research Database (Denmark)

    Kongjan, Prawit; O-Thong, Sompong; Angelidaki, Irini

    2011-01-01

    The two-stage process for extreme thermophilic hydrogen and thermophilic methane production from wheat straw hydrolysate was investigated in up-flow anaerobic sludge bed (UASB) reactors. Specific hydrogen and methane yields of 89ml-H2/g-VS (190ml-H2/g-sugars) and 307ml-CH4/g-VS, respectively were...... energy of 13.4kJ/g-VS. Dominant hydrogen-producing bacteria in the H2-UASB reactor were Thermoanaerobacter wiegelii, Caldanaerobacter subteraneus, and Caloramator fervidus. Meanwhile, the CH4-UASB reactor was dominated with methanogens of Methanosarcina mazei and Methanothermobacter defluvii. The results...

  18. Thermophilic biofiltration of benzene and toluene.

    Science.gov (United States)

    Cho, Kyung-Suk; Yoo, Sun-Kyung; Ryu, Hee Wook

    2007-12-01

    In the current studies, we characterized the degradation of a hot mixture of benzene and toluene (BT) gases by a thermophilic biofilter using polyurethane as packing material and high-temperature compost as a microbial source. We also examined the effect of supplementing the biofilter with yeast extract (YE). We found that YE substantially enhanced microbial activity in the thermophilic biofilter. The degrading activity of the biofilter supplied with YE was stable during long-term operation (approximately 100 d) without accumulating excess biomass. The maximum elimination capacity (1,650 g x m(-3) h(-1)) in the biofilter supplemented with YE was 3.5 times higher than that in the biofilter without YE (470 g g x m(-3) h(-1)). At similar retention times, the capacity to eliminate BT for the YE-supplemented biofilter was higher than for previously reported mesophilic biofilters. Thus, thermophilic biofiltration can be used to degrade hydrophobic compounds such as a BT mixture. Finally, 16S rDNA polymerase chain reaction-DGGE (PCR-DGGE) fingerprinting revealed that the thermophilic bacteria in the biofilter included Rubrobacter sp. and Mycobacterium sp.

  19. Molecular analysis of the microbial community structures in water-flooding petroleum reservoirs with different temperatures

    Science.gov (United States)

    Wang, L.-Y.; Duan, R.-Y.; Liu, J.-F.; Yang, S.-Z.; Gu, J.-D.; Mu, B.-Z.

    2012-04-01

    Temperature is one of the most important environmental factors regulating the activity and determining the composition of the microbial community. Analysis of microbial communities from six water-flooding petroleum reservoirs at temperatures from 20 to 63 °C by 16S rRNA gene clone libraries indicates the presence of physiologically diverse and temperature-dependent microorganisms in these subterrestrial ecosystems. In high-temperature petroleum reservoirs, most of the archaeal sequences belong to the thermophilic archaea including the genera Thermococcus, Methanothermobacter and Thermoplasmatales, most of the bacterial sequences belong to the phyla Firmicutes, Thermotogae and Thermodesulfobacteria; in low-temperature petroleum reservoirs, most of the archaeal sequences are affiliated with the genera Methanobacterium, Methanoculleus and Methanocalculus, most of the bacterial sequences to the phyla Proteobacteria, Bacteroidetes and Actinobacteria. Canonical correspondence analysis (CCA) revealed that temperature, mineralization, ionic type as well as volatile fatty acids showed correlation with the microbial community structures. These organisms may be adapted to the environmental conditions of these petroleum reservoirs over geologic time by metabolizing buried organic matter from the original deep subsurface environment and became the common inhabitants in subsurface environments.

  20. Community phylogenetic analysis of moderately thermophilic cyanobacterial mats from China, the Philippines and Thailand.

    Science.gov (United States)

    Hongmei, Jing; Aitchison, Jonathan C; Lacap, Donnabella C; Peerapornpisal, Yuwadee; Sompong, Udomluk; Pointing, Stephen B

    2005-08-01

    Most community molecular studies of thermophilic cyanobacterial mats to date have focused on Synechococcus occurring at temperatures of approximately 50-65 degrees C. These reveal that molecular diversity exceeds that indicated by morphology, and that phylogeographic lineages exist. The moderately thermophilic and generally filamentous cyanobacterial mat communities occurring at lower temperatures have not previously been investigated at the community molecular level. Here we report community diversity in mats of 42-53 degrees C recovered from previously unstudied geothermal locations. Separation of 16S rRNA gene-defined genotypes from community DNA was achieved by DGGE. Genotypic diversity was greater than morphotype diversity in all mats sampled, although genotypes generally corresponded to observed morphotypes. Thirty-six sequences were recovered from DGGE bands. Phylogenetic analyses revealed these to form novel thermophilic lineages distinct from their mesophilic counterparts, within Calothrix, Cyanothece, Fischerella, Phormidium, Pleurocapsa, Oscillatoria and Synechococcus. Where filamentous cyanobacterial sequences belonging to the same genus were recovered from the same site, these were generally closely affiliated. Location-specific sequences were observed for some genotypes recovered from geochemically similar yet spatially separated sites, thus providing evidence for phylogeographic lineages that evolve in isolation. Other genotypes were more closely affiliated to geographically remote counterparts from similar habitats suggesting that adaptation to certain niches is also important.

  1. Ecology and biotechnological potential of the thermophilic fermentative Coprothermobacter spp.

    Science.gov (United States)

    Gagliano, M C; Braguglia, C M; Petruccioli, M; Rossetti, S

    2015-05-01

    Thermophilic bacteria have been isolated from several terrestrial, marine and industrial environments. Anaerobic digesters treating organic wastes are often an important source of these microorganisms, which catalyze a wide array of metabolic processes. Moreover, organic wastes are primarily composed of proteins, whose degradation is often incomplete. Coprothermobacter spp. are proteolytic anaerobic thermophilic microbes identified in several studies focused on the analysis of the microbial community structure in anaerobic thermophilic reactors. They are currently classified in the phylum Firmicutes; nevertheless, several authors showed that the Coprothermobacter group is most closely related to the phyla Dictyoglomi and Thermotoga. Since only a few proteolytic anaerobic thermophiles have been characterized so far, this microorganism has attracted the attention of researchers for its potential applications with high-temperature environments. In addition to proteolysis, Coprothermobacter spp. showed several metabolic abilities and may have a biotechnological application either as source of thermostable enzymes or as inoculum in anaerobic processes. Moreover, they can improve protein degradation by establishing a syntrophy with hydrogenotrophic archaea. To gain a better understanding of the phylogenesis, metabolic capabilities and adaptations of these microorganisms, it is of importance to better define the role in thermophilic environments and to disclose properties not yet investigated. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Thermophilic archaeal community succession and function change associated with the leaching rate in bioleaching of chalcopyrite.

    Science.gov (United States)

    Zhu, Wei; Xia, Jin-lan; Yang, Yi; Nie, Zhen-yuan; Peng, An-an; Liu, Hong-chang; Qiu, Guan-zhou

    2013-04-01

    The community succession and function change of thermophilic archaea Acidianus brierleyi, Metallosphaera sedula, Acidianus manzaensis and Sulfolobus metallicus were studied by denaturing gradient gel electrophoresis (DGGE) analysis of amplifying 16S rRNA genes fragments and real-time qPCR analysis of amplifying sulfur-oxidizing soxB gene associated with chalcopyrite bioleaching rate at different temperatures and initial pH values. The analysis results of the community succession indicated that temperature and initial pH value had a significant effect on the consortium, and S. metallicus was most sensitive to the environmental change, A. brierleyi showed the best adaptability and sulfur oxidation ability and predominated in various leaching systems. Meanwhile, the leaching rate of chalcopyrite closely related to the consortium function embodied by soxB gene, which could prove a desirable way for revealing microbial sulfur oxidation difference and tracking the function change of the consortium, and for optimizing the leaching parameters and improving the recovery of valuable metals. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream

    Science.gov (United States)

    Nishizawa, Manabu; Koba, Keisuke; Makabe, Akiko; Yoshida, Naohiro; Kaneko, Masanori; Hirao, Shingo; Ishibashi, Jun-ichiro; Yamanaka, Toshiro; Shibuya, Takazo; Kikuchi, Tohru; Hirai, Miho; Miyazaki, Junichi; Nunoura, Takuro; Takai, Ken

    2013-07-01

    We report here the concurrence and interaction among forms of nitrogen metabolism in thermophilic microbial mat communities that developed in an ammonium-abundant subsurface geothermal stream. First, the physical and chemical conditions of the stream water at several representative microbial mat habitats (including upper, middle and downstream sites) were characterized. A thermodynamic calculation using these physical and chemical conditions predicted that nitrification consisting of ammonia and nitrite oxidations would provide one of the largest energy yields of chemolithotrophic metabolisms. Second, near-complete prokaryotic 16S rRNA gene clone analysis was conducted for representative microbial mat communities at the upper, middle and downstream sites. The results indicated a dynamic shift in the 16S rRNA gene phylotype composition through physical and chemical variations of the stream water. The predominant prokaryotic components varied from phylotypes related to hydrogeno (H2)- and thio (S)-trophic Aquificales, thermophilic methanotrophs and putative ammonia-oxidizing Archaea (AOA) located upstream (72 °C) to the phylotypes affiliated with putative AOA and nitrite-oxidizing bacteria (NOB) located at the middle and downstream sites (65 and 57 °C, respectively). In addition, the potential in situ metabolic activities of different forms of nitrogen metabolism were estimated through laboratory experiments using bulk microbial mat communities. Finally, the compositional and isotopic variation in nitrogen compounds was investigated in the stream water flowing over the microbial mats and in the interstitial water inside the mats. Although the stream water was characterized by a gradual decrease in the total ammonia concentration (ΣNH3: the sum of ammonia and ammonium concentrations) and a gradual increase in the total concentration of nitrite and nitrate (NO2- + NO3-), the total inorganic nitrogen concentration (TIN: the sum of ΣNH3, NO2- and NO3- concentrations

  4. The structural and functional contributions of β-glucosidase-producing microbial communities to cellulose degradation in composting.

    Science.gov (United States)

    Zang, Xiangyun; Liu, Meiting; Fan, Yihong; Xu, Jie; Xu, Xiuhong; Li, Hongtao

    2018-01-01

    Compost habitats sustain a vast ensemble of microbes that engender the degradation of cellulose, which is an important part of global carbon cycle. β-Glucosidase is the rate-limiting enzyme of degradation of cellulose. Thus, analysis of regulation of β-glucosidase gene expression in composting is beneficial to a better understanding of cellulose degradation mechanism. Genetic diversity and expression of β-glucosidase-producing microbial communities, and relationships of cellulose degradation, metabolic products and the relative enzyme activity during natural composting and inoculated composting were evaluated. Compared with natural composting, adding inoculation agent effectively improved the degradation of cellulose, and maintained high level of the carboxymethyl cellulose (CMCase) and β-glucosidase activities in thermophilic phase. Gene expression analysis showed that glycoside hydrolase family 1 (GH1) family of β-glucosidase genes contributed more to β-glucosidase activity in the later thermophilic phase in inoculated compost. In the cooling phase of natural compost, glycoside hydrolase family 3 (GH3) family of β-glucosidase genes contributed more to β-glucosidase activity. Intracellular β-glucosidase activity played a crucial role in the regulation of β-glucosidase gene expression, and upregulation or downregulation was also determined by extracellular concentration of glucose. At sufficiently high glucose concentrations, the functional microbial community in compost was altered, which may contribute to maintaining β-glucosidase activity despite the high glucose content. This research provides an ecological functional map of microorganisms involved in carbon metabolism in cattle manure-rice straw composting. The performance of the functional microbial groups in the two composting treatments is different, which is related to the cellulase activity and cellulose degradation, respectively.

  5. Previously unclassified bacteria dominate during thermophilic and mesophilic anaerobic pre-treatment of primary sludge.

    Science.gov (United States)

    Pervin, Hasina M; Batstone, Damien J; Bond, Philip L

    2013-06-01

    Thermophilic biological pre-treatment enables enhanced anaerobic digestion for treatment of wastewater sludges but, at present, there is limited understanding of the hydrolytic-acidogenic microbial composition and its contribution to this process. In this study, the process was assessed by comparing the microbiology of thermophilic (50-65 °C) and mesophilic (35 °C) pre-treatment reactors treating primary sludge. A full-cycle approach for the 16S rRNA genes was applied in order to monitor the diversity of bacteria and their abundance in a thermophilic pre-treatment reactor treating primary sludge. For the thermophilic pre-treatment (TP), over 90% of the sequences were previously undetected and these had less than 97% sequence similarity to cultured organisms. During the first 83 days, members of the Betaproteobacteria dominated the community sequences and a newly designed probe was used to monitor a previously unknown bacterium affiliated with the genus Brachymonas. Between days 85 and 183, three phylotypes that affiliated with the genera Comamonas, Clostridium and Lysobacter were persistently dominant in the TP community, as revealed by terminal-restriction fragment length polymorphism (T-RFLP). Hydrolytic and fermentative functions have been speculated for these bacteria. Mesophilic pre-treatment (MP) and TP communities were different but they were both relatively dynamic. Statistical correlation analysis and the function of closely allied reference organisms indicated that previously unclassified bacteria dominated the TP community and may have been functionally involved in the enhanced hydrolytic performance of thermophilic anaerobic pre-treatment. This study is the first to reveal the diversity and dynamics of bacteria during anaerobic digestion of primary sludge. Copyright © 2013 Elsevier GmbH. All rights reserved.

  6. Bioprospecting thermophiles for cellulase production: a review.

    Science.gov (United States)

    Acharya, Somen; Chaudhary, Anita

    2012-07-01

    Most of the potential bioprospecting is currently related to the study of the extremophiles and their potential use in industrial processes. Recently microbial cellulases find applications in various industries and constitute a major group of industrial enzymes. Considerable amount of work has been done on microbial cellulases, especially with resurgence of interest in biomass ethanol production employing cellulases and use of cellulases in textile and paper industry. Most efficient method of lignocellulosic biomass hydrolysis is through enzymatic saccharification using cellulases. Significant information has also been gained about the physiology of thermophilic cellulases producers and process development for enzyme production and biomass saccharification. The review discusses the current knowledge on cellulase producing thermophilic microorganisms, their physiological adaptations and control of cellulase gene expression. It discusses the industrial applications of thermophilic cellulases, their cost of production and challenges in cellulase research especially in the area of improving process economics of enzyme production.

  7. Microbial Communities of the Okinawa Backarc Basin Subvent Biosphere

    Science.gov (United States)

    Brandt, L. D.; House, C. H.

    2014-12-01

    IODP Expedition 331 to the Okinawa backarc basin provided an opportunity to study the microbial stratigraphy within the sediments surrounding a hydrothermal vent. The Okinawa backarc basin is a sedimented region of the seafloor located on a continental margin, and also hosts a hydrothermal network within the subsurface. Site C0014 within the Iheya North hydrothermal field is located 450 m east of the active vent and has a surface temperature of 5°C with no evidence of hydrothermal alteration within the top 10 m. Temperature increases with depth at an estimated rate of 3°C/m and transitions from non-hydrothermal margin sediments to a hydrothermally altered regime below 10 m. Site C0014 is a unique location to study changes in microbial communities with depth, as the hydrothermal system generates a thermally and geochemically restrictive subvent biosphere. In this study, we utilized deep 16S rRNA sequencing of DNA from IODP Expedition 331 Site C0014 sediment horizons in order to assess diversity throughout the sediment column as well as determine the potential limits of the biosphere. Analysis of the amplicon data suggests that Archaea represent a significant proportion of the indigenous community throughout the top 15 m of sediment, where Archaea then abruptly disappear. Furthermore, a deeper classification of Archaeal sequences suggests a transition from a mesophilic community to a potentially thermophilic one, where there is an increasingly stronger signal of Miscellaneous Crenarchaeotic Group (MCG) followed by Terrestrial Hot Spring Crenarchaeotic Group (THSCG). Additionally, there are several horizons in which methanotrophy is likely supported, indicated by peaks in anaerobic methanotrophic Archaea. The cessation of Archaea as well as Chloroflexi, a common marine subsurface bacterial phylum, at approximately 15 meters below seafloor (mbsf) is suggestive of a potential boundary within Site C0014 in which the environmental conditions have become too restrictive

  8. Bioprospecting thermophiles for cellulase production: a review

    Directory of Open Access Journals (Sweden)

    Somen Acharya

    2012-09-01

    Full Text Available Most of the potential bioprospecting is currently related to the study of the extremophiles and their potential use in industrial processes. Recently microbial cellulases find applications in various industries and constitute a major group of industrial enzymes. Considerable amount of work has been done on microbial cellulases, especially with resurgence of interest in biomass ethanol production employing cellulases and use of cellulases in textile and paper industry. Most efficient method of lignocellulosic biomass hydrolysis is through enzymatic saccharification using cellulases. Significant information has also been gained about the physiology of thermophilic cellulases producers and process development for enzyme production and biomass saccharification. The review discusses the current knowledge on cellulase producing thermophilic microorganisms, their physiological adaptations and control of cellulase gene expression. It discusses the industrial applications of thermophilic cellulases, their cost of production and challenges in cellulase research especially in the area of improving process economics of enzyme production.

  9. The performance of a thermophilic microbial fuel cell fed with synthesis gas.

    Science.gov (United States)

    Hussain, A; Mehta, P; Raghavan, V; Wang, H; Guiot, S R; Tartakovsky, B

    2012-08-10

    This study demonstrated electricity generation in a thermophilic microbial fuel cell (MFC) operated on synthesis gas (syngas) as the sole electron donor. At 50°C, a volumetric power output of 30-35 mWL(R)(-1) and a syngas conversion efficiency of 87-98% was achieved. The observed pathway of syngas conversion to electricity primarily consisted of a two-step process, where the carbon monoxide and hydrogen were first converted to acetate, which was then consumed by the anodophilic bacteria to produce electricity. A denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rDNA revealed the presence of Geobacter species, Acetobacter, methanogens and several uncultured bacteria and archaea in the anodic chamber. Crown Copyright © 2012. Published by Elsevier Inc. All rights reserved.

  10. Comprehensive microbial analysis of combined mesophilic anaerobic-thermophilic aerobic process treating high-strength food wastewater.

    Science.gov (United States)

    Jang, Hyun Min; Ha, Jeong Hyub; Park, Jong Moon; Kim, Mi-Sun; Sommer, Sven G

    2015-04-15

    A combined mesophilic anaerobic-thermophilic aerobic process was used to treat high-strength food wastewater in this study. During the experimental period, most of solid residue from the mesophilic anaerobic reactor (R1) was separated by centrifugation and introduced into the thermophilic aerobic reactor (R2) for further digestion. Then, thermophilic aerobically-digested sludge was reintroduced into R1 to enhance reactor performance. The combined process was operated with two different Runs: Run I with hydraulic retention time (HRT) = 40 d (corresponding OLR = 3.5 kg COD/m(3) d) and Run II with HRT = 20 d (corresponding OLR = 7 kg COD/m(3)). For a comparison, a single-stage mesophilic anaerobic reactor (R3) was operated concurrently with same OLRs and HRTs as the combined process. During the overall digestion, all reactors showed high stability without pH control. The combined process demonstrated significantly higher organic matter removal efficiencies (over 90%) of TS, VS and COD and methane production than did R3. Quantitative real-time PCR (qPCR) results indicated that higher populations of both bacteria and archaea were maintained in R1 than in R3. Pyrosequencing analysis revealed relatively high abundance of phylum Actinobacteria in both R1 and R2, and a predominance of phyla Synergistetes and Firmicutes in R3 during Run II. Furthermore, R1 and R2 shared genera (Prevotella, Aminobacterium, Geobacillus and Unclassified Actinobacteria), which suggests synergy between mesophilic anaerobic digestion and thermophilic aerobic digestion. For archaea, in R1 methanogenic archaea shifted from genus Methanosaeta to Methanosarcina, whereas genera Methanosaeta, Methanobacterium and Methanoculleus were predominant in R3. The results demonstrated dynamics of key microbial populations that were highly consistent with an enhanced reactor performance of the combined process. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Characterization of thermophilic fungal community associated with pile fermentation of Pu-erh tea.

    Science.gov (United States)

    Zhang, Wei; Yang, Ruijuan; Fang, Wenjun; Yan, Liang; Lu, Jun; Sheng, Jun; Lv, Jie

    2016-06-16

    This study aimed to characterize the thermophilic fungi in pile-fermentation process of Pu-erh tea. Physicochemical analyses showed that the high temperature and low pH provided optimal conditions for propagation of fungi. A number of fungi, including Blastobotrys adeninivorans, Thermomyces lanuginosus, Rasamsonia emersonii, Aspergillus fumigatus, Rhizomucor pusillus, Rasamsonia byssochlamydoides, Rasamsonia cylindrospora, Aspergillus tubingensis, Aspergillus niger, Candida tropicalis and Fusarium graminearum were isolated as thermophilic fungi under combination of high temperature and acid culture conditions from Pu-erh tea pile-fermentation. The fungal communities were analyzed by PCR-DGGE. Results revealed that those fungi are closely related to Debaryomyces hansenii, Cladosporium cladosporioides, A. tubingensis, R. emersonii, R. pusillus, A. fumigatus and A. niger, and the last four presented as dominant species in the pile process. These four preponderant thermophilic fungi reached the order of magnitude of 10(7), 10(7), 10(7) and 10(6)copies/g dry tea, respectively, measured by real-time quantitative PCR (q-PCR). The results indicate that the thermophilic fungi play an important role in Pu-erh tea pile fermentation. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. ENDOSPORES OF THERMOPHILIC FERMENTATIVE BACTERIA

    DEFF Research Database (Denmark)

    Volpi, Marta

    2016-01-01

    solely based on endospores of sulphate-reducing bacteria (SRB), which presumably constitute only a small fraction of the total thermophilic endospore community reaching cold environments. My PhD project developed an experimental framework for using thermophilic fermentative endospores (TFEs) to trace...

  13. Bioleaching of a low-grade nickel-copper sulfide by mixture of four thermophiles.

    Science.gov (United States)

    Li, Shuzhen; Zhong, Hui; Hu, Yuehua; Zhao, Jiancun; He, Zhiguo; Gu, Guohua

    2014-02-01

    This study investigated thermophilic bioleaching of a low grade nickel-copper sulfide using mixture of four acidophilic thermophiles. Effects of 0.2g/L l-cysteine on the bioleaching process were further evaluated. It aimed at offering new alternatives for enhancing metal recoveries from nickel-copper sulfide. Results showed a recovery of 80.4% nickel and 68.2% copper in 16-day bioleaching without l-cysteine; while 83.7% nickel and 81.4% copper were recovered in the presence of l-cysteine. Moreover, nickel recovery was always higher than copper recovery. l-Cysteine was found contributing to lower pH value, faster microbial growth, higher Oxidation-Reduction Potential (ORP), higher zeta potential and absorbing on the sulfide surfaces through amino, carboxyl and sulfhydryl groups. X-ray Diffraction (XRD) patterns of leached residues showed generation of S, jarosite and ammoniojarosite. Denaturing Gradient Gel Electrophoresis (DGGE) results revealed that l-cysteine could have variant impacts on different microorganisms and changed the microbial community composition dramatically during nickel-copper sulfide bioleaching. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. In-Drift Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    D. Jolley

    2000-11-09

    As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses.

  15. In-Drift Microbial Communities

    International Nuclear Information System (INIS)

    Jolley, D.

    2000-01-01

    As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses

  16. A comparative study of composting the solid fraction of dairy manure with or without bulking material: Performance and microbial community dynamics.

    Science.gov (United States)

    Zhong, Xiao-Zhong; Ma, Shi-Chun; Wang, Shi-Peng; Wang, Ting-Ting; Sun, Zhao-Yong; Tang, Yue-Qin; Deng, Yu; Kida, Kenji

    2018-01-01

    The present study compared the development of various physicochemical properties and the composition of microbial communities involved in the composting process in the solid fraction of dairy manure (SFDM) with a sawdust-regulated SFDM (RDM). The changes in several primary physicochemical properties were similar in the two composting processes, and both resulted in mature end-products within 48days. The bacterial communities in both composting processes primarily comprised Proteobacteria and Bacteroidetes. Firmicutes were predominant in the thermophilic phase, whereas Chloroflexi, Planctomycetes, and Nitrospirae were more abundant in the final mature phase. Furthermore, the succession of bacteria in both groups proceeded in a similar pattern, suggesting that the effects of the bulking material on bacterial dynamics were minor. These results demonstrate the feasibility of composting using only the SFDM, reflected by the evolution of physicochemical properties and the microbial communities involved in the composting process. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Effects of sludge inoculum and organic feedstock on active microbial communities and methane yield during anaerobic digestion

    Directory of Open Access Journals (Sweden)

    David eWilkins

    2015-10-01

    Full Text Available Anaerobic digestion (AD is a widespread microbial technology used to treat organic waste and recover energy in the form of methane (biogas. While most AD systems have been designed to treat a single input, mixtures of digester sludge and solid organic waste are emerging as a means to improve efficiency and methane yield. We examined laboratory anaerobic cultures of AD sludge from two sources amended with food waste, xylose, and xylan at mesophilic temperatures, and with cellulose at meso- and thermophilic temperatures, to determine whether and how the inoculum and substrate affect biogas yield and community composition. All substrate and inoculum combinations yielded methane, with food waste most productive by mass. Pyrosequencing of transcribed bacterial and archaeal 16S rRNA showed that community composition varied across substrates and inocula, with differing ratios of hydrogenotrophic/acetoclastic methanogenic archaea associated with syntrophic partners. While communities did not cluster by either inoculum or substrate, additional sequencing of the bacterial 16S rRNA gene in the source sludge revealed that the bacterial communities were influenced by their inoculum. These results suggest that complete and efficient AD systems could potentially be assembled from different microbial inocula and consist of taxonomically diverse communities that nevertheless perform similar functions.

  18. What is microbial community ecology?

    Science.gov (United States)

    Konopka, Allan

    2009-11-01

    The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.

  19. Invasion in microbial communities: Role of community composition and assembly processes

    DEFF Research Database (Denmark)

    Kinnunen, Marta

    of microbial community assembly. Biotic factors include interactions between different microbial groups as well as the community response to alien species – invaders. Microbial invasions can have significant effects on the composition and functioning of resident communities. There is, however, lack......Microbes contribute to all biogeochemical cycles on earth and are responsible for key biological processes that support the survival of plants and animals. There is increased interest in controlling and managing microbial communities in different ecosystems in order to make targeted microbiological...... processes more effective. In order to manage microbial communities, it is essential to understand the factors that shape and influence microbial community composition. In addition to abiotic factors, such as environmental conditions and resource availability, biotic factors also shape the dynamics...

  20. Start-up strategies for thermophilic anaerobic digestion of pig manure

    International Nuclear Information System (INIS)

    Moset, V.; Bertolini, E.; Cerisuelo, A.; Cambra, M.; Olmos, A.; Cambra-López, M.

    2014-01-01

    Sludge physicochemical composition, methane (CH 4 ) yield, and methanogenic community structure and dynamics using quantitative real-time polymerase chain reaction were determined after start-up of anaerobic digestion of pig manure. Eight thermophilic continuous stirred anaerobic digesters were used during 126 days. Four management strategies were investigated: a feedless and a non-feedless period followed by a gradual or an abrupt addition of pig manure (two digesters per strategy). During the first 43 days, VFA (volatile fatty acids) accumulations and low CH 4 yield were observed in all digesters. After this period, digesters recovered their initial status being propionic acid the last parameter to be re-established. Non-feedless digesters with an abrupt addition of pig manure showed the best performances (lower VFA accumulation and higher CH 4 yield). Differences in microbial orders and dynamics, however, were less evident among treatments. Hydrogenotrophic methanogenesis, Methanomicrobiales first and Methanobacteriales second, was the dominant metabolic pathway in all digesters. Further research is needed to clarify the role and activity of hydrogenotrophic methanogens during the recovery start-up period and to identify the best molecular tools and methodologies to monitor microbial populations and dynamics reliably and accurately in anaerobic digesters. - Highlights: • Four start-up strategies for thermophilic anaerobic digestion of pig manure were tested. • Physicochemical composition, methane yield and methanogenic community were determined. • During the first 43 days, a decline in reactor's performance occurred. • The best start-up strategy was non-feedless with an abrupt addition of pig slurry. • Hydrogenotrophic methanogenesis was the dominant metabolic pathway

  1. Characterization of the planktonic microbiome in upflow anaerobic sludge blanket reactors during adaptation of mesophilic methanogenic granules to thermophilic operational conditions

    DEFF Research Database (Denmark)

    Zhu, Xinyu; Treu, Laura; Kougias, Panagiotis

    2017-01-01

    Upflow anaerobic sludge blanket (UASB) technology refers to reactor technology where granules, i.e. self-immobilised microbial associations, are the biological catalysts involved in the anaerobic digestion process. During the start-up period, UASB reactors operate at relatively long HRT and there......Upflow anaerobic sludge blanket (UASB) technology refers to reactor technology where granules, i.e. self-immobilised microbial associations, are the biological catalysts involved in the anaerobic digestion process. During the start-up period, UASB reactors operate at relatively long HRT...... and therefore the liquid phase of the reactor becomes a favourable environment for microbial growth. The current study aimed to elucidate the dynamicity of the suspended microbial community in UASB reactors, during the transition from mesophilic to thermophilic conditions. High throughput 16S rRNA amplicon...... sequencing was used to characterize the taxonomic composition of the microbiome. The results showed that the microbial community was mainly composed by hydrolytic and fermentative bacteria. Results revealed relevant shifts in the microbial community composition, which is mainly determined by the operational...

  2. Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

    NARCIS (Netherlands)

    Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

    2012-01-01

    The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into

  3. Benefits to decomposition rates when using digestate as compost co-feedstock: Part II - Focus on microbial community dynamics.

    Science.gov (United States)

    Arab, Golnaz; Razaviarani, Vahid; Sheng, Zhiya; Liu, Yang; McCartney, Daryl

    2017-10-01

    Linkage between composting reactor performance and microbial community dynamics was investigated during co-composting of digestate and fresh feedstock (organic fraction of municipal solid waste) using 25L reactors. Previously, the relationship between composting performance and various physicochemical parameters were reported in Part I of the study (Arab and McCartney, 2017). Three digestate to fresh feedstock ratios (0, 40, and 100%; wet weight basis) were selected for analysis of microbial community dynamics. The 40% ratio was selected because it was found to perform the best (Arab and McCartney, 2017). Illumina sequencing results revealed that the reactor with a greater composting performance (higher organic matter degradation and higher heat generation; 40% ratio) was associated with higher microbial diversity. Two specific bacterial orders that might result in higher performance were Thermoactinomycetaceae and Actinomycetales with a higher sequence abundance during thermophilic composting phase and during the maturing composting phase, respectively. Galactomyces, Pichia, Chaetomium, and Acremonium were the four fungal genera that are probably also involved in higher organic matter degradation in the reactor with better performance. The redundancy analysis (RDA) biplot indicated that among the studied environmental variables, temperature, total ammonia nitrogen and nitrate concentration accounted for much of the major shifts in microbial sequence abundance during the co-composting process. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

  4. Microbial Communities of Terrestrial Springs in Extensional Settings of the Western U.S.A.

    Science.gov (United States)

    Takacs-Vesbach, C.; Hall, J.; Crossey, L. J.; Karlstrom, K. E.; Fischer, T.; Cron, B.

    2008-12-01

    Gas and water chemistry from hot springs, gas vents, travertine-bearing cool springs, and high-pCO2 groundwaters of the western U.S. indicate a regionally extensive flux of deeply sourced volatiles through spring vents. We use the term "continental smokers" to emphasize and test analogs to mid-ocean vent systems, and are currently concentrating on vents in the Rocky Mountain/Colorado Plateau region as part of the Colorado Rockies and Experiment and Seismic transects (CREST). Measurable mantle-derived helium components (3He/4He = 0.10 to 2.1 RA) occur in nearly all springs in Colorado and New Mexico suggesting direct fast fluid pathways from the mantle to the surface hydrologic system. Important components of the CO2 are also derived from the mantle. We surveyed the geochemistry and microbial diversity of more than forty deeply sourced terrestrial springs that ranged in temperatures from 9° to 70°C. We hypothesize that degassing in continental extensional settings supports microbial assemblages that are analogous to chemolithotrophic communities at mid-ocean ridges and continental volcanic hydrothermal systems. Geochemical characteristics of the fluids and gases structure and sustain distinctive geomicrobiological communities as indicated by the widespread presence of archaea and thermophilic organisms in cool as well as hot springs.

  5. Biogas Upgrading via Hydrogenotrophic Methanogenesis in Two-Stage Continuous Stirred Tank Reactors at Mesophilic and Thermophilic Conditions

    DEFF Research Database (Denmark)

    Bassani, Ilaria; Kougias, Panagiotis; Treu, Laura

    2015-01-01

    This study proposes an innovative setup composed by two stage reactors to achieve biogas upgrading coupling the CO2 in the biogas with external H2 and subsequent conversion into CH4 by hydrogenotrophic methanogenesis. In this configuration, the biogas produced in the first reactor was transferred...... production and CO2 conversion was recorded. The consequent increase of pH did not inhibit the process indicating adaptation of microorganisms to higher pH levels. The effects of H2 on the microbial community were studied using high-throughput Illumina random sequences and full-length 16S rRNA genes extracted...... to the second one, where H2 was injected. This configuration was tested at both mesophilic and thermophilic conditions. After H2 addition, the produced biogas was upgraded to average CH4 content of 89% in the mesophilic reactor and 85% in the thermophilic. At thermophilic conditions, a higher efficiency of CH4...

  6. Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

    OpenAIRE

    Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

    2012-01-01

    The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) w...

  7. Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

    OpenAIRE

    Timmers, Ruud A.; Rothballer, Michael; Strik, David P. B. T. B.; Engel, Marion; Schulz, Stephan; Schloter, Michael; Hartmann, Anton; Hamelers, Bert; Buisman, Cees

    2012-01-01

    The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode–rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) w...

  8. Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years.

    Science.gov (United States)

    de Rezende, Júlia Rosa; Kjeldsen, Kasper Urup; Hubert, Casey R J; Finster, Kai; Loy, Alexander; Jørgensen, Bo Barker

    2013-01-01

    Patterns of microbial biogeography result from a combination of dispersal, speciation and extinction, yet individual contributions exerted by each of these mechanisms are difficult to isolate and distinguish. The influx of endospores of thermophilic microorganisms to cold marine sediments offers a natural model for investigating passive dispersal in the ocean. We investigated the activity, diversity and abundance of thermophilic endospore-forming sulfate-reducing bacteria (SRB) in Aarhus Bay by incubating pasteurized sediment between 28 and 85 °C, and by subsequent molecular diversity analyses of 16S rRNA and of the dissimilatory (bi)sulfite reductase (dsrAB) genes within the endospore-forming SRB genus Desulfotomaculum. The thermophilic Desulfotomaculum community in Aarhus Bay sediments consisted of at least 23 species-level 16S rRNA sequence phylotypes. In two cases, pairs of identical 16S rRNA and dsrAB sequences in Arctic surface sediment 3000 km away showed that the same phylotypes are present in both locations. Radiotracer-enhanced most probable number analysis revealed that the abundance of endospores of thermophilic SRB in Aarhus Bay sediment was ca. 10(4) per cm(3) at the surface and decreased exponentially to 10(0) per cm(3) at 6.5 m depth, corresponding to 4500 years of sediment age. Thus, a half-life of ca. 300 years was estimated for the thermophilic SRB endospores deposited in Aarhus Bay sediments. These endospores were similarly detected in the overlying water column, indicative of passive dispersal in water masses preceding sedimentation. The sources of these thermophiles remain enigmatic, but at least one source may be common to both Aarhus Bay and Arctic sediments.

  9. Oxygen and carbon dioxide mass transfer and the aerobic, autotrophic cultivation of moderate and extreme thermophiles : a case study related to the microbial desulfurization of coal

    NARCIS (Netherlands)

    Boogerd, F C; Bos, P; Kuenen, J.G.; Heijnen, J.; van der Lans, R G

    Mass transfers of O(2), CO(2), and water vapor are among the key processes in the aerobic, autotrophic cultivation of moderate and extreme thermophiles. The dynamics and kinetics of these processes are, in addition to the obvious microbial kinetics, of crucial importance for the industrial

  10. Antibiotic Resistance Genes and Correlations with Microbial Community and Metal Resistance Genes in Full-Scale Biogas Reactors As Revealed by Metagenomic Analysis

    DEFF Research Database (Denmark)

    Luo, Gang; Li, Bing; Li, Li-Guan

    2017-01-01

    resistance genes (MRGs). The total abundance of ARGs in all the samples varied from 7 × 10-3 to 1.08 × 10-1 copy of ARG/copy of 16S-rRNA gene, and the samples obtained from thermophilic biogas reactors had a lower total abundance of ARGs, indicating the superiority of thermophilic anaerobic digestion......Digested residues from biogas plants are often used as biofertilizers for agricultural crops cultivation. The antibiotic resistance genes (ARGs) in digested residues pose a high risk to public health due to their potential spread to the disease-causing microorganisms and thus reduce...... the susceptibility of disease-causing microorganisms to antibiotics in medical treatment. A high-throughput sequencing (HTS)-based metagenomic approach was used in the present study to investigate the variations of ARGs in full-scale biogas reactors and the correlations of ARGs with microbial communities and metal...

  11. Soil microbial community structure across a thermal gradient following a geothermal heating event.

    Science.gov (United States)

    Norris, Tracy B; Wraith, Jon M; Castenholz, Richard W; McDermott, Timothy R

    2002-12-01

    In this study microbial species diversity was assessed across a landscape in Yellowstone National Park, where an abrupt increase in soil temperature had occurred due to recent geothermal activity. Soil temperatures were measured, and samples were taken across a temperature gradient (35 to 65 degrees C at a 15-cm depth) that spanned geothermally disturbed and unimpacted soils; thermally perturbed soils were visually apparent by the occurrence of dead or dying lodgepole pine trees. Changes in soil microbial diversity across the temperature gradient were qualitatively assessed based on 16S rRNA sequence variation as detected by denaturing gradient gel electrophoresis (DGGE) using both ribosomal DNA (rDNA) and rRNA as PCR templates and primers specific for the Bacteria or Archaea domain. The impact of the major heating disturbance was apparent in that DGGE profiles from heated soils appeared less complex than those from the unaffected soils. Phylogenetic analysis of a bacterial 16S rDNA PCR clone library from a recently heated soil showed that a majority of the clones belonged to the Acidobacterium (51%) and Planctomyces (18%) divisions. Agar plate counts of soil suspensions cultured on dilute yeast extract and R2A agar media incubated at 25 or 50 degrees C revealed that thermophile populations were two to three orders of magnitude greater in the recently heated soil. A soil microcosm laboratory experiment simulated the geothermal heating event. As determined by both RNA- and DNA-based PCR coupled with DGGE, changes in community structure (marked change in the DGGE profile) of soils incubated at 50 degrees C occurred within 1 week and appeared to stabilize after 3 weeks. The results of our molecular and culture data suggest that thermophiles or thermotolerant species are randomly distributed in this area within Yellowstone National Park and that localized thermal activity selects for them.

  12. Marine Subsurface Microbial Communities Across a Hydrothermal Gradient in Okinawa Trough Sediments

    Science.gov (United States)

    Brandt, L. D.; Hser Wah Saw, J.; Ettema, T.; House, C. H.

    2015-12-01

    IODP Expedition 331 to the Okinawa backarc basin provided an opportunity to study the microbial stratigraphy within the sediments surrounding a hydrothermal vent. The Okinawa backarc basin is a sedimented region of the seafloor located on a continental margin, and also hosts a hydrothermal network within the subsurface. Site C0014 within the Iheya North hydrothermal field is located 450 m east of the active vent and has a surface temperature of 5°C with no evidence of hydrothermal alteration within the top 10 meters below sea floor (mbsf). Temperature increases with depth at an estimated rate of 3°C/m and transitions from non-hydrothermal margin sediments to a hydrothermally altered regime below 10 mbsf. In this study, we utilized deep 16S rRNA sequencing of DNA from IODP Expedition 331 Site C0014 sediment horizons in order to assess diversity throughout the sediment column as well as determine the potential limits of the biosphere. Analysis of the amplicon data shows a shift over 15 mbsf from a heterogeneous community of cosmopolitan marine subsurface taxa toward an archaeal-dominated community in the deepest horizons of the predicted biosphere. Notably, the phylum Chloroflexi represents a substantial taxon through most horizons, where it appears to be replaced below 10 mbsf by punctuations of thermophilic and methanotrophic Archaea and Miscellaneous Crenarchaeotic Group abundances. DNA from the aforementioned transition horizons was further analyzed using metagenomic sequencing. Preliminary taxonomic analysis of the metagenomic data agrees well with amplicon data in capturing the shift in relative abundance of Archaea increasing with depth. Additionally, reverse gyrase, a gene found exclusively in hyperthermophilic microorganisms, was recovered only in the metagenome of the deepest horizon. A BLAST search of this protein sequence against the GenBank non-redudnant protein database produced top hits with reverse gyrase from Thermococcus and Pyrococcus, which are

  13. Microbial community functional change during vertebrate carrion decomposition.

    Directory of Open Access Journals (Sweden)

    Jennifer L Pechal

    Full Text Available Microorganisms play a critical role in the decomposition of organic matter, which contributes to energy and nutrient transformation in every ecosystem. Yet, little is known about the functional activity of epinecrotic microbial communities associated with carrion. The objective of this study was to provide a description of the carrion associated microbial community functional activity using differential carbon source use throughout decomposition over seasons, between years and when microbial communities were isolated from eukaryotic colonizers (e.g., necrophagous insects. Additionally, microbial communities were identified at the phyletic level using high throughput sequencing during a single study. We hypothesized that carrion microbial community functional profiles would change over the duration of decomposition, and that this change would depend on season, year and presence of necrophagous insect colonization. Biolog EcoPlates™ were used to measure the variation in epinecrotic microbial community function by the differential use of 29 carbon sources throughout vertebrate carrion decomposition. Pyrosequencing was used to describe the bacterial community composition in one experiment to identify key phyla associated with community functional changes. Overall, microbial functional activity increased throughout decomposition in spring, summer and winter while it decreased in autumn. Additionally, microbial functional activity was higher in 2011 when necrophagous arthropod colonizer effects were tested. There were inconsistent trends in the microbial function of communities isolated from remains colonized by necrophagous insects between 2010 and 2011, suggesting a greater need for a mechanistic understanding of the process. These data indicate that functional analyses can be implemented in carrion studies and will be important in understanding the influence of microbial communities on an essential ecosystem process, carrion decomposition.

  14. PCR-DGGE analysis of the microbial communities in three different Chinese "Baiyunbian" liquor fermentation starters.

    Science.gov (United States)

    Xiong, Xiaomao; Hu, Yuanliang; Yan, Nanfeng; Huang, Yingna; Peng, Nan; Liang, Yunxiang; Zhao, Shumiao

    2014-08-01

    A systematic investigation was performed on the bacterial, Bacillus, fungal, and yeast communities of the three types of Daqu (mechanically prepared, manually prepared, and mixed prepared) used in Baiyunbian Company by reconditioning PCR-denaturing gradient gel electrophoresis (PCR-DGGE). The DGGE results showed that the microbes in the three types of Daqu were mainly thermotolerant and thermophilic microbes, and the most dominant bacterial species were Bacillus and Virgibacillus, followed by Lactobacillus and Trichococcus. Furthermore, the dominant fungi were found to be molds, such as Rasamsonia, Penicillium, Aspergillus, and Monascus, and the dominant yeasts were Saccharomyces cerevisiae, Saccharomycopsis fibuligera, Pichia anomala, and Debaryomyces hansenii. In general, the three types of Daqu showed slight differences in microbial communities, and the Shannon indexes (H') of the manually prepared and mechanically prepared Daqu were similar. The results suggest that mechanically prepared Daqu can replace manually prepared Daqu in liquor production, and this research provides useful information for liquor production and process improvement.

  15. Effect of alkaline pretreatment on mesophilic and thermophilic anaerobic digestion of a submerged macrophyte: Inhibition and recovery against dissolved lignin during semi-continuous operation.

    Science.gov (United States)

    Koyama, Mitsuhiko; Watanabe, Keiko; Kurosawa, Norio; Ishikawa, Kanako; Ban, Syuhei; Toda, Tatsuki

    2017-08-01

    The long-term effect of alkaline pretreatment on semi-continuous anaerobic digestion (AD) of the lignin-rich submerged macrophyte Potamogeton maackianus was investigated using mesophilic and thermophilic conditions. In pretreated reactors, dissolved lignin accumulated to high levels. CH 4 production under the pretreated condition was higher than that of the untreated condition, but decreased from Days 22 (mesophilic) and 42 (thermophilic). However, CH 4 production subsequently recovered, although dissolved lignin accumulated. Further, the change in the microbial community was observed between conditions. These results suggest that dissolved lignin temporarily inhibited AD, although acclimatization to dissolved lignin occurred during long-term operation. During the steady state period, mesophilic conditions achieved a 42% increase in the CH 4 yield using pretreatment, while thermophilic conditions yielded an 8% increment. Because volatile fatty acids accumulated even after acclimatization during the thermophilic pretreated condition and was discharged with the effluent, improvement of the methanogenic step would enable enhanced CH 4 recovery. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Glycoside Hydrolases across Environmental Microbial Communities.

    Directory of Open Access Journals (Sweden)

    Renaud Berlemont

    2016-12-01

    Full Text Available Across many environments microbial glycoside hydrolases support the enzymatic processing of carbohydrates, a critical function in many ecosystems. Little is known about how the microbial composition of a community and the potential for carbohydrate processing relate to each other. Here, using 1,934 metagenomic datasets, we linked changes in community composition to variation of potential for carbohydrate processing across environments. We were able to show that each ecosystem-type displays a specific potential for carbohydrate utilization. Most of this potential was associated with just 77 bacterial genera. The GH content in bacterial genera is best described by their taxonomic affiliation. Across metagenomes, fluctuations of the microbial community structure and GH potential for carbohydrate utilization were correlated. Our analysis reveals that both deterministic and stochastic processes contribute to the assembly of complex microbial communities.

  17. Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester.

    Science.gov (United States)

    Hagen, Live H; Frank, Jeremy A; Zamanzadeh, Mirzaman; Eijsink, Vincent G H; Pope, Phillip B; Horn, Svein J; Arntzen, Magnus Ø

    2017-01-15

    In this study, we used multiple meta-omic approaches to characterize the microbial community and the active metabolic pathways of a stable industrial biogas reactor with food waste as the dominant feedstock, operating at thermophilic temperatures (60°C) and elevated levels of free ammonia (367 mg/liter NH 3 -N). The microbial community was strongly dominated (76% of all 16S rRNA amplicon sequences) by populations closely related to the proteolytic bacterium Coprothermobacter proteolyticus. Multiple Coprothermobacter-affiliated strains were detected, introducing an additional level of complexity seldom explored in biogas studies. Genome reconstructions provided metabolic insight into the microbes that performed biomass deconstruction and fermentation, including the deeply branching phyla Dictyoglomi and Planctomycetes and the candidate phylum "Atribacteria" These biomass degraders were complemented by a synergistic network of microorganisms that convert key fermentation intermediates (fatty acids) via syntrophic interactions with hydrogenotrophic methanogens to ultimately produce methane. Interpretation of the proteomics data also suggested activity of a Methanosaeta phylotype acclimatized to high ammonia levels. In particular, we report multiple novel phylotypes proposed as syntrophic acetate oxidizers, which also exert expression of enzymes needed for both the Wood-Ljungdahl pathway and β-oxidation of fatty acids to acetyl coenzyme A. Such an arrangement differs from known syntrophic oxidizing bacteria and presents an interesting hypothesis for future studies. Collectively, these findings provide increased insight into active metabolic roles of uncultured phylotypes and presents new synergistic relationships, both of which may contribute to the stability of the biogas reactor. Biogas production through anaerobic digestion of organic waste provides an attractive source of renewable energy and a sustainable waste management strategy. A comprehensive understanding

  18. Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

    Directory of Open Access Journals (Sweden)

    Darine Trabelsi

    2013-01-01

    Full Text Available The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research.

  19. Phylogenetic and Physiological Diversity of Subseafloor Microbial Communities at Axial Seamount, Juan de Fuca Ridge: Summary of Results From the New Millenium Observatory (NeMO), 1998-2004

    Science.gov (United States)

    Baross, J. A.; Huber, J. A.; Mehta, M. P.; Opatkiewicz, A.; Bolton, S. A.; Butterfield, D. A.; Sogin, M. L.; Embley, R. W.

    2005-12-01

    Axial Seamount (45 ° 58' N; 130 ° 00' W) is an active submarine volcano located on the Juan de Fuca Ridge, approximately 300 miles off the coast of Oregon. Lying at the intersection of a seamount chain and a spreading axis, Axial is a unique study site from both the geological and biological perspective. In January of 1998, Axial experienced a week-long series of earthquakes, and subsequent water column and seafloor observations on the southeast portion of the caldera found temperature and chemical anomalies, extensive new seafloor lava flows, large "snow blower" type vents, and other characteristics commonly associated with diking-eruptive events. Due to its high activity and close proximity to shore, Axial was chosen as a site for a multi-year observatory (New Millenium Observatory, NeMO) to document changes and interactions between geology, chemistry, and biology on the mid-ocean ridge system. From 1998 through 2004, we extensively sampled diffuse vents at Axial Seamount to determine the physiological and phylogenetic diversity of subseafloor microbial communities and their relationship to the geochemical environment. Here we present a summary of those studies, including molecular-based phylogenetic surveys of bacteria, archaea, and potential nitrogen-fixing organisms, culturing results of thermophiles and hyperthermophiles from over 20 sites, and the distribution of one particular group of hyperthermophiles at diffuse vents throughout the caldera and how that distribution may be linked to the geochemical habitat. Results indicate that Axial supports a diverse subseafloor microbial community, including hydrogen and sulfur oxidizers, hyperthermophilic methane producers and heterotrophs, and many organisms with the potential to fix nitrogen. In addition, we find that the species composition of the microbial community changes in response to changes in the physical and chemical conditions at each vent site. The extent of seawater mixing with hydrothermal fluids

  20. Microbial reduction of structural Fe3+ in nontronite by a thermophilic bacterium and its role in promoting the smectite to illite reaction

    Science.gov (United States)

    Zhang, G.; Dong, H.; Kim, J.; Eberl, D.D.

    2007-01-01

    The illitization process of Fe-rich smectite (nontronite NAu-2) promoted by microbial reduction of structural Fe3+ was investigated by using a thermophilic metal-reducing bacterium, Thermoanaerobacter ethanolicus, isolated from the deep subsurface. T. ethanolicus was incubated with lactate as the sole electron donor and structural Fe3+ in nontronite as the sole electron acceptor, and anthraquinone-2, 6-disulfonate (AQDS) as an electron shuttle in a growth medium (pH 6.2 and 9.2, 65 ??C) with or without an external supply of Al and K sources. With an external supply of Al and K, the extent of reduction of Fe3+ in NAu-2 was 43.7 and 40.4% at pH 6.2 and 9.2, respectively. X-ray diffraction and scanning and transmission electron microscopy revealed formation of discrete illite at pH 9.2 with external Al and K sources, while mixed layers of illite/smectite or highly charged smectite were detected under other conditions. The morphology of biogenic illite evolved from lath and flake to pseudo-hexagonal shape. An external supply of Al and K under alkaline conditions enhances the smectite-illite reaction during microbial Fe3+ reduction of smectite. Biogenic SiO2 was observed as a result of bioreduction under all conditions. The microbially promoted smectite-illite reaction proceeds via dissolution of smectite and precipitation of illite. Thermophilic iron reducing bacteria have a significant role in promoting the smectite to illite reaction under conditions common in sedimentary basins.

  1. Thermophilic xylanases: from bench to bottle.

    Science.gov (United States)

    Basit, Abdul; Liu, Junquan; Rahim, Kashif; Jiang, Wei; Lou, Huiqiang

    2018-01-17

    Lignocellulosic biomass is a valuable raw material. As technology has evolved, industrial interest in new ways to take advantage of this raw material has grown. Biomass is treated with different microbial cells or enzymes under ideal industrial conditions to produce the desired products. Xylanases are the key enzymes that degrade the xylosidic linkages in the xylan backbone of the biomass, and commercial enzymes are categorized into different glycoside hydrolase families. Thermophilic microorganisms are excellent sources of industrially relevant thermostable enzymes that can withstand the harsh conditions of industrial processing. Thermostable xylanases display high-specific activity at elevated temperatures and distinguish themselves in biochemical properties, structures, and modes of action from their mesophilic counterparts. Natural xylanases can be further improved through genetic engineering. Rapid progress with genome editing, writing, and synthetic biological techniques have provided unlimited potential to produce thermophilic xylanases in their natural hosts or cell factories including bacteria, yeasts, and filamentous fungi. This review will discuss the biotechnological potential of xylanases from thermophilic microorganisms and the ways they are being optimized and produced for various industrial applications.

  2. Spatial and Temporal Changes in Fluid Chemistry and Microbial Community Diversity in Subseafloor Habitats at Axial Seamount Following the 1998 Eruption

    Science.gov (United States)

    Opatkiewicz, A. D.; Butterfield, D. A.; Baross, J. A.

    2006-12-01

    The subseafloor associated with hydrothermal vents has the potential to contribute significantly to primary production and biogeochemical cycling in the ocean. However, too little is known about the phylogenetic and physiological diversity of the microbial communities or their in situ activity to assess this potential. There are previous reports that subseafloor environments at active vent sites harbor a high diversity of microorganisms that include different thermal and metabolic groups of Bacteria and Archaea. However, little is known about how these communities change over time (minutes to years), at different vent sites, or in response to perturbations. In an effort to address these issues, the subseafloor microbial community diversity was examined from five diffuse-flow hydrothermal vent sites (distributed geographically over the seamount between three distinguishable vent fields) over the course of six years following the 1998 eruption at Axial Seamount (45° 58'N; 130° 00' W). PCR-based Terminal Restriction Fragment Length Polymorphism (TRFLP) analyses were used to follow changes in the microbial community structure. 16S rRNA gene sequence analysis was used to identify the specific groups of Bacteria and Archaea from the TRFLP analyses. Deep-sea background seawater microorganisms were detected in hydrothermal fluid samples (Bacteria: Alpha and Gamma Proteobacteria, Archaea: Marine Group I Crenarchaeota and Marine Group II Euryarchaeota). The unique subseafloor phylotypes detected included Epsilon, Delta and Beta Proteobacteria, Methanococcales and thermophilic Euryarchaeota. Temperature and key chemical species, which indicate the degree of mixing of hydrothermal fluid with seawater in the subsurface, have been shown previously to be important in affecting the diversity of the microbial communities (Huber et al., 2003). This work substantiates these earlier findings and furthermore presents evidence that additional chemical species, distinguishing the

  3. A Combination of Stable Isotope Probing, Illumina Sequencing, and Co-occurrence Network to Investigate Thermophilic Acetate- and Lactate-Utilizing Bacteria.

    Science.gov (United States)

    Sun, Weimin; Krumins, Valdis; Dong, Yiran; Gao, Pin; Ma, Chunyan; Hu, Min; Li, Baoqin; Xia, Bingqing; He, Zijun; Xiong, Shangling

    2018-01-01

    Anaerobic digestion is a complicated microbiological process that involves a wide diversity of microorganisms. Acetate is one of the most important intermediates, and interactions between acetate-oxidizing bacteria and archaea could play an important role in the formation of methane in anoxic environments. Anaerobic digestion at thermophilic temperatures is known to increase methane production, but the effects on the microbial community are largely unknown. In the current study, stable isotope probing was used to characterize acetate- and lactate-oxidizing bacteria in thermophilic anaerobic digestion. In microcosms fed 13 C-acetate, bacteria related to members of Clostridium, Hydrogenophaga, Fervidobacterium, Spirochaeta, Limnohabitans, and Rhodococcus demonstrated elevated abundances of 13 C-DNA fractions, suggesting their activities in acetate oxidation. In the treatments fed 13 C-lactate, Anaeromyxobacter, Desulfobulbus, Syntrophus, Cystobacterineae, and Azospira were found to be the potential thermophilic lactate utilizers. PICRUSt predicted that enzymes related to nitrate and nitrite reduction would be enriched in 13 C-DNA fractions, suggesting that the acetate and lactate oxidation may be coupled with nitrate and/or nitrite reduction. Co-occurrence network analysis indicated bacterial taxa not enriched in 13 C-DNA fractions that may also play a critical role in thermophilic anaerobic digestion.

  4. Seasonality in ocean microbial communities.

    Science.gov (United States)

    Giovannoni, Stephen J; Vergin, Kevin L

    2012-02-10

    Ocean warming occurs every year in seasonal cycles that can help us to understand long-term responses of plankton to climate change. Rhythmic seasonal patterns of microbial community turnover are revealed when high-resolution measurements of microbial plankton diversity are applied to samples collected in lengthy time series. Seasonal cycles in microbial plankton are complex, but the expansion of fixed ocean stations monitoring long-term change and the development of automated instrumentation are providing the time-series data needed to understand how these cycles vary across broad geographical scales. By accumulating data and using predictive modeling, we gain insights into changes that will occur as the ocean surface continues to warm and as the extent and duration of ocean stratification increase. These developments will enable marine scientists to predict changes in geochemical cycles mediated by microbial communities and to gauge their broader impacts.

  5. Systems biology of Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    Navid, A; Ghim, C; Fenley, A; Yoon, S; Lee, S; Almaas, E

    2008-04-11

    Microbes exist naturally in a wide range of environments, spanning the extremes of high acidity and high temperature to soil and the ocean, in communities where their interactions are significant. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.

  6. Space agriculture for habitation on Mars with hyper-thermophilic aerobic composting bacteria

    Science.gov (United States)

    Space Agriculture Task Force; Ishikawa, Y.; Tomita-Yokotani, K.; Hashimoto, H.; Kitaya, Y.; Yamashita, M.; Nagatomo, M.; Oshima, T.; Wada, H.

    Manned Mars exploration, especially for extended periods of time, will require recycle of materials to support human life. Here, a conceptual design is developed for a Martian agricultural system driven by biologically regenerative functions. One of the core biotechnologies function is the use of hyper-thermophilic aerobic composting bacterial ecology. These thermophilic bacteria can play an important role in increasing the effectiveness of the processing of human metabolic waste and inedible biomass and of converting them to fertilizer for the cultivation of plants. This microbial technology has been already well established for the purpose of processing sewage and waste materials for small local communities in Japan. One of the characteristics of the technology is that the metabolic heat release that occurs during bacterial fermentation raises the processing temperature sufficiently high at 80 100 °C to support hyper-thermophilic bacteria. Such a hyper-thermophilic system is found to have great capability of decomposing wastes including even their normally recalcitrant components, in a reasonably short period of time and of providing a better quality of fertilizer as an end-product. High quality compost has been shown to be a key element in creating a healthy regenerative food production system. In ground-based studies, the soil microbial ecology after the addition of high quality compost was shown to improve plant growth and promote a healthy symbiosis of arbuscular mycorrhizal fungi. Another advantage of such high processing temperature is the ability to sterilize the pathogenic organisms through the fermentation process and thus to secure the hygienic safety of the system. Plant cultivation is one of the other major systems. It should fully utilize solar energy received on the Martian surface for supplying energy for photosynthesis. Subsurface water and atmospheric carbon dioxide mined on Mars should be also used in the plant cultivation system. Oxygen and

  7. Anaerobic Thermophiles

    Directory of Open Access Journals (Sweden)

    Francesco Canganella

    2014-02-01

    Full Text Available The term “extremophile” was introduced to describe any organism capable of living and growing under extreme conditions. With the further development of studies on microbial ecology and taxonomy, a variety of “extreme” environments have been found and an increasing number of extremophiles are being described. Extremophiles have also been investigated as far as regarding the search for life on other planets and even evaluating the hypothesis that life on Earth originally came from space. The first extreme environments to be largely investigated were those characterized by elevated temperatures. The naturally “hot environments” on Earth range from solar heated surface soils and water with temperatures up to 65 °C, subterranean sites such as oil reserves and terrestrial geothermal with temperatures ranging from slightly above ambient to above 100 °C, to submarine hydrothermal systems with temperatures exceeding 300 °C. There are also human-made environments with elevated temperatures such as compost piles, slag heaps, industrial processes and water heaters. Thermophilic anaerobic microorganisms have been known for a long time, but scientists have often resisted the belief that some organisms do not only survive at high temperatures, but actually thrive under those hot conditions. They are perhaps one of the most interesting varieties of extremophilic organisms. These microorganisms can thrive at temperatures over 50 °C and, based on their optimal temperature, anaerobic thermophiles can be subdivided into three main groups: thermophiles with an optimal temperature between 50 °C and 64 °C and a maximum at 70 °C, extreme thermophiles with an optimal temperature between 65 °C and 80 °C, and finally hyperthermophiles with an optimal temperature above 80 °C and a maximum above 90 °C. The finding of novel extremely thermophilic and hyperthermophilic anaerobic bacteria in recent years, and the fact that a large fraction of them belong

  8. Two-stage pretreatment of excess sludge for electricity generation in microbial fuel cell.

    Science.gov (United States)

    Zhang, Yi; Zhao, Yang-Guo; Guo, Liang; Gao, Mengchun

    2018-01-12

    Thermophiles hydrolysis and acidogens fermentation were sequentially adopted to pretreat excess sludge for microbial fuel cell (MFC) electricity production. The results indicated that MFC fed with the thermophiles-acidogens pretreated sludge (MFC AB), reached a higher removal of ammonia nitrogen than the MFC fed with the heating hydrolysis and acidogens fermentation pretreated sludge (MFC NB). However, compared with the MFC AB, MFC NB presented a better performance for removal of soluble chemical oxygen demand (SCOD) (90.08%) and protein (82.42%). As for the electricity production, MFC NB obtained higher voltage of 0.632 V and maximum power density with 1.05 W/m 3 while MFC AB reached maximum voltage of 0.373 V and maximum power density of 0.58 W/m 3 . Bacterial 16S rRNA-based molecular microbial techniques showed that microbial communities on both MFC anode biofilms was diverse and different. The cooperation of fermentation bacteria and electricigen Shewanella baltica in the MFC NB may have contributed towards the improvement of electricity generation.

  9. [Characterization and microbial community shifts of rice strawdegrading microbial consortia].

    Science.gov (United States)

    Wang, Chunfang; Ma, Shichun; Huang, Yan; Liu, Laiyan; Fan, Hui; Deng, Yu

    2016-12-04

    To study the relationship between microbial community and degradation rate of rice straw, we compared and analyzed cellulose-decomposing ability, microbial community structures and shifts of microbial consortia F1 and F2. We determined exoglucanase activity by 3, 5-dinitrosalicylic acid colorimetry. We determined content of cellulose, hemicellulose and lignin in rice straw by Van Soest method, and calculated degradation rates of rice straw by the weight changes before and after a 10-day incubation. We analyzed and compared the microbial communities and functional microbiology shifts by clone libraries, Miseq analysis and real time-PCR based on the 16S rRNA gene and cel48 genes. Total degradation rate, cellulose, and hemicellulose degradation rate of microbial consortia F1 were significantly higher than that of F2. The variation trend of exoglucanase activity in both microbial consortia F1 and F2 was consistent with that of cel48 gene copies. Microbial diversity of F1 was complex with aerobic bacteria as dominant species, whereas that of F2 was simple with a high proportion of anaerobic cellulose decomposing bacteria in the later stage of incubation. In the first 4 days, unclassified Bacillales and Bacillus were dominant in both F1 and F2. The dominant species and abundance became different after 4-day incubation, Bacteroidetes and Firmicutes were dominant phyla of F1 and F2, respectively. Although Petrimonas and Pusillimonas were common dominant species in F1 and F2, abundance of Petrimonas in F2 (38.30%) was significantly higher than that in F1 (9.47%), and the abundance of Clostridiales OPB54 in F2 increased to 14.85% after 8-day incubation. The abundance of cel48 gene related with cellulose degradation rate and exoglucanase activity, and cel48 gene has the potential as a molecular marker to monitor the process of cellulose degradation. Microbial community structure has a remarkable impact on the degradation efficiency of straw cellulose, and Petrimonas

  10. High-resolution phylogenetic microbial community profiling

    Energy Technology Data Exchange (ETDEWEB)

    Singer, Esther; Coleman-Derr, Devin; Bowman, Brett; Schwientek, Patrick; Clum, Alicia; Copeland, Alex; Ciobanu, Doina; Cheng, Jan-Fang; Gies, Esther; Hallam, Steve; Tringe, Susannah; Woyke, Tanja

    2014-03-17

    The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance our knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.

  11. DNA metabarcoding of microbial communities for healthcare

    Directory of Open Access Journals (Sweden)

    Zaets I. Ye.

    2016-02-01

    Full Text Available High-throughput sequencing allows obtaining DNA barcodes of multiple species of microorganisms from single environmental samples. Next Generation Sequencing (NGS-based profiling provides new opportunities to evaluate the human health effect of microbial community members affiliated to probiotics. The DNA metabarcoding may serve to a quality control of microbial communities, comprising complex probiotics and other fermented foods. A detailed inventory of complex communities is a pre-requisite of understanding their functionality as whole entities that makes it possible to design more effective bio-products by precise replacement of one community member by others. The present paper illustrates how the NGS-based DNA metabarcoding aims at the profiling of both wild and hybrid multi-microbial communities with the example of kombucha probiotic beverage fermented by yeast-bacterial partners.

  12. Temporal change of composition and potential activity of the thermophilic archaeal community during the composting of organic material.

    Science.gov (United States)

    Thummes, Kathrin; Kämpfer, Peter; Jäckel, Udo

    2007-07-01

    To date, composting has been regarded as an aerobic process but it has been shown that composting piles are often sources of atmospheric methane. In order to gain a more comprehensive view on the diversity of methanogenic Archaea in compost, gas chromatographical methods and molecular cloning were used to study relationships of thermophilic archaeal communities and changes in methane production potential during compost maturation. According to the thermophilic methane production potential, wide differences could be detected between differently aged compost materials. In material derived from 3- and 4-week-old piles, low and no thermophilic methane production potential, respectively, was observed at 50 degrees C. Material from a 6-week-old pile showed the maximum methane production. With compost maturation, the production slowly decreased again with 6 weeks, 8 weeks, and mature compost showing an optimum methane production potential at 60 degrees C. At 70 degrees C, only 6-week-old material showed a comparable high production of methane. The 16S rRNA-based phylogenetic surveys revealed an increase of archaeal diversity with compost maturation. In the 6-week-old material, 86% of the sequences in the archaeal 16S rRNA library had the highest sequence similarities to Methanothermobacter spp. and the remaining 14% of the clones were related to Methanosarcina thermophila. Quantification of methanogens in 6-week-old material, on the basis of the methane production rate, resulted in values of about 2x10(7) cells per gram fresh weight. In 8-week-old and mature compost material, the proportion of sequences similar to Methanothermobacter spp. decreased to 34% and 0%, respectively. The mature compost material showed the highest variation in identified sequences, although 33% could be assigned to as yet uncultured Archaea (e.g. Rice cluster I, III, and IV). Our results indicate that compost harbours a diverse community of thermophilic methanogens, with changing composition

  13. Rapid startup of thermophilic anaerobic digester to remove tetracycline and sulfonamides resistance genes from sewage sludge.

    Science.gov (United States)

    Xu, Rui; Yang, Zhao-Hui; Wang, Qing-Peng; Bai, Yang; Liu, Jian-Bo; Zheng, Yue; Zhang, Yan-Ru; Xiong, Wei-Ping; Ahmad, Kito; Fan, Chang-Zheng

    2018-01-15

    Spread of antibiotic resistance genes (ARGs) originating from sewage sludge is highlighted as an eminent health threat. This study established a thermophilic anaerobic digester using one-step startup strategy to quickly remove tetracycline and sulfonamides resistance genes from sewage sludge. At least 20days were saved in the startup period from mesophilic to thermophilic condition. Based on the results of 16S rDNA amplicons sequencing and predicted metagenomic method, the successful startup largely relied on the fast colonization of core thermophilic microbial population (e.g. Firmicutes, Proteobacteria, Actinobacteria). Microbial metabolic gene pathways for substrate degradation and methane production was also increased by one-step mode. In addition, real-time quantitative PCR approach revealed that most targeted tetracycline and sulfonamides resistance genes ARGs (sulI, tetA, tetO, tetX) were substantially removed during thermophilic digestion (removal efficiency>80%). Network analysis showed that the elimination of ARGs was attributed to the decline of their horizontal (intI1 item) and vertical (potential hosts) transfer-related elements under high-temperature. This research demonstrated that rapid startup thermophilic anaerobic digestion of wastewater solids would be a suitable technology for reducing quantities of various ARGs. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Development of a multiplex real time PCR to detect thermophilic lactic acid bacteria in natural whey starters.

    Science.gov (United States)

    Bottari, Benedetta; Agrimonti, Caterina; Gatti, Monica; Neviani, Erasmo; Marmiroli, Nelson

    2013-01-01

    A multiplex real time PCR (mRealT-PCR) useful to rapidly screen microbial composition of thermophilic starter cultures for hard cooked cheeses and to compare samples with potentially different technological properties was developed. Novel primers directed toward pheS gene were designed and optimized for multiple detection of Lactobacillus helveticus, Lactobacillus delbrueckii, Streptococcus thermophilus and Lactobacillus fermentum. The assay was based on SYBR Green chemistry followed by melting curves analysis. The method was then evaluated for applications in the specific detection of the 4 lactic acid bacteria (LAB) in 29 different natural whey starters for Parmigiano Reggiano cheese production. The results obtained by mRealT-PCR were also compared with those obtained on the same samples by Fluorescence in Situ Hybridization (FISH) and Length-Heterogeneity PCR (LH-PCR). The mRealT-PCR developed in this study, was found to be effective for analyzing species present in the samples with an average sensitivity down to less than 600 copies of DNA and therefore sensitive enough to detect even minor LAB community members of thermophilic starter cultures. The assay was able to describe the microbial population of all the different natural whey starter samples analyzed, despite their natural variability. A higher number of whey starter samples with S. thermophilus and L. fermentum present in their microbial community were revealed, suggesting that these species could be more frequent in Parmigiano Reggiano natural whey starter samples than previously shown. The method was more effective than LH-PCR and FISH and, considering that these two techniques have to be used in combination to detect the less abundant species, the mRealT-PCR was also faster. Providing a single step sensitive detection of L. helveticus, L. delbrueckii, S. thermophilus and L. fermentum, the developed mRealT-PCR could be used for screening thermophilic starter cultures and to follow the presence of

  15. [Effects of grape seed addition in swine manure-wheat straw composting on the compost microbial community and carbon and nitrogen contents].

    Science.gov (United States)

    Huang, Yi-Mei; Liu, Xue-Ling; Jiang, Ji-Shao; Huang, Hua; Liu, Dong

    2012-08-01

    Taking substrates swine manure and wheat straw (fresh mass ratio 10.5:1) as the control (PMW), a composting experiment was conducted in a self-made aerated static composting bin to study the effects of adding 8% grape seed (treatment PMW + G) on the succession of microbial community and the transformation of carbon and nitrogen in the substrates during the composting. Seven samples were collected from each treatment, according to the temperature of the compost during the 30 d composting period. The microbial population and physiological groups were determined, and the NH4(+)-N, NO3(-)-N, organic N, and organic C concentrations in the compost were measured. Grape seed addition induced a slight increase of bacterial count and a significant increase of actinomycetes count, but decreased the fungal count significantly. Grape seed addition also decreased the ratio of bacteria to actinomycetes and the counts of ammonifiers and denitrifiers, but increased the counts of nitrifiers, N-fixing bacteria, and cellulose-decomposing microorganisms. The contents of NH4(+)-N and organic C decreased, while that of NO3(-)-N increased obviously. The NO3(-)-N content in the compost was positively correlated with the actinomycetes count. During composting, the compost temperature in treatment PMW + G increased more rapidly, and remained steady in thermophilic phase, while the water content changed little, which provided a stable and higher population of actinomycetes and nitrifiers in thermophilic phase, being beneficial to the increase of compost nitrate N.

  16. Microbial life in volcanic/geothermal areas: how soil geochemistry shapes microbial communities

    Science.gov (United States)

    Gagliano, Antonina Lisa; D'Alessandro, Walter; Franzetti, Andrea; Parello, Francesco; Tagliavia, Marcello; Quatrini, Paola

    2015-04-01

    Extreme environments, such as volcanic/geothermal areas, are sites of complex interactions between geosphere and biosphere. Although biotic and abiotic components are strictly related, they were separately studied for long time. Nowadays, innovative and interdisciplinary approaches are available to explore microbial life thriving in these environments. Pantelleria island (Italy) hosts a high enthalpy geothermal system characterized by high CH4 and low H2S fluxes. Two selected sites, FAV1 and FAV2, located at Favara Grande, the main exhalative area of the island, show similar physical conditions with a surface temperature close to 60° C and a soil gas composition enriched in CH4, H2 and CO2. FAV1 soil is characterized by harsher conditions (pH 3.4 and 12% of H2O content); conversely, milder conditions were recorded at site FAV2 (pH 5.8 and 4% of H2O content). High methanotrophic activity (59.2 nmol g-1 h-1) and wide diversity of methanotrophic bacteria were preliminary detected at FAV2, while no activity was detected at FAV1(1). Our aim was to investigate how the soil microbial communities of these two close geothermal sites at Pantelleria island respond to different geochemical conditions. Bacterial and Archaeal communities of the sites were investigated by MiSeq Illumina sequencing of hypervariable regions of the 16S rRNA gene. More than 33,000 reads were obtained for Bacteria and Archaea from soil samples of the two sites. At FAV1 99% of the bacterial sequences were assigned to four main phyla (Proteobacteria, Firmicutes, Actinobacteria and Chloroflexi). FAV2 sequences were distributed in the same phyla with the exception of Chloroflexi that was represented below 1%. Results indicate a high abundance of thermo-acidophilic chemolithotrophs in site FAV1 dominated by Acidithiobacillus ferrooxidans (25%), Nitrosococcus halophilus (10%), Alicyclobacillus spp. (7%) and the rare species Ktedonobacter racemifer (11%). The bacterial community at FAV2 soil is dominated by

  17. Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting

    Science.gov (United States)

    Lemos, Leandro N.; Pereira, Roberta V.; Quaggio, Ronaldo B.; Martins, Layla F.; Moura, Livia M. S.; da Silva, Amanda R.; Antunes, Luciana P.; da Silva, Aline M.; Setubal, João C.

    2017-01-01

    Microbial consortia selected from complex lignocellulolytic microbial communities are promising alternatives to deconstruct plant waste, since synergistic action of different enzymes is required for full degradation of plant biomass in biorefining applications. Culture enrichment also facilitates the study of interactions among consortium members, and can be a good source of novel microbial species. Here, we used a sample from a plant waste composting operation in the São Paulo Zoo (Brazil) as inoculum to obtain a thermophilic aerobic consortium enriched through multiple passages at 60°C in carboxymethylcellulose as sole carbon source. The microbial community composition of this consortium was investigated by shotgun metagenomics and genome-centric analysis. Six near-complete (over 90%) genomes were reconstructed. Similarity and phylogenetic analyses show that four of these six genomes are novel, with the following hypothesized identifications: a new Thermobacillus species; the first Bacillus thermozeamaize genome (for which currently only 16S sequences are available) or else the first representative of a new family in the Bacillales order; the first representative of a new genus in the Paenibacillaceae family; and the first representative of a new deep-branching family in the Clostridia class. The reconstructed genomes from known species were identified as Geobacillus thermoglucosidasius and Caldibacillus debilis. The metabolic potential of these recovered genomes based on COG and CAZy analyses show that these genomes encode several glycoside hydrolases (GHs) as well as other genes related to lignocellulose breakdown. The new Thermobacillus species stands out for being the richest in diversity and abundance of GHs, possessing the greatest potential for biomass degradation among the six recovered genomes. We also investigated the presence and activity of the organisms corresponding to these genomes in the composting operation from which the consortium was built

  18. Effects of heavy metals on soil microbial community

    Science.gov (United States)

    Chu, Dian

    2018-02-01

    Soil is one of the most important environmental natural resources for human beings living, which is of great significance to the quality of ecological environment and human health. The study of the function of arable soil microbes exposed to heavy metal pollution for a long time has a very important significance for the usage of farmland soil. In this paper, the effects of heavy metals on soil microbial community were reviewed. The main contents were as follows: the effects of soil microbes on soil ecosystems; the effects of heavy metals on soil microbial activity, soil enzyme activities and the composition of soil microbial community. In addition, a brief description of main methods of heavy metal detection for soil pollution is given, and the means of researching soil microbial community composition are introduced as well. Finally, it is concluded that the study of soil microbial community can well reflect the degree of soil heavy metal pollution and the impact of heavy metal pollution on soil ecology.

  19. Permissiveness of soil microbial communities towards broad host range plasmids

    DEFF Research Database (Denmark)

    Klümper, Uli

    . Plasmids are implicated in the rapid spread of antibiotic resistance and the emergence of multi-resistant pathogenic bacteria, making it crucial to be able to quantify, understand, and, ideally, control plasmid transfer in mixed microbial communities. The fate of plasmids in microbial communities...... of microbial communities may be directly interconnected through transfer of BHR plasmids at a so far unrecognized level. The developed method furthermore enabled me to explore how agronomic practices may affect gene transfer in soil microbial communities. I compared bacterial communities extracted from plots...

  20. Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments

    Science.gov (United States)

    Saxena, Rituja; Dhakan, Darshan B.; Mittal, Parul; Waiker, Prashant; Chowdhury, Anirban; Ghatak, Arundhuti; Sharma, Vineet K.

    2017-01-01

    Extreme ecosystems such as hot springs are of great interest as a source of novel extremophilic species, enzymes, metabolic functions for survival and biotechnological products. India harbors hundreds of hot springs, the majority of which are not yet explored and require comprehensive studies to unravel their unknown and untapped phylogenetic and functional diversity. The aim of this study was to perform a large-scale metagenomic analysis of three major hot springs located in central India namely, Badi Anhoni, Chhoti Anhoni, and Tattapani at two geographically distinct regions (Anhoni and Tattapani), to uncover the resident microbial community and their metabolic traits. Samples were collected from seven distinct sites of the three hot spring locations with temperature ranging from 43.5 to 98°C. The 16S rRNA gene amplicon sequencing of V3 hypervariable region and shotgun metagenome sequencing uncovered a unique taxonomic and metabolic diversity of the resident thermophilic microbial community in these hot springs. Genes associated with hydrocarbon degradation pathways, such as benzoate, xylene, toluene, and benzene were observed to be abundant in the Anhoni hot springs (43.5–55°C), dominated by Pseudomonas stutzeri and Acidovorax sp., suggesting the presence of chemoorganotrophic thermophilic community with the ability to utilize complex hydrocarbons as a source of energy. A high abundance of genes belonging to methane metabolism pathway was observed at Chhoti Anhoni hot spring, where methane is reported to constitute >80% of all the emitted gases, which was marked by the high abundance of Methylococcus capsulatus. The Tattapani hot spring, with a high-temperature range (61.5–98°C), displayed a lower microbial diversity and was primarily dominated by a nitrate-reducing archaeal species Pyrobaculum aerophilum. A higher abundance of cell metabolism pathways essential for the microbial survival in extreme conditions was observed at Tattapani. Taken together

  1. A conceptual framework for invasion in microbial communities

    KAUST Repository

    Kinnunen, Marta; Dechesne, Arnaud; Proctor, Caitlin; Hammes, Frederik; Johnson, David; Quintela-Baluja, Marcos; Graham, David; Daffonchio, Daniele; Fodelianakis, Stylianos; Hahn, Nicole; Boon, Nico; Smets, Barth F

    2016-01-01

    There is a growing interest in controlling-promoting or avoiding-the invasion of microbial communities by new community members. Resource availability and community structure have been reported as determinants of invasion success. However, most invasion studies do not adhere to a coherent and consistent terminology nor always include rigorous interpretations of the processes behind invasion. Therefore, we suggest that a consistent set of definitions and a rigorous conceptual framework are needed. We define invasion in a microbial community as the establishment of an alien microbial type in a resident community and argue how simple criteria to define aliens, residents, and alien establishment can be applied for a wide variety of communities. In addition, we suggest an adoption of the community ecology framework advanced by Vellend (2010) to clarify potential determinants of invasion. This framework identifies four fundamental processes that control community dynamics: dispersal, selection, drift and diversification. While selection has received ample attention in microbial community invasion research, the three other processes are often overlooked. Here, we elaborate on the relevance of all four processes and conclude that invasion experiments should be designed to elucidate the role of dispersal, drift and diversification, in order to obtain a complete picture of invasion as a community process.

  2. A conceptual framework for invasion in microbial communities

    Science.gov (United States)

    Kinnunen, Marta; Dechesne, Arnaud; Proctor, Caitlin; Hammes, Frederik; Johnson, David; Quintela-Baluja, Marcos; Graham, David; Daffonchio, Daniele; Fodelianakis, Stilianos; Hahn, Nicole; Boon, Nico; Smets, Barth F

    2016-01-01

    There is a growing interest in controlling—promoting or avoiding—the invasion of microbial communities by new community members. Resource availability and community structure have been reported as determinants of invasion success. However, most invasion studies do not adhere to a coherent and consistent terminology nor always include rigorous interpretations of the processes behind invasion. Therefore, we suggest that a consistent set of definitions and a rigorous conceptual framework are needed. We define invasion in a microbial community as the establishment of an alien microbial type in a resident community and argue how simple criteria to define aliens, residents, and alien establishment can be applied for a wide variety of communities. In addition, we suggest an adoption of the community ecology framework advanced by Vellend (2010) to clarify potential determinants of invasion. This framework identifies four fundamental processes that control community dynamics: dispersal, selection, drift and diversification. While selection has received ample attention in microbial community invasion research, the three other processes are often overlooked. Here, we elaborate on the relevance of all four processes and conclude that invasion experiments should be designed to elucidate the role of dispersal, drift and diversification, in order to obtain a complete picture of invasion as a community process. PMID:27137125

  3. A conceptual framework for invasion in microbial communities

    KAUST Repository

    Kinnunen, Marta

    2016-05-03

    There is a growing interest in controlling-promoting or avoiding-the invasion of microbial communities by new community members. Resource availability and community structure have been reported as determinants of invasion success. However, most invasion studies do not adhere to a coherent and consistent terminology nor always include rigorous interpretations of the processes behind invasion. Therefore, we suggest that a consistent set of definitions and a rigorous conceptual framework are needed. We define invasion in a microbial community as the establishment of an alien microbial type in a resident community and argue how simple criteria to define aliens, residents, and alien establishment can be applied for a wide variety of communities. In addition, we suggest an adoption of the community ecology framework advanced by Vellend (2010) to clarify potential determinants of invasion. This framework identifies four fundamental processes that control community dynamics: dispersal, selection, drift and diversification. While selection has received ample attention in microbial community invasion research, the three other processes are often overlooked. Here, we elaborate on the relevance of all four processes and conclude that invasion experiments should be designed to elucidate the role of dispersal, drift and diversification, in order to obtain a complete picture of invasion as a community process.

  4. Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents.

    Science.gov (United States)

    Anderson, Rika E; Sogin, Mitchell L; Baross, John A

    2015-01-01

    Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in very low abundance. However, the ecological role and distribution of rare and abundant lineages, particularly in deep, hot subsurface environments, remain unclear. Here, we use 16S rRNA tag sequencing to describe biogeographic patterning and microbial community structure of both rare and abundant archaea and bacteria in hydrothermal vent systems. We show that while rare archaeal lineages and almost all bacterial lineages displayed geographically restricted community structuring patterns, the abundant lineages of archaeal communities displayed a much more cosmopolitan distribution. Finally, analysis of one high-volume, high-temperature fluid sample representative of the deep hot biosphere described a unique microbial community that differed from microbial populations in diffuse flow fluid or sulfide samples, yet the rare thermophilic archaeal groups showed similarities to those that occur in sulfides. These results suggest that while most archaeal and bacterial lineages in vents are rare and display a highly regional distribution, a small percentage of lineages, particularly within the archaeal domain, are successful at widespread dispersal and colonization. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell.

    Science.gov (United States)

    Timmers, Ruud A; Rothballer, Michael; Strik, David P B T B; Engel, Marion; Schulz, Stephan; Schloter, Michael; Hartmann, Anton; Hamelers, Bert; Buisman, Cees

    2012-04-01

    The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) were located on the root surfaces, but they were more abundant colonising the graphite granular electrode. Anaerobic cellulolytic bacteria dominated the area where most of the EAB were found, indicating that the current was probably generated via the hydrolysis of cellulose. Due to the presence of oxygen and nitrate, short-chain fatty acid-utilising denitrifiers were the major competitors for the electron donor. Acetate-utilising methanogens played a minor role in the competition for electron donor, probably due to the availability of graphite granules as electron acceptors.

  6. Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

    Energy Technology Data Exchange (ETDEWEB)

    Timmers, Ruud A.; Strik, David P.B.T.B.; Hamelers, Bert; Buisman, Cees [Wageningen Univ. (Netherlands). Sub-dept. of Environmental Technology; Rothballer, Michael; Hartmann, Anton [Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg (Germany). Dept. Microbe-Plant Interactions; Engel, Marion; Schulz, Stephan; Schloter, Michael [Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg (Germany). Dept. Terrestrial Ecogenetics

    2012-04-15

    The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) were located on the root surfaces, but they were more abundant colonising the graphite granular electrode. Anaerobic cellulolytic bacteria dominated the area where most of the EAB were found, indicating that the current was probably generated via the hydrolysis of cellulose. Due to the presence of oxygen and nitrate, short-chain fatty acid-utilising denitrifiers were the major competitors for the electron donor. Acetate-utilising methanogens played a minor role in the competition for electron donor, probably due to the availability of graphite granules as electron acceptors. (orig.)

  7. A conceptual framework for invasion in microbial communities

    DEFF Research Database (Denmark)

    Kinnunen, Marta; Dechesne, Arnaud; Proctor, Caitlin

    2016-01-01

    and consistent terminology nor always include rigorous interpretations of the processes behind invasion. Therefore, we suggest that a consistent set of definitions and a rigorous conceptual framework are needed. We define invasion in a microbial community as the establishment of an alien microbial type...... in a resident community and argue how simple criteria to define aliens, residents, and alien establishment can be applied for a wide variety of communities. In addition, we suggest an adoption of the community ecology framework advanced by Vellend (2010) to clarify potential determinants of invasion....... This framework identifies four fundamental processes that control community dynamics: dispersal, selection, drift and diversification. While selection has received ample attention in microbial community invasion research, the three other processes are often overlooked. Here, we elaborate on the relevance of all...

  8. Biomass production and energy source of thermophiles in a Japanese alkaline geothermal pool.

    Science.gov (United States)

    Kimura, Hiroyuki; Mori, Kousuke; Nashimoto, Hiroaki; Hattori, Shohei; Yamada, Keita; Koba, Keisuke; Yoshida, Naohiro; Kato, Kenji

    2010-02-01

    Microbial biomass production has been measured to investigate the contribution of planktonic bacteria to fluxations in dissolved organic matter in marine and freshwater environments, but little is known about biomass production of thermophiles inhabiting geothermal and hydrothermal regions. The biomass production of thermophiles inhabiting an 85 degrees C geothermal pool was measured by in situ cultivation using diffusion chambers. The thermophiles' growth rates ranged from 0.43 to 0.82 day(-1), similar to those of planktonic bacteria in marine and freshwater habitats. Biomass production was estimated based on cellular carbon content measured directly from the thermophiles inhabiting the geothermal pool, which ranged from 5.0 to 6.1 microg C l(-1) h(-1). This production was 2-75 times higher than that of planktonic bacteria in other habitats, because the cellular carbon content of the thermophiles was much higher. Quantitative PCR and phylogenetic analysis targeting 16S rRNA genes revealed that thermophilic H2-oxidizing bacteria closely related to Calderobacterium and Geothermobacterium were dominant in the geothermal pool. Chemical analysis showed the presence of H2 in gases bubbling from the bottom of the geothermal pool. These results strongly suggested that H2 plays an important role as a primary energy source of thermophiles in the geothermal pool.

  9. Mesophilic and thermophilic anaerobic digestion of biologically pretreated abattoir wastewaters in an upflow anaerobic filter

    International Nuclear Information System (INIS)

    Gannoun, H.; Bouallagui, H.; Okbi, A.; Sayadi, S.; Hamdi, M.

    2009-01-01

    The hydrolysis pretreatment of abattoir wastewaters (AW), rich in organic suspended solids (fats and protein) was studied in static and stirred batch reactors without aeration in the presence of natural microbial population acclimated in a storage tank of AW. Microbial analysis showed that the major populations which contribute to the pretreatment of AW belong to the genera Bacillus. Contrary to the static pretreatment, the stirred conditions favoured the hydrolysis and solubilization of 80% of suspended matter into soluble pollution. The pretreated AW, in continuous stirred tank reactor (CSTR) at a hydraulic retention time (HRT) of 2 days, was fed to an upflow anaerobic filter (UAF) at an HRT of 2 days. The performance of anaerobic digestion of biologically pretreated AW was examined under mesophilic (37 deg. C) and thermophilic (55 deg. C) conditions. The shifting from a mesophilic to a thermophilic environment in the UAF was carried out with a short start-up of thermophilic condition. The UAF ran at organic loading rates (OLRs) ranging from 0.9 to 6 g COD/L d in mesophilic conditions and at OLRs from 0.9 to 9 g COD/L d in thermophilic conditions. COD removal efficiencies of 80-90% were achieved for OLRs up to 4.5 g COD/L d in mesophilic conditions, while the highest OLRs i.e. 9 g COD/L d led to efficiencies of 70-72% in thermophilic conditions. The biogas yield in thermophilic conditions was about 0.32-0.45 L biogas/g of COD removed for OLRs up to 4.5 g COD/L d. For similar OLR, the UAF in mesophilic conditions showed lower percentage of methanization. Mesophilic anaerobic digestion has been shown to destroy pathogens partially, whereas the thermophilic process was more efficient in the removal of indicator microorganisms and pathogenic bacteria at different organic loading rates.

  10. Stochastic Community Assembly: Does It Matter in Microbial Ecology?

    Science.gov (United States)

    Zhou, Jizhong; Ning, Daliang

    2017-12-01

    Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research. Copyright © 2017 American Society for Microbiology.

  11. Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant

    Science.gov (United States)

    Liu, Dongming; Li, Mingxiao; Xi, Beidou; Zhao, Yue; Wei, Zimin; Song, Caihong; Zhu, Chaowei

    2015-01-01

    Composting is an appropriate management alternative for municipal solid waste; however, our knowledge about the microbial regulation of this process is still scare. We employed metaproteomics to elucidate the main biodegradation pathways in municipal solid waste composting system across the main phases in a large-scale composting plant. The investigation of microbial succession revealed that Bacillales, Actinobacteria and Saccharomyces increased significantly with respect to abundance in composting process. The key microbiologic population for cellulose degradation in different composting stages was different. Fungi were found to be the main producers of cellulase in earlier phase. However, the cellulolytic fungal communities were gradually replaced by a purely bacterial one in active phase, which did not support the concept that the thermophilic fungi are active through the thermophilic phase. The effective decomposition of cellulose required the synergy between bacteria and fungi in the curing phase. PMID:25989417

  12. Improved cellulose conversion to bio-hydrogen with thermophilic bacteria and characterization of microbial community in continuous bioreactor

    International Nuclear Information System (INIS)

    Jiang, Hongyu; Gadow, Samir I.; Tanaka, Yasumitsu; Cheng, Jun; Li, Yu-You

    2015-01-01

    Thermophilic hydrogen fermentation of cellulose was evaluated by a long term continuous experiment and batch experiments. The continuous experiment was conducted under 55 °C using a continuously stirred tank reactor (CSTR) at a hydraulic retention time (HRT) of 10 day. A stable hydrogen yield of 15.4 ± 0.23 mol kg −1 of cellulose consumed was maintained for 190 days with acetate and butyrate as the main soluble byproducts. An analysis of the 16S rRNA sequences showed that the hydrogen-producing thermophilic cellulolytic microorganisms (HPTCM) were close to Thermoanaerobacterium thermosaccharolyticum, Clostridium sp. and Enterobacter cloacae. Batch experiment demonstrated that the highest H 2 producing activity was obtained at 55 °C and the ultimate hydrogen yield and the metabolic by-products were influenced greatly by temperatures. The effect of temperature variation showed that the activation energy for cellulose and glucose were estimated at 103 and 98.8 kJ mol −1 , respectively. - Highlights: • Continuous cellulosic-hydrogen fermentation was conducted at 55 °C. • Hydrogen yield was improved to 15.4 mol kg −1 of consumed-cellulose. • The cellulosic hydrogen bacteria were close to Clostridia and Enterobacter genus. • The mixed microflora produced H 2 within a wide range of temperatures (35 °C–65 °C). • Activation energy of cellulose and glucose were 103 and 98.8 kJ mol −1 , respectively

  13. Thermal pretreatment of the solid fraction of manure: Impact on the biogas reactor performance and microbial community

    DEFF Research Database (Denmark)

    Mladenovska, Z; Hartmann, H.; Kvist, T.

    2006-01-01

    Application of thermal treatment at 100-140 degrees C as a pretreatment method prior to anaerobic digestion of a mixture of cattle and swine manure was investigated. In a batch test, biogasification of manure with thermally pretreated solid fraction proceeded faster and resulted in the increase...... of methane yield. The performances of two thermophilic continuously stirred tank reactors (CSTR) treating manure with solid fraction pretreated for 40 minutes at 140 degrees C and non-treated manure were compared. The digester fed with the thermally pretreated manure had a higher methane productivity...... and butyrate - was low. The kinetic parameters of the VFA conversion revealed a reduced affinity of the microbial community from the CSTR fed with thermally pre-treated manure for acetate, propionate and butyrate. The bacterial and archaeal populations identified by t-RLFP analysis of 16S rRNA genes were found...

  14. Mangrove succession enriches the sediment microbial community in South China.

    Science.gov (United States)

    Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai

    2016-06-06

    Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession.

  15. Thermophilic campylobacters in surface waters around Lancaster, UK: negative correlation with Campylobacter infections in the community.

    Science.gov (United States)

    Jones, K; Betaieb, M; Telford, D R

    1990-11-01

    The incidence of campylobacter enteritis in Lancaster City Health Authority is three times the UK average for similar sizes of population and has marked seasonal peaks in May and June. Environmental monitoring of surface waters around Lancaster showed that thermophilic campylobacters were absent from drinking water from the fells and from the clean upper reaches of the River Conder but were present in the main rivers entering Morecambe Bay, the lower reaches of the River Conder, the Lancaster canal, and seawater from the Lune estuary and Morecambe Bay. All the surface waters tested showed the same seasonality, namely, higher numbers in the winter months and low numbers or none in May, June and July. The absence of thermophilic campylobacters in the summer months may be due to high sunshine levels because experiments on the effects of light showed that campylobacters in sewage effluent and seawater were eliminated within 60 and 30 min of daylight respectively but survived for 24 h in darkness. As the concentrations of campylobacters in surface waters were at their lowest precisely at the time of peak infections in the community it is unlikely that surface waters form Lancaster's reservoir of campylobacter infection for the community.

  16. Influence of feedstock-to-inoculum ratio on performance and microbial community succession during solid-state thermophilic anaerobic co-digestion of pig urine and rice straw.

    Science.gov (United States)

    Meng, Lingyu; Xie, Li; Kinh, Co Thi; Suenaga, Toshikazu; Hori, Tomoyuki; Riya, Shohei; Terada, Akihiko; Hosomi, Masaaki

    2018-03-01

    This study investigated the effect of the feedstock-to-inoculum (F/I) ratio on performance of the solid-state anaerobic co-digestion of pig urine and rice straw inoculated with a solid digestate, and clarified the microbial community succession. A 44-day biochemical methane potential test at F/I ratios of 0.5, 1, 2 and 3 at 55 °C and a 35-day large-scale batch test at F/I ratios of 0.5 and 3 at 55 °C were conducted to investigate the effects of F/I ratio on anaerobic digestibility and analyze microbial community succession, respectively. The highest cumulative methane yield was 353.7 m 3 /t VS in the large-scale batch test. Volatile fatty acids did not accumulate at any F/I ratios. The volatile solids reduction rate was highest at a F/I ratio of 0.5. Microbial community structures were similar between F/I ratios of 3 and 0.5, despite differences in digestion performance, suggesting that stable operation can be achieved at these ratios. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Diversity of bacteria and glycosyl hydrolase family 48 genes in cellulolytic consortia enriched from thermophilic biocompost.

    Science.gov (United States)

    Izquierdo, Javier A; Sizova, Maria V; Lynd, Lee R

    2010-06-01

    The enrichment from nature of novel microbial communities with high cellulolytic activity is useful in the identification of novel organisms and novel functions that enhance the fundamental understanding of microbial cellulose degradation. In this work we identify predominant organisms in three cellulolytic enrichment cultures with thermophilic compost as an inoculum. Community structure based on 16S rRNA gene clone libraries featured extensive representation of clostridia from cluster III, with minor representation of clostridial clusters I and XIV and a novel Lutispora species cluster. Our studies reveal different levels of 16S rRNA gene diversity, ranging from 3 to 18 operational taxonomic units (OTUs), as well as variability in community membership across the three enrichment cultures. By comparison, glycosyl hydrolase family 48 (GHF48) diversity analyses revealed a narrower breadth of novel clostridial genes associated with cultured and uncultured cellulose degraders. The novel GHF48 genes identified in this study were related to the novel clostridia Clostridium straminisolvens and Clostridium clariflavum, with one cluster sharing as little as 73% sequence similarity with the closest known relative. In all, 14 new GHF48 gene sequences were added to the known diversity of 35 genes from cultured species.

  18. Indigenous microbial capability in solid manure residues to start-up solid-phase anaerobic digesters.

    Science.gov (United States)

    Yap, S D; Astals, S; Jensen, P D; Batstone, D J; Tait, S

    2017-06-01

    Batch solid-phase anaerobic digestion is a technology for sustainable on-farm treatment of solid residues, but is an emerging technology that is yet to be optimised with respect to start-up and inoculation. In the present study, spent bedding from two piggeries (site A and B) were batch digested at total solids (TS) concentration of 5, 10 and 20% at mesophilic (37°C) and thermophilic (55°C) temperatures, without adding an external inoculum. The results showed that the indigenous microbial community present in spent bedding was able to recover the full methane potential of the bedding (140±5 and 227±6L CH 4 kgVS fed -1 for site A and B, respectively), but longer treatment times were required than for digestion with an added external inoculum. Nonetheless, at high solid loadings (i.e. TS level>10%), the digestion performance was affected by chemical inhibition due to ammonia and/or humic acid. Thermophilic temperatures did not influence digestion performance but did increase start-up failure risk. Further, inoculation of residues from the batch digestion to subsequent batch enhanced start-up and achieved full methane potential recovery of the bedding. Inoculation with liquid residue (leachate) was preferred over a solid residue, to preserve treatment capacity for fresh substrate. Overall, the study highlighted that indigenous microbial community in the solid manure residue was capable of recovering full methane potential and that solid-phase digestion was ultimately limited by chemical inhibition rather than lack of suitable microbial community. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Linkages between mineralogy, fluid chemistry, and microbial communities within hydrothermal chimneys from the Endeavour Segment, Juan de Fuca Ridge

    Science.gov (United States)

    Lin, T. J.; Ver Eecke, H. C.; Breves, E. A.; Dyar, M. D.; Jamieson, J. W.; Hannington, M. D.; Dahle, H.; Bishop, J. L.; Lane, M. D.; Butterfield, D. A.; Kelley, D. S.; Lilley, M. D.; Baross, J. A.; Holden, J. F.

    2016-02-01

    Rock and fluid samples were collected from three hydrothermal chimneys at the Endeavour Segment, Juan de Fuca Ridge to evaluate linkages among mineralogy, fluid chemistry, and microbial community composition within the chimneys. Mössbauer, midinfrared thermal emission, and visible-near infrared spectroscopies were utilized for the first time to characterize vent mineralogy, in addition to thin-section petrography, X-ray diffraction, and elemental analyses. A 282°C venting chimney from the Bastille edifice was composed primarily of sulfide minerals such as chalcopyrite, marcasite, and sphalerite. In contrast, samples from a 300°C venting chimney from the Dante edifice and a 321°C venting chimney from the Hot Harold edifice contained a high abundance of the sulfate mineral anhydrite. Geochemical modeling of mixed vent fluids suggested the oxic-anoxic transition zone was above 100°C at all three vents, and that the thermodynamic energy available for autotrophic microbial redox reactions favored aerobic sulfide and methane oxidation. As predicted, microbes within the Dante and Hot Harold chimneys were most closely related to mesophilic and thermophilic aerobes of the Betaproteobacteria and Gammaproteobacteria and sulfide-oxidizing autotrophic Epsilonproteobacteria. However, most of the microbes within the Bastille chimney were most closely related to mesophilic and thermophilic anaerobes of the Deltaproteobacteria, especially sulfate reducers, and anaerobic hyperthermophilic archaea. The predominance of anaerobes in the Bastille chimney indicated that other environmental factors promote anoxic conditions. Possibilities include the maturity or fluid flow characteristics of the chimney, abiotic Fe2+ and S2- oxidation in the vent fluids, or O2 depletion by aerobic respiration on the chimney outer wall.

  20. Microbial community analysis of ambient temperature anaerobic digesters

    Energy Technology Data Exchange (ETDEWEB)

    Ciotola, R. [Ohio State Univ., Columbus, OH (United States). Dept. of Food, Agriculture and Biological Engineering

    2010-07-01

    This paper reported on a study in which designs for Chinese and Indian fixed-dome anaerobic digesters were modified in an effort to produce smaller and more affordable digesters. While these types of systems are common in tropical regions of developing countries, they have not been used in colder climates because of the low biogas yield during the winter months. Although there is evidence that sufficient biogas production can be maintained in colder temperatures through design and operational changes, there is a lack of knowledge about the seasonal changes in the composition of the microbial communities in ambient temperature digesters. More knowledge is needed to design and operate systems for maximum biogas yield in temperate climates. The purpose of this study was to cultivate a microbial community that maximizes biogas production at psychrophilic temperatures. The study was conducted on a 300 gallon experimental anaerobic digester on the campus of Ohio State University. Culture-independent methods were used on weekly samples collected from the digester in order to examine microbial community response to changes in ambient temperature. Microbial community profiles were established using universal bacterial and archaeal primers that targeted the 16S rRNA gene. In addition to the methanogenic archaea, this analysis also targeted some of the other numerically and functionally important microbial taxa in anaerobic digesters, such as hydrolytic, fermentative, acetogenic and sulfate reducing bacteria. According to preliminary results, the composition of the microbial community shifts with changes in seasonal temperature.

  1. Diversity and activity of benthic microbial communities at the North Alex mud volcano, Eastern Mediterranean

    Science.gov (United States)

    Makarow, Dorothee; Feseker, Tomas; Schmitz, Ruth; Treude, Tina

    2010-05-01

    North Alex mud volcano, located on the upper slope of the western Nile deep-sea fan, is characterized by an active seepage center transporting pore fluids, hydrocarbons and gases from deep subsurface sources to the sediment-water interface. Surface sediments feature steep temperature gradient of 8.5°C m-1. We sampled the top 40 cm of the sediments at different locations between the center and rim of the mud volcano to study the diversity, activity, and physiological characteristics of benthic microorganisms. The sediments revealed the activity of anaerobic oxidation of methane coupled to sulfate reduction with a mesophilic temperature optimum. Organisms involved in the process include consortia of methanotrophic archaea (ANME-2 group) and an unknown bacterial partner. Besides methanotrophic organisms the sediments harbored a variety of other bacterial and archaeal groups - including potentially thermophilic bacteria that could be involved in sulfur cycling. This poster presentation will provide an overview of microbial activities and community compositions of North Alex mud volcano sediments.

  2. Microbial communities in blueberry soils

    Science.gov (United States)

    Microbial communities thrive in the soil of the plant root zone and it is clear that these communities play a role in plant health. Although blueberry fields can be productive for decades, yields are sometimes below expectations and fields that are replanted sometimes underperform and/or take too lo...

  3. Microorganisms with a Taste for Vanilla: Microbial Ecology of Traditional Indonesian Vanilla Curing

    Science.gov (United States)

    Röling, Wilfred F. M.; Kerler, Josef; Braster, Martin; Apriyantono, Anton; Stam, Hein; van Verseveld, Henk W.

    2001-01-01

    The microbial ecology of traditional postharvesting processing of vanilla beans (curing) was examined using a polyphasic approach consisting of conventional cultivation, substrate utilization-based and molecular identification of isolates, and cultivation-independent community profiling by 16S ribosomal DNA based PCR-denaturing gradient gel electrophoresis. At two different locations, a batch of curing beans was monitored. In both batches a major shift in microbial communities occurred after short-term scalding of the beans in hot water. Fungi and yeast disappeared, although regrowth of fungi occurred in one batch during a period in which process conditions were temporarily not optimal. Conventional plating showed that microbial communities consisting of thermophilic and thermotolerant bacilli (mainly closely related to Bacillus subtilis, B. licheniformis,, and B. smithii) developed under the high temperatures (up to 65°C) that were maintained for over a week after scalding. Only small changes in the communities of culturable bacteria occurred after this period. Molecular analysis revealed that a proportion of the microbial communities could not be cultured on conventional agar medium, especially during the high-temperature period. Large differences between both batches were observed in the numbers of microorganisms, in species composition, and in the enzymatic abilities of isolated bacteria. These large differences indicate that the effects of microbial activities on the development of vanilla flavor could be different for each batch of cured vanilla beans. PMID:11319073

  4. Resistance and Resilience of Soil Microbial Communities Exposed to Petroleum-Derived Compounds

    DEFF Research Database (Denmark)

    Modrzynski, Jakub Jan

    Functioning of soil microbial communities is generally considered resilient to disturbance, including chemical stress. Activities of soil microbial communities are often sustained in polluted environments due to exceptional plasticity of microbial communities and functional redundancy. Pollution......-induced community tolerance (PICT) often develops following chemical stress. Nonetheless, environmental pollution may severely disturb functioning of soil microbial communities, thereby threatening provision of important ecosystem services provided by microorganisms. Pollution with petroleum and petroleum......-derived compounds (PDCs) is a significant environmental problem on a global scale. Research addressing interactions between microorganisms and PDC pollution is dominated by studies of biodegradation, with less emphasis on microbial ecotoxicology. Soil microbial communities are generally considered highly resilient...

  5. Reprint of Design of synthetic microbial communities for biotechnological production processes.

    Science.gov (United States)

    Jagmann, Nina; Philipp, Bodo

    2014-12-20

    In their natural habitats microorganisms live in multi-species communities, in which the community members exhibit complex metabolic interactions. In contrast, biotechnological production processes catalyzed by microorganisms are usually carried out with single strains in pure cultures. A number of production processes, however, may be more efficiently catalyzed by the concerted action of microbial communities. This review will give an overview of organismic interactions between microbial cells and of biotechnological applications of microbial communities. It focuses on synthetic microbial communities that consist of microorganisms that have been genetically engineered. Design principles for such synthetic communities will be exemplified based on plausible scenarios for biotechnological production processes. These design principles comprise interspecific metabolic interactions via cross-feeding, regulation by interspecific signaling processes via metabolites and autoinducing signal molecules, and spatial structuring of synthetic microbial communities. In particular, the implementation of metabolic interdependencies, of positive feedback regulation and of inducible cell aggregation and biofilm formation will be outlined. Synthetic microbial communities constitute a viable extension of the biotechnological application of metabolically engineered single strains and enlarge the scope of microbial production processes. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Population dynamics during startup of thermophilic anaerobic digesters: The mixing factor

    KAUST Repository

    Ghanimeh, Sophia A.

    2013-11-01

    Two thermophilic digesters were inoculated with manure and started-up under mixed and stagnant conditions. The Archaea in the mixed digester (A) were dominated by hydrogenotrophic Methanobateriaceae (61%) with most of the methane being produced via syntrophic pathways. Methanosarcinales (35%) were the only acetoclastic methanogens present. Acetate dissipation seems to depend on balanced hydrogenotrophic-to-acetotrophic abundance, which in turn was statistically correlated to free ammonia levels. Relative abundance of bacterial community was associated with the loading rate. However, in the absence of mixing (digester B), the relationship between microbial composition and operating parameters was not discernible. This was attributed to the development of microenvironments where environmental conditions are significantly different from average measured parameters. The impact of microenvironments was accentuated by the use of a non-acclimated seed that lacks adequate propionate degraders. Failure to disperse the accumulated propionate, and other organics, created high concentration niches where competitive and inhibiting conditions developed and favored undesired genera, such as Halobacteria (65% in B). As a result, digester B experienced higher acid levels and lower allowable loading rate. Mixing was found necessary to dissipate potential inhibitors, and improve stability and loading capacity, particularly when a non-acclimated seed, often lacking balanced thermophilic microflora, is used. © 2013 Elsevier Ltd.

  7. Population dynamics during startup of thermophilic anaerobic digesters: the mixing factor.

    Science.gov (United States)

    Ghanimeh, Sophia A; Saikaly, Pascal E; Li, Dong; El-Fadel, Mutasem

    2013-11-01

    Two thermophilic digesters were inoculated with manure and started-up under mixed and stagnant conditions. The Archaea in the mixed digester (A) were dominated by hydrogenotrophic Methanobateriaceae (61%) with most of the methane being produced via syntrophic pathways. Methanosarcinales (35%) were the only acetoclastic methanogens present. Acetate dissipation seems to depend on balanced hydrogenotrophic-to-acetotrophic abundance, which in turn was statistically correlated to free ammonia levels. Relative abundance of bacterial community was associated with the loading rate. However, in the absence of mixing (digester B), the relationship between microbial composition and operating parameters was not discernible. This was attributed to the development of microenvironments where environmental conditions are significantly different from average measured parameters. The impact of microenvironments was accentuated by the use of a non-acclimated seed that lacks adequate propionate degraders. Failure to disperse the accumulated propionate, and other organics, created high concentration niches where competitive and inhibiting conditions developed and favored undesired genera, such as Halobacteria (65% in B). As a result, digester B experienced higher acid levels and lower allowable loading rate. Mixing was found necessary to dissipate potential inhibitors, and improve stability and loading capacity, particularly when a non-acclimated seed, often lacking balanced thermophilic microflora, is used. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Soil microbial community successional patterns during forest ecosystem restoration.

    Science.gov (United States)

    Banning, Natasha C; Gleeson, Deirdre B; Grigg, Andrew H; Grant, Carl D; Andersen, Gary L; Brodie, Eoin L; Murphy, D V

    2011-09-01

    Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables.

  9. Relating Anaerobic Digestion Microbial Community and Process Function.

    Science.gov (United States)

    Venkiteshwaran, Kaushik; Bocher, Benjamin; Maki, James; Zitomer, Daniel

    2015-01-01

    Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure-function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community-activity relationships or improve engineered bioprocesses.

  10. Habitat constraints on the functional significance of soil microbial communities

    Science.gov (United States)

    Nunan, Naoise; Leloup, Julie; Ruamps, Léo; Pouteau, Valérie; Chenu, Claire

    2017-04-01

    An underlying assumption of most ecosystem models is that soil microbial communities are functionally equivalent; in other words, that microbial activity under given set of conditions is not dependent on the composition or diversity of the communities. Although a number of studies have suggested that this assumption is incorrect, ecosystem models can adequately describe ecosystem processes, such as soil C dynamics, without an explicit description of microbial functioning. Here, we provide a mechanistic basis for reconciling this apparent discrepancy. In a reciprocal transplant experiment, we show that microbial communities are not always functionally equivalent. The data suggest that when the supply of substrate is restricted, then the functioning of different microbial communities cannot be distinguished, but when the supply is less restricted, the intrinsic functional differences among communities can be expressed. When the supply of C is restricted then C dynamics are related to the properties of the physical and chemical environment of the soil. We conclude that soil C dynamics may depend on microbial community structure or diversity in environments such as the rhizosphere or the litter layer, but are less likely to do so in oligotrophic environments such as the mineral layers of soil.

  11. Potential and utilization of thermophiles and thermostable enzymes in biorefining

    Directory of Open Access Journals (Sweden)

    Karlsson Eva

    2007-03-01

    Full Text Available Abstract In today's world, there is an increasing trend towards the use of renewable, cheap and readily available biomass in the production of a wide variety of fine and bulk chemicals in different biorefineries. Biorefineries utilize the activities of microbial cells and their enzymes to convert biomass into target products. Many of these processes require enzymes which are operationally stable at high temperature thus allowing e.g. easy mixing, better substrate solubility, high mass transfer rate, and lowered risk of contamination. Thermophiles have often been proposed as sources of industrially relevant thermostable enzymes. Here we discuss existing and potential applications of thermophiles and thermostable enzymes with focus on conversion of carbohydrate containing raw materials. Their importance in biorefineries is explained using examples of lignocellulose and starch conversions to desired products. Strategies that enhance thermostablity of enzymes both in vivo and in vitro are also assessed. Moreover, this review deals with efforts made on developing vectors for expressing recombinant enzymes in thermophilic hosts.

  12. Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

    Science.gov (United States)

    Ha, Connie WY; Lam, Yan Y; Holmes, Andrew J

    2014-01-01

    Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

  13. Microbial community structure characteristics associated membrane fouling in A/O-MBR system.

    Science.gov (United States)

    Gao, Da-Wen; Wen, Zhi-Dan; Li, Bao; Liang, Hong

    2014-02-01

    The study demonstrated the potential relationship between microbial community structure and membrane fouling in an anoxic-oxic membrane bioreactor (A/O-MBR). The results showed that the microbial community structure in biocake was different with aerobic mixture, and the dominant populations were out of sync during the fouling process. Based on microbial community structure and metabolites analysis, the results showed that the succession of microbial community might be the leading factor to the variation of metabolites, and it might be the primary cause of membrane fouling. The rise of Shannon diversity index (H) of the microbial community in A/O-MBR went with the gradually serious membrane fouling. Pareto-Lorenz curve was used to describe the evenness of microbial distribution in A/O-MBR, and the result indicated when community evenness was low, the membrane fouling took place smoothly or slightly, otherwise, high evenness of microbial community would lead to more seriously membrane fouling. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Microbial Communities Model Parameter Calculation for TSPA/SR

    International Nuclear Information System (INIS)

    D. Jolley

    2001-01-01

    This calculation has several purposes. First the calculation reduces the information contained in ''Committed Materials in Repository Drifts'' (BSC 2001a) to useable parameters required as input to MING V1.O (CRWMS M and O 1998, CSCI 30018 V1.O) for calculation of the effects of potential in-drift microbial communities as part of the microbial communities model. The calculation is intended to replace the parameters found in Attachment II of the current In-Drift Microbial Communities Model revision (CRWMS M and O 2000c) with the exception of Section 11-5.3. Second, this calculation provides the information necessary to supercede the following DTN: M09909SPAMING1.003 and replace it with a new qualified dataset (see Table 6.2-1). The purpose of this calculation is to create the revised qualified parameter input for MING that will allow ΔG (Gibbs Free Energy) to be corrected for long-term changes to the temperature of the near-field environment. Calculated herein are the quadratic or second order regression relationships that are used in the energy limiting calculations to potential growth of microbial communities in the in-drift geochemical environment. Third, the calculation performs an impact review of a new DTN: M00012MAJIONIS.000 that is intended to replace the currently cited DTN: GS9809083 12322.008 for water chemistry data used in the current ''In-Drift Microbial Communities Model'' revision (CRWMS M and O 2000c). Finally, the calculation updates the material lifetimes reported on Table 32 in section 6.5.2.3 of the ''In-Drift Microbial Communities'' AMR (CRWMS M and O 2000c) based on the inputs reported in BSC (2001a). Changes include adding new specified materials and updating old materials information that has changed

  15. Does iron inhibit cryptoendolithic microbial communities?

    Science.gov (United States)

    Johnston, C. G.; Vestal, J. R.; Friedmann, E. I. (Principal Investigator)

    1988-01-01

    Photosynthetic activity of three cryptoendolithic microbial communities was studied under controlled conditions in the laboratory. In two of these communities, the dominant organisms were lichens, collected from Linnaeus Terrace and from Battleship Promontory. The third community, dominated by cyanobacteria, was collected from Battleship Promontory. Both sites are in the ice-free valleys of southern Victoria Land. Previous efforts have shown how physical conditions can influence metabolic activity in endolithic communities (Kappen and Friedmann 1983; Kappen, Friedmann, and Garty 1981; Vestal, Federle, and Friedmann 1984). Biological activity can also be strongly influenced by the chemical environment. Inorganic nutrients such as nitrate, ammonia, and phosphate are often limiting factors, so their effects on photosynthetic carbon-14 bicarbonate incorporation were investigated. Iron and manganese are two metals present in Linnaeus Terrace and Battleship Promontory sandstones, and their effects on photosynthesis were also studied. The results may add to our understanding of biogeochemical interactions within this unique microbial community.

  16. Community genomics among stratified microbial assemblages in the ocean's interior

    DEFF Research Database (Denmark)

    DeLong, Edward F; Preston, Christina M; Mincer, Tracy

    2006-01-01

    Microbial life predominates in the ocean, yet little is known about its genomic variability, especially along the depth continuum. We report here genomic analyses of planktonic microbial communities in the North Pacific Subtropical Gyre, from the ocean's surface to near-sea floor depths. Sequence......, and host-viral interactions. Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics....

  17. Microbial Communities Are Well Adapted to Disturbances in Energy Input.

    Science.gov (United States)

    Fernandez-Gonzalez, Nuria; Huber, Julie A; Vallino, Joseph J

    2016-01-01

    Although microbial systems are well suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20-day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function were used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply. We observed that microbial communities appeared inherently well adapted to disturbances in energy input and that changes in community structure in both treatments were more dependent on internal dynamics than on external forcing. The results also showed that the rare biosphere was critical to seeding the internal community dynamics, perhaps due to cross-feeding or other strategies. We conclude that in our experimental system, internal feedbacks were more important than external drivers in shaping the community dynamics over time, suggesting that ecosystems can maintain their function despite inherently unstable community dynamics. IMPORTANCE Within the broader ecological context, biological communities are often viewed as stable and as only experiencing succession or replacement when subject to external perturbations, such as changes in food availability or the introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic "unstable" communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and manipulating

  18. Biochemical characterization of thermophilic lignocellulose degrading enzymes and their potential for biomass bioprocessing

    Energy Technology Data Exchange (ETDEWEB)

    Zambare, Vasudeo; Zambare, Archana; Christopher, Lew P. [Center for Bioprocessing Research & Development, South Dakota School of Mines and Technology, Rapid City 57701, SD (United States); Muthukumarappan, Kasiviswanath [Center for Bioprocessing Research & Development, South Dakota State University, Brookings 57007, SD (United States)

    2011-07-01

    A thermophilic microbial consortium (TMC) producing hydrolytic (cellulolytic and xylanolytic) enzymes was isolated from yard waste compost following enrichment with carboxymethyl cellulose and birchwood xylan. When grown on 5% lignocellulosic substrates (corn stover and prairie cord grass) at 60C, the thermophilic consortium produced more xylanase (up to 489 U/l on corn stover) than cellulase activity (up to 367 U/l on prairie cord grass). Except for the carboxymethyl cellulose-enriched consortium, thermo-mechanical extrusion pretreatment of these substrates had a positive effect on both activities with up to 13% and 21% increase in the xylanase and cellulase production, respectively. The optimum temperatures of the crude cellulase and xylanase were 60C and 70C with half-lives of 15 h and 18 h, respectively, suggesting higher thermostability for the TMC xylanase. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the crude enzyme exhibited protein bands of 25-77 kDa with multiple enzyme activities containing 3 cellulases and 3 xylanases. The substrate specificity declined in the following descending order: avicel>birchwood xylan>microcrystalline cellulose>filter paper>pine wood saw dust>carboxymethyl cellulose. The crude enzyme was 77% more active on insoluble than soluble cellulose. The Km and Vmax values were 36.49 mg/ml and 2.98 U/mg protein on avicel (cellulase), and 22.25 mg/ml and 2.09 U/mg protein, on birchwood xylan (xylanase). A total of 50 TMC isolates were screened for cellulase and xylanase secretion on agar plates. All single isolates showed significantly lower enzyme activities when compared to the thermophilic consortia. This is indicative of the strong synergistic interactions that exist within the thermophilic microbial consortium and enhance its hydrolytic capabilities. It was further demonstrated that the thermostable enzyme-generated lignocellulosic hydrolyzates can be fermented to bioethanol by a recombinant strain of Escherichia coli

  19. Perspective for Aquaponic Systems: "Omic" Technologies for Microbial Community Analysis.

    Science.gov (United States)

    Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Torres-Pacheco, Irineo; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V; Garcia-Trejo, Juan F; Guevara-Gonzalez, Ramon G

    2015-01-01

    Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the "Omic" technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. "Omic" technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current "Omic" tools to characterize the microbial community in aquaponic systems.

  20. Evaluation of microbial community composition in thermophilic methane-producing incubation of production water from a high-temperature oil reservoir.

    Science.gov (United States)

    Zhou, Fang; Mbadinga, Serge Maurice; Liu, Jin-Feng; Gu, Ji-Dong; Mu, Bo-Zhong

    2013-01-01

    Investigation of petroleum microbes is fundamental for the development and utilization of oil reservoirs' microbial resources, and also provides great opportunities for research and development of bio-energy. Production water from a high-temperature oil reservoir was incubated anaerobically at 55 degrees C for more than 400 days without amendment of any nutrients. Over the time of incubation, about 1.6 mmol of methane and up to 107 micromol of hydrogen (H2) were detected in the headspace. Methane formation indicated that methanogenesis was likely the predominant process in spite of the presence of 23.4 mM SO4(2-) in the production water. Microbial community composition of the incubation was characterized by means of 16S rRNA gene clone libraries construction. Bacterial composition changed from Pseudomonales as the dominant population initially to Hydrogenophilales-related microorganisms affiliated to Petrobacter spp. closely. After 400 days of incubation, other bacterial members detected were related to Anareolineales, beta-, gamma-, and delta-Proteobacteria. The archaeal composition of the original production water was essentially composed of obligate acetoclastic methanogens of the genus Methanosaeta, but the incubation was predominantly composed of CO2-reducing methanogens of the genus Methanothermobacter and Crenarchaeotes-related microorganisms. Our results suggest that methanogenesis could be more active than expected in oil reservoir environments and methane formation from CO2-reduction played a significant role in the methanogenic community. This conclusion is consistent with the predominant role played by H2-oxidizing methanogens in the methanogenic conversion of organic matter in high-temperature petroleum reservoirs.

  1. The Role of Soil Organic Matter, Nutrients, and Microbial Community Structure on the Performance of Microbial Fuel Cells

    Science.gov (United States)

    Rooney-Varga, J. N.; Dunaj, S. J.; Vallino, J. J.; Hines, M. E.; Gay, M.; Kobyljanec, C.

    2011-12-01

    Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful, natural, and renewable resource: soil organic carbon. In the current study, we analyzed microbial community structure, MFC performance, and soil characteristics in different microhabitats (bulk soil, anode, and cathode) within MFCs constructed from agricultural or forest soils in order to determine how soil type and microbial dynamics influence MFC performance. MFCs were constructed with soils from agricultural and hardwood forest sites at Harvard Forest (Petersham, MA). The bulk soil characteristics were analyzed, including polyphenols, short chain fatty acids, total organic C and N, abiotic macronutrients, N and P mineralization rates, CO2 respiration rates, and MFC power output. Microbial community structure of the anodes, cathodes, and bulk soils was determined with molecular fingerprinting methods, which included terminal restriction length polymorphism (T-RFLP) analysis and 16S rRNA gene sequencing analysis. Our results indicated that MFCs constructed from agricultural soil had power output about 17 times that of forest soil-based MFCs and respiration rates about 10 times higher than forest soil MFCs. Agricultural soil MFCs had lower C:N ratios, polyphenol content, and acetate concentrations than forest soil MFCs, suggesting that active agricultural MFC microbial communities were supported by higher quality organic carbon. Microbial community profile data indicate that the microbial communities at the anode of the high power MFCs were less diverse than in low power MFCs and were dominated by Deltaproteobacteria, Geobacter, and, to a lesser extent, Clostridia, while low-power MFC anode communities were dominated by Clostridia. These data suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic microbial

  2. Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times.

    Science.gov (United States)

    Neher, Deborah A; Weicht, Thomas R; Bates, Scott T; Leff, Jonathan W; Fierer, Noah

    2013-01-01

    Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed

  3. Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India.

    Science.gov (United States)

    Badhai, Jhasketan; Ghosh, Tarini S; Das, Subrata K

    2015-01-01

    This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40-58°C; pH: 7.2-7.4) with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate), total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis, and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria.

  4. Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India

    Directory of Open Access Journals (Sweden)

    Subrata K Das

    2015-10-01

    Full Text Available This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40-58 °C; pH: 7.2-7.4 with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate, total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria.

  5. [Oxidation of sulfur-containing substrates by aboriginal and experimentally designed microbial communities].

    Science.gov (United States)

    Pivovarova, T A; Bulaev, A G; Roshchupko, P V; Belyĭ, A V; Kondrat'eva, T F

    2012-01-01

    Aboriginal and experimental (constructed of pure microbial cultures) communities of acidophilic chemolithotrophs have been studied. The oxidation of elemental sulfur, sodium thiosulfate, and potassium tetrathionate as sole sources of energy has been monitored. The oxidation rate of the experimental community is higher as compared to the aboriginal community isolated from a flotation concentrate of pyrrhotine-containing pyrite-arsenopyrite gold-arsenic sulfide ore. The degree of oxidation of the mentioned S substrates amounts to 17.91, 68.30, and 93.94% for the experimental microbial community and to 10.71, 56.03, and 79.50% for the aboriginal community, respectively. The degree of oxidation of sulfur sulfide forms in the ore flotation concentrate is 59.15% by the aboriginal microbial community and 49.40% by the experimental microbial community. Despite a higher rate of oxidation of S substrates as a sole source of energy by the experimental microbial community, the aboriginal community oxidizes S substrates at a higher rate in the flotation concentrate of pyrrhotine-containing pyrite-arsenopyrite gold-arsenic sulfide ore, from which it was isolated. Bacterial-chemical oxidation of the flotation concentrate by the aboriginal microbial community allows for the extraction of an additional 32.3% of gold from sulfide minerals, which is by 5.7% larger compared to the yield obtained by the experimental microbial community.

  6. Hydraulic retention time affects stable acetate production from tofu processing wastewater in extreme-thermophilic (70°C) mixed culture fermentation.

    Science.gov (United States)

    Chen, Yun; Zhang, Fang; Wang, Ting; Shen, Nan; Yu, Zhong-Wei; Zeng, Raymond J

    2016-09-01

    Acetate is an important industrial chemical and its production from wastes via mixed culture fermentation (MCF) is economic. In this work, the effect of hydraulic retention time (HRT) on acetate production from tofu processing wastewater (TPW) in extreme-thermophilic (70°C) MCF was first investigated. It was found that long HRT (>3days) could lead to less acetate production while stable acetate production was achieved at short HRT (3days) with the yield of 0.57g-COD/g-CODTPW. The microbial community analysis showed that hydrogenotrophic methanogens (mainly Methanothermobacter) occupied up to 90% of archaea at both HRTs of 3 and 5days. However, Coprothermobacter, the main acetate-degraders, decreased from 35.74% to 10.58% of bacteria when HRT decreased from 5 to 3days, supporting the aggravation of syntrophic acetate oxidation in long HRT. This work demonstrated that HRT was a crucial factor to maintain stable acetate production from TPW in extreme-thermophilic MCF. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Mesophilic and thermophilic biotreatment of BTEX-polluted air in reactors.

    Science.gov (United States)

    Mohammad, Balsam T; Veiga, María C; Kennes, Christian

    2007-08-15

    This study compares the removal of a mixture of benzene, toluene, ethylbenzene, and all three xylene isomers (BTEX) in mesophilic and thermophilic (50 degrees C) bioreactors. In the mesophilic reactor fungi became dominant after long-term operation, while bacteria dominated in the thermophilic unit. Microbial acclimation was achieved by exposing the biofilters to initial BTEX loads of 2-15 g m(-3) h(-1), at an empty bed residence time of 96 s. After adaptation, the elimination capacities ranged from 3 to 188 g m(-3) h(-1), depending on the inlet load, for the mesophilic biofilter with removal efficiencies reaching 96%. On the other hand, in the thermophilic reactor the average removal efficiency was 83% with a maximum elimination capacity of 218 g m(-3) h(-1). There was a clear positive relationship between temperature gradients as well as CO(2) production and elimination capacities across the biofilters. The gas phase was sampled at different depths along the reactors observing that the percentage pollutant removal in each section was strongly dependant on the load applied. The fate of individual alkylbenzene compounds was checked, showing the unusually high biodegradation rate of benzene at high loads under thermophilic conditions (100%) compared to its very low removal in the mesophilic reactor at such load (<10%). Such difference was less pronounced for the other pollutants. After 210 days of operation, the dry biomass content for the mesophilic and thermophilic reactors were 0.300 and 0.114 g g(-1) (support), respectively, reaching higher removals under thermophilic conditions with a lower biomass accumulation, that is, lower pressure drop. (c) 2007 Wiley Periodicals, Inc.

  8. Response of soil microbial activities and microbial community structure to vanadium stress.

    Science.gov (United States)

    Xiao, Xi-Yuan; Wang, Ming-Wei; Zhu, Hui-Wen; Guo, Zhao-Hui; Han, Xiao-Qing; Zeng, Peng

    2017-08-01

    High levels of vanadium (V) have long-term, hazardous impacts on soil ecosystems and biological processes. In the present study, the effects of V on soil enzymatic activities, basal respiration (BR), microbial biomass carbon (MBC), and the microbial community structure were investigated through 12-week greenhouse incubation experiments. The results showed that V content affected soil dehydrogenase activity (DHA), BR, and MBC, while urease activity (UA) was less sensitive to V stress. The average median effective concentration (EC 50 ) thresholds of V were predicted using a log-logistic dose-response model, and they were 362mgV/kg soil for BR and 417mgV/kg soil for DHA. BR and DHA were more sensitive to V addition and could be used as biological indicators for soil V pollution. According to a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis, the structural diversity of the microbial community decreased for soil V contents ranged between 254 and 1104mg/kg after 1 week of incubation. As the incubation time increased, the diversity of the soil microbial community structure increased for V contents ranged between 354 and 1104mg/kg, indicating that some new V-tolerant bacterial species might have replicated under these conditions. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Microbial community composition affects soil fungistasis.

    Science.gov (United States)

    de Boer, Wietse; Verheggen, Patrick; Klein Gunnewiek, Paulien J A; Kowalchuk, George A; van Veen, Johannes A

    2003-02-01

    Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.

  10. Lipid Biomarkers for a Hypersaline Microbial Mat Community

    Science.gov (United States)

    Jahnke, Linda L.; Embaye, Tsege; Turk, Kendra A.

    2003-01-01

    The use of lipid biomarkers and their carbon isotopic compositions are valuable tools for establishing links to ancient microbial ecosystems. As witnessed by the stromatolite record, benthic microbial mats grew in shallow water lagoonal environments where microorganisms had virtually no competition apart from the harsh conditions of hypersalinity, desiccation and intense light. Today, the modern counterparts of these microbial ecosystems find appropriate niches in only a few places where extremes eliminate eukaryotic grazers. Answers to many outstanding questions about the evolution of microorganisms and their environments on early Earth are best answered through study of these extant analogs. Lipids associated with various groups of bacteria can be valuable biomarkers for identification of specific groups of microorganisms both in ancient organic-rich sedimentary rocks (geolipids) and contemporary microbial communities (membrane lipids). Use of compound specific isotope analysis adds additional refinement to the identification of biomarker source, so that it is possible to take advantage of the 3C-depletions associated with various functional groups of organisms (i.e. autotrophs, heterotrophs, methanotrophs, methanogens) responsible for the cycling of carbon within a microbial community. Our recent work has focused on a set of hypersaline evaporation ponds at Guerrero Negro, Baja California Sur, Mexico which support the abundant growth of Microcoleus-dominated microbial mats. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface.

  11. Reactor performances and microbial communities of biogas reactors: effects of inoculum sources.

    Science.gov (United States)

    Han, Sheng; Liu, Yafeng; Zhang, Shicheng; Luo, Gang

    2016-01-01

    Anaerobic digestion is a very complex process that is mediated by various microorganisms, and the understanding of the microbial community assembly and its corresponding function is critical in order to better control the anaerobic process. The present study investigated the effect of different inocula on the microbial community assembly in biogas reactors treating cellulose with various inocula, and three parallel biogas reactors with the same inoculum were also operated in order to reveal the reproducibility of both microbial communities and functions of the biogas reactors. The results showed that the biogas production, volatile fatty acid (VFA) concentrations, and pH were different for the biogas reactors with different inocula, and different steady-state microbial community patterns were also obtained in different biogas reactors as reflected by Bray-Curtis similarity matrices and taxonomic classification. It indicated that inoculum played an important role in shaping the microbial communities of biogas reactor in the present study, and the microbial community assembly in biogas reactor did not follow the niche-based ecology theory. Furthermore, it was found that the microbial communities and reactor performances of parallel biogas reactors with the same inoculum were different, which could be explained by the neutral-based ecology theory and stochastic factors should played important roles in the microbial community assembly in the biogas reactors. The Bray-Curtis similarity matrices analysis suggested that inoculum affected more on the microbial community assembly compared to stochastic factors, since the samples with different inocula had lower similarity (10-20 %) compared to the samples from the parallel biogas reactors (30 %).

  12. Microbial Community Structure of an Alluvial Aquifer Treated to Encourage Microbial Induced Calcite Precipitation

    Science.gov (United States)

    Ohan, J.; Saneiyan, S.; Lee, J.; Ntarlagiannis, D.; Burns, S.; Colwell, F. S.

    2017-12-01

    An oligotrophic aquifer in the Colorado River floodplain (Rifle, CO) was treated with molasses and urea to encourage microbial induced calcite precipitation (MICP). This would stabilize the soil mass by reducing porosity and strengthening the mineral fabric. Over the course of a 15-day treatment period, microbial biomass was collected from monitoring well groundwater for DNA extraction and sequencing. Bromide, a conservative tracer, was co-injected and subsequently detected in downgradient wells, confirming effective nutrient delivery. Conductivity increased during the injection regime and an overall decrease in pH was observed. Groundwater chemistry showed a marked increase in ammonia, suggesting urea hydrolysis - a process catalyzed by the enzyme urease - the primary enzyme implicated in MICP. Additionally, soluble iron was detected, suggesting a general increase in microbial activity; possibly as iron-reducing bacteria changed insoluble ferric oxide to soluble ferrous hydroxide in the anoxic aquifer. DNA sequencing of the 16S rRNA gene confirmed the presence of iron reducing bacteria, including Shewanella and Desulfuromonadales. Generally, a decrease in microbial community diversity was observed when pre-injection community taxa were compared with post-injection community taxa. Phyla indicative of anoxic aquifers were represented in accordance with previous literature at the Rifle site. Linear discriminant analysis showed significant differences in representative phyla over the course of the injection series. Geophysical monitoring of the site further suggested changes that could be due to MICP. Induced polarization increased the phase shift in the primary treated area, in agreement with laboratory experiments. Cross-hole seismic testing confirmed that the shear wave velocities increased in the treated soil mass, implying the soil matrix became more stable. Future investigations will help elucidate the viability and efficacy of MICP treatment in changing

  13. How microbial community composition regulates coral disease development.

    Directory of Open Access Journals (Sweden)

    Justin Mao-Jones

    2010-03-01

    Full Text Available Reef coral cover is in rapid decline worldwide, in part due to bleaching (expulsion of photosynthetic symbionts and outbreaks of infectious disease. One important factor associated with bleaching and in disease transmission is a shift in the composition of the microbial community in the mucus layer surrounding the coral: the resident microbial community-which is critical to the healthy functioning of the coral holobiont-is replaced by pathogenic microbes, often species of Vibrio. In this paper we develop computational models for microbial community dynamics in the mucus layer in order to understand how the surface microbial community responds to changes in environmental conditions, and under what circumstances it becomes vulnerable to overgrowth by pathogens. Some of our model's assumptions and parameter values are based on Vibrio spp. as a model system for other established and emerging coral pathogens. We find that the pattern of interactions in the surface microbial community facilitates the existence of alternate stable states, one dominated by antibiotic-producing beneficial microbes and the other pathogen-dominated. A shift to pathogen dominance under transient stressful conditions, such as a brief warming spell, may persist long after environmental conditions have returned to normal. This prediction is consistent with experimental findings that antibiotic properties of Acropora palmata mucus did not return to normal long after temperatures had fallen. Long-term loss of antibiotic activity eliminates a critical component in coral defense against disease, giving pathogens an extended opportunity to infect and spread within the host, elevating the risk of coral bleaching, disease, and mortality.

  14. How microbial community composition regulates coral disease development.

    Science.gov (United States)

    Mao-Jones, Justin; Ritchie, Kim B; Jones, Laura E; Ellner, Stephen P

    2010-03-30

    Reef coral cover is in rapid decline worldwide, in part due to bleaching (expulsion of photosynthetic symbionts) and outbreaks of infectious disease. One important factor associated with bleaching and in disease transmission is a shift in the composition of the microbial community in the mucus layer surrounding the coral: the resident microbial community-which is critical to the healthy functioning of the coral holobiont-is replaced by pathogenic microbes, often species of Vibrio. In this paper we develop computational models for microbial community dynamics in the mucus layer in order to understand how the surface microbial community responds to changes in environmental conditions, and under what circumstances it becomes vulnerable to overgrowth by pathogens. Some of our model's assumptions and parameter values are based on Vibrio spp. as a model system for other established and emerging coral pathogens. We find that the pattern of interactions in the surface microbial community facilitates the existence of alternate stable states, one dominated by antibiotic-producing beneficial microbes and the other pathogen-dominated. A shift to pathogen dominance under transient stressful conditions, such as a brief warming spell, may persist long after environmental conditions have returned to normal. This prediction is consistent with experimental findings that antibiotic properties of Acropora palmata mucus did not return to normal long after temperatures had fallen. Long-term loss of antibiotic activity eliminates a critical component in coral defense against disease, giving pathogens an extended opportunity to infect and spread within the host, elevating the risk of coral bleaching, disease, and mortality.

  15. Diversity of Cultured Thermophilic Anaerobes in Hot Springs of Yunnan Province, China

    Science.gov (United States)

    Lin, L.; Lu, Y.; Dong, X.; Liu, X.; Wei, Y.; Ji, X.; Zhang, C.

    2010-12-01

    Thermophilic anaerobes including Archaea and Bacteria refer to those growing optimally at temperatures above 50°C and do not use oxygen as the terminal electron acceptor for growth. Study on thermophilic anaerobes will help to understand how life thrives under extreme conditions. Meanwhile thermophilic anaerobes are of importance in potential application and development of thermophilic biotechnology. We have surveyed culturable thermophilic anaerobes in hot springs (pH6.5-7.5; 70 - 94°C) in Rehai of Tengchong, Bangnazhang of Longlin, Eryuan of Dali,Yunnan, China. 50 strains in total were cultured from the hot springs water using Hungate anaerobic technique, and 30 strains were selected based on phenotypic diversity for analysis of 16S rDNA sequences. Phylogenetic analysis showed that 28 strains belonged to the members of five genera: Caldanaerobacter, Calaramator, Thermoanaerobacter, Dictyoglomus and Fervidobacterium, which formed five branches on the phylogenetic tree. Besides, 2 strains of methanogenic archaea were obtained. The majority of the isolates were the known species, however, seven strains were identified as novel species affiliated to the five genera based on the lower 16S rDNA sequence similarities (less than 93 - 97%) with the described species. This work would provide the future study on their diversity, distribution among different regions and the potential application of thermophilic enzyme. Supported by State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences(SKLMR-080605)and the Foundation of State Natural Science (30660009, 30960022, 31081220175).

  16. Microbial Interactions With Dissolved Organic Matter Drive Carbon Dynamics and Community Succession

    Directory of Open Access Journals (Sweden)

    Xiaoqin Wu

    2018-06-01

    Full Text Available Knowledge of dynamic interactions between natural organic matter (NOM and microbial communities is critical not only to delineate the routes of NOM degradation/transformation and carbon (C fluxes, but also to understand microbial community evolution and succession in ecosystems. Yet, these processes in subsurface environments are usually studied independently, and a comprehensive view has been elusive thus far. In this study, we fed sediment-derived dissolved organic matter (DOM to groundwater microbes and continually analyzed microbial transformation of DOM over a 50-day incubation. To document fine-scale changes in DOM chemistry, we applied high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS and soft X-ray absorption spectroscopy (sXAS. We also monitored the trajectory of microbial biomass, community structure and activity over this time period. Together, these analyses provided an unprecedented comprehensive view of interactions between sediment-derived DOM and indigenous subsurface groundwater microbes. Microbial decomposition of labile C in DOM was immediately evident from biomass increase and total organic carbon (TOC decrease. The change of microbial composition was closely related to DOM turnover: microbial community in early stages of incubation was influenced by relatively labile tannin- and protein-like compounds; while in later stages the community composition evolved to be most correlated with less labile lipid- and lignin-like compounds. These changes in microbial community structure and function, coupled with the contribution of microbial products to DOM pool affected the further transformation of DOM, culminating in stark changes to DOM composition over time. Our study demonstrates a distinct response of microbial communities to biotransformation of DOM, which improves our understanding of coupled interactions between sediment-derived DOM, microbial processes, and community structure in

  17. Cyanobacterial composition of microbial mats from an Australian thermal spring: a polyphasic evaluation.

    Science.gov (United States)

    McGregor, Glenn B; Rasmussen, J Paul

    2008-01-01

    Cyanobacterial composition of microbial mats from an alkaline thermal spring issuing at 43-71 degrees C from tropical north-eastern Australia are described using a polyphasic approach. Eight genera and 10 species from three cyanobacterial orders were identified based on morphological characters. These represented taxa previously known as thermophilic from other continents. Ultrastructural analysis of the tower mats revealed two filamentous morphotypes contributed the majority of the biomass. Both types had ultrastructural characteristics of the family Pseudanabaenaceae. DNA extracts were made from sections of the tentaculiform towers and the microbial community analysed by 16S cyanobacteria-specific PCR and denaturing-gradient gel electrophoresis. Five significant bands were identified and sequenced. Two bands clustered closely with Oscillatoria amphigranulata isolated from New Zealand hot springs; one unique phylotype had only moderate similarity to a range of Leptolyngbya species; and one phylotype was closely related to a number of Geitlerinema species. Generally the approaches yielded complementary information, however the results suggest that species designation based on morphological and ultrastructural criteria alone often fails to recognize their true phylogenetic position. Conversely some molecular techniques may fail to detect rare taxa suggesting that the widest possible suite of techniques be applied when conducting analyses of cyanobacterial diversity of natural populations. This is the first polyphasic evaluation of thermophilic cyanobacterial communities from the Australian continent.

  18. Sediment Microbial Communities Influenced by Cool Hydrothermal Fluid Migration

    Directory of Open Access Journals (Sweden)

    Laura A. Zinke

    2018-06-01

    Full Text Available Cool hydrothermal systems (CHSs are prevalent across the seafloor and discharge fluid volumes that rival oceanic input from rivers, yet the microbial ecology of these systems are poorly constrained. The Dorado Outcrop on the ridge flank of the Cocos Plate in the northeastern tropical Pacific Ocean is the first confirmed CHS, discharging minimally altered <15°C fluid from the shallow lithosphere through diffuse venting and seepage. In this paper, we characterize the resident sediment microbial communities influenced by cool hydrothermal advection, which is evident from nitrate and oxygen concentrations. 16S rRNA gene sequencing revealed that Thaumarchaea, Proteobacteria, and Planctomycetes were the most abundant phyla in all sediments across the system regardless of influence from seepage. Members of the Thaumarchaeota (Marine Group I, Alphaproteobacteria (Rhodospirillales, Nitrospirae, Nitrospina, Acidobacteria, and Gemmatimonadetes were enriched in the sediments influenced by CHS advection. Of the various geochemical parameters investigated, nitrate concentrations correlated best with microbial community structure, indicating structuring based on seepage of nitrate-rich fluids. A comparison of microbial communities from hydrothermal sediments, seafloor basalts, and local seawater at Dorado Outcrop showed differences that highlight the distinct niche space in CHS. Sediment microbial communities from Dorado Outcrop differ from those at previously characterized, warmer CHS sediment, but are similar to deep-sea sediment habitats with surficial ferromanganese nodules, such as the Clarion Clipperton Zone. We conclude that cool hydrothermal venting at seafloor outcrops can alter the local sedimentary oxidation–reduction pathways, which in turn influences the microbial communities within the fluid discharge affected sediment.

  19. A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal.

    Science.gov (United States)

    Courtens, Emilie Np; Spieck, Eva; Vilchez-Vargas, Ramiro; Bodé, Samuel; Boeckx, Pascal; Schouten, Stefan; Jauregui, Ruy; Pieper, Dietmar H; Vlaeminck, Siegfried E; Boon, Nico

    2016-09-01

    The increasing production of nitrogen-containing fertilizers is crucial to meet the global food demand, yet high losses of reactive nitrogen associated with the food production/consumption chain progressively deteriorate the natural environment. Currently, mesophilic nitrogen-removing microbes eliminate nitrogen from wastewaters. Although thermophilic nitrifiers have been separately enriched from natural environments, no bioreactors are described that couple these processes for the treatment of nitrogen in hot wastewaters. Samples from composting facilities were used as inoculum for the batch-wise enrichment of thermophilic nitrifiers (350 days). Subsequently, the enrichments were transferred to a bioreactor to obtain a stable, high-rate nitrifying process (560 days). The community contained up to 17% ammonia-oxidizing archaea (AOAs) closely related to 'Candidatus Nitrososphaera gargensis', and 25% nitrite-oxidizing bacteria (NOBs) related to Nitrospira calida. Incorporation of (13)C-derived bicarbonate into the respective characteristic membrane lipids during nitrification supported their activity as autotrophs. Specific activities up to 198±10 and 894±81 mg N g(-1) VSS per day for AOAs and NOBs were measured, where NOBs were 33% more sensitive to free ammonia. The NOBs were extremely sensitive to free nitrous acid, whereas the AOAs could only be inhibited by high nitrite concentrations, independent of the free nitrous acid concentration. The observed difference in product/substrate inhibition could facilitate the development of NOB inhibition strategies to achieve more cost-effective processes such as deammonification. This study describes the enrichment of autotrophic thermophilic nitrifiers from a nutrient-rich environment and the successful operation of a thermophilic nitrifying bioreactor for the first time, facilitating opportunities for thermophilic nitrogen removal biotechnology.

  20. Lignocellulose-derived thin stillage composition and efficient biological treatment with a high-rate hybrid anaerobic bioreactor system

    KAUST Repository

    Oosterkamp, Margreet J.; Mé ndez-Garcí a, Celia; Kim, Chang-H.; Bauer, Stefan; Ibá ñ ez, Ana B.; Zimmerman, Sabrina; Hong, Pei-Ying; Cann, Isaac K.; Mackie, Roderick I.

    2016-01-01

    Results showed that thin stillage contains easily degradable compounds suitable for anaerobic digestion and that hybrid reactors can efficiently convert thin stillage to methane under mesophilic and thermophilic conditions. Furthermore, we found that optimal conditions for biological treatment of thin stillage were similar for both mesophilic and thermophilic reactors. Bar-coded pyrosequencing of the 16S rRNA gene identified different microbial communities in mesophilic and thermophilic reactors and these differences in the microbial communities could be linked to the composition of the thin stillage.

  1. Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

    Science.gov (United States)

    Haverkamp, Thomas H A; Hammer, Øyvind; Jakobsen, Kjetill S

    2014-01-01

    Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.

  2. Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

    Directory of Open Access Journals (Sweden)

    Thomas H A Haverkamp

    Full Text Available Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm sediment communities are affected by local conditions within the sediment.

  3. Copper removal and microbial community analysis in single-chamber microbial fuel cell.

    Science.gov (United States)

    Wu, Yining; Zhao, Xin; Jin, Min; Li, Yan; Li, Shuai; Kong, Fanying; Nan, Jun; Wang, Aijie

    2018-04-01

    In this study, copper removal and electricity generation were investigated in a single-chamber microbial fuel cell (MFC). Result showed that copper was efficiently removed in the membrane-less MFC with removal efficiency of 98.3% at the tolerable Cu 2+ concentration of 12.5 mg L -1 , the corresponding open circuit voltage and maximum power density were 0.78 V and 10.2 W m -3 , respectively. The mechanism analysis demonstrated that microbial electrochemical reduction contributed to the copper removal with the products of Cu and Cu 2 O deposited at biocathode. Moreover, the microbial community analysis indicated that microbial communities changed with different copper concentrations. The dominant phyla were Proteobacteria and Bacteroidetes which could play key roles in electricity generation, while Actinobacteria and Acidobacteria were also observed which were responsible for Cu-resistant and copper removal. It will be of important guiding significance for the recovery of copper from low concentration wastewater through single-chamber MFC with simultaneous energy recovery. Copyright © 2018 Elsevier Ltd. All rights reserved.

  4. Metagenomics of Kamchatkan hot spring filaments reveal two new major (hyper)thermophilic lineages related to Thaumarchaeota.

    Science.gov (United States)

    Eme, Laura; Reigstad, Laila J; Spang, Anja; Lanzén, Anders; Weinmaier, Thomas; Rattei, Thomas; Schleper, Christa; Brochier-Armanet, Céline

    2013-06-01

    Based on phylogenetic analyses and gene distribution patterns of a few complete genomes, a new distinct phylum within the Archaea, the Thaumarchaeota, has recently been proposed. Here we present analyses of six archaeal fosmid sequences derived from a microbial hot spring community in Kamchatka. The phylogenetic analysis of informational components (ribosomal RNAs and proteins) reveals two major (hyper-)thermophilic clades ("Hot Thaumarchaeota-related Clade" 1 and 2, HTC1 and HTC2) related to Thaumarchaeota, representing either deep branches of this phylum or a new archaeal phylum and provides information regarding the ancient evolution of Archaea and their evolutionary links with Eukaryotes. Copyright © 2013 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  5. Diversity and ubiquity of thermophilic methanogenic archaea in temperate anoxic soils.

    Science.gov (United States)

    Wu, Xiao-Lei; Friedrich, Michael W; Conrad, Ralf

    2006-03-01

    Temperate rice field soil from Vercelli (Italy) contains moderately thermophilic methanogens of the yet uncultivated rice cluster I (RC-I), which become prevalent upon incubation at temperatures of 45-50 degrees C. We studied whether such thermophilic methanogens were ubiquitously present in anoxic soils. Incubation of different rice field soils (from Italy, China and the Philippines) and flooded riparian soils (from the Netherlands) at 45 degrees C resulted in vigorous CH(4) production after a lag phase of about 10 days. The archaeal community structure in the soils was analysed by terminal restriction fragment length polymorphism (T-RFLP) targeting the SSU rRNA genes retrieved from the soil, and by cloning and sequencing. Clones of RC-I methanogens mostly exhibited T-RF of 393 bp, but also terminal restriction fragment (T-RF) of 158 and 258 bp length, indicating a larger diversity than previously assumed. No RC-I methanogens were initially found in flooded riparian soils. However, these archaea became abundant upon incubation of the soil at 45 degrees C. Thermophilic RC-I methanogens were also found in the rice field soils from Pavia, Pila and Gapan. However, the archaeal communities in these soils also contained other methanogenic archaea at high temperature. Rice field soil from Buggalon, on the other hand, only contained thermophilic Methanomicrobiales rather than RC-I methanogens, and rice field soil from Jurong mostly Methanomicrobiales and only a few RC-I methanogens. The archaeal community of rice field soil from Zhenjiang almost exclusively consisted of Methanosarcinaceae when incubated at high temperature. Our results show that moderately thermophilic methanogens are common in temperate soils. However, RC-I methanogens are not always dominating or ubiquitous.

  6. Strong linkage between active microbial communities and microbial carbon usage in a deglaciated terrain of the High Arctic

    Science.gov (United States)

    Kim, M.; Gyeong, H. R.; Lee, Y. K.

    2017-12-01

    Soil microorganisms play pivotal roles in ecosystem development and carbon cycling in newly exposed glacier forelands. However, little is known about carbon utilization pattern by metabolically active microbes over the course of ecosystem succession in these nutrient-poor environments. We investigated RNA-based microbial community dynamics and its relation to microbial carbon usage along the chronosequence of a High Arctic glacier foreland. Among microbial taxa surveyed (bacteria, archaea and fungi), bacteria are among the most metabolically active taxa with a dominance of Cyanobacteria and Actinobacteria. There was a strong association between microbial carbon usage and active Actinobacterial communities, suggesting that member of Actinobacteria are actively involved in organic carbon degradation in glacier forelands. Both bacterial community and microbial carbon usage are converged towards later stage of succession, indicating that the composition of soil organic carbon plays important roles in structuring bacterial decomposer communities during ecosystem development.

  7. Perspective for Aquaponic Systems: “Omic” Technologies for Microbial Community Analysis

    Directory of Open Access Journals (Sweden)

    Perla Munguia-Fragozo

    2015-01-01

    Full Text Available Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the “Omic” technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS. However, microbial community composition of aquaponics is still unknown. “Omic” technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current “Omic” tools to characterize the microbial community in aquaponic systems.

  8. Perspective for Aquaponic Systems: “Omic” Technologies for Microbial Community Analysis

    Science.gov (United States)

    Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V.; Garcia-Trejo, Juan F.; Guevara-Gonzalez, Ramon G.

    2015-01-01

    Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the “Omic” technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. “Omic” technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current “Omic” tools to characterize the microbial community in aquaponic systems. PMID:26509157

  9. Microbial community assembly and metabolic function during mammalian corpse decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Metcalf, J. L.; Xu, Z. Z.; Weiss, S.; Lax, S.; Van Treuren, W.; Hyde, E. R.; Song, S. J.; Amir, A.; Larsen, P.; Sangwan, N.; Haarmann, D.; Humphrey, G. C.; Ackermann, G.; Thompson, L. R.; Lauber, C.; Bibat, A.; Nicholas, C.; Gebert, M. J.; Petrosino, J. F.; Reed, S. C.; Gilbert, J. A.; Lynne, A. M.; Bucheli, S. R.; Carter, D. O.; Knight, R.

    2015-12-10

    Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

  10. Microbial community assembly and metabolic function during mammalian corpse decomposition

    Science.gov (United States)

    Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R.; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C.; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

    2016-01-01

    Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

  11. Toward Understanding the Dynamics of Microbial Communities in an Estuarine System

    KAUST Repository

    Zhang, Weipeng; Bougouffa, Salim; Wang, Yong; Lee, On On; Yang, Jiangke; Chan, Colin; Song, Xingyu; Qian, Pei-Yuan

    2014-01-01

    Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE). The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.

  12. Toward understanding the dynamics of microbial communities in an estuarine system.

    Directory of Open Access Journals (Sweden)

    Weipeng Zhang

    Full Text Available Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE. The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.

  13. Toward Understanding the Dynamics of Microbial Communities in an Estuarine System

    KAUST Repository

    Zhang, Weipeng

    2014-04-14

    Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE). The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.

  14. Microbial degradation and impact of Bracken toxin ptaquiloside on microbial communities in soil

    DEFF Research Database (Denmark)

    Engel, Pernille; Brandt, Kristian Koefoed; Rasmussen, Lars Holm

    2007-01-01

    ), but not in the NZ soil (weak acid loamy Entisol). In the DK soil PTA turnover was predominantly due to microbial degradation (biodegradation); chemical hydrolysis was occurring mainly in the uppermost A horizon where pH was very low (3.4). Microbial activity (basal respiration) and growth ([3H]leucine incorporation...... assay) increased after PTA exposure, indicating that the Bracken toxin served as a C substrate for the organotrophic microorganisms. On the other hand, there was no apparent impact of PTA on community size as measured by substrate-induced respiration or composition as indicated by community......-level physiological profiles. Our results demonstrate that PTA stimulates microbial activity and that microorganisms play a predominant role for rapid PTA degradation in Bracken-impacted soils....

  15. Responses of Microbial Community Composition to Temperature Gradient and Carbon Steel Corrosion in Production Water of Petroleum Reservoir

    Directory of Open Access Journals (Sweden)

    Xiao-Xiao Li

    2017-12-01

    Full Text Available Oil reservoir production systems are usually associated with a temperature gradient and oil production facilities frequently suffer from pipeline corrosion failures. Both bacteria and archaea potentially contribute to biocorrosion of the oil production equipment. Here the response of microbial populations from the petroleum reservoir to temperature gradient and corrosion of carbon steel coupons were investigated under laboratory condition. Carbon steel coupons were exposed to production water from a depth of 1809 m of Jiangsu petroleum reservoir (China and incubated for periods of 160 and 300 days. The incubation temperatures were set at 37, 55, and 65°C to monitoring mesophilic, thermophilic and hyperthermophilic microorganisms associated with anaerobic carbon steel corrosion. The results showed that corrosion rate at 55°C (0.162 ± 0.013 mm year-1 and 37°C (0.138 ± 0.008 mm year-1 were higher than that at 65°C (0.105 ± 0.007 mm year-1, and a dense biofilm was observed on the surface of coupons under all biotic incubations. The microbial community analysis suggests a high frequency of bacterial taxa associated with families Porphyromonadaceae, Enterobacteriaceae, and Spirochaetaceae at all three temperatures. While the majority of known sulfate-reducing bacteria, in particular Desulfotignum, Desulfobulbus and Desulfovibrio spp., were predominantly observed at 37°C; Desulfotomaculum spp., Thermotoga spp. and Thermanaeromonas spp. as well as archaeal members closely related to Thermococcus and Archaeoglobus spp. were substantially enriched at 65°C. Hydrogenotrophic methanogens of the family Methanobacteriaceae were dominant at both 37 and 55°C; acetoclastic Methanosaeta spp. and methyltrophic Methanolobus spp. were enriched at 37°C. These observations show that temperature changes significantly alter the microbial community structure in production fluids and also affected the biocorrosion of carbon steel under anaerobic conditions.

  16. Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil.

    Science.gov (United States)

    Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2016-06-15

    The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Seasonality and vertical structure of microbial communities in an ocean gyre.

    Science.gov (United States)

    Treusch, Alexander H; Vergin, Kevin L; Finlay, Liam A; Donatz, Michael G; Burton, Robert M; Carlson, Craig A; Giovannoni, Stephen J

    2009-10-01

    Vertical, seasonal and geographical patterns in ocean microbial communities have been observed in many studies, but the resolution of community dynamics has been limited by the scope of data sets, which are seldom up to the task of illuminating the highly structured and rhythmic patterns of change found in ocean ecosystems. We studied vertical and temporal patterns in the microbial community composition in a set of 412 samples collected from the upper 300 m of the water column in the northwestern Sargasso Sea, on cruises between 1991 and 2004. The region sampled spans the extent of deep winter mixing and the transition between the euphotic and the upper mesopelagic zones, where most carbon fixation and reoxidation occurs. A bioinformatic pipeline was developed to de-noise, normalize and align terminal restriction fragment length polymorphism (T-RFLP) data from three restriction enzymes and link T-RFLP peaks to microbial clades. Non-metric multidimensional scaling statistics resolved three microbial communities with distinctive composition during seasonal stratification: a surface community in the region of lowest nutrients, a deep chlorophyll maximum community and an upper mesopelagic community. A fourth microbial community was associated with annual spring blooms of eukaryotic phytoplankton that occur in the northwestern Sargasso Sea as a consequence of winter convective mixing that entrains nutrients to the surface. Many bacterial clades bloomed in seasonal patterns that shifted with the progression of stratification. These richly detailed patterns of community change suggest that highly specialized adaptations and interactions govern the success of microbial populations in the oligotrophic ocean.

  18. Comparison of the active and resident community of a coastal microbial mat

    OpenAIRE

    Cardoso, Daniela Clara; Sandionigi, Anna; Cretoiu, Mariana Silvia; Casiraghi, Maurizio; Stal, Lucas; Bolhuis, Henk

    2017-01-01

    Coastal microbial mats form a nearly closed micro-scale ecosystem harboring a complex microbial community. Previous DNA based analysis did not necessarily provide information about the active fraction of the microbial community because it includes dormant, inactive cells as well as a potential stable pool of extracellular DNA. Here we focused on the active microbial community by comparing 16S rRNA sequences obtained from the ribosomal RNA pool with gene sequences obtained from the DNA fractio...

  19. Effects of pesticides on community composition and activity of sediment microbes - responses at various levels of microbial community organization

    International Nuclear Information System (INIS)

    Widenfalk, Anneli; Bertilsson, Stefan; Sundh, Ingvar; Goedkoop, Willem

    2008-01-01

    A freshwater sediment was exposed to the pesticides captan, glyphosate, isoproturon, and pirimicarb at environmentally relevant and high concentrations. Effects on sediment microorganisms were studied by measuring bacterial activity, fungal and total microbial biomass as community-level endpoints. At the sub-community level, microbial community structure was analysed (PLFA composition and bacterial 16S rRNA genotyping, T-RFLP). Community-level endpoints were not affected by pesticide exposure. At lower levels of microbial community organization, however, molecular methods revealed treatment-induced changes in community composition. Captan and glyphosate exposure caused significant shifts in bacterial community composition (as T-RFLP) at environmentally relevant concentrations. Furthermore, differences in microbial community composition among pesticide treatments were found, indicating that test compounds and exposure concentrations induced multidirectional shifts. Our study showed that community-level end points failed to detect these changes, underpinning the need for application of molecular techniques in aquatic ecotoxicology. - Molecular techniques revealed pesticide-induced changes at lower levels of microbial community organization that were not detected by community-level end points

  20. Effects of pesticides on community composition and activity of sediment microbes - responses at various levels of microbial community organization

    Energy Technology Data Exchange (ETDEWEB)

    Widenfalk, Anneli [Department of Environmental Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, SE-750 07 Uppsala (Sweden)], E-mail: anneli.widenfalk@kemi.se; Bertilsson, Stefan [Limnology/Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvaegen 20, SE-752 36 Uppsala (Sweden); Sundh, Ingvar [Department of Microbiology, Swedish University of Agricultural Sciences, P.O. Box 7025, SE-750 07 Uppsala (Sweden); Goedkoop, Willem [Department of Environmental Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, SE-750 07 Uppsala (Sweden)

    2008-04-15

    A freshwater sediment was exposed to the pesticides captan, glyphosate, isoproturon, and pirimicarb at environmentally relevant and high concentrations. Effects on sediment microorganisms were studied by measuring bacterial activity, fungal and total microbial biomass as community-level endpoints. At the sub-community level, microbial community structure was analysed (PLFA composition and bacterial 16S rRNA genotyping, T-RFLP). Community-level endpoints were not affected by pesticide exposure. At lower levels of microbial community organization, however, molecular methods revealed treatment-induced changes in community composition. Captan and glyphosate exposure caused significant shifts in bacterial community composition (as T-RFLP) at environmentally relevant concentrations. Furthermore, differences in microbial community composition among pesticide treatments were found, indicating that test compounds and exposure concentrations induced multidirectional shifts. Our study showed that community-level end points failed to detect these changes, underpinning the need for application of molecular techniques in aquatic ecotoxicology. - Molecular techniques revealed pesticide-induced changes at lower levels of microbial community organization that were not detected by community-level end points.

  1. The effects of micro-aeration on the phylogenetic diversity of microorganisms in a thermophilic anaerobic municipal solid-waste digester.

    Science.gov (United States)

    Tang, Yueqin; Shigematsu, Toru; Ikbal; Morimura, Shigeru; Kida, Kenji

    2004-05-01

    We demonstrated previously that micro-aeration allows construction of an effective thermophilic methane-fermentation system for treatment of municipal solid waste (MSW) without production of H(2)S. In the present study, we compared the microbial communities in a thermophilic MSW digester without aeration and with micro-aeration by fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), phylogenetic analysis of libraries of 16S rRNA gene clones and quantitative real-time PCR. Moreover, we studied the activity of sulfate-reducing bacteria (SRB) by analysis of the transcription of the gene for dissimilatory sulfite reductase (dsr). Experiments using FISH revealed that microorganisms belonging to the domain Bacteria dominated in the digester both without aeration and with micro-aeration. Phylogenetic analysis based on 16S rRNA gene and analysis of bacteria by DGGE did not reveal any obvious difference within the microbial communities under the two aeration conditions, and bacteria affiliated with the phylum Firmicutes were dominant. In Archaea, the population of Methanosarcina decreased while the population of Methanoculleus increased as a result of micro-aerations as revealed by the analysis of 16S rRNA gene clones and quantitative real-time PCR. Reverse transcription and PCR (RT-PCR) demonstrated the transcription of dsrA not only in the absence of aeration but also in the presence of micro-aeration, even under conditions where no H(2)S was detected in the biogas. In conclusion, micro-aeration has no obvious effects on the phylogenetic diversity of microorganisms. Furthermore, the activity of SRBs in the digester was not repressed even though the concentration of H(2)S in the biogas was very low under the micro-aeration conditions.

  2. Molecular Analysis of Endolithic Microbial Communities in Volcanic Glasses

    Science.gov (United States)

    di Meo, C. A.; Giovannoni, S.; Fisk, M.

    2002-12-01

    Terrestrial and marine volcanic glasses become mineralogically and chemically altered, and in many cases this alteration has been attributed to microbial activity. We have used molecular techniques to study the resident microbial communities from three different volcanic environments that may be responsible for this crustal alteration. Total microbial DNA was extracted from rhyolite glass of the 7 million year old Rattlesnake Tuff in eastern Oregon. The DNA was amplified using the polymerase chain reaction (PCR) with bacterial primers targeting the 16S rRNA gene. This 16S rDNA was cloned and screened with restriction fragment length polymorphism (RFLP). Out of 89 total clones screened, 46 belonged to 13 different clone families containing two or more members, while 43 clones were unique. Sequences of eight clones representing the most dominant clone families in the library were 92 to 97% similar to soil bacterial species. In a separate study, young pillow basalts (rock- and seawater-associated archaea. The six rock community profiles were quite similar to each other, and the background water communities were also similar, respectively. Both the rock and water communities shared the same dominant peak. To identify the T-RFLP peaks corresponding to the individual members of the rock and seawater communities, clone libraries of the archaeal 16S rDNA for one basalt sample (Dive 3718) and its corresponding background water sample were constructed. The most abundant archaeal genes were closely related to uncultured Group I marine Crenarchaeota that have been previously identified from similar deep-sea habitats. These archaeal genes collectively correspond to the dominant T-RFLP peak present in both the rock and water samples. In a third study, we investigated the microbial community residing in a Hawaiian Scientific Drilling Program core collected near Hilo, Hawaii. Total microbial DNA was extracted from a depth of 1351 m in the drill core (ambient temperature in the

  3. Ecological restoration alters microbial communities in mine tailings profiles.

    Science.gov (United States)

    Li, Yang; Jia, Zhongjun; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

    2016-04-29

    Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0-30 cm soils and altered the bacterial communities at 0-20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30-60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0-20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.

  4. Ecological restoration alters microbial communities in mine tailings profiles

    Science.gov (United States)

    Li, Yang; Jia, Zhongjun; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

    2016-04-01

    Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0-30 cm soils and altered the bacterial communities at 0-20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30-60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0-20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.

  5. Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities.

    Science.gov (United States)

    Mahadevan, Radhakrishnan; Henson, Michael A

    2012-01-01

    Biotechnology research is traditionally focused on individual microbial strains that are perceived to have the necessary metabolic functions, or the capability to have these functions introduced, to achieve a particular task. For many important applications, the development of such omnipotent microbes is an extremely challenging if not impossible task. By contrast, nature employs a radically different strategy based on synergistic combinations of different microbial species that collectively achieve the desired task. These natural communities have evolved to exploit the native metabolic capabilities of each species and are highly adaptive to changes in their environments. However, microbial communities have proven difficult to study due to a lack of suitable experimental and computational tools. With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.

  6. Engineering chemical interactions in microbial communities.

    Science.gov (United States)

    Kenny, Douglas J; Balskus, Emily P

    2018-03-05

    Microbes living within host-associated microbial communities (microbiotas) rely on chemical communication to interact with surrounding organisms. These interactions serve many purposes, from supplying the multicellular host with nutrients to antagonizing invading pathogens, and breakdown of chemical signaling has potentially negative consequences for both the host and microbiota. Efforts to engineer microbes to take part in chemical interactions represent a promising strategy for modulating chemical signaling within these complex communities. In this review, we discuss prominent examples of chemical interactions found within host-associated microbial communities, with an emphasis on the plant-root microbiota and the intestinal microbiota of animals. We then highlight how an understanding of such interactions has guided efforts to engineer microbes to participate in chemical signaling in these habitats. We discuss engineering efforts in the context of chemical interactions that enable host colonization, promote host health, and exclude pathogens. Finally, we describe prominent challenges facing this field and propose new directions for future engineering efforts.

  7. Citrate and malonate increase microbial activity and alter microbial community composition in uncontaminated and diesel-contaminated soil microcosms

    Science.gov (United States)

    Martin, Belinda C.; George, Suman J.; Price, Charles A.; Shahsavari, Esmaeil; Ball, Andrew S.; Tibbett, Mark; Ryan, Megan H.

    2016-09-01

    Petroleum hydrocarbons (PHCs) are among the most prevalent sources of environmental contamination. It has been hypothesized that plant root exudation of low molecular weight organic acid anions (carboxylates) may aid degradation of PHCs by stimulating heterotrophic microbial activity. To test their potential implication for bioremediation, we applied two commonly exuded carboxylates (citrate and malonate) to uncontaminated and diesel-contaminated microcosms (10 000 mg kg-1; aged 40 days) and determined their impact on the microbial community and PHC degradation. Every 48 h for 18 days, soil received 5 µmol g-1 of (i) citrate, (ii) malonate, (iii) citrate + malonate or (iv) water. Microbial activity was measured daily as the flux of CO2. After 18 days, changes in the microbial community were assessed by a community-level physiological profile (CLPP) and 16S rRNA bacterial community profiles determined by denaturing gradient gel electrophoresis (DGGE). Saturated PHCs remaining in the soil were assessed by gas chromatography-mass spectrometry (GC-MS). Cumulative soil respiration increased 4- to 6-fold with the addition of carboxylates, while diesel contamination resulted in a small, but similar, increase across all carboxylate treatments. The addition of carboxylates resulted in distinct changes to the microbial community in both contaminated and uncontaminated soils but only a small increase in the biodegradation of saturated PHCs as measured by the n-C17 : pristane biomarker. We conclude that while the addition of citrate and malonate had little direct effect on the biodegradation of saturated hydrocarbons present in diesel, their effect on the microbial community leads us to suggest further studies using a variety of soils and organic acids, and linked to in situ studies of plants, to investigate the role of carboxylates in microbial community dynamics.

  8. Soil Microbial Community Structure Evolution along Halophyte Succession in Bohai Bay Wetland

    Directory of Open Access Journals (Sweden)

    Mingyang Cong

    2014-01-01

    Full Text Available It is urgent to recover Bohai Bay costal wetland ecosystem because of covering a large area of severe saline-alkali soil. To explore the relationship between halophyte herbaceous succession and microbial community structure, we chose four local communities which played an important role in improving soil microenvironment. We performed phospholipid fatty acid analysis, measured soil parameters, and evaluated shifts of microbial community structure. Results showed that microbial community structure changed significantly along succession and bacteria community was dominant. Total phospholipid fatty acid content increased in different successional stages but decreased with depth, with similar variations in bacterial and fungal biomass. Soil organic carbon and especially total nitrogen were positively correlated with microbial biomass. Colonization of pioneering salt-tolerant plants Suaeda glauca in saline-alkali bare land changed total soil microorganism content and composition. These results showed that belowground processes were strongly related with aboveground halophyte succession. Fungal/bacterial ratio, Gram-negative/Gram-positive bacteria ratio, total microbial biomass, and fungi and bacteria content could indicate the degree of succession stages in Bohai Bay wetland ecosystem. And also these findings demonstrated that microbial community biomass and composition evolved along with vegetation succession environmental variables.

  9. Rapid Response of Eastern Mediterranean Deep Sea Microbial Communities to Oil

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Jiang; Techtmann, Stephen M.; Woo, Hannah L.; Ning, Daliang; Fortney, Julian L.; Hazen, Terry C.

    2017-07-18

    Deep marine oil spills like the Deepwater Horizon (DWH) in the Gulf of Mexico have the potential to drastically impact marine systems. Crude oil contamination in marine systems remains a concern, especially for countries around the Mediterranean Sea with off shore oil production. The goal of this study was to investigate the response of indigenous microbial communities to crude oil in the deep Eastern Mediterranean Sea (E. Med.) water column and to minimize potential bias associated with storage and shifts in microbial community structure from sample storage. 16S rRNA amplicon sequencing was combined with GeoChip metagenomic analysis to monitor the microbial community changes to the crude oil and dispersant in on-ship microcosms set up immediately after water collection. After 3 days of incubation at 14 °C, the microbial communities from two different water depths: 824 m and 1210 m became dominated by well-known oil degrading bacteria. The archaeal population and the overall microbial community diversity drastically decreased. Similarly, GeoChip metagenomic analysis revealed a tremendous enrichment of genes related to oil biodegradation, which was consistent with the results from the DWH oil spill. These results highlight a rapid microbial adaption to oil contamination in the deep E. Med., and indicate strong oil biodegradation potentia

  10. Generation of Electricity and Analysis of Microbial Communities in Wheat Straw Biomass-Powered Microbial Fuel Cells

    DEFF Research Database (Denmark)

    Zhang, Yifeng; Min, Booki; Huang, L.

    2009-01-01

    Electricity generation from wheat straw hydrolysate and the microbial ecology of electricity producing microbial communities developed in two chamber microbial fuel cells (MFCs) were investigated. Power density reached 123 mW/m2 with an initial hydrolysate concentration of 1000 mg-COD/L while...

  11. mcaGUI: microbial community analysis R-Graphical User Interface (GUI).

    Science.gov (United States)

    Copeland, Wade K; Krishnan, Vandhana; Beck, Daniel; Settles, Matt; Foster, James A; Cho, Kyu-Chul; Day, Mitch; Hickey, Roxana; Schütte, Ursel M E; Zhou, Xia; Williams, Christopher J; Forney, Larry J; Abdo, Zaid

    2012-08-15

    Microbial communities have an important role in natural ecosystems and have an impact on animal and human health. Intuitive graphic and analytical tools that can facilitate the study of these communities are in short supply. This article introduces Microbial Community Analysis GUI, a graphical user interface (GUI) for the R-programming language (R Development Core Team, 2010). With this application, researchers can input aligned and clustered sequence data to create custom abundance tables and perform analyses specific to their needs. This GUI provides a flexible modular platform, expandable to include other statistical tools for microbial community analysis in the future. The mcaGUI package and source are freely available as part of Bionconductor at http://www.bioconductor.org/packages/release/bioc/html/mcaGUI.html

  12. Linking the development and functioning of a carnivorous pitcher plant's microbial digestive community.

    Science.gov (United States)

    Armitage, David W

    2017-11-01

    Ecosystem development theory predicts that successional turnover in community composition can influence ecosystem functioning. However, tests of this theory in natural systems are made difficult by a lack of replicable and tractable model systems. Using the microbial digestive associates of a carnivorous pitcher plant, I tested hypotheses linking host age-driven microbial community development to host functioning. Monitoring the yearlong development of independent microbial digestive communities in two pitcher plant populations revealed a number of trends in community succession matching theoretical predictions. These included mid-successional peaks in bacterial diversity and metabolic substrate use, predictable and parallel successional trajectories among microbial communities, and convergence giving way to divergence in community composition and carbon substrate use. Bacterial composition, biomass, and diversity positively influenced the rate of prey decomposition, which was in turn positively associated with a host leaf's nitrogen uptake efficiency. Overall digestive performance was greatest during late summer. These results highlight links between community succession and ecosystem functioning and extend succession theory to host-associated microbial communities.

  13. Application of biocathode in microbial fuel cells: cell performance and microbial community

    Energy Technology Data Exchange (ETDEWEB)

    Guo-Wei, Chen [Pusan National Univ. (Korea). Dept. of Environmental Engineering; Hefei Univ. of Technology (China). School of Civil Engineering; Choi, Soo-Jung; Lee, Tae-Ho; Lee, Gil-Young; Cha, Jae-Hwan; Kim, Chang-Won [Pusan National Univ. (Korea). Dept. of Environmental Engineering

    2008-06-15

    Instead of the utilization of artificial redox mediators or other catalysts, a biocathode has been applied in a two-chamber microbial fuel cell in this study, and the cell performance and microbial community were analyzed. After a 2-month startup, the microorganisms of each compartment in microbial fuel cell were well developed, and the output of microbial fuel cell increased and became stable gradually, in terms of electricity generation. At 20 ml/min flow rate of the cathodic influent, the maximum power density reached 19.53 W/m{sup 3}, while the corresponding current and cell voltage were 15.36 mA and 223 mV at an external resistor of 14.9 {omega}, respectively. With the development of microorganisms in both compartments, the internal resistance decreased from initial 40.2 to 14.0 {omega}, too. Microbial community analysis demonstrated that five major groups of the clones were categorized among those 26 clone types derived from the cathode microorganisms. Betaproteobacteria was the most abundant division with 50.0% (37 of 74) of the sequenced clones in the cathode compartment, followed by 21.6% (16 of 74) Bacteroidetes, 9.5% (7 of 74) Alphaproteobacteria, 8.1% (6 of 74) Chlorobi, 4.1% (3 of 74) Deltaproteobacteria, 4.1% (3 of 74) Actinobacteria, and 2.6% (2 of 74) Gammaproteobacteria. (orig.)

  14. Boom clay pore water, home of a diverse microbial community

    International Nuclear Information System (INIS)

    Wouters, Katinka; Moors, Hugo; Leys, Natalie

    2012-01-01

    Document available in extended abstract form only. Boom Clay pore water (BCPW) has been studied in the framework of geological disposal of nuclear waste for over two decades, thereby mainly addressing its geochemical properties. A reference composition for synthetic clay water has been derived earlier by modelling and spatial calibration efforts, mainly based on interstitial water sampled from different layers within the Boom clay. However, since microbial activity is found in a range of extreme circumstances, the possibility of microbes interacting with future radioactive waste in a host formation like Boom Clay, cannot be ignored. In this respect, BCPW was sampled from different Boom Clay layers using the Morpheus piezometer and subsequently analysed by a complementary set of microbiological and molecular techniques, in search for overall shared and abundant microorganisms. Similar to the previous characterization of the 'average' BCPW chemical composition, the primary aim of this microbiological study is to determine a representative BCPW microbial community which can be used in laboratory studies. Secondly, the in situ activity and the metabolic properties of members of this community were addressed, aiming to assess their survival and proliferation chances in repository conditions. In a first approach, total microbial DNA of the community was extracted from the BCPW samples. This molecular approach allows a broad insight in the total microbial ecology of the BCPW samples. By polymerase chain reaction (PCR) on the highly conserved 16S rRNA genes in this DNA pool and subsequent sequencing and bio-informatics analysis, operational taxonomic units (OTUs) could be assigned to the microbial community. The bacterial community was found to be quite diverse, with OTUs belonging to 8 different phyla (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chlorobi, Spirochetes, Chloroflexi and Deinococcus-Thermus). These results provide an overall view of the

  15. Boom clay pore water, home of a diverse microbial community

    Energy Technology Data Exchange (ETDEWEB)

    Wouters, Katinka; Moors, Hugo; Leys, Natalie [SCK.CEN, Environment, Health and Safety Institute, B-2400 Mol (Belgium)

    2012-10-15

    Document available in extended abstract form only. Boom Clay pore water (BCPW) has been studied in the framework of geological disposal of nuclear waste for over two decades, thereby mainly addressing its geochemical properties. A reference composition for synthetic clay water has been derived earlier by modelling and spatial calibration efforts, mainly based on interstitial water sampled from different layers within the Boom clay. However, since microbial activity is found in a range of extreme circumstances, the possibility of microbes interacting with future radioactive waste in a host formation like Boom Clay, cannot be ignored. In this respect, BCPW was sampled from different Boom Clay layers using the Morpheus piezometer and subsequently analysed by a complementary set of microbiological and molecular techniques, in search for overall shared and abundant microorganisms. Similar to the previous characterization of the 'average' BCPW chemical composition, the primary aim of this microbiological study is to determine a representative BCPW microbial community which can be used in laboratory studies. Secondly, the in situ activity and the metabolic properties of members of this community were addressed, aiming to assess their survival and proliferation chances in repository conditions. In a first approach, total microbial DNA of the community was extracted from the BCPW samples. This molecular approach allows a broad insight in the total microbial ecology of the BCPW samples. By polymerase chain reaction (PCR) on the highly conserved 16S rRNA genes in this DNA pool and subsequent sequencing and bio-informatics analysis, operational taxonomic units (OTUs) could be assigned to the microbial community. The bacterial community was found to be quite diverse, with OTUs belonging to 8 different phyla (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chlorobi, Spirochetes, Chloroflexi and Deinococcus-Thermus). These results provide an overall view of the

  16. Establishment of markerless gene deletion tools in thermophilic Bacillus smithii and construction of multiple mutant strains

    NARCIS (Netherlands)

    Bosma, E.F.; Weijer, van de A.H.P.; Vlist, L.; Vos, de W.M.; Oost, van der J.; Kranenburg, van R.

    2015-01-01

    BACKGROUND: Microbial conversion of biomass to fuels or chemicals is an attractive alternative for fossil-based fuels and chemicals. Thermophilic microorganisms have several operational advantages as a production host over mesophilic organisms, such as low cooling costs, reduced contamination risks

  17. Thermophilic subseafloor microorganisms from the 1996 North Gorda Ridge eruption

    Science.gov (United States)

    Summit, Melanie; Baross, John A.

    1998-12-01

    High-temperature microbes were present in two hydrothermal event plumes (EP96A and B) resulting from the February-March 1996 eruptions along the North Gorda Ridge. Anaerobic thermophiles were cultured from 17 of 22 plume samples at levels exceeding 200 organisms per liter; no thermophiles were cultured from any of 12 samples of background seawater. As these microorganisms grow at temperatures of 50-90°C, they could not have grown in the event plume and instead most probably derived from a subseafloor environment tapped by the event plume source fluids. Event plumes are thought to derive from a pre-existing subseafloor fluid reservoir, which implies that these thermophiles are members of a native subseafloor community that was present before the eruptive event. Thermophiles also were cultured from continuous chronic-style hydrothermal plumes in April 1996; these plumes may have formed from cooling lava piles. To better understand the nutritional, chemical, and physical constraints of pre-eruptive crustal environments, seven coccoidal isolates from the two event plumes were partially characterized. Results from nutritional and phylogenetic studies indicate that these thermophiles are heterotrophic archaea that represent new species, and probably a new genus, within the Thermococcales.

  18. Genome-reconstruction for eukaryotes from complex natural microbial communities.

    Science.gov (United States)

    West, Patrick T; Probst, Alexander J; Grigoriev, Igor V; Thomas, Brian C; Banfield, Jillian F

    2018-04-01

    Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k -mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities. © 2018 West et al.; Published by Cold Spring Harbor Laboratory Press.

  19. Cellulolytic potential under environmental changes in microbial communities from grassland litter

    Directory of Open Access Journals (Sweden)

    Renaud eBerlemont

    2014-11-01

    Full Text Available In many ecosystems, global changes are likely to profoundly affect microorganisms. In Southern California, changes in precipitation and nitrogen deposition may influence the composition and functional potential of microbial communities and their resulting ability to degrade plant material. To test whether environmental changes impact the distribution of functional groups involved in leaf litter degradation, we determined how the genomic diversity of microbial communities in a semi-arid grassland ecosystem changed under reduced precipitation or increased N deposition. We monitored communities seasonally over a period of two years to place environmental change responses into the context of natural variation. Fungal and bacterial communities displayed strong seasonal patterns, Fungi being mostly detected during the dry season whereas Bacteria were common during wet periods. Most putative cellulose degraders were associated with 33 bacterial genera and constituted ~18.2% of the microbial community. Precipitation reduction reduced bacterial abundance and cellulolytic potential whereas nitrogen addition did not affect the cellulolytic potential of the microbial community. Finally, we detected a strong correlation between the frequencies of genera putative cellulose degraders and cellulase genes. Thus, microbial taxonomic composition was predictive of cellulolytic potential. This work provides a framework for how environmental changes affect microorganisms responsible for plant litter deconstruction.

  20. The electric picnic: synergistic requirements for exoelectrogenic microbial communities

    KAUST Repository

    Kiely, Patrick D; Regan, John M; Logan, Bruce E

    2011-01-01

    (BESs). Analysis of the community profiles of exoelectrogenic microbial consortia in BESs fed different substrates gives a clearer picture of the different microbial populations present in these exoelectrogenic biofilms. Rapid utilization of fermentation

  1. Temporal and Spatial Distribution of the Microbial Community of Winogradsky Columns.

    Directory of Open Access Journals (Sweden)

    David J Esteban

    Full Text Available Winogradsky columns are model microbial ecosystems prepared by adding pond sediment to a clear cylinder with additional supplements and incubated with light. Environmental gradients develop within the column creating diverse niches that allow enrichment of specific bacteria. The enrichment culture can be used to study soil and sediment microbial community structure and function. In this study we used a 16S rRNA gene survey to characterize the microbial community dynamics during Winogradsky column development to determine the rate and extent of change from the source sediment community. Over a period of 60 days, the microbial community changed from the founding pond sediment population: Cyanobacteria, Chloroflexi, Nitrospirae, and Planctomycetes increased in relative abundance over time, while most Proteobacteria decreased in relative abundance. A unique, light-dependent surface biofilm community formed by 60 days that was less diverse and dominated by a few highly abundant bacteria. 67-72% of the surface community was comprised of highly enriched taxa that were rare in the source pond sediment, including the Cyanobacteria Anabaena, a member of the Gemmatimonadetes phylum, and a member of the Chloroflexi class Anaerolinea. This indicates that rare taxa can become abundant under appropriate environmental conditions and supports the hypothesis that rare taxa serve as a microbial seed bank. We also present preliminary findings that suggest that bacteriophages may be active in the Winogradsky community. The dynamics of certain taxa, most notably the Cyanobacteria, showed a bloom-and-decline pattern, consistent with bacteriophage predation as predicted in the kill-the-winner hypothesis. Time-lapse photography also supported the possibility of bacteriophage activity, revealing a pattern of colony clearance similar to formation of viral plaques. The Winogradsky column, a technique developed early in the history of microbial ecology to enrich soil

  2. Halotolerant PGPRs Prevent Major Shifts in Indigenous Microbial Community Structure Under Salinity Stress.

    Science.gov (United States)

    Bharti, Nidhi; Barnawal, Deepti; Maji, Deepamala; Kalra, Alok

    2015-07-01

    The resilience of soil microbial populations and processes to environmental perturbation is of increasing interest as alteration in rhizosphere microbial community dynamics impacts the combined functions of plant-microbe interactions. The present study was conducted to investigate the effect of inoculation with halotolerant rhizobacteria Bacillus pumilus (STR2), Halomonas desiderata (STR8), and Exiguobacterium oxidotolerans (STR36) on the indigenous root-associated microbial (bacterial and fungal) communities in maize under non-saline and salinity stress. Plants inoculated with halotolerant rhizobacteria recorded improved growth as illustrated by significantly higher shoot and root dry weight and elongation in comparison to un-inoculated control plants under both non-saline and saline conditions. Additive main effect and multiplicative interaction ordination analysis revealed that plant growth promoting rhizobacteria (PGPR) inoculations as well as salinity are major drivers of microbial community shift in maize rhizosphere. Salinity negatively impacts microbial community as analysed through diversity indices; among the PGPR-inoculated plants, STR2-inoculated plants recorded higher values of diversity indices. As observed in the terminal-restriction fragment length polymorphism analysis, the inoculation of halotolerant rhizobacteria prevents major shift of the microbial community structure, thus enhancing the resilience capacity of the microbial communities.

  3. Shift in soil microbial communities with shrub encroachment in Inner Mongolia grasslands, China

    Science.gov (United States)

    Shen, H.; Li, H.; Zhang, J.; Hu, H.; Chen, L.; Zhu, Y.; Fang, J.

    2017-12-01

    The ongoing expansion of shrub encroachment into grasslands represents a unique form of land cover change. How this process affects soil microbial communities is poorly understood. In this study, we aim to assess the effects of shrub encroachment on soil microbial biomass, abundance and composition by comparing data between shrub patches and neighboring herb patches in shrub-encroached grasslands (SEGs) in Inner Mongolia, China. Fourteen SEG sites from two ecosystem types (typical and desert grasslands) were investigated. The phospholipid fatty acid (PLFA) method was used to analyze the composition and biomass of the soil microbial community. Our results showed that the top-soil microbial biomass and abundances of gram-negative bacteria, arbuscular mycorrhizal fungi, and actinomycetes were significantly higher in shrub patches than in herb patches in both typical and desert grasslands (P fungi to bacteria ratio was significantly higher in shrub patches than in herb patches in desert grassland (P soil microbial communities, which makes the microbial communities toward a fresh organic carbon-based structure. This study highlights the importance of edaphic and climate factors in microbial community shifts in SEGs.

  4. Bacterial community profiles in low microbial abundance sponges

    KAUST Repository

    Giles, Emily

    2012-09-04

    It has long been recognized that sponges differ in the abundance of associated microorganisms, and they are therefore termed either \\'low microbial abundance\\' (LMA) or \\'high microbial abundance\\' (HMA) sponges. Many previous studies concentrated on the dense microbial communities in HMA sponges, whereas little is known about microorganisms in LMA sponges. Here, two LMA sponges from the Red Sea, two from the Caribbean and one from the South Pacific were investigated. With up to only five bacterial phyla per sponge, all LMA sponges showed lower phylum-level diversity than typical HMA sponges. Interestingly, each LMA sponge was dominated by a large clade within either Cyanobacteria or different classes of Proteobacteria. The overall similarity of bacterial communities among LMA sponges determined by operational taxonomic unit and UniFrac analysis was low. Also the number of sponge-specific clusters, which indicate bacteria specifically associated with sponges and which are numerous in HMA sponges, was low. A biogeographical or host-dependent distribution pattern was not observed. In conclusion, bacterial community profiles of LMA sponges are clearly different from profiles of HMA sponges and, remarkably, each LMA sponge seems to harbour its own unique bacterial community. © 2012 Federation of European Microbiological Societies.

  5. mcaGUI: microbial community analysis R-Graphical User Interface (GUI)

    OpenAIRE

    Copeland, Wade K.; Krishnan, Vandhana; Beck, Daniel; Settles, Matt; Foster, James A.; Cho, Kyu-Chul; Day, Mitch; Hickey, Roxana; Schütte, Ursel M.E.; Zhou, Xia; Williams, Christopher J.; Forney, Larry J.; Abdo, Zaid

    2012-01-01

    Summary: Microbial communities have an important role in natural ecosystems and have an impact on animal and human health. Intuitive graphic and analytical tools that can facilitate the study of these communities are in short supply. This article introduces Microbial Community Analysis GUI, a graphical user interface (GUI) for the R-programming language (R Development Core Team, 2010). With this application, researchers can input aligned and clustered sequence data to create custom abundance ...

  6. Physiology of thermophilic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Ljungdahl, L G

    1979-01-01

    Thermophilic micro-organisms have all of the properties normally found in mesophilic micro-organisms. These include metabolic pathways, regulatory mechanisms such as allosteric or feedback control, repression and induction of protein synthesis, growth yields and metabolic rates. The main difference between thermophiles and mesophiles is the former's capacity to grow at high temperatures. The basis for this capacity is the thermophile's capability to synthesize proteins, complex structures and membranes that are stable or are stabilized and functional at thermophilic temperatures. It is proposed that the maximum and minimum growth temperatures are normally determined by properties associated with proteins, and that the membrane plays a lesser role in determining these temperatures. Enzymes and other proteins from thermophiles, except for having higher thermostability, are very similar to corresponding proteins from mesophiles. The higher thermostability is generally dependent on subtle changes in the composition and sequence of the amino acids and rarely dependent on non-proteinaceous factors. Although over 100 proteins have been purified from thermophiles and compared with corresponding proteins from mesophiles, the exact nature of the higher thermostability has yet to be determined in a protein from a thermophile.

  7. Impact of long-term Diesel Contamination on Soil Microbial Community Structure

    NARCIS (Netherlands)

    Sutton, N.B.; Maphosa, F.; Morillo, J.A.; Abu Al-Soud, W.; Langenhoff, A.A.M.; Grotenhuis, J.T.C.; Rijnaarts, H.H.M.; Smidt, H.

    2013-01-01

    Microbial community composition and diversity at a diesel-contaminated railway site were investigated by pyrosequencing of bacterial and archaeal 16S rRNA gene fragments to understand the interrelationships among microbial community composition, pollution level, and soil geochemical and physical

  8. Geomicrobiology of Archaeal Communities Isolated from an Off-axis Abyssal Hill Fault Scarp on the East Pacific Rise Flank at 9° 27'N

    Science.gov (United States)

    Ehrhardt, C. J.; Haymon, R.; Holden, P.; Lamontagne, M.

    2003-12-01

    Although heat flow studies suggest that ~70% of the hydrothermal heat loss in the oceans occurs in the abyssal hill terrain on the flanks of mid-ocean ridges, very few off-axis hydrothermal sites have been discovered. In May 2002, sedimentary blowout structures of probable hydrothermal origin were discovered along East Pacific Rise at 9° 27'N on an off-axis abyssal hill bounded by a fault scarp covered with orange-brown microbial flocculations. Recovered samples of these flocculations have presented an opportunity to study the unknown nature and role of thermophilic and hyperthermophilic microbial communities on the ridge flanks. Furthermore, the archaeal communities that we have identified in the samples are useful "microbial tracers" which can be used to locate off-axis areas of moderate-to-high temperature fluid flow (>50° C). In this study, we used molecular techniques to isolate, amplify, and sequence community archaeal RNA sequences from fault scarp flocculations collected with a slurp pump system mounted in the Alvin basket. Molecular phylogenies based on 16S rRNA were constructed. Phylogenetic relationships of isolated clones were used to infer temperature preferences of archaeal communities. We identified 12 clones that clustered within thermophilic or hyperthermophilic clades within Archaea suggesting that moderately high temperature fluid (>50° C) exited the seafloor along this abyssal hill fault scarp. Our studies also suggest that these communities mediate the formation of Fe-sulfide mineral phases. Analysis of the samples with an Environmental Scanning Electron Microscope (ESEM) and X-ray energy dispersive analysis (EDS) revealed unique iron sulfide mineral phases with anomalously low Fe/S ratios in direct association with microbial communities.

  9. Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration ▿†

    Science.gov (United States)

    Banning, Natasha C.; Gleeson, Deirdre B.; Grigg, Andrew H.; Grant, Carl D.; Andersen, Gary L.; Brodie, Eoin L.; Murphy, D. V.

    2011-01-01

    Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables. PMID:21724890

  10. Microbial Life in an Underground Gas Storage Reservoir

    Science.gov (United States)

    Bombach, Petra; van Almsick, Tobias; Richnow, Hans H.; Zenner, Matthias; Krüger, Martin

    2015-04-01

    While underground gas storage is technically well established for decades, the presence and activity of microorganisms in underground gas reservoirs have still hardly been explored today. Microbial life in underground gas reservoirs is controlled by moderate to high temperatures, elevated pressures, the availability of essential inorganic nutrients, and the availability of appropriate chemical energy sources. Microbial activity may affect the geochemical conditions and the gas composition in an underground reservoir by selective removal of anorganic and organic components from the stored gas and the formation water as well as by generation of metabolic products. From an economic point of view, microbial activities can lead to a loss of stored gas accompanied by a pressure decline in the reservoir, damage of technical equipment by biocorrosion, clogging processes through precipitates and biomass accumulation, and reservoir souring due to a deterioration of the gas quality. We present here results from molecular and cultivation-based methods to characterize microbial communities inhabiting a porous rock gas storage reservoir located in Southern Germany. Four reservoir water samples were obtained from three different geological horizons characterized by an ambient reservoir temperature of about 45 °C and an ambient reservoir pressure of about 92 bar at the time of sampling. A complementary water sample was taken at a water production well completed in a respective horizon but located outside the gas storage reservoir. Microbial community analysis by Illumina Sequencing of bacterial and archaeal 16S rRNA genes indicated the presence of phylogenetically diverse microbial communities of high compositional heterogeneity. In three out of four samples originating from the reservoir, the majority of bacterial sequences affiliated with members of the genera Eubacterium, Acetobacterium and Sporobacterium within Clostridiales, known for their fermenting capabilities. In

  11. Extreme CO2 disturbance and the resilience of soil microbial communities

    Science.gov (United States)

    McFarland, Jack W.; Waldrop, Mark P.; Haw, Monica

    2013-01-01

    Carbon capture and storage (CSS) technology has the potential to inadvertently release large quantities of CO2 through geologic substrates and into surrounding soils and ecosystems. Such a disturbance has the potential to not only alter the structure and function of plant and animal communities, but also soils, soil microbial communities, and the biogeochemical processes they mediate. At Mammoth Mountain, we assessed the soil microbial community response to CO2 disturbance (derived from volcanic ‘cold’ CO2) that resulted in localized tree kill; soil CO2 concentrations in our study area ranged from 0.6% to 60%. Our objectives were to examine how microbial communities and their activities are restructured by extreme CO2 disturbance, and assess the response of major microbial taxa to the reintroduction of limited plant communities following an extensive period (15–20 years) with no plants. We found that CO2-induced tree kill reduced soil carbon (C) availability along our sampling transect. In response, soil microbial biomass decreased by an order of magnitude from healthy forest to impacted areas. Soil microorganisms were most sensitive to changes in soil organic C, which explained almost 60% of the variation for microbial biomass C (MBC) along the CO2gradient. We employed phospholipid fatty acid analysis and quantitative PCR (qPCR) to determine compositional changes among microbial communities in affected areas and found substantial reductions in microbial biomass linked to the loss of soil fungi. In contrast, archaeal populations responded positively to the CO2 disturbance, presumably due to reduced competition of bacteria and fungi, and perhaps unique adaptations to energy stress. Enzyme activities important in the cycling of soil C, nitrogen (N), and phosphorus (P) declined with increasing CO2, though specific activities (per unit MBC) remained stable or increased suggesting functional redundancy among restructured communities. We conclude that both the

  12. The electric picnic: synergistic requirements for exoelectrogenic microbial communities

    KAUST Repository

    Kiely, Patrick D

    2011-06-01

    Characterization of the various microbial populations present in exoelectrogenic biofilms provides insight into the processes required to convert complex organic matter in wastewater streams into electrical current in bioelectrochemical systems (BESs). Analysis of the community profiles of exoelectrogenic microbial consortia in BESs fed different substrates gives a clearer picture of the different microbial populations present in these exoelectrogenic biofilms. Rapid utilization of fermentation end products by exoelectrogens (typically Geobacter species) relieves feedback inhibition for the fermentative consortia, allowing for rapid metabolism of organics. Identification of specific syntrophic processes and the communities characteristic of these anodic biofilms will be a valuable aid in improving the performance of BESs. © 2011 Elsevier Ltd.

  13. Microbial community dynamics in diesel waste biodegradation using ...

    African Journals Online (AJOL)

    Microbial community dynamics in diesel waste biodegradation using sequencing batch bioreactor operation mode (SBR) ... African Journal of Biotechnology ... Oxygen uptake rate (OUR) indicated increases in microbial activity from cycle one to cycle two (124.9 to 252.9 mgO2/L/h) and decreases in cycles three and four ...

  14. A constant flux of diverse thermophilic bacteria into the cold arctic seabed

    DEFF Research Database (Denmark)

    Hubert, Casey; Loy, Alexander; Nickel, Maren

    2009-01-01

    Microorganisms have been repeatedly discovered in environments that do not support their metabolic activity. Identifying and quantifying these misplaced organisms can reveal dispersal mechanisms that shape natural microbial diversity. Using endospore germination experiments, we estimated a stable...... supply of thermophilic bacteria into permanently cold Arctic marine sediment at a rate exceeding 108 spores per square meter per year. These metabolically and phylogenetically diverse Firmicutes show no detectable activity at cold in situ temperatures but rapidly mineralize organic matter by hydrolysis......, fermentation, and sulfate reduction upon induction at 50°C. The closest relatives to these bacteria come from warm subsurface petroleum reservoir and ocean crust ecosystems, suggesting that seabed fluid flow from these environments is delivering thermophiles to the cold ocean. These transport pathways may...

  15. Effect of cerium dioxide, titanium dioxide, silver, and gold nanoparticles on the activity of microbial communities intended in wastewater treatment

    International Nuclear Information System (INIS)

    García, Ana; Delgado, Lucía; Torà, Josep A.; Casals, Eudald; González, Edgar; Puntes, Víctor; Font, Xavier; Carrera, Julián; Sánchez, Antoni

    2012-01-01

    Highlights: ► Toxicity of TiO 2 , CeO 2 , Ag and Au nanoparticles (NP) has been studied. ► NP were synthesized in the lab and stabilized to prevent agglomeration. ► Toxicity was studied in all the communities used for the wastewater treatment. ► Heterotrophic, nitrifying and anaerobic organisms were studied for nanotoxicology. ► Au and TiO 2 NP were not toxic, but Ag and CeO 2 NP were inhibitory. - Abstract: Growth in production and use of nanoparticles (NPs) will result increased concentrations of these in industrial and urban wastewaters and, consequently, in wastewater-treatment facilities. The effect of this increase on the performance of the wastewater-treatment process has not been studied systematically and including all the microbial communities involved in wastewater treatment. The present work investigates, by using respiration tests and biogas-production analysis, the inhibitory effect of four different commonly used metal oxide (CeO 2 and TiO 2 ) and zero-valent metal (Ag and Au) nanoparticles on the activity of the most important microbial communities present in a modern wastewater-treatment plant. Specifically, the actions of ordinary heterotrophic organisms, ammonia oxidizing bacteria, and thermophilic and mesophilic anaerobic bacteria were tested in the presence and absence of the nanoparticles. In general, CeO 2 nanoparticles caused the greatest inhibition in biogas production (nearly 100%) and a strong inhibitory action of other biomasses; Ag nanoparticles caused an intermediate inhibition in biogas production (within 33–50%) and a slight inhibition in the action of other biomasses, and Au and TiO 2 nanoparticles caused only slight or no inhibition for all tested biomasses.

  16. Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond

    Directory of Open Access Journals (Sweden)

    Zarraz M.-P. Lee

    2017-05-01

    Full Text Available Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on microbial communities in CCB, a mesocosm experiment was implemented in a stoichiometrically imbalanced pond, Lagunita, which has an average TN:TP ratio of 122 (atomic. The experiment had four treatments, each with five spatial replicates – unamended controls and three fertilization treatments with different nitrogen:phosphorus (N:P regimes (P only, N:P = 16 and N:P = 75 by atoms. In the water column, quantitative PCR of the 16S rRNA gene indicated that P enrichment alone favored proliferation of bacterial taxa with high rRNA gene copy number, consistent with a previously hypothesized but untested connection between rRNA gene copy number and P requirement. Bacterial and microbial eukaryotic community structure was investigated by pyrosequencing of 16S and 18S rRNA genes from the planktonic and surficial sediment samples. Nutrient enrichment shifted the composition of the planktonic community in a treatment-specific manner and promoted the growth of previously rare bacterial taxa at the expense of the more abundant, potentially endemic, taxa. The eukaryotic community was highly enriched with phototrophic populations in the fertilized treatment. The sediment microbial community exhibited high beta diversity among replicates within treatments, which obscured any changes due to fertilization. Overall, these results showed that nutrient stoichiometry can be an important factor in shaping microbial community structure.

  17. GENOME-BASED MODELING AND DESIGN OF METABOLIC INTERACTIONS IN MICROBIAL COMMUNITIES

    Directory of Open Access Journals (Sweden)

    Radhakrishnan Mahadevan

    2012-10-01

    With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.

  18. Soil microbial community response to land use and various soil ...

    African Journals Online (AJOL)

    Soil microbial community response to land use and various soil elements in a city landscape of north China. ... African Journal of Biotechnology ... Legumes played an important role in stimulating the growth and reproduction of various soil microbial populations, accordingly promoting the microbial catabolic activity.

  19. Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology.

    Directory of Open Access Journals (Sweden)

    Łukasz Jałowiecki

    Full Text Available The aim of the study was to determine the potential of community-level physiological profiles (CLPPs methodology as an assay for characterization of the metabolic diversity of wastewater samples and to link the metabolic diversity patterns to efficiency of select onsite biological wastewater facilities. Metabolic fingerprints obtained from the selected samples were used to understand functional diversity implied by the carbon substrate shifts. Three different biological facilities of onsite wastewater treatment were evaluated: fixed bed reactor (technology A, trickling filter/biofilter system (technology B, and aerated filter system (the fluidized bed reactor, technology C. High similarities of the microbial community functional structures were found among the samples from the three onsite wastewater treatment plants (WWTPs, as shown by the diversity indices. Principal components analysis (PCA showed that the diversity and CLPPs of microbial communities depended on the working efficiency of the wastewater treatment technologies. This study provided an overall picture of microbial community functional structures of investigated samples in WWTPs and discerned the linkages between microbial communities and technologies of onsite WWTPs used. The results obtained confirmed that metabolic profiles could be used to monitor treatment processes as valuable biological indicators of onsite wastewater treatment technologies efficiency. This is the first step toward understanding relations of technology types with microbial community patterns in raw and treated wastewaters.

  20. Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers.

    Science.gov (United States)

    Kleinsteuber, Sabine; Schleinitz, Kathleen M; Vogt, Carsten

    2012-05-01

    Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, "omics" approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.

  1. Water regime history drives responses of soil Namib Desert microbial communities to wetting events

    Science.gov (United States)

    Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A.

    2015-07-01

    Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel “dry condition” control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.

  2. Microbial community functional structures in wastewater treatment plants as characterized by GeoChip.

    Science.gov (United States)

    Wang, Xiaohui; Xia, Yu; Wen, Xianghua; Yang, Yunfeng; Zhou, Jizhong

    2014-01-01

    Biological WWTPs must be functionally stable to continuously and steadily remove contaminants which rely upon the activity of complex microbial communities. However, knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables. To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and to understand the effects of environmental factors on their structure. 12 activated sludge samples were collected from four WWTPs in Beijing. A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and sulfur cycles, metal resistance, antibiotic resistance and organic contaminant degradation. High similarities of the microbial community functional structures were found among activated sludge samples from the four WWTPs, as shown by both diversity indices and the overlapped genes. For individual gene category, such as egl, amyA, lip, nirS, nirK, nosZ, ureC, ppx, ppk, aprA, dsrA, sox and benAB, there were a number of microorganisms shared by all 12 samples. Canonical correspondence analysis (CCA) showed that the microbial functional patterns were highly correlated with water temperature, dissolved oxygen (DO), ammonia concentrations and loading rate of chemical oxygen demand (COD). Based on the variance partitioning analyses (VPA), a total of 53% of microbial community variation from GeoChip data can be explained by wastewater characteristics (25%) and operational parameters (23%), respectively. This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs.

  3. Microbial community functional structures in wastewater treatment plants as characterized by GeoChip.

    Directory of Open Access Journals (Sweden)

    Xiaohui Wang

    Full Text Available BACKGROUND: Biological WWTPs must be functionally stable to continuously and steadily remove contaminants which rely upon the activity of complex microbial communities. However, knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables. AIMS: To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs and to understand the effects of environmental factors on their structure. METHODS: 12 activated sludge samples were collected from four WWTPs in Beijing. A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and sulfur cycles, metal resistance, antibiotic resistance and organic contaminant degradation. RESULTS: High similarities of the microbial community functional structures were found among activated sludge samples from the four WWTPs, as shown by both diversity indices and the overlapped genes. For individual gene category, such as egl, amyA, lip, nirS, nirK, nosZ, ureC, ppx, ppk, aprA, dsrA, sox and benAB, there were a number of microorganisms shared by all 12 samples. Canonical correspondence analysis (CCA showed that the microbial functional patterns were highly correlated with water temperature, dissolved oxygen (DO, ammonia concentrations and loading rate of chemical oxygen demand (COD. Based on the variance partitioning analyses (VPA, a total of 53% of microbial community variation from GeoChip data can be explained by wastewater characteristics (25% and operational parameters (23%, respectively. CONCLUSIONS: This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs.

  4. Research Progress on the Relationship Between Oral Microbial Community and Tumor

    Directory of Open Access Journals (Sweden)

    Ma Shujun

    2016-03-01

    Full Text Available Significant progress was observed in studies of the relationship between oral Helicobacter pylori and gastric cancer and tumors. Based on three distinct and close relationships, namely, the relationship between oral H. pylori and gastric cancer, between oral microbial communities and oral squamous cell carcinoma, and between oral microbial communities of human immunodeficiency virus-infected patients and tumors, this work reviews the relationship between oral microbial communities and tumors. This research also provides reference for further analysis of the relationship between oral microorganisms and tumors to realize early diagnosis of tumor patients through detecting oral microorganisms under adjuvant therapy.

  5. Manipulating soil microbial communities in extensive green roof substrates.

    Science.gov (United States)

    Molineux, Chloe J; Connop, Stuart P; Gange, Alan C

    2014-09-15

    There has been very little investigation into the soil microbial community on green roofs, yet this below ground habitat is vital for ecosystem functioning. Green roofs are often harsh environments that would greatly benefit from having a healthy microbial system, allowing efficient nutrient cycling and a degree of drought tolerance in dry summer months. To test if green roof microbial communities could be manipulated, we added mycorrhizal fungi and a microbial mixture ('compost tea') to green roof rootzones, composed mainly of crushed brick or crushed concrete. The study revealed that growing media type and depth play a vital role in the microbial ecology of green roofs. There are complex relationships between depth and type of substrate and the biomass of different microbial groups, with no clear pattern being observed. Following the addition of inoculants, bacterial groups tended to increase in biomass in shallower substrates, whereas fungal biomass change was dependent on depth and type of substrate. Increased fungal biomass was found in shallow plots containing more crushed concrete and deeper plots containing more crushed brick where compost tea (a live mixture of beneficial bacteria) was added, perhaps due to the presence of helper bacteria for arbuscular mycorrhizal fungi (AMF). Often there was not an additive affect of the microbial inoculations but instead an antagonistic interaction between the added AM fungi and the compost tea. This suggests that some species of microbes may not be compatible with others, as competition for limited resources occurs within the various substrates. The overall results suggest that microbial inoculations of green roof habitats are sustainable. They need only be done once for increased biomass to be found in subsequent years, indicating that this is a novel and viable method of enhancing roof community composition. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Life in the "plastisphere": microbial communities on plastic marine debris.

    Science.gov (United States)

    Zettler, Erik R; Mincer, Tracy J; Amaral-Zettler, Linda A

    2013-07-02

    Plastics are the most abundant form of marine debris, with global production rising and documented impacts in some marine environments, but the influence of plastic on open ocean ecosystems is poorly understood, particularly for microbial communities. Plastic marine debris (PMD) collected at multiple locations in the North Atlantic was analyzed with scanning electron microscopy (SEM) and next-generation sequencing to characterize the attached microbial communities. We unveiled a diverse microbial community of heterotrophs, autotrophs, predators, and symbionts, a community we refer to as the "Plastisphere". Pits visualized in the PMD surface conformed to bacterial shapes suggesting active hydrolysis of the hydrocarbon polymer. Small-subunit rRNA gene surveys identified several hydrocarbon-degrading bacteria, supporting the possibility that microbes play a role in degrading PMD. Some Plastisphere members may be opportunistic pathogens (the authors, unpublished data) such as specific members of the genus Vibrio that dominated one of our plastic samples. Plastisphere communities are distinct from surrounding surface water, implying that plastic serves as a novel ecological habitat in the open ocean. Plastic has a longer half-life than most natural floating marine substrates, and a hydrophobic surface that promotes microbial colonization and biofilm formation, differing from autochthonous substrates in the upper layers of the ocean.

  7. Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

    Science.gov (United States)

    Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

    2016-06-01

    Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural

  8. Mineralogic control on abundance and diversity of surface-adherent microbial communities

    Science.gov (United States)

    Mauck, Brena S.; Roberts, Jennifer A.

    2007-01-01

    In this study, we investigated the role of mineral-bound P and Fe in defining microbial abundance and diversity in a carbon-rich groundwater. Field colonization experiments of initially sterile mineral surfaces were combined with community structure characterization of the attached microbial population. Silicate minerals containing varying concentrations of P (∼1000 ppm P) and Fe (∼4 wt % Fe 2 O3), goethite (FeOOH), and apatite [Ca5(PO4)3(OH)] were incubated for 14 months in three biogeochemically distinct zones within a petroleum-contaminated aquifer. Phospholipid fatty acid analysis of incubated mineral surfaces and groundwater was used as a measure of microbial community structure and biomass. Microbial biomass on minerals exhibited distinct trends as a function of mineralogy depending on the environment of incubation. In the carbon-rich, aerobic groundwater attached biomass did not correlate to the P- or Fe- content of the mineral. In the methanogenic groundwater, however, biomass was most abundant on P-containing minerals. Similarly, in the Fe-reducing groundwater a correlation between Fe-content and biomass was observed. The community structure of the mineral-adherent microbial population was compared to the native groundwater community. These two populations were significantly different regardless of mineralogy, suggesting differentiation of the planktonic community through attachment, growth, and death of colonizing cells. Biomarkers specific for dissimilatory Fe-reducing bacteria native to the aquifer were identified only on Fe-containing minerals in the Fe-reducing groundwater. These results demonstrate that the trace nutrient content of minerals affects both the abundance and diversity of surface-adherent microbial communities. This behavior may be a means to access limiting nutrients from the mineral, creating a niche for a particular microbial population. These results suggest that heterogeneity of microbial populations and their associated

  9. Microbial examination of anaerobic sludge adaptation to animal slurry.

    Science.gov (United States)

    Moset, V; Cerisuelo, A; Ferrer, P; Jimenez, A; Bertolini, E; Cambra-López, M

    2014-01-01

    The objective of this study was to evaluate changes in the microbial population of anaerobic sludge digesters during the adaptation to pig slurry (PS) using quantitative real-time polymerase chain reaction (qPCR) and qualitative scanning electron microscopy (SEM). Additionally, the relationship between microbial parameters and sludge physicochemical composition and methane yield was examined. Results showed that the addition of PS to an unadapted thermophilic anaerobic digester caused an increase in volatile fatty acids (VFA) concentration, a decrease in removal efficiency and CH4 yield. Additionally, increases in total bacteria and total archaea were observed using qPCR. Scanning electron micrographs provided a general overview of the sludge's cell morphology, morphological diversity and degree of organic matter degradation. A change in microbial morphotypes from homogeneous cell morphologies to a higher morphological diversity, similar to that observed in PS, was observed with the addition of PS by SEM. Therefore, the combination of qPCR and SEM allowed expanding the knowledge about the microbial adaptation to animal slurry in thermophilic anaerobic digesters.

  10. Microbial diversity and community structure in an antimony-rich tailings dump.

    Science.gov (United States)

    Xiao, Enzong; Krumins, Valdis; Dong, Yiran; Xiao, Tangfu; Ning, Zengping; Xiao, Qingxiang; Sun, Weimin

    2016-09-01

    To assess the impact of antimony (Sb) on microbial community structure, 12 samples were taken from an Sb tailings pile in Guizhou Province, Southwest China. All 12 samples exhibited elevated Sb concentrations, but the mobile and bioaccessible fractions were small in comparison to total Sb concentrations. Besides the geochemical analyses, microbial communities inhabiting the tailing samples were characterized to investigate the interplay between the microorganisms and environmental factors in mine tailings. In all samples, Proteobacteria and Actinobacteria were the most dominant phyla. At the genus level, Thiobacillus, Limnobacter, Nocardioides, Lysobacter, Phormidium, and Kaistobacter demonstrated relatively high abundances. The two most abundant genera, Thiobacillus and Limnobacter, are characterized as sulfur-oxidizing bacteria and thiosulfate-oxidizing bacteria, respectively, while the genus Lysobacter contains arsenic (As)-resistant bacteria. Canonical correspondence analysis (CCA) indicates that TOC and the sulfate to sulfide ratio strongly shaped the microbial communities, suggesting the influence of the environmental factors in the indigenous microbial communities.

  11. Changes in microbial community structure in the wake of Hurricanes Katrina and Rita.

    Science.gov (United States)

    Amaral-Zettler, Linda A; Rocca, Jennifer D; Lamontagne, Michael G; Dennett, Mark R; Gast, Rebecca J

    2008-12-15

    Hurricanes have the potential to alter the structures of coastal ecosystems and generate pathogen-laden floodwaters thatthreaten public health. To examine the impact of hurricanes on urban systems, we compared microbial community structures in samples collected after Hurricane Katrina and before and after Hurricane Rita. We extracted environmental DNA and sequenced small-subunit rRNA (SSU rRNA) gene clone libraries to survey microbial communities in floodwater, water, and sediment samples collected from Lake Charles, Lake Pontchartrain, the 17th Street and Industrial Canals in New Orleans, and raw sewage. Correspondence analysis showed that microbial communities associated with sediments formed one cluster while communities associated with lake and Industrial Canal water formed a second. Communities associated with water from the 17th Street Canal and floodwaters collected in New Orleans showed similarity to communities in raw sewage and contained a number of sequences associated with possible pathogenic microbes. This suggests that a distinct microbial community developed in floodwaters following Hurricane Katrina and that microbial community structures as a whole might be sensitive indicators of ecosystem health and serve as "sentinels" of water quality in the environment.

  12. Micro-Food Web Structure Shapes Rhizosphere Microbial Communities and Growth in Oak

    Directory of Open Access Journals (Sweden)

    Hazel R. Maboreke

    2018-03-01

    Full Text Available The multitrophic interactions in the rhizosphere impose significant impacts on microbial community structure and function, affecting nutrient mineralisation and consequently plant performance. However, particularly for long-lived plants such as forest trees, the mechanisms by which trophic structure of the micro-food web governs rhizosphere microorganisms are still poorly understood. This study addresses the role of nematodes, as a major component of the soil micro-food web, in influencing the microbial abundance and community structure as well as tree growth. In a greenhouse experiment with Pedunculate Oak seedlings were grown in soil, where the nematode trophic structure was manipulated by altering the proportion of functional groups (i.e., bacterial, fungal, and plant feeders in a full factorial design. The influence on the rhizosphere microbial community, the ectomycorrhizal symbiont Piloderma croceum, and oak growth, was assessed. Soil phospholipid fatty acids were employed to determine changes in the microbial communities. Increased density of singular nematode functional groups showed minor impact by increasing the biomass of single microbial groups (e.g., plant feeders that of Gram-negative bacteria, except fungal feeders, which resulted in a decline of all microorganisms in the soil. In contrast, inoculation of two or three nematode groups promoted microbial biomass and altered the community structure in favour of bacteria, thereby counteracting negative impact of single groups. These findings highlight that the collective action of trophic groups in the soil micro-food web can result in microbial community changes promoting the fitness of the tree, thereby alleviating the negative effects of individual functional groups.

  13. Response of soil microbial communities and microbial interactions to long-term heavy metal contamination.

    Science.gov (United States)

    Li, Xiaoqi; Meng, Delong; Li, Juan; Yin, Huaqun; Liu, Hongwei; Liu, Xueduan; Cheng, Cheng; Xiao, Yunhua; Liu, Zhenghua; Yan, Mingli

    2017-12-01

    Due to the persistence of metals in the ecosystem and their threat to all living organisms, effects of heavy metal on soil microbial communities were widely studied. However, little was known about the interactions among microorganisms in heavy metal-contaminated soils. In the present study, microbial communities in Non (CON), moderately (CL) and severely (CH) contaminated soils were investigated through high-throughput Illumina sequencing of 16s rRNA gene amplicons, and networks were constructed to show the interactions among microbes. Results showed that the microbial community composition was significantly, while the microbial diversity was not significantly affected by heavy metal contamination. Bacteria showed various response to heavy metals. Bacteria that positively correlated with Cd, e.g. Acidobacteria_Gp and Proteobacteria_thiobacillus, had more links between nodes and more positive interactions among microbes in CL- and CH-networks, while bacteria that negatively correlated with Cd, e.g. Longilinea, Gp2 and Gp4 had fewer network links and more negative interactions in CL and CH-networks. Unlike bacteria, members of the archaeal domain, i.e. phyla Crenarchaeota and Euryarchaeota, class Thermoprotei and order Thermoplasmatales showed only positive correlation with Cd and had more network interactions in CH-networks. The present study indicated that (i) the microbial community composition, as well as network interactions was shift to strengthen adaptability of microorganisms to heavy metal contamination, (ii) archaea were resistant to heavy metal contamination and may contribute to the adaption to heavy metals. It was proposed that the contribution might be achieved either by improving environment conditions or by cooperative interactions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Spatial Distribution of Viruses Associated with Planktonic and Attached Microbial Communities in Hydrothermal Environments

    Science.gov (United States)

    Nunoura, Takuro; Kazama, Hiromi; Noguchi, Takuroh; Inoue, Kazuhiro; Akashi, Hironori; Yamanaka, Toshiro; Toki, Tomohiro; Yamamoto, Masahiro; Furushima, Yasuo; Ueno, Yuichiro; Yamamoto, Hiroyuki; Takai, Ken

    2012-01-01

    Viruses play important roles in marine surface ecosystems, but little is known about viral ecology and virus-mediated processes in deep-sea hydrothermal microbial communities. In this study, we examined virus-like particle (VLP) abundances in planktonic and attached microbial communities, which occur in physical and chemical gradients in both deep and shallow submarine hydrothermal environments (mixing waters between hydrothermal fluids and ambient seawater and dense microbial communities attached to chimney surface areas or macrofaunal bodies and colonies). We found that viruses were widely distributed in a variety of hydrothermal microbial habitats, with the exception of the interior parts of hydrothermal chimney structures. The VLP abundance and VLP-to-prokaryote ratio (VPR) in the planktonic habitats increased as the ratio of hydrothermal fluid to mixing water increased. On the other hand, the VLP abundance in attached microbial communities was significantly and positively correlated with the whole prokaryotic abundance; however, the VPRs were always much lower than those for the surrounding hydrothermal waters. This is the first report to show VLP abundance in the attached microbial communities of submarine hydrothermal environments, which presented VPR values significantly lower than those in planktonic microbial communities reported before. These results suggested that viral lifestyles (e.g., lysogenic prevalence) and virus interactions with prokaryotes are significantly different among the planktonic and attached microbial communities that are developing in the submarine hydrothermal environments. PMID:22210205

  15. Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota

    Science.gov (United States)

    Pereira-Marques, Joana; Pinto-Ribeiro, Ines; Costa, Jose L; Carneiro, Fatima; Machado, Jose C

    2018-01-01

    Objective Gastric carcinoma development is triggered by Helicobacter pylori. Chronic H. pylori infection leads to reduced acid secretion, which may allow the growth of a different gastric bacterial community. This change in the microbiome may increase aggression to the gastric mucosa and contribute to malignancy. Our aim was to evaluate the composition of the gastric microbiota in chronic gastritis and in gastric carcinoma. Design The gastric microbiota was retrospectively investigated in 54 patients with gastric carcinoma and 81 patients with chronic gastritis by 16S rRNA gene profiling, using next-generation sequencing. Differences in microbial composition of the two patient groups were assessed using linear discriminant analysis effect size. Associations between the most relevant taxa and clinical diagnosis were validated by real-time quantitative PCR. Predictive functional profiling of microbial communities was obtained with PICRUSt. Results The gastric carcinoma microbiota was characterised by reduced microbial diversity, by decreased abundance of Helicobacter and by the enrichment of other bacterial genera, mostly represented by intestinal commensals. The combination of these taxa into a microbial dysbiosis index revealed that dysbiosis has excellent capacity to discriminate between gastritis and gastric carcinoma. Analysis of the functional features of the microbiota was compatible with the presence of a nitrosating microbial community in carcinoma. The major observations were confirmed in validation cohorts from different geographic origins. Conclusions Detailed analysis of the gastric microbiota revealed for the first time that patients with gastric carcinoma exhibit a dysbiotic microbial community with genotoxic potential, which is distinct from that of patients with chronic gastritis. PMID:29102920

  16. Discovery of enzymes for toluene synthesis from anoxic microbial communities

    DEFF Research Database (Denmark)

    Beller, Harry R.; Rodrigues, Andria V.; Zargar, Kamrun

    2018-01-01

    Microbial toluene biosynthesis was reported in anoxic lake sediments more than three decades ago, but the enzyme catalyzing this biochemically challenging reaction has never been identified. Here we report the toluene-producing enzyme PhdB, a glycyl radical enzyme of bacterial origin that catalyzes...... phenylacetate decarboxylation, and its cognate activating enzyme PhdA, a radical S-adenosylmethionine enzyme, discovered in two distinct anoxic microbial communities that produce toluene. The unconventional process of enzyme discovery from a complex microbial community (>300,000 genes), rather than from...... a microbial isolate, involved metagenomics- and metaproteomics-enabled biochemistry, as well as in vitro confirmation of activity with recombinant enzymes. This work expands the known catalytic range of glycyl radical enzymes (only seven reaction types had been characterized previously) and aromatic...

  17. Properties of thermophilic microorganisms

    International Nuclear Information System (INIS)

    Ljungdahl, L.G.

    1984-01-01

    Microorganisms are called thermophilic or extreme thermophilic (caldo-active) if they grow and reproduce over 47 0 C and 70 0 C, respectively. A survey of growth characteristics of thermophiles is presented and it includes those which also live at extreme pH. The prevalent but not completely emcompassing theory of the ability of thermophiles to grow at high temperatures is that they have macromolecules and cell organelles with high thermostability. Work on some proteins and cell organelles from thermophiles is reviewed. The thermostabilities of these components are compared with those of the living cells, and factors which may govern optimum as well as minimum growth temperatures of microorganisms are discussed. Examples are from the literature but also include enzymes involved in tetrahydrofolate metabolism and other proteins of acetogenic therhmophilic bacteria which are presently studied in the author's laboratory

  18. Comparison of bacterial community structure and dynamics during the thermophilic composting of different types of solid wastes: anaerobic digestion residue, pig manure and chicken manure

    Science.gov (United States)

    Song, Caihong; Li, Mingxiao; Jia, Xuan; Wei, Zimin; Zhao, Yue; Xi, Beidou; Zhu, Chaowei; Liu, Dongming

    2014-01-01

    This study investigated the impact of composting substrate types on the bacterial community structure and dynamics during composting processes. To this end, pig manure (PM), chicken manure (CM), a mixture of PM and CM (PM + CM), and a mixture of PM, CM and anaerobic digestion residue (ADR) (PM + CM + ADR) were selected for thermophilic composting. The bacterial community structure and dynamics during the composting process were detected and analysed by polymerase chain reaction–denaturing gradient gel electrophoresis (DGGE) coupled with a statistic analysis. The physical-chemical analyses indicated that compared to single-material composting (PM, CM), co-composting (PM + CM, PM + CM + ADR) could promote the degradation of organic matter and strengthen the ability of conserving nitrogen. A DGGE profile and statistical analysis demonstrated that co-composting, especially PM + CM + ADR, could improve the bacterial community structure and functional diversity, even in the thermophilic stage. Therefore, co-composting could weaken the screening effect of high temperature on bacterial communities. Dominant sequencing analyses indicated a dramatic shift in the dominant bacterial communities from single-material composting to co-composting. Notably, compared with PM, PM + CM increased the quantity of xylan-degrading bacteria and reduced the quantity of human pathogens. PMID:24963997

  19. The role of macrobiota in structuring microbial communities along rocky shores

    Directory of Open Access Journals (Sweden)

    Catherine A. Pfister

    2014-10-01

    Full Text Available Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.

  20. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

    Science.gov (United States)

    Fierer, Noah; Leff, Jonathan W; Adams, Byron J; Nielsen, Uffe N; Bates, Scott Thomas; Lauber, Christian L; Owens, Sarah; Gilbert, Jack A; Wall, Diana H; Caporaso, J Gregory

    2012-12-26

    For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.

  1. The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature.

    Science.gov (United States)

    Auffret, Marc D; Karhu, Kristiina; Khachane, Amit; Dungait, Jennifer A J; Fraser, Fiona; Hopkins, David W; Wookey, Philip A; Singh, Brajesh K; Freitag, Thomas E; Hartley, Iain P; Prosser, James I

    2016-01-01

    Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited.

  2. Environmental controls on microbial communities in continental serpentinite fluids

    Directory of Open Access Journals (Sweden)

    Melitza eCrespo-Medina

    2014-11-01

    Full Text Available Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite–hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate and formate, with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the three month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems.

  3. Metagenomics meets time series analysis: unraveling microbial community dynamics

    NARCIS (Netherlands)

    Faust, K.; Lahti, L.M.; Gonze, D.; Vos, de W.M.; Raes, J.

    2015-01-01

    The recent increase in the number of microbial time series studies offers new insights into the stability and dynamics of microbial communities, from the world's oceans to human microbiota. Dedicated time series analysis tools allow taking full advantage of these data. Such tools can reveal periodic

  4. Mapping and determinism of soil microbial community distribution across an agricultural landscape.

    Science.gov (United States)

    Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

    2015-06-01

    Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  5. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession.

    Science.gov (United States)

    Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

    2015-05-06

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth's biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

  6. Microbial population dynamics during startup of a full-scale anaerobic digester treating industrial food waste in Kyoto eco-energy project.

    Science.gov (United States)

    Ike, Michihiko; Inoue, Daisuke; Miyano, Tomoki; Liu, Tong Tong; Sei, Kazunari; Soda, Satoshi; Kadoshin, Shiro

    2010-06-01

    The microbial community in a full-scale anaerobic digester (2300m3) treating industrial food waste in the Kyoto Eco-Energy Project was analyzed using terminal restriction fragment length polymorphism for eubacterial and archaeal 16S rRNA genes. Both thermophilic and mesophilic sludge of treated swine waste were seeded to the digestion tank. During the 150-day startup period, coffee grounds as a main food waste, along with potato, kelp and boiled beans, tofu, bean curd lees, and deep-fried bean curd were fed to the digestion process step-by-step (max. 40t/d). Finally, the methane yield reached 360m3/t-feed with 40days' retention time, although temporary accumulation of propionate was observed. Eubacterial communities that formed in the thermophilic digestion tank differed greatly from both thermophilic and mesophilic types of seed sludge. Results suggest that the Actinomyces/Thermomonospora and Ralstonia/Shewanella were contributors for hydrolyzation and degradation of food waste into volatile fatty acids. Acetate-utilizing methanogens, Methanosaeta, were dominant in seed sludges of both types, but they decreased drastically during processing in the digestion tank. Methanosarcina and Methanobrevibacter/Methanobacterium were, respectively, possible main contributors for methane production from acetate and H2 plus CO2. Copyright 2010 Elsevier Ltd. All rights reserved.

  7. [Microbial Community Structure on the Root Surface of Patients with Periodontitis.

    Science.gov (United States)

    Zhang, Ju-Mei; Zhou, Jian-Ye; Bo, Lei; Hu, Xiao-Pan; Jiao, Kang-Li; Li, Zhi-Jie; Li, Yue-Hong; Li, Zhi-Qiang

    2016-11-01

    To study the microbial community structure on the root surface of patients with periodontitis. Bacterial plaque and tissues from the root neck (RN group),root middle (RM group) and root tine (RT group) of six teeth with mobility 3 in one patient with periodontitis were sampled.The V3V4 region of 16S rRNA was sequenced on the Illumina MiSeq platform.The microbial community structure was analyzed by Mothur,Qiime and SPSS software. The principal component analysis (PCoA) results indicated that the RM samples had a similar microbial community structure as that of the RT samples,which was significant different from that of the RN samples.Thirteen phyla were detected in the three groups of samples,which included 7 dominant phyla.29 dominant genera were detected in 184 genera.The abundance of Bacteroidetes _[G-6] and Peptostre ptococcaceae _[XI][G-4] had a positive correlation with the depth of the collection site of samples ( P microbial community structure on the root surface of patients with periodontitis.

  8. High taxonomic variability despite stable functional structure across microbial communities.

    Science.gov (United States)

    Louca, Stilianos; Jacques, Saulo M S; Pires, Aliny P F; Leal, Juliana S; Srivastava, Diane S; Parfrey, Laura Wegener; Farjalla, Vinicius F; Doebeli, Michael

    2016-12-05

    Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate 'miniature' aquatic ecosystems contained within the foliage of wild bromeliads. We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups. We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable. Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift. Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.

  9. Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

    Directory of Open Access Journals (Sweden)

    Jerome eBabauta

    2014-01-01

    Full Text Available Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode with tip size ~20 µm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode in the mat. Subsequently, to characterize the microelectrode-associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1-V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community.

  10. Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat.

    Science.gov (United States)

    Babauta, Jerome T; Atci, Erhan; Ha, Phuc T; Lindemann, Stephen R; Ewing, Timothy; Call, Douglas R; Fredrickson, James K; Beyenal, Haluk

    2014-01-01

    Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode-associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1-V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community.

  11. Bacillus sp. JR3 esterase LipJ: A new mesophilic enzyme showing traces of a thermophilic past.

    Directory of Open Access Journals (Sweden)

    Judit Ribera

    Full Text Available A search for extremophile enzymes from ancient volcanic soils in El Hierro Island (Canary Islands, Spain allowed isolation of a microbial sporulated strain collection from which several enzymatic activities were tested. Isolates were obtained after sample cultivation under several conditions of nutrient contents and temperature. Among the bacterial isolates, supernatants from the strain designated JR3 displayed high esterase activity at temperatures ranging from 30 to 100°C, suggesting the presence of at least a hyper-thermophilic extracellular lipase. Sequence alignment of known thermophilic lipases allowed design of degenerated consensus primers for amplification and cloning of the corresponding lipase, named LipJ. However, the cloned enzyme displayed maximum activity at 30°C and pH 7, showing a different profile from that observed in supernatants of the parental strain. Sequence analysis of the cloned protein showed a pentapeptide motif -GHSMG- distinct from that of thermophilic lipases, and much closer to that of esterases. Nevertheless, the 3D structural model of LipJ displayed the same folding as that of thermophilic lipases, suggesting a common evolutionary origin. A phylogenetic study confirmed this possibility, positioning LipJ as a new member of the thermophilic family of bacterial lipases I.5. However, LipJ clusters in a clade close but separated from that of Geobacillus sp. thermophilic lipases. Comprehensive analysis of the cloned enzyme suggests a common origin of LipJ and other bacterial thermophilic lipases, and highlights the most probable divergent evolutionary pathway followed by LipJ, which during the harsh past times would have probably been a thermophilic enzyme, having lost these properties when the environment changed to more benign conditions.

  12. Bacillus sp. JR3 esterase LipJ: A new mesophilic enzyme showing traces of a thermophilic past.

    Science.gov (United States)

    Ribera, Judit; Estupiñán, Mónica; Fuentes, Alba; Fillat, Amanda; Martínez, Josefina; Diaz, Pilar

    2017-01-01

    A search for extremophile enzymes from ancient volcanic soils in El Hierro Island (Canary Islands, Spain) allowed isolation of a microbial sporulated strain collection from which several enzymatic activities were tested. Isolates were obtained after sample cultivation under several conditions of nutrient contents and temperature. Among the bacterial isolates, supernatants from the strain designated JR3 displayed high esterase activity at temperatures ranging from 30 to 100°C, suggesting the presence of at least a hyper-thermophilic extracellular lipase. Sequence alignment of known thermophilic lipases allowed design of degenerated consensus primers for amplification and cloning of the corresponding lipase, named LipJ. However, the cloned enzyme displayed maximum activity at 30°C and pH 7, showing a different profile from that observed in supernatants of the parental strain. Sequence analysis of the cloned protein showed a pentapeptide motif -GHSMG- distinct from that of thermophilic lipases, and much closer to that of esterases. Nevertheless, the 3D structural model of LipJ displayed the same folding as that of thermophilic lipases, suggesting a common evolutionary origin. A phylogenetic study confirmed this possibility, positioning LipJ as a new member of the thermophilic family of bacterial lipases I.5. However, LipJ clusters in a clade close but separated from that of Geobacillus sp. thermophilic lipases. Comprehensive analysis of the cloned enzyme suggests a common origin of LipJ and other bacterial thermophilic lipases, and highlights the most probable divergent evolutionary pathway followed by LipJ, which during the harsh past times would have probably been a thermophilic enzyme, having lost these properties when the environment changed to more benign conditions.

  13. Impact of long-term diesel contamination on soil microbial community structure

    DEFF Research Database (Denmark)

    Sutton, Nora; Maphosa, Farai; Morillo, Jose

    2013-01-01

    Microbial community composition and diversity at a diesel-contaminated railway site were investigated by pyrosequencing of bacterial and archaeal 16S rRNA gene fragments to understand the interrelationships among microbial community composition, pollution level, and soil geochemical and physical...... properties. To this end, 26 soil samples from four matrix types with various geochemical characteristics and contaminant concentrations were investigated. The presence of diesel contamination significantly impacted microbial community composition and diversity, regardless of the soil matrix type. Clean...... observed in contaminated samples. Redundancy analysis indicated that increased relative abundances of the phyla Chloroflexi, Firmicutes, and Euryarchaeota correlated with the presence of contamination. Shifts in the chemical composition of diesel constituents across the site and the abundance of specific...

  14. Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass

    Science.gov (United States)

    Guo, Xue; Zhou, Xishu; Hale, Lauren; Yuan, Mengting; Feng, Jiajie; Ning, Daliang; Shi, Zhou; Qin, Yujia; Liu, Feifei; Wu, Liyou; He, Zhili; Van Nostrand, Joy D.; Liu, Xueduan; Luo, Yiqi; Tiedje, James M.; Zhou, Jizhong

    2018-01-01

    Clipping, removal of aboveground plant biomass, is an important issue in grassland ecology. However, few studies have focused on the effect of clipping on belowground microbial communities. Using integrated metagenomic technologies, we examined the taxonomic and functional responses of soil microbial communities to annual clipping (2010–2014) in a grassland ecosystem of the Great Plains of North America. Our results indicated that clipping significantly (P microbial respiration rates. Annual temporal variation within the microbial communities was much greater than the significant changes introduced by clipping, but cumulative effects of clipping were still observed in the long-term scale. The abundances of some bacterial and fungal lineages including Actinobacteria and Bacteroidetes were significantly (P microbial communities were significantly correlated with soil respiration and plant productivity. Intriguingly, clipping effects on microbial function may be highly regulated by precipitation at the interannual scale. Altogether, our results illustrated the potential of soil microbial communities for increased soil organic matter decomposition under clipping land-use practices. PMID:29904372

  15. Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

    Energy Technology Data Exchange (ETDEWEB)

    Terence L. Marsh

    2004-05-26

    The goals of this study were: (1) survey the microbial community in soil samples from a site contaminated with heavy metals using new rapid molecular techniques that are culture-independent; (2) identify phylogenetic signatures of microbial populations that correlate with metal ion contamination; and (3) cultivate these diagnostic strains using traditional as well as novel cultivation techniques in order to identify organisms that may be of value in site evaluation/management or bioremediation.

  16. Microbial community analysis of fouled reverse osmosis membranes used in water recycling

    KAUST Repository

    Ayache, C.; Manes, Carmem Lara De O; Pidou, Marc; Croue, Jean-Philippe; Gernjak, Wolfgang

    2013-01-01

    Biofouling on RO membranes has major cost implications in water reclamation. In this study membranes and water samples were collected from a RO pilot-plant operated on two sites to study the differences in microbial communities in order to develop a better understanding of the biofouling. For the two sites studied, the examination of the front membrane of the first stage and the tail membrane of the second stage of the RO train using 16S rRNA gene-based molecular technique showed that bacteria were similar on both stages and no significant effect of the membrane location within the RO train on the biofilm development could be discerned. However, the comparison of the identified bacteria from membrane samples between the two sites showed that each site is specific, leading to a different composition of microbial communities. The different nutrient concentrations in the RO feed water due to the different biological pre-treatments are one potential explanation for the observed differences in the microbial communities. Seasonal variations also play a major role in the development of microbial communities as shown by the significant differences observed between the communities measured in the samples in winter and summer on the second site. The results did not show similarity between the species identified on the RO membranes and in the feed water. Hence, the relationship of microbial community between the water generated during the pre-treatment process and RO membranes is not obvious. From this study, results showed that there is an actual need to investigate the development of microbial communities on membrane surface in real conditions in order to suggest tailored solutions for biofouling control and removal. © 2013 Elsevier Ltd.

  17. Microbial community analysis of fouled reverse osmosis membranes used in water recycling

    KAUST Repository

    Ayache, C.

    2013-06-01

    Biofouling on RO membranes has major cost implications in water reclamation. In this study membranes and water samples were collected from a RO pilot-plant operated on two sites to study the differences in microbial communities in order to develop a better understanding of the biofouling. For the two sites studied, the examination of the front membrane of the first stage and the tail membrane of the second stage of the RO train using 16S rRNA gene-based molecular technique showed that bacteria were similar on both stages and no significant effect of the membrane location within the RO train on the biofilm development could be discerned. However, the comparison of the identified bacteria from membrane samples between the two sites showed that each site is specific, leading to a different composition of microbial communities. The different nutrient concentrations in the RO feed water due to the different biological pre-treatments are one potential explanation for the observed differences in the microbial communities. Seasonal variations also play a major role in the development of microbial communities as shown by the significant differences observed between the communities measured in the samples in winter and summer on the second site. The results did not show similarity between the species identified on the RO membranes and in the feed water. Hence, the relationship of microbial community between the water generated during the pre-treatment process and RO membranes is not obvious. From this study, results showed that there is an actual need to investigate the development of microbial communities on membrane surface in real conditions in order to suggest tailored solutions for biofouling control and removal. © 2013 Elsevier Ltd.

  18. The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem

    Directory of Open Access Journals (Sweden)

    William P. Inskeep

    2013-05-01

    Full Text Available The Yellowstone geothermal complex contains over 10,000 diverse geothermal features that host numerous phylogenetically deeply-rooted and poorly understood archaea, bacteria and viruses. Microbial communities in high-temperature environments are generally less diverse than soil, marine, sediment or lake habitats and therefore offer a tremendous opportunity for studying the structure and function of different model microbial communities using environmental metagenomics. One of the broader goals of this study was to establish linkages among microbial distribution, metabolic potential and environmental variables. Twenty geochemically distinct geothermal ecosystems representing a broad spectrum of Yellowstone hot-spring environments were used for metagenomic and geochemical analysis and included approximately equal numbers of: (1 phototrophic mats, (2 ‘filamentous streamer’ communities, and (3 archaeal-dominated sediments. The metagenomes were analyzed using a suite of complementary and integrative bioinformatic tools, including phylogenetic and functional analysis of both individual sequence reads and assemblies of predominant phylotypes. This volume identifies major environmental determinants of a large number of thermophilic microbial lineages, many of which have not been fully described in the literature nor previously cultivated to enable functional and genomic analyses. Moreover, protein family abundance comparisons and in-depth analyses of specific genes and metabolic pathways relevant to these hot-spring environments reveal hallmark signatures of metabolic capabilities that parallel the distribution of phylotypes across specific types of geochemical environments.

  19. Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes.

    Directory of Open Access Journals (Sweden)

    John F Heidelberg

    Full Text Available CRISPR arrays and associated cas genes are widespread in bacteria and archaea and confer acquired resistance to viruses. To examine viral immunity in the context of naturally evolving microbial populations we analyzed genomic data from two thermophilic Synechococcus isolates (Syn OS-A and Syn OS-B' as well as a prokaryotic metagenome and viral metagenome derived from microbial mats in hotsprings at Yellowstone National Park. Two distinct CRISPR types, distinguished by the repeat sequence, are found in both the Syn OS-A and Syn OS-B' genomes. The genome of Syn OS-A contains a third CRISPR type with a distinct repeat sequence, which is not found in Syn OS-B', but appears to be shared with other microorganisms that inhabit the mat. The CRISPR repeats identified in the microbial metagenome are highly conserved, while the spacer sequences (hereafter referred to as "viritopes" to emphasize their critical role in viral immunity were mostly unique and had no high identity matches when searched against GenBank. Searching the viritopes against the viral metagenome, however, yielded several matches with high similarity some of which were within a gene identified as a likely viral lysozyme/lysin protein. Analysis of viral metagenome sequences corresponding to this lysozyme/lysin protein revealed several mutations all of which translate into silent or conservative mutations which are unlikely to affect protein function, but may help the virus evade the host CRISPR resistance mechanism. These results demonstrate the varied challenges presented by a natural virus population, and support the notion that the CRISPR/viritope system must be able to adapt quickly to provide host immunity. The ability of metagenomics to track population-level variation in viritope sequences allows for a culture-independent method for evaluating the fast co-evolution of host and viral genomes and its consequence on the structuring of complex microbial communities.

  20. Vertically distinct microbial communities in the Mariana and Kermadec trenches

    Science.gov (United States)

    Donaldson, Sierra; Osuntokun, Oladayo; Xia, Qing; Nelson, Alex; Blanton, Jessica; Allen, Eric E.; Church, Matthew J.; Bartlett, Douglas H.

    2018-01-01

    Hadal trenches, oceanic locations deeper than 6,000 m, are thought to have distinct microbial communities compared to those at shallower depths due to high hydrostatic pressures, topographical funneling of organic matter, and biogeographical isolation. Here we evaluate the hypothesis that hadal trenches contain unique microbial biodiversity through analyses of the communities present in the bottom waters of the Kermadec and Mariana trenches. Estimates of microbial protein production indicate active populations under in situ hydrostatic pressures and increasing adaptation to pressure with depth. Depth, trench of collection, and size fraction are important drivers of microbial community structure. Many putative hadal bathytypes, such as members related to the Marinimicrobia, Rhodobacteraceae, Rhodospirilliceae, and Aquibacter, are similar to members identified in other trenches. Most of the differences between the two trench microbiomes consists of taxa belonging to the Gammaproteobacteria whose distributions extend throughout the water column. Growth and survival estimates of representative isolates of these taxa under deep-sea conditions suggest that some members may descend from shallower depths and exist as a potentially inactive fraction of the hadal zone. We conclude that the distinct pelagic communities residing in these two trenches, and perhaps by extension other trenches, reflect both cosmopolitan hadal bathytypes and ubiquitous genera found throughout the water column. PMID:29621268

  1. Exploring optimal conditions for thermophilic fermentative hydrogen production from cassava stillage

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Gang; Zou, Zhonghai; Wang, Wen [Key Laboratory of Yangtze River Water Environment, Ministry(Tongji University), Siping Road no 1239, Shanghai 200092 (China); Xie, Li; Zhou, Qi [Key Laboratory of Yangtze River Water Environment, Ministry(Tongji University), Siping Road no 1239, Shanghai 200092 (China); UNEP-Tongji University Institute of Environment for Sustainable Development, Siping Road no 1239, Shanghai 200092 (China)

    2010-06-15

    This study investigated the effects of seed sludges, alkalinity and HRT on the thermophilic fermentative hydrogen production from cassava stillage. Five different kinds of sludges were used as inocula without any pretreatment. Though batch experiments showed that mesophilic anaerobic sludge was the best inoculum, the hydrogen yields with different seed sludges were quite similar in continuous experiments in the range of 82.9-92.3 ml H{sub 2}/gVS without significant differences which could be attributed to the establishment of Uncultured Thermoanaerobacteriaceae bacterium-dominant microbial communities in all reactors. It is indicated that results obtained from batch experiments are not consistent with those from continuous experiments and all the tested seed sludges are good sources for continuous thermophilic hydrogen production from cassava stillage. The influent alkalinity of 6 g NaHCO{sub 3}/L and HRT 24 h were optimal for hydrogen production with hydrogen yield of 76 ml H{sub 2}/gVS and hydrogen production rate of 3215 ml H{sub 2}/L/d. Butyrate was the predominant metabolite in all experiments. With the increase in alkalinity of more than 6 g/L, the concentration of VFA/ethanol increased while hydrogen yield decreased due to the higher concentration of acetate and propionate. The decrease in HRT resulted in the higher hydrogen production rate but lower hydrogen yield. Variation of hydrogen yields were quite correlated with butyrate/acetate (B/A) ratio with different influent alkalinities, however, butyrate was important parameter to justify the hydrogen yields with various HRTs. (author)

  2. Temperature sensitivity of soil respiration rates enhanced by microbial community response.

    Science.gov (United States)

    Karhu, Kristiina; Auffret, Marc D; Dungait, Jennifer A J; Hopkins, David W; Prosser, James I; Singh, Brajesh K; Subke, Jens-Arne; Wookey, Philip A; Agren, Göran I; Sebastià, Maria-Teresa; Gouriveau, Fabrice; Bergkvist, Göran; Meir, Patrick; Nottingham, Andrew T; Salinas, Norma; Hartley, Iain P

    2014-09-04

    Soils store about four times as much carbon as plant biomass, and soil microbial respiration releases about 60 petagrams of carbon per year to the atmosphere as carbon dioxide. Short-term experiments have shown that soil microbial respiration increases exponentially with temperature. This information has been incorporated into soil carbon and Earth-system models, which suggest that warming-induced increases in carbon dioxide release from soils represent an important positive feedback loop that could influence twenty-first-century climate change. The magnitude of this feedback remains uncertain, however, not least because the response of soil microbial communities to changing temperatures has the potential to either decrease or increase warming-induced carbon losses substantially. Here we collect soils from different ecosystems along a climate gradient from the Arctic to the Amazon and investigate how microbial community-level responses control the temperature sensitivity of soil respiration. We find that the microbial community-level response more often enhances than reduces the mid- to long-term (90 days) temperature sensitivity of respiration. Furthermore, the strongest enhancing responses were observed in soils with high carbon-to-nitrogen ratios and in soils from cold climatic regions. After 90 days, microbial community responses increased the temperature sensitivity of respiration in high-latitude soils by a factor of 1.4 compared to the instantaneous temperature response. This suggests that the substantial carbon stores in Arctic and boreal soils could be more vulnerable to climate warming than currently predicted.

  3. Metagenome reveals potential microbial degradation of hydrocarbon coupled with sulfate reduction in an oil-immersed chimney from Guaymas Basin

    Directory of Open Access Journals (Sweden)

    Ying eHe

    2013-06-01

    Full Text Available Deep-sea hydrothermal vent chimneys contain a high diversity of microorganisms, yet the metabolic activity and the ecological functions of the microbial communities remain largely unexplored. In this study, a metagenomic approach was applied to characterize the metabolic potential in a Guaymas hydrothermal vent chimney and to conduct comparative genomic analysis among a variety of environments with sequenced metagenomes. Complete clustering of functional gene categories with a comparative metagenomic approach showed that this Guaymas chimney metagenome was clustered most closely with a chimney metagenome from Juan de Fuca. All chimney samples were enriched with genes involved in recombination and repair, chemotaxis and flagellar assembly, highlighting their roles in coping with the fluctuating extreme deep-sea environments. A high proportion of transposases was observed in all the metagenomes from deep-sea chimneys, supporting the previous hypothesis that horizontal gene transfer may be common in the deep-sea vent chimney biosphere. In the Guaymas chimney metagenome, thermophilic sulfate reducing microorganisms including bacteria and archaea were found predominant, and genes coding for the degradation of refractory organic compounds such as cellulose, lipid, pullullan, as well as a few hydrocarbons including toluene, ethylbenzene and o-xylene were identified. Therefore, this oil-immersed chimney supported a thermophilic microbial community capable of oxidizing a range of hydrocarbons that served as electron donors for sulphate reduction under anaerobic conditions.

  4. Utilization of Alternate Chirality Enantiomers in Microbial Communities

    Science.gov (United States)

    Pikuta, Elena V.; Hoover, Richard B.

    2010-01-01

    Our previous study of chirality led to interesting findings for some anaerobic extremophiles: the ability to metabolize substrates with alternate chirality enantiomers of amino acids and sugars. We have subsequently found that not just separate microbial species or strains but entire microbial communities have this ability. The functional division within a microbial community on proteo- and sugarlytic links was also reflected in a microbial diet with L-sugars and D-amino acids. Several questions are addressed in this paper. Why and when was this feature developed in a microbial world? Was it a secondary de novo adaptation in a bacterial world? Or is this a piece of genetic information that has been left in modern genomes as an atavism? Is it limited exclusively to prokaryotes, or does this ability also occur in eukaryotes? In this article, we have used a broader approach to study this phenomenon using anaerobic extremophilic strains from our laboratory collection. A series of experiments were performed on physiologically different groups of extremophilic anaerobes (pure and enrichment cultures). The following characteristics were studied: 1) the ability to grow on alternate chirality enantiomers -- L-sugars and D- amino acids; 2) Growth-inhibitory effect of alternate chirality enantiomers; 3) Stickland reaction with alternate chirality amino acids. The results of this research are presented in this paper.

  5. Thermophilic lignocellulose deconstruction.

    Science.gov (United States)

    Blumer-Schuette, Sara E; Brown, Steven D; Sander, Kyle B; Bayer, Edward A; Kataeva, Irina; Zurawski, Jeffrey V; Conway, Jonathan M; Adams, Michael W W; Kelly, Robert M

    2014-05-01

    Thermophilic microorganisms are attractive candidates for conversion of lignocellulose to biofuels because they produce robust, effective, carbohydrate-degrading enzymes and survive under harsh bioprocessing conditions that reflect their natural biotopes. However, no naturally occurring thermophile is known that can convert plant biomass into a liquid biofuel at rates, yields and titers that meet current bioprocessing and economic targets. Meeting those targets requires either metabolically engineering solventogenic thermophiles with additional biomass-deconstruction enzymes or engineering plant biomass degraders to produce a liquid biofuel. Thermostable enzymes from microorganisms isolated from diverse environments can serve as genetic reservoirs for both efforts. Because of the sheer number of enzymes that are required to hydrolyze plant biomass to fermentable oligosaccharides, the latter strategy appears to be the preferred route and thus has received the most attention to date. Thermophilic plant biomass degraders fall into one of two categories: cellulosomal (i.e. multienzyme complexes) and noncellulosomal (i.e. 'free' enzyme systems). Plant-biomass-deconstructing thermophilic bacteria from the genera Clostridium (cellulosomal) and Caldicellulosiruptor (noncellulosomal), which have potential as metabolic engineering platforms for producing biofuels, are compared and contrasted from a systems biology perspective. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  6. Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories.

    Science.gov (United States)

    Wigneswaran, Vinoth; Amador, Cristina Isabel; Jelsbak, Lotte; Sternberg, Claus; Jelsbak, Lars

    2016-01-01

    Microbial activities are most often shaped by interactions between co-existing microbes within mixed-species communities. Dissection of the molecular mechanisms of species interactions within communities is a central issue in microbial ecology, and our ability to engineer and control microbial communities depends, to a large extent, on our knowledge of these interactions. This review highlights the recent advances regarding molecular characterization of microbe-microbe interactions that modulate community structure, activity, and stability, and aims to illustrate how these findings have helped us reach an engineering-level understanding of microbial communities in relation to both human health and industrial biotechnology.

  7. Long-term oil contamination causes similar changes in microbial communities of two distinct soils.

    Science.gov (United States)

    Liao, Jingqiu; Wang, Jie; Jiang, Dalin; Wang, Michael Cai; Huang, Yi

    2015-12-01

    Since total petroleum hydrocarbons (TPH) are toxic and persistent in environments, studying the impact of oil contamination on microbial communities in different soils is vital to oil production engineering, effective soil management and pollution control. This study analyzed the impact of oil contamination on the structure, activity and function in carbon metabolism of microbial communities of Chernozem soil from Daqing oil field and Cinnamon soil from Huabei oil field through both culture-dependent techniques and a culture-independent technique-pyrosequencing. Results revealed that pristine microbial communities in these two soils presented disparate patterns, where Cinnamon soil showed higher abundance of alkane, (polycyclic aromatic hydrocarbons) PAHs and TPH degraders, number of cultivable microbes, bacterial richness, bacterial biodiversity, and stronger microbial activity and function in carbon metabolism than Chernozem soil. It suggested that complicated properties of microbes and soils resulted in the difference in soil microbial patterns. However, the changes of microbial communities caused by oil contamination were similar in respect of two dominant phenomena. Firstly, the microbial community structures were greatly changed, with higher abundance, higher bacterial biodiversity, occurrence of Candidate_division_BRC1 and TAO6, disappearance of BD1-5 and Candidate_division_OD1, dominance of Streptomyces, higher percentage of hydrocarbon-degrading groups, and lower percentage of nitrogen-transforming groups. Secondly, microbial activity and function in carbon metabolism were significantly enhanced. Based on the characteristics of microbial communities in the two soils, appropriate strategy for in situ bioremediation was provided for each oil field. This research underscored the usefulness of combination of culture-dependent techniques and next-generation sequencing techniques both to unravel the microbial patterns and understand the ecological impact of

  8. A thermophilic bacterial origin and subsequent constraints by redox, light and salinity on the evolution of the microbial mercuric reductase.

    Science.gov (United States)

    Barkay, Tamar; Kritee, K; Boyd, Eric; Geesey, Gill

    2010-11-01

    Mercuric reductase (MerA) is central to the mercury (Hg) resistance (mer) system, catalyzing the reduction of ionic Hg to volatile Hg(0). A total of 213 merA homologues were identified in sequence databases, the majority of which belonged to microbial lineages that occupy oxic environments. merA was absent among phototrophs and in lineages that inhabit anoxic environments. Phylogenetic reconstructions of MerA indicate that (i) merA originated in a thermophilic bacterium following the divergence of the Archaea and Bacteria with a subsequent acquisition in Archaea via horizontal gene transfer (HGT), (ii) HGT of merA was rare across phylum boundaries and (iii) MerA from marine bacteria formed distinct and strongly supported lineages. Collectively, these observations suggest that a combination of redox, light and salinity conditions constrain MerA to microbial lineages that occupy environments where the most oxidized and toxic form of Hg, Hg(II), predominates. Further, the taxon-specific distribution of MerA with and without a 70 amino acid N-terminal extension may reflect intracellular levels of thiols. In conclusion, MerA likely evolved following the widespread oxygenation of the biosphere in a thermal environment and its subsequent evolution has been modulated by the interactions of Hg with the intra- and extracellular environment of the organism. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

  9. Cultivation Of Deep Subsurface Microbial Communities

    Science.gov (United States)

    Obrzut, Natalia; Casar, Caitlin; Osburn, Magdalena R.

    2018-01-01

    The potential habitability of surface environments on other planets in our solar system is limited by exposure to extreme radiation and desiccation. In contrast, subsurface environments may offer protection from these stressors and are potential reservoirs for liquid water and energy that support microbial life (Michalski et al., 2013) and are thus of interest to the astrobiology community. The samples used in this project were extracted from the Deep Mine Microbial Observatory (DeMMO) in the former Homestake Mine at depths of 800 to 2000 feet underground (Osburn et al., 2014). Phylogenetic data from these sites indicates the lack of cultured representatives within the community. We used geochemical data to guide media design to cultivate and isolate organisms from the DeMMO communities. Media used for cultivation varied from heterotrophic with oxygen, nitrate or sulfate to autotrophic media with ammonia or ferrous iron. Environmental fluid was used as inoculum in batch cultivation and strains were isolated via serial transfers or dilution to extinction. These methods resulted in isolating aerobic heterotrophs, nitrate reducers, sulfate reducers, ammonia oxidizers, and ferric iron reducers. DNA sequencing of these strains is underway to confirm which species they belong to. This project is part of the NASA Astrobiology Institute Life Underground initiative to detect and characterize subsurface microbial life; by characterizing the intraterrestrials, the life living deep within Earth’s crust, we aim to understand the controls on how and where life survives in subsurface settings. Cultivation of terrestrial deep subsurface microbes will provide insight into the survival mechanisms of intraterrestrials guiding the search for these life forms on other planets.

  10. Modeling adaptation of carbon use efficiency in microbial communities

    Directory of Open Access Journals (Sweden)

    Steven D Allison

    2014-10-01

    Full Text Available In new microbial-biogeochemical models, microbial carbon use efficiency (CUE is often assumed to decline with increasing temperature. Under this assumption, soil carbon losses under warming are small because microbial biomass declines. Yet there is also empirical evidence that CUE may adapt (i.e. become less sensitive to warming, thereby mitigating negative effects on microbial biomass. To analyze potential mechanisms of CUE adaptation, I used two theoretical models to implement a tradeoff between microbial uptake rate and CUE. This rate-yield tradeoff is based on thermodynamic principles and suggests that microbes with greater investment in resource acquisition should have lower CUE. Microbial communities or individuals could adapt to warming by reducing investment in enzymes and uptake machinery. Consistent with this idea, a simple analytical model predicted that adaptation can offset 50% of the warming-induced decline in CUE. To assess the ecosystem implications of the rate-yield tradeoff, I quantified CUE adaptation in a spatially-structured simulation model with 100 microbial taxa and 12 soil carbon substrates. This model predicted much lower CUE adaptation, likely due to additional physiological and ecological constraints on microbes. In particular, specific resource acquisition traits are needed to maintain stoichiometric balance, and taxa with high CUE and low enzyme investment rely on low-yield, high-enzyme neighbors to catalyze substrate degradation. In contrast to published microbial models, simulations with greater CUE adaptation also showed greater carbon storage under warming. This pattern occurred because microbial communities with stronger CUE adaptation produced fewer degradative enzymes, despite increases in biomass. Thus the rate-yield tradeoff prevents CUE adaptation from driving ecosystem carbon loss under climate warming.

  11. Influence of soil zinc concentrations on zinc sensitivity and functional diversity of microbial communities

    International Nuclear Information System (INIS)

    Lock, K.; Janssen, C.R.

    2005-01-01

    Pollution induced community tolerance (PICT) is based on the phenomenon that toxic effects reduce survival of the most sensitive organisms, thus increasing community tolerance. Community tolerance for a contaminant is thus a strong indicator for the presence of that contaminant at the level of adverse concentrations. Here we assessed PICT in 11 soils contaminated with zinc runoff from galvanised electricity pylons and 11 reference soils sampled at 10 m distance from these pylons. Using PICT, the influence of background concentration and bioavailability of zinc on zinc sensitivity and functional diversity of microbial communities was assessed. Zinc sensitivity of microbial communities decreased significantly with increasing zinc concentrations in pore water and calcium chloride extracted fraction while no significant relationship was found with total zinc concentration in the soil. It was also found that functional diversity of microbial communities decreased with increasing zinc concentrations, indicating that increased tolerance is indeed an undesirable phenomenon when environmental quality is considered. The hypothesis that zinc sensitivity of microbial communities is related to background zinc concentration in pore water could not be confirmed. - Zinc sensitivity of microbial communities and functional diversity decrease with increasing zinc concentration in the pore water

  12. Comparative microbiological-hygienic studies in mesophilic and thermophilic fouling of sewage sludge

    Energy Technology Data Exchange (ETDEWEB)

    Pohlig-Schmitt, M.; Philipp, W.; Wekerle, J.; Strauch, D.

    Investigations concerning the inactivation of microbial pathogens (bacteria, viruses and parasites) during anaerobic, alkaline dignestion of sludge are described. A thermophilic (54/sup 0/C) and a mesophilic (34/sup 0/C) operated biogas model plant were compared from the point of view of hygiene. Is was found that in the thermophilic process Salmonella senftenberg survived 13,5 h, Streptococcus faecium 55 h, Streptococcus faecalis 42 h and Klebsiella pneumoniae 0,5 h. Within 30 min eggs of Ascaris suum lost their infectivity Bovine Parvovirus was inactivated after 1 d to 2 d treatment. Survival times under mesophilic conditions of 13 d for Salmonella senftenberg and more than 8 mouth for Streptococcus faecium were found. Poliovirus Type 1 was inactivated in 8 d while Bovine Parvovirus survived no longer than 15 d. The results obtained in the thermophilic process were compared to those after heat treatment of the test microorganisms in ampules exposed in a wather-bath under defined conditions to 54/sup 0/C. It was found, that the bacteria survived only about half the time in this case. Poliovirus Type 1 was inactivated after 0,75 h and Bovine Parvovirus after 7 d exposure. (orig.RB)

  13. Comparative Metagenomic Analysis of Electrogenic Microbial Communities in Differentially Inoculated Swine Wastewater-Fed Microbial Fuel Cells

    Directory of Open Access Journals (Sweden)

    Irina V. Khilyas

    2017-01-01

    Full Text Available Bioelectrochemical systems such as microbial fuel cells (MFCs are promising new technologies for efficient removal of organic compounds from industrial wastewaters, including that generated from swine farming. We inoculated two pairs of laboratory-scale MFCs with sludge granules from a beer wastewater-treating anaerobic digester (IGBS or from sludge taken from the bottom of a tank receiving swine wastewater (SS. The SS-inoculated MFC outperformed the IGBS-inoculated MFC with regard to COD and VFA removal and electricity production. Using a metagenomic approach, we describe the microbial diversity of the MFC planktonic and anodic communities derived from the different inocula. Proteobacteria (mostly Deltaproteobacteria became the predominant phylum in both MFC anodic communities with amplification of the electrogenic genus Geobacter being the most pronounced. Eight dominant and three minor species of Geobacter were found in both MFC anodic communities. The anodic communities of the SS-inoculated MFCs had a higher proportion of Clostridium and Bacteroides relative to those of the IGBS-inoculated MFCs, which were enriched with Pelobacter. The archaeal populations of the SS- and IGBS-inoculated MFCs were dominated by Methanosarcina barkeri and Methanothermobacter thermautotrophicus, respectively. Our results show a long-term influence of inoculum type on the performance and microbial community composition of swine wastewater-treating MFCs.

  14. Shifts of microbial communities of wheat (Triticum aestivum L.) cultivation in a closed artificial ecosystem.

    Science.gov (United States)

    Qin, Youcai; Fu, Yuming; Dong, Chen; Jia, Nannan; Liu, Hong

    2016-05-01

    The microbial communities of plant ecosystems are in relation to plant growing environment, but the alteration in biodiversity of rhizosphere and phyllosphere microbial communities in closed and controlled environments is unknown. The purpose of this study is to analyze the change regularity of microbial communities with wheat plants dependent-cultivated in a closed artificial ecosystem. The microbial community structures in closed-environment treatment plants were investigated by a culture-dependent approach, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), and Illumina Miseq high-throughput sequencing. The results indicated that the number of microbes decreased along with time, and the magnitude of bacteria, fungi, and actinomycetes were 10(7)-10(8), 10(5), and 10(3)-10(4) CFU/g (dry weight), respectively. The analysis of PCR-DGGE and Illumina Miseq revealed that the wheat leaf surface and near-root substrate had different microbial communities at different periods of wheat ecosystem development and showed that the relative highest diversity of microbial communities appeared at late and middle periods of the plant ecosystem, respectively. The results also indicated that the wheat leaf and substrate had different microbial community compositions, and the wheat substrate had higher richness of microbial community than the leaf. Flavobacterium, Pseudomonas, Paenibacillus, Enterobacter, Penicillium, Rhodotorula, Acremonium, and Alternaria were dominant in the wheat leaf samples, and Pedobacter, Flavobacterium, Halomonas, Marinobacter, Salinimicrobium, Lysobacter, Pseudomonas, Halobacillus, Xanthomonas, Acremonium, Monographella, and Penicillium were dominant populations in the wheat near-root substrate samples.

  15. ANALYSIS OF AQUATIC MICROBIAL COMMUNITIES IMPACTED BY LARGE POULTRY FORMS

    Science.gov (United States)

    Microbial communities often respond more rapidly and extensively to environmental change than communities of higher organisms. Thus, characterizing shifts in the structure of native bacterial communities as a response to changes in nutrients, antimicrobials, and invading pathogen...

  16. Environmental drivers of differences in microbial community structure in crude oil reservoirs across a methanogenic gradient

    Directory of Open Access Journals (Sweden)

    Jenna L Shelton

    2016-09-01

    Full Text Available Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, and formation water chemistry. Twenty-two oil production wells from north central Louisiana, USA, were sampled for analysis of microbial community structure and fluid geochemistry. Archaea were the dominant microbial community in the majority of the wells sampled. Methanogens, including hydrogenotrophic and methylotrophic organisms, were numerically dominant in every well, accounting for, on average, over 98% of the total archaea present. The dominant Bacteria groups were Pseudomonas, Acinetobacter, Enterobacteriaceae, and Clostridiales, which have also been identified in other microbially-altered oil reservoirs. Comparing microbial community structure to fluid (gas, water, and oil geochemistry revealed that the relative extent of biodegradation, salinity, and spatial location were the major drivers of microbial diversity. Archaeal relative abundance was independent of the extent of methanogenesis, but closely correlated to the extent of crude oil biodegradation; therefore, microbial community structure is likely not a good sole predictor of methanogenic activity, but may predict the extent of crude oil biodegradation. However, when the shallow, highly biodegraded, low salinity wells were excluded from the statistical analysis, no environmental parameters could explain the differences in microbial community structure. This suggests that the microbial community structure of the 5 shallow up-dip wells was different than the 17 deeper, down-dip wells, and that

  17. Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates.

    Science.gov (United States)

    Patel, Vrutika; Sharma, Anukriti; Lal, Rup; Al-Dhabi, Naif Abdullah; Madamwar, Datta

    2016-03-22

    Gauging the microbial community structures and functions become imperative to understand the ecological processes. To understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across Kadi, near Ahmedabad, India. Soil collected was hence used for metagenomic DNA extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation. Taxonomic profiling was carried out by two different complementary approaches i.e. 16S rDNA and lowest common ancestor. The community profiling revealed the enrichment of phylum "Proteobacteria" and genus "Chromobacterium," respectively for polluted soil sample. Our results indicated that soil microbial diversity (Shannon diversity index) decreased significantly with contamination. Further, assignment of obtained metagenome reads to Clusters of Orthologous Groups (COG) of protein and Kyoto Encyclopedia of Genes and Genomes (KEGG) hits revealed metabolic potential of indigenous microbial community. Enzymes were mapped on fatty acid biosynthesis pathway to elucidate their roles in possible catalytic reactions. To the best of our knowledge this is first study for influence of edible oil on soil microbial communities via shotgun sequencing. The results indicated that long-term oil contamination significantly affects soil microbial community structure by acting as an environmental filter to decrease the regional differences distinguishing soil microbial communities.

  18. Exocellular electron transfer in anaerobic microbial communities.

    Science.gov (United States)

    Stams, Alfons J M; de Bok, Frank A M; Plugge, Caroline M; van Eekert, Miriam H A; Dolfing, Jan; Schraa, Gosse

    2006-03-01

    Exocellular electron transfer plays an important role in anaerobic microbial communities that degrade organic matter. Interspecies hydrogen transfer between microorganisms is the driving force for complete biodegradation in methanogenic environments. Many organic compounds are degraded by obligatory syntrophic consortia of proton-reducing acetogenic bacteria and hydrogen-consuming methanogenic archaea. Anaerobic microorganisms that use insoluble electron acceptors for growth, such as iron- and manganese-oxide as well as inert graphite electrodes in microbial fuel cells, also transfer electrons exocellularly. Soluble compounds, like humic substances, quinones, phenazines and riboflavin, can function as exocellular electron mediators enhancing this type of anaerobic respiration. However, direct electron transfer by cell-cell contact is important as well. This review addresses the mechanisms of exocellular electron transfer in anaerobic microbial communities. There are fundamental differences but also similarities between electron transfer to another microorganism or to an insoluble electron acceptor. The physical separation of the electron donor and electron acceptor metabolism allows energy conservation in compounds as methane and hydrogen or as electricity. Furthermore, this separation is essential in the donation or acceptance of electrons in some environmental technological processes, e.g. soil remediation, wastewater purification and corrosion.

  19. Exocellular electron transfer in anaerobic microbial communities

    NARCIS (Netherlands)

    Stams, A.J.M.; Bok, de F.A.M.; Plugge, C.M.; Eekert, van M.H.A.; Dolfing, J.; Schraa, G.

    2006-01-01

    Exocellular electron transfer plays an important role in anaerobic microbial communities that degrade organic matter. Interspecies hydrogen transfer between microorganisms is the driving force for complete biodegradation in methanogenic environments. Many organic compounds are degraded by obligatory

  20. Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration ▿†

    OpenAIRE

    Banning, Natasha C.; Gleeson, Deirdre B.; Grigg, Andrew H.; Grant, Carl D.; Andersen, Gary L.; Brodie, Eoin L.; Murphy, D. V.

    2011-01-01

    Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mini...

  1. Impact of electrokinetic remediation on microbial communities within PCP contaminated soil

    International Nuclear Information System (INIS)

    Lear, G.; Harbottle, M.J.; Sills, G.; Knowles, C.J.; Semple, K.T.; Thompson, I.P.

    2007-01-01

    Electrokinetic techniques have been used to stimulate the removal of organic pollutants within soil, by directing contaminant migration to where remediation may be more easily achieved. The effect of this and other physical remediation techniques on the health of soil microbial communities has been poorly studied and indeed, largely ignored. This study reports the impact on soil microbial communities during the application of an electric field within ex situ laboratory soil microcosms contaminated with pentachlorophenol (PCP; 100 mg kg -1 oven dry soil). Electrokinetics reduced counts of culturable bacteria and fungi, soil microbial respiration and carbon substrate utilisation, especially close to the acidic anode where PCP accumulated (36 d), perhaps exacerbated by the greater toxicity of PCP at lower soil pH. There is little doubt that a better awareness of the interactions between soil electrokinetic processes and microbial communities is key to improving the efficacy and sustainability of this remediation strategy. - Electrokinetics negatively impacted soil

  2. Temporal Microbial Community Dynamics in Microbial Electrolysis Cells – Influence of Acetate and Propionate Concentration

    KAUST Repository

    Rao, Hari Ananda

    2017-07-20

    Microbial electrolysis cells (MECs) are widely considered as a next generation wastewater treatment system. However, fundamental insight on the temporal dynamics of microbial communities associated with MEC performance under different organic types with varied loading concentrations is still unknown, nevertheless this knowledge is essential for optimizing this technology for real-scale applications. Here, the temporal dynamics of anodic microbial communities associated with MEC performance was examined at low (0.5 g COD/L) and high (4 g COD/L) concentrations of acetate or propionate, which are important intermediates of fermentation of municipal wastewaters and sludge. The results showed that acetate-fed reactors exhibited higher performance in terms of maximum current density (I: 4.25 ± 0.23 A/m), coulombic efficiency (CE: 95 ± 8%), and substrate degradation rate (98.8 ± 1.2%) than propionate-fed reactors (I: 2.7 ± 0.28 A/m; CE: 68 ± 9.5%; substrate degradation rate: 84 ± 13%) irrespective of the concentrations tested. Despite of the repeated sampling of the anodic biofilm over time, the high-concentration reactors demonstrated lower and stable performance in terms of current density (I: 1.1 ± 0.14 to 4.2 ± 0.21 A/m), coulombic efficiency (CE: 44 ± 4.1 to 103 ± 7.2%) and substrate degradation rate (64.9 ± 6.3 to 99.7 ± 0.5%), while the low-concentration reactors produced higher and dynamic performance (I: 1.1 ± 0.12 to 4.6 ± 0.1 A/m; CE: 52 ± 2.5 to 105 ± 2.7%; substrate degradation rate: 87.2 ± 0.2 to 99.9 ± 0.06%) with the different substrates tested. Correlating reactor\\'s performance with temporal dynamics of microbial communities showed that relatively similar anodic microbial community composition but with varying relative abundances was observed in all the reactors despite differences in the substrate and concentrations tested. Particularly, Geobacter was the predominant bacteria on the anode biofilm of all MECs over time suggesting its

  3. Impacts of zero valent iron, natural zeolite and Dnase on the fate of antibiotic resistance genes during thermophilic and mesophilic anaerobic digestion of swine manure.

    Science.gov (United States)

    Zhang, Junya; Sui, Qianwen; Zhong, Hui; Meng, Xiaoshan; Wang, Ziyue; Wang, Yawei; Wei, Yuansong

    2018-06-01

    This study investigated the fate of antibiotic resistance genes (ARGs) during mesophilic (mAD) and thermophilic digestion (tAD) of swine manure through zero valent iron (ZVI), natural zeolite and Dnase addition. Changes of microbial community, intI1, heavy metal resistance genes (MRGs) and virulence factors (VFs) were followed to clarify the influencing factors to ARGs reduction. Results showed that AD could realize ARGs reduction with tAD superior to mAD, and ZVI and natural zeolite could further enhance the reduction, especially for natural zeolite addition at mAD. The reduction efficiency of the relative abundance of ARGs was increased by 33.3% and 138.5% after ZVI and natural zeolite addition, respectively, but Dnase deteriorated ARGs reduction at mAD. Most of ARGs could be reduced effectively except sulII and tetM. Network analysis and partial redundancy analysis indicated that co-occurrence of MRGs followed by microbial community contributed the most to the variation of ARGs fate among treatments. Copyright © 2018 Elsevier Ltd. All rights reserved.

  4. Differential sensitivity of total and active soil microbial communities to drought and forest management.

    Science.gov (United States)

    Bastida, Felipe; Torres, Irene F; Andrés-Abellán, Manuela; Baldrian, Petr; López-Mondéjar, Rubén; Větrovský, Tomáš; Richnow, Hans H; Starke, Robert; Ondoño, Sara; García, Carlos; López-Serrano, Francisco R; Jehmlich, Nico

    2017-10-01

    Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning-that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 6 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community-based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought-plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial

  5. Anode microbial communities produced by changing from microbial fuel cell to microbial electrolysis cell operation using two different wastewaters

    KAUST Repository

    Kiely, Patrick D.; Cusick, Roland; Call, Douglas F.; Selembo, Priscilla A.; Regan, John M.; Logan, Bruce E.

    2011-01-01

    Conditions in microbial fuel cells (MFCs) differ from those in microbial electrolysis cells (MECs) due to the intrusion of oxygen through the cathode and the release of H2 gas into solution. Based on 16S rRNA gene clone libraries, anode communities in reactors fed acetic acid decreased in species richness and diversity, and increased in numbers of Geobacter sulfurreducens, when reactors were shifted from MFCs to MECs. With a complex source of organic matter (potato wastewater), the proportion of Geobacteraceae remained constant when MFCs were converted into MECs, but the percentage of clones belonging to G. sulfurreducens decreased and the percentage of G. metallireducens clones increased. A dairy manure wastewater-fed MFC produced little power, and had more diverse microbial communities, but did not generate current in an MEC. These results show changes in Geobacter species in response to the MEC environment and that higher species diversity is not correlated with current. © 2010 Elsevier Ltd.

  6. PanFP: pangenome-based functional profiles for microbial communities.

    Science.gov (United States)

    Jun, Se-Ran; Robeson, Michael S; Hauser, Loren J; Schadt, Christopher W; Gorin, Andrey A

    2015-09-26

    For decades there has been increasing interest in understanding the relationships between microbial communities and ecosystem functions. Current DNA sequencing technologies allows for the exploration of microbial communities in two principle ways: targeted rRNA gene surveys and shotgun metagenomics. For large study designs, it is often still prohibitively expensive to sequence metagenomes at both the breadth and depth necessary to statistically capture the true functional diversity of a community. Although rRNA gene surveys provide no direct evidence of function, they do provide a reasonable estimation of microbial diversity, while being a very cost-effective way to screen samples of interest for later shotgun metagenomic analyses. However, there is a great deal of 16S rRNA gene survey data currently available from diverse environments, and thus a need for tools to infer functional composition of environmental samples based on 16S rRNA gene survey data. We present a computational method called pangenome-based functional profiles (PanFP), which infers functional profiles of microbial communities from 16S rRNA gene survey data for Bacteria and Archaea. PanFP is based on pangenome reconstruction of a 16S rRNA gene operational taxonomic unit (OTU) from known genes and genomes pooled from the OTU's taxonomic lineage. From this lineage, we derive an OTU functional profile by weighting a pangenome's functional profile with the OTUs abundance observed in a given sample. We validated our method by comparing PanFP to the functional profiles obtained from the direct shotgun metagenomic measurement of 65 diverse communities via Spearman correlation coefficients. These correlations improved with increasing sequencing depth, within the range of 0.8-0.9 for the most deeply sequenced Human Microbiome Project mock community samples. PanFP is very similar in performance to another recently released tool, PICRUSt, for almost all of survey data analysed here. But, our method is unique

  7. Horizontal gene transfer in an acid mine drainage microbial community.

    Science.gov (United States)

    Guo, Jiangtao; Wang, Qi; Wang, Xiaoqi; Wang, Fumeng; Yao, Jinxian; Zhu, Huaiqiu

    2015-07-04

    Horizontal gene transfer (HGT) has been widely identified in complete prokaryotic genomes. However, the roles of HGT among members of a microbial community and in evolution remain largely unknown. With the emergence of metagenomics, it is nontrivial to investigate such horizontal flow of genetic materials among members in a microbial community from the natural environment. Because of the lack of suitable methods for metagenomics gene transfer detection, microorganisms from a low-complexity community acid mine drainage (AMD) with near-complete genomes were used to detect possible gene transfer events and suggest the biological significance. Using the annotation of coding regions by the current tools, a phylogenetic approach, and an approximately unbiased test, we found that HGTs in AMD organisms are not rare, and we predicted 119 putative transferred genes. Among them, 14 HGT events were determined to be transfer events among the AMD members. Further analysis of the 14 transferred genes revealed that the HGT events affected the functional evolution of archaea or bacteria in AMD, and it probably shaped the community structure, such as the dominance of G-plasma in archaea in AMD through HGT. Our study provides a novel insight into HGT events among microorganisms in natural communities. The interconnectedness between HGT and community evolution is essential to understand microbial community formation and development.

  8. Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau.

    Science.gov (United States)

    Chen, Yong-Liang; Deng, Ye; Ding, Jin-Zhi; Hu, Hang-Wei; Xu, Tian-Le; Li, Fei; Yang, Gui-Biao; Yang, Yuan-He

    2017-12-01

    Permafrost represents an important understudied genetic resource. Soil microorganisms play important roles in regulating biogeochemical cycles and maintaining ecosystem function. However, our knowledge of patterns and drivers of permafrost microbial communities is limited over broad geographic scales. Using high-throughput Illumina sequencing, this study compared soil bacterial, archaeal and fungal communities between the active and permafrost layers on the Tibetan Plateau. Our results indicated that microbial alpha diversity was significantly higher in the active layer than in the permafrost layer with the exception of fungal Shannon-Wiener index and Simpson's diversity index, and microbial community structures were significantly different between the two layers. Our results also revealed that environmental factors such as soil fertility (soil organic carbon, dissolved organic carbon and total nitrogen contents) were the primary drivers of the beta diversity of bacterial, archaeal and fungal communities in the active layer. In contrast, environmental variables such as the mean annual precipitation and total phosphorus played dominant roles in driving the microbial beta diversity in the permafrost layer. Spatial distance was important for predicting the bacterial and archaeal beta diversity in both the active and permafrost layers, but not for fungal communities. Collectively, these results demonstrated different driving factors of microbial beta diversity between the active layer and permafrost layer, implying that the drivers of the microbial beta diversity observed in the active layer cannot be used to predict the biogeographic patterns of the microbial beta diversity in the permafrost layer. © 2017 John Wiley & Sons Ltd.

  9. Agroforestry management in vineyards: effects on soil microbial communities

    Science.gov (United States)

    Montagne, Virginie; Nowak, Virginie; Guilland, Charles; Gontier, Laure; Dufourcq, Thierry; Guenser, Josépha; Grimaldi, Juliette; Bourgade, Emilie; Ranjard, Lionel

    2017-04-01

    Some vineyard practices (tillage, chemical weeding or pest management) are generally known to impact the environment with particular negative effects on the diversity and the abundance of soil microorganisms, and cause water and soil pollutions. In an agro-ecological context, innovative cropping systems have been developed to improve ecosystem services. Among them, agroforestry offers strategies of sustainable land management practices. It consists in intercropping trees with annual/perennial/fodder crop on the same plot but it is weakly referenced with grapevine. The present study assesses the effects of intercropped and neighbouring trees on the soil of three agroforestry vineyards, in south-western France regions. More precisely soils of the different plots were sampled and the impact of the distance to the tree or to the neighbouring trees (forest) on soil microbial community has been considered. Indigenous soil microbial communities were characterized by a metagenomic approach that consisted in extracting the molecular microbial biomass, then in calculating the soil fungi/bacteria ratio - obtained by qPCR - and then in characterizing the soil microbial diversity - through Illumina sequencing of 16S and 18S regions. Our results showed a significant difference between the soil of agroforestry vineyards and the soil sampled in the neighbouring forest in terms of microbial abundance and diversity. However, only structure and composition of bacterial community seem to be influenced by the implanted trees in the vine plots. In addition, the comparison of microbial co-occurrence networks between vine and forest plots as well as inside vine plots according to distance to the tree allow revealing a more sensitive impact of agroforestry practices. Altogether, the results we obtained build up the first references for concerning the soil of agroforestry vineyards which will be interpreted in terms of soil quality, functioning and sustainability.

  10. Modular spectral imaging system for discrimination of pigments in cells and microbial communities.

    Science.gov (United States)

    Polerecky, Lubos; Bissett, Andrew; Al-Najjar, Mohammad; Faerber, Paul; Osmers, Harald; Suci, Peter A; Stoodley, Paul; de Beer, Dirk

    2009-02-01

    Here we describe a spectral imaging system for minimally invasive identification, localization, and relative quantification of pigments in cells and microbial communities. The modularity of the system allows pigment detection on spatial scales ranging from the single-cell level to regions whose areas are several tens of square centimeters. For pigment identification in vivo absorption and/or autofluorescence spectra are used as the analytical signals. Along with the hardware, which is easy to transport and simple to assemble and allows rapid measurement, we describe newly developed software that allows highly sensitive and pigment-specific analyses of the hyperspectral data. We also propose and describe a number of applications of the system for microbial ecology, including identification of pigments in living cells and high-spatial-resolution imaging of pigments and the associated phototrophic groups in complex microbial communities, such as photosynthetic endolithic biofilms, microbial mats, and intertidal sediments. This system provides new possibilities for studying the role of spatial organization of microorganisms in the ecological functioning of complex benthic microbial communities or for noninvasively monitoring changes in the spatial organization and/or composition of a microbial community in response to changing environmental factors.

  11. Comparison of bacterial community structure and dynamics during the thermophilic composting of different types of solid wastes: anaerobic digestion residue, pig manure and chicken manure

    OpenAIRE

    Song, Caihong; Li, Mingxiao; Jia, Xuan; Wei, Zimin; Zhao, Yue; Xi, Beidou; Zhu, Chaowei; Liu, Dongming

    2015-01-01

    This study investigated the impact of composting substrate types on the bacterial community structure and dynamics during composting processes. To this end, pig manure (PM), chicken manure (CM), a mixture of PM and CM (PM + CM), and a mixture of PM, CM and anaerobic digestion residue (ADR) (PM + CM + ADR) were selected for thermophilic composting. The bacterial community structure and dynamics during the composting process were detected and analysed by polymerase chain reaction–denaturing gra...

  12. Metabarcoding of the kombucha microbial community grown in different microenvironments.

    Science.gov (United States)

    Reva, Oleg N; Zaets, Iryna E; Ovcharenko, Leonid P; Kukharenko, Olga E; Shpylova, Switlana P; Podolich, Olga V; de Vera, Jean-Pierre; Kozyrovska, Natalia O

    2015-12-01

    Introducing of the DNA metabarcoding analysis of probiotic microbial communities allowed getting insight into their functioning and establishing a better control on safety and efficacy of the probiotic communities. In this work the kombucha poly-microbial probiotic community was analysed to study its flexibility under different growth conditions. Environmental DNA sequencing revealed a complex and flexible composition of the kombucha microbial culture (KMC) constituting more bacterial and fungal organisms in addition to those found by cultural method. The community comprised bacterial and yeast components including cultured and uncultivable microorganisms. Culturing the KMC under different conditions revealed the core part of the community which included acetobacteria of two genera Komagataeibacter (former Gluconacetobacter) and Gluconobacter, and representatives of several yeast genera among which Brettanomyces/Dekkera and Pichia (including former Issatchenkia) were dominant. Herbaspirillum spp. and Halomonas spp., which previously had not been described in KMC, were found to be minor but permanent members of the community. The community composition was dependent on the growth conditions. The bacterial component of KMC was relatively stable, but may include additional member-lactobacilli. The yeast species composition was significantly variable. High-throughput sequencing showed complexity and variability of KMC that may affect the quality of the probiotic drink. It was hypothesized that the kombucha core community might recruit some environmental bacteria, particularly lactobacilli, which potentially may contribute to the fermentative capacity of the probiotic drink. As many KMC-associated microorganisms cannot be cultured out of the community, a robust control for community composition should be provided by using DNA metabarcoding.

  13. Exploring ancient microbial community assemblages by creating complex lipid biomarker profiles for stromatolites and microbial mats in Hamelin Pool, Shark Bay, Australia

    Science.gov (United States)

    Myers, E.; Summons, R. E.; Schubotz, F.; Matys, E. D.

    2015-12-01

    Stromatolites that are biogenic in origin, a characteristic that can be determined by the coexistence of microbial mats (active microbial communities) and stromatolites (lithified structures) like in Hamelin Pool, comprise one of the best modern analogs to ancient microbial community assemblages. Comprehensive lipid biomarker profiles that include lipids of varying persistence in the rock record can help determine how previously living microbial communities are represented in lithified stromatolites. To create these profiles, the samples analyzed included non-lithified smooth, pustular, and colloform microbial mats, as well as smooth and colloform stromatolites. Select samples were separated into upper and lower layers of 5cm depth each. Intact polar lipids, glycerol dialkyl glycerol tetraethers, and bacteriohopanepolyols were analyzed via liquid chromatography-mass spectrometry (LC-MS) coupled to a Quadropole Time-of-Flight (QTOF) mass spectrometer; additionally, fatty acids from each sample were analyzed using gas chromatography-mass spectrometry (GC-MS) to prove consistent signatures with those determined by Allen et al. in 2010 for similar microbial mat samples. In accordance with those findings, 2-methylhopanoids were detected, as well as limited signals from higher (vascular) plants, the latter of which suggests terrestrial inputs, potentially from runoff. The rarely detected presence of 3-methylhopanoids appears in a significant portion of the samples, though further isolations of the molecule are needed to confirm. While all lipid profiles were relatively similar, certain differences in relative composition are likely attributable to morphological differences of the mats, some of which allow deeper oxygen and/or sunlight penetration, which influence the microbial community. However, overall similarities of transient and persistent lipids suggest that the microbial communities of both the non-lithified microbial mats and stromatolites are similar.

  14. Microbial activities and communities in oil sands tailings ponds

    Energy Technology Data Exchange (ETDEWEB)

    Gieg, Lisa; Ramos, Esther; Clothier, Lindsay; Bordenave, Sylvain; Lin, Shiping; Voordouw, Gerrit; Dong, Xiaoli; Sensen, Christoph [University of Calgary (Canada)

    2011-07-01

    This paper discusses how the microbial communities and their activity play a vital role in tailings ponds. The ponds contain microorganisms along with metals, hydrocarbon diluent, naphthenic acid and others. The ponds play an important role in mining operations because they store bitumen extraction waste and also allow water to be re-used in the bitumen extraction process. Pond management presents a few challenges that include, among others, gas emissions and the presence of toxic and corrosive acids. Microbial activities and communities help in managing these ponds. Microbial activity measurement in active and inactive ponds is described and analyzed and the results are presented. The conditions for reducing sulfate, nitrate and iron are also presented. From the results it can be concluded that naphthenic acids can potentially serve as substrates for anaerobic populations in tailings ponds.

  15. Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge.

    Science.gov (United States)

    Dahle, Håkon; Økland, Ingeborg; Thorseth, Ingunn H; Pederesen, Rolf B; Steen, Ida H

    2015-07-01

    Methods developed in geochemical modelling combined with recent advances in molecular microbial ecology provide new opportunities to explore how microbial communities are shaped by their chemical surroundings. Here, we present a framework for analyses of how chemical energy availability shape chemotrophic microbial communities in hydrothermal systems through an investigation of two geochemically different basalt-hosted hydrothermal systems on the Arctic Mid-Ocean Ridge: the Soria Moria Vent field (SMVF) and the Loki's Castle Vent Field (LCVF). Chemical energy landscapes were evaluated through modelling of the Gibbs energy from selected redox reactions under different mixing ratios between seawater and hydrothermal fluids. Our models indicate that the sediment-influenced LCVF has a much higher potential for both anaerobic and aerobic methane oxidation, as well as aerobic ammonium and hydrogen oxidation, than the SMVF. The modelled energy landscapes were used to develop microbial community composition models, which were compared with community compositions in environmental samples inside or on the exterior of hydrothermal chimneys, as assessed by pyrosequencing of partial 16S rRNA genes. We show that modelled microbial communities based solely on thermodynamic considerations can have a high predictive power and provide a framework for analyses of the link between energy availability and microbial community composition.

  16. Microbial Insight into a Pilot-Scale Enhanced Two-Stage High-Solid Anaerobic Digestion System Treating Waste Activated Sludge.

    Science.gov (United States)

    Wu, Jing; Cao, Zhiping; Hu, Yuying; Wang, Xiaolu; Wang, Guangqi; Zuo, Jiane; Wang, Kaijun; Qian, Yi

    2017-11-30

    High solid anaerobic digestion (HSAD) is a rapidly developed anaerobic digestion technique for treating municipal sludge, and has been widely used in Europe and Asia. Recently, the enhanced HSAD process with thermal treatment showed its advantages in both methane production and VS reduction. However, the understanding of the microbial community is still poor. This study investigated microbial communities in a pilot enhanced two-stage HSAD system that degraded waste activated sludge at 9% solid content. The system employed process "thermal pre-treatment (TPT) at 70 °C, thermophilic anaerobic digestion (TAD), and mesophilic anaerobic digestion (MAD)". Hydrogenotrophic methanogens Methanothermobacter spp. dominated the system with relative abundance up to about 100% in both TAD and MAD. Syntrophic acetate oxidation (SAO) bacteria were discovered in TAD, and they converted acetate into H₂ and CO₂ to support hydrogenotrophic methanogenesis. The microbial composition and conversion route of this system are derived from the high solid content and protein content in raw sludge, as well as the operational conditions. This study could facilitate the understanding of the enhanced HSAD process, and is of academic and industrial importance.

  17. Characterization of fatty acid-producing wastewater microbial communities using next generation sequencing technologies

    Science.gov (United States)

    While wastewater represents a viable source of bacterial biodiesel production, very little is known on the composition of these microbial communities. We studied the taxonomic diversity and succession of microbial communities in bioreactors accumulating fatty acids using 454-pyro...

  18. Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc

    Directory of Open Access Journals (Sweden)

    Kevin W. Hager

    2017-08-01

    Full Text Available The Mariana region exhibits a rich array of hydrothermal venting conditions in a complex geological setting, which provides a natural laboratory to study the influence of local environmental conditions on microbial community structure as well as large-scale patterns in microbial biogeography. We used high-throughput amplicon sequencing of the bacterial small subunit (SSU rRNA gene from 22 microbial mats collected from four hydrothermally active locations along the Mariana Arc and back-arc to explore the structure of lithotrophically-based microbial mat communities. The vent effluent was classified as iron- or sulfur-rich corresponding with two distinct community types, dominated by either Zetaproteobacteria or Epsilonproteobacteria, respectively. The Zetaproteobacterial-based communities had the highest richness and diversity, which supports the hypothesis that Zetaproteobacteria function as ecosystem engineers creating a physical habitat within a chemical environment promoting enhanced microbial diversity. Gammaproteobacteria were also high in abundance within the iron-dominated mats and some likely contribute to primary production. In addition, we also compare sampling scale, showing that bulk sampling of microbial mats yields higher diversity than micro-scale sampling. We present a comprehensive analysis and offer new insights into the community structure and diversity of lithotrophically-driven microbial mats from a hydrothermal region associated with high microbial biodiversity. Our study indicates an important functional role of for the Zetaproteobacteria altering the mat habitat and enhancing community interactions and complexity.

  19. Effects of biochar blends on microbial community composition in two coastal plain soils

    Science.gov (United States)

    The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure....

  20. Responses of Soil Microbial Community Structure and Diversity to Agricultural Deintensification

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wei-Jian; S.HU; RUI Wen-Yi; C.TU; H.G.DIAB; F.J.LOUWS; J.P.MUELLER; N.CREAMER; M.BELL; M.G.WAGGER

    2005-01-01

    Using a scheme of agricultural fields with progressively less intensive management (deintensification), different management practices in six agroecosystems located near Goldsboro, NC, USA were tested in a large-scale experiment, including two cash-grain cropping systems employing either tillage (CT) or no-tillage (NT), an organic farming system (OR), an integrated cropping system with animals (IN), a successional field (SU), and a plantation woodlot (WO). Microbial phospholipid fatty acid (PLFA) profiles and substrate utilization patterns (BIOLOG ECO plates) were measured to examine the effects of deintensification on the structure and diversity of soil microbial communities. Principle component analyses of PLFA and BIOLOG data showed that the microbial community structure diverged among the soils of the six systems.Lower microbial diversity was found in lowly managed ecosystem than that in intensive and moderately managed agroecosystems, and both fungal contribution to the total identified PLFAs and the ratio of microbial biomass C/N increased along with agricultural deintensification. Significantly higher ratios of C/N (P < 0.05) were found in the WO and SU systems, and for fungal/bacterial PLFAs in the WO system (P < 0.05). There were also significant decreases (P < 0.05)along with agricultural deintensification for contributions of total bacterial and gram positive (G+) bacterial PLFAs.Agricultural deintensification could facilitate the development of microbial communities that favor soil fungi over bacteria.

  1. 16S rRNA targeted DGGE fingerprinting of microbial communities

    NARCIS (Netherlands)

    Tzeneva, V.A.; Heilig, G.H.J.; Vliet, van W.M.; Akkermans, A.D.L.; Vos, de W.M.; Smidt, H.

    2008-01-01

    The past decades have seen the staggering development of molecular microbial ecology as a discipline that uses the detection of so-called biomarkers to monitor microbial communities in environment samples. A variety of molecules can be used as biomarkers, including cell-wall components, proteins,

  2. Metagenomic insights into evolution of heavy metal-contaminated groundwater microbial community

    Energy Technology Data Exchange (ETDEWEB)

    Hemme, C.L.; Deng, Y.; Gentry, T.J.; Fields, M.W.; Wu, L.; Barua, S.; Barry, K.; Green-Tringe, S.; Watson, D.B.; He, Z.; Hazen, T.C.; Tiedje, J.M.; Rubin, E.M.; Zhou, J.

    2010-07-01

    Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents ({approx}50 years) has resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying {gamma}- and {beta}-proteobacterial populations. The resulting community is overabundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could have a key function in rapid response and adaptation to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

  3. Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau.

    Science.gov (United States)

    Zhang, Yuguang; Lu, Zhenmei; Liu, Shanshan; Yang, Yunfeng; He, Zhili; Ren, Zuohua; Zhou, Jizhong; Li, Diqiang

    2013-03-29

    GeoChip 3.0, a microbial functional gene array, containing ~28,000 oligonucleotide probes and targeting ~57,000 sequences from 292 functional gene families, provided a powerful tool for researching microbial community structure in natural environments. The alpine meadow is a dominant plant community in the Qinghai-Tibetan plateau, hence it is important to profile the unique geographical flora and assess the response of the microbial communities to environmental variables. In this study, Geochip 3.0 was employed to understand the microbial functional gene diversity and structure, and metabolic potential and the major environmental factors in shaping microbial communities structure of alpine meadow soil in Qinghai-Tibetan Plateau. A total of 6143 microbial functional genes involved in carbon degradation, carbon fixation, methane oxidation and production, nitrogen cycling, phosphorus utilization, sulphur cycling, organic remediation, metal resistance, energy process and other category were detected in six soil samples and high diversity was observed. Interestingly, most of the detected genes associated with carbon degradation were derived from cultivated organisms. To identify major environmental factors in shaping microbial communities, Mantel test and CCA Statistical analyses were performed. The results indicated that altitude, C/N, pH and soil organic carbon were significantly (P the microbial functional structure and a total of 80.97% of the variation was significantly explained by altitude, C/N and pH. The C/N contributed 38.2% to microbial functional gene variation, which is in accordance with the hierarchical clustering of overall microbial functional genes. High overall functional genes and phylogenetic diversity of the alpine meadow soil microbial communities existed in the Qinghai-Tibetan Plateau. Most of the genes involved in carbon degradation were derived from characterized microbial groups. Microbial composition and structures variation were

  4. Isolation and Phylogenetic Analysis of Thermophile Community Within Tanjung Sakti Hot Spring, South Sumatera, Indonesia

    Directory of Open Access Journals (Sweden)

    Heni Yohandini

    2015-07-01

    Full Text Available A community of thermophiles within Tanjung Sakti Hot Spring (South Sumatera have been cultivated and identified based on 16S ribosomal RNA gene sequence. The hot spring has temperature 80 °C–91 °C and pH 7–8. We used a simple method for culturing the microbes, by enriching the spring water with nutrient broth media. Phylogenetic analysis showed that the method could recover microbes, which clustered within four distinct taxonomic groups: Anoxybacillus, Geobacillus, Brevibacillus, and Bacillus. These microbes closely related to Anoxybacillus rupiensis, Anoxybacillus flavithermus, Geobacillus pallidus, Brevibacillus thermoruber, Bacillus licheniformis, and Bacillus thermoamylovorans. The 16S ribosomal RNA gene sequence of one isolate only had 96% similarity with Brevibacillus sequence in GenBank.

  5. Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities

    Science.gov (United States)

    Li, Jun-Min; Jin, Ze-Xin; Hagedorn, Frank; Li, Mai-He

    2014-11-01

    Native parasitic plants may be used to infect and control invasive plants. We established microcosms with invasive Mikania micrantha and native Coix lacryma-jobi growing in mixture on native soils, with M. micrantha being infected by parasitic Cuscuta campestris at four intensity levels for seven weeks to estimate the top-down effects of plant parasitism on the biomass and functional diversity of soil microbial communities. Parasitism significantly decreased root biomass and altered soil microbial communities. Soil microbial biomass decreased, but soil respiration increased at the two higher infection levels, indicating a strong stimulation of soil microbial metabolic activity (+180%). Moreover, a Biolog assay showed that the infection resulted in a significant change in the functional diversity indices of soil microbial communities. Pearson correlation analysis indicated that microbial biomass declined significantly with decreasing root biomass, particularly of the invasive M. micrantha. Also, the functional diversity indices of soil microbial communities were positively correlated with soil microbial biomass. Therefore, the negative effects on the biomass, activity and functional diversity of soil microbial community by the seven week long plant parasitism was very likely caused by decreased root biomass and root exudation of the invasive M. micrantha.

  6. Thermophilic Biohydrogen Production

    DEFF Research Database (Denmark)

    Karakashev, Dimitar Borisov; Angelidaki, Irini

    2011-01-01

    Dark fermentative hydrogen production at thermophilic conditions is attractive process for biofuel production. From thermodynamic point of view, higher temperatures favor biohydrogen production. Highest hydrogen yields are always associated with acetate, or with mixed acetate- butyrate type...... fermentation. On the contrary the hydrogen yield decreases, with increasing concentrations of lactate, ethanol or propionate. Major factors affecting dark fermentative biohydrogen production are organic loading rate (OLR), pH, hydraulic retention time (HRT), dissolved hydrogen and dissolved carbon dioxide...... concentrations, and soluble metabolic profile (SMP). A number of thermophilic and extreme thermophilic cultures (pure and mixed) have been studied for biohydrogen production from different feedstocks - pure substrates and waste/wastewaters. Variety of process technologies (operational conditions...

  7. Performance and methanogenic community of rotating disk reactor packed with polyurethane during thermophilic anaerobic digestion

    International Nuclear Information System (INIS)

    Yang, Yingnan; Tsukahara, Kenichiro; Sawayama, Shigeki

    2007-01-01

    A newly developed anaerobic rotating disk reactor (ARDR) packed with polyurethane was used in continuous mode for organic waste removal under thermophilic (55 o C) anaerobic conditions. This paper reports the effects of the rotational speed on the methanogenic performance and community in an ARDR supplied with acetic acid synthetic wastewater as the organic substrate. The best performance was obtained from the ARDR with the rotational speed (ω) of 30 rpm. The average removal of dissolved organic carbon was 98.5%, and the methane production rate was 393 ml/l-reactor/day at an organic loading rate of 2.69 g/l-reactor/day. Under these operational conditions, the reactor had a greater biomass retention capacity and better reactor performance than those at other rotational speeds (0, 5 and 60 rpm). The results of 16S rRNA phylogenetic analysis indicated that the major methanogens in the reactor belonged to the genus Methanosarcina spp. The results of real-time polymerase chain reaction (PCR) analysis suggested that the cell density of methanogenic archaea immobilized on the polyurethane foam disk could be concentrated more than 2000 times relative to those in the original thermophilic sludge. Scanning electron microphotographs showed that there were more immobilized microbes at ω of 30 rpm than 60 rpm. A rotational speed on the outer layer of the disk of 6.6 m/min could be appropriate for anaerobic digestion using the polyurethane ARDR

  8. Polyphasic characterization of a PCP-to-phenol dechlorinating microbial community enriched from paddy soil

    Energy Technology Data Exchange (ETDEWEB)

    Yoshida, Naoko [EcoTopia Science Institute, Nagoya University Nagoya 464-8603 (Japan)]. E-mail: ysd75@esi.nagoya-u.ac.jp; Yoshida, Yukina [Graduate School of Engineering, Nagoya University, Nagoya 464-8603 (Japan); Handa, Yuko [Graduate School of Engineering, Nagoya University, Nagoya 464-8603 (Japan); Kim, Hyo-Keun [Korea Ginseng and Tobacco Research Institute, Taejon 305-345 (Korea, Republic of); Ichihara, Shigeyuki [Faculty of Agriculture, Meijo University, Nagoya 468-8502 (Japan); Katayama, Arata [EcoTopia Science Institute, Nagoya University Nagoya 464-8603 (Japan); Graduate School of Engineering, Nagoya University, Nagoya 464-8603 (Japan)

    2007-08-01

    Dechlorination of PCP has been observed previously under anaerobic condition in paddy soil. However, there is poor information about the dechlorination pathway of PCP and the microbial community associated with the PCP dechlorination in paddy soil. In this study, an anaerobic microbial community dechlorinating PCP was enriched by serial transfers from a paddy soil using a medium containing PCP, lactate and the steam-sterilized paddy soil. The enriched microbial community dechlorinated PCP completely to phenol under the anaerobic condition by a dechlorinating pathway as follows; PCP {sup {yields}} 2,3,4,5-tetrachlorophenol {sup {yields}} 3,4,5-trichlorophenol {sup {yields}} 3,5-dichlorophenol {sup {yields}} 3-chlorophenol {sup {yields}} phenol. Intermediate products such as 3-chlorophenol were not accumulated, which were immediately dechlorinated to phenol. The enriched microbial community was characterized physiologically by testing the effects of electron donors and electron acceptors on the dechlorinating activity. The dechlorinating activity was promoted with lactate, pyruvate, and hydrogen as electron donors but not with acetate. Electron acceptors, nitrate and sulphate, inhibited the dechlorinating activity competitively but not iron (III). The microbial group associated with the anaerobic dechlorination was characterized by the effect of specific inhibitors on the PCP dechlorination. Effects of specific metabolic inhibitors and antibiotics indicated the involvement of Gram-positive spore-forming bacteria with the PCP dechlorinating activity, which was represented as bacteria of phylum Firmicutes. The structure of the microbial community was characterized by fluorescence in situ hybridization, quinone profiling, and PCR-DGGE (denaturing gel gradient electrophoresis). The combined results indicated the predominance of Clostridium species of phylum Firmicutes in the microbial community. Desulfitobacterium spp. known as anaerobic Gram-positive spore

  9. Polyphasic characterization of a PCP-to-phenol dechlorinating microbial community enriched from paddy soil

    International Nuclear Information System (INIS)

    Yoshida, Naoko; Yoshida, Yukina; Handa, Yuko; Kim, Hyo-Keun; Ichihara, Shigeyuki; Katayama, Arata

    2007-01-01

    Dechlorination of PCP has been observed previously under anaerobic condition in paddy soil. However, there is poor information about the dechlorination pathway of PCP and the microbial community associated with the PCP dechlorination in paddy soil. In this study, an anaerobic microbial community dechlorinating PCP was enriched by serial transfers from a paddy soil using a medium containing PCP, lactate and the steam-sterilized paddy soil. The enriched microbial community dechlorinated PCP completely to phenol under the anaerobic condition by a dechlorinating pathway as follows; PCP → 2,3,4,5-tetrachlorophenol → 3,4,5-trichlorophenol → 3,5-dichlorophenol → 3-chlorophenol → phenol. Intermediate products such as 3-chlorophenol were not accumulated, which were immediately dechlorinated to phenol. The enriched microbial community was characterized physiologically by testing the effects of electron donors and electron acceptors on the dechlorinating activity. The dechlorinating activity was promoted with lactate, pyruvate, and hydrogen as electron donors but not with acetate. Electron acceptors, nitrate and sulphate, inhibited the dechlorinating activity competitively but not iron (III). The microbial group associated with the anaerobic dechlorination was characterized by the effect of specific inhibitors on the PCP dechlorination. Effects of specific metabolic inhibitors and antibiotics indicated the involvement of Gram-positive spore-forming bacteria with the PCP dechlorinating activity, which was represented as bacteria of phylum Firmicutes. The structure of the microbial community was characterized by fluorescence in situ hybridization, quinone profiling, and PCR-DGGE (denaturing gel gradient electrophoresis). The combined results indicated the predominance of Clostridium species of phylum Firmicutes in the microbial community. Desulfitobacterium spp. known as anaerobic Gram-positive spore-forming bacteria dechlorinating PCP were not detected by PCR using a

  10. Monitoring of microbial communities in anaerobic digestion sludge for biogas optimisation.

    Science.gov (United States)

    Lim, Jun Wei; Ge, Tianshu; Tong, Yen Wah

    2018-01-01

    This study characterised and compared the microbial communities of anaerobic digestion (AD) sludge using three different methods - (1) Clone library; (2) Pyrosequencing; and (3) Terminal restriction fragment length polymorphism (T-RFLP). Although high-throughput sequencing techniques are becoming increasingly popular and affordable, the reliance of such techniques for frequent monitoring of microbial communities may be a financial burden for some. Furthermore, the depth of microbial analysis revealed by high-throughput sequencing may not be required for monitoring purposes. This study aims to develop a rapid, reliable and economical approach for the monitoring of microbial communities in AD sludge. A combined approach where genetic information of sequences from clone library was used to assign phylogeny to T-RFs determined experimentally was developed in this study. In order to assess the effectiveness of the combined approach, microbial communities determined by the combined approach was compared to that characterised by pyrosequencing. Results showed that both pyrosequencing and clone library methods determined the dominant bacteria phyla to be Proteobacteria, Firmicutes, Bacteroidetes, and Thermotogae. Both methods also found that sludge A and B were predominantly dominated by acetogenic methanogens followed by hydrogenotrophic methanogens. The number of OTUs detected by T-RFLP was significantly lesser than that detected by the clone library. In this study, T-RFLP analysis identified majority of the dominant species of the archaeal consortia. However, many of the more highly diverse bacteria consortia were missed. Nevertheless, the combined approach developed in this study where clone sequences from the clone library were used to assign phylogeny to T-RFs determined experimentally managed to accurately predict the same dominant microbial groups for both sludge A and sludge B, as compared to the pyrosequencing results. Results showed that the combined approach of

  11. Metagenomic analysis of microbial communities and beyond

    DEFF Research Database (Denmark)

    Schreiber, Lars

    2014-01-01

    From small clone libraries to large next-generation sequencing datasets – the field of community genomics or metagenomics has developed tremendously within the last years. This chapter will summarize some of these developments and will also highlight pitfalls of current metagenomic analyses...... heterologous expression of metagenomic DNA fragments to discover novel metabolic functions. Lastly, the chapter will shortly discuss the meta-analysis of gene expression of microbial communities, more precisely metatranscriptomics and metaproteomics....

  12. Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes.

    Science.gov (United States)

    Yang, Jian; Ma, Li'an; Jiang, Hongchen; Wu, Geng; Dong, Hailiang

    2016-04-26

    Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions.

  13. Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories

    DEFF Research Database (Denmark)

    Wigneswaran, Vinoth; Amador Hierro, Cristina Isabel; Jelsbak, Lotte

    2016-01-01

    Microbial activities are most often shaped by interactions between co-existing microbes within mixed-species communities. Dissection of the molecular mechanisms of species interactions within communities is a central issue in microbial ecology, and our ability to engineer and control microbial co...

  14. Earthworms modify microbial community structure and accelerate maize stover decomposition during vermicomposting.

    Science.gov (United States)

    Chen, Yuxiang; Zhang, Yufen; Zhang, Quanguo; Xu, Lixin; Li, Ran; Luo, Xiaopei; Zhang, Xin; Tong, Jin

    2015-11-01

    In the present study, maize stover was vermicomposted with the epigeic earthworm Eisenia fetida. The results showed that, during vermicomposting process, the earthworms promoted decomposition of maize stover. Analysis of microbial communities of the vermicompost by high-throughput pyrosequencing showed more complex bacterial community structure in the substrate treated by the earthworms than that in the control group. The dominant microbial genera in the treatment with the earthworms were Pseudoxanthomonas, Pseudomonas, Arthrobacter, Streptomyces, Cryptococcus, Guehomyces, and Mucor. Compared to the control group, the relative abundance of lignocellulose degradation microorganisms increased. The results indicated that the earthworms modified the structure of microbial communities during vermicomposting process, activated the growth of lignocellulose degradation microorganisms, and triggered the lignocellulose decomposition.

  15. Quorum sensing alters the microbial community of electrode-respiring bacteria and hydrogen scavengers toward improving hydrogen yield in microbial electrolysis cells

    International Nuclear Information System (INIS)

    Cai, Weiwei; Zhang, Zhaojing; Ren, Ge; Shen, Qiuxuan; Hou, Yanan; Ma, Anzhou; Deng, Ye; Wang, Aijie; Liu, Wenzong

    2016-01-01

    Highlights: • Enhanced hydrogen yield has been achieved with addition of AHL. • AHL regulated exoelectrogens resulting in electrochemical activity enhancement. • Microbial community shift in cathodic biofilm inhibited hydrogen loss. - Abstract: Quorum sensing has been widely applied to enhance the energy recovery of bioelectrochemical system as a sustainable pathway to enhance communication between cells and electrodes. However, how signalling molecules (acyl-homoserine lactones, AHLs) regulate the microbial community to improve hydrogen generation in microbial electrolysis cells (MECs) is not well understood, especially the subsequent influence on interspecies relationships among not only electrode-respiring bacteria but also hydrogen scavengers. Understanding AHL regulation in a complicated and actual biofilm system will be valuable for future applications of microbial electrochemical technology. Herein, we added short-chain AHLs (3OC6) to regulate the biofilm community on bio-electrodes in MECs. As a result, hydrogen yields were enhanced with AHL addition, increasing by 5.57%, 38.68%, and 81.82% with varied external voltages (0.8 V, 0.6 V, and 0.4 V, respectively). Accordingly, overall reactor performance was enhanced, including coulombic efficiency, electron recovery efficiency, and energy efficiency. Based on an electrochemical impedance spectra analysis, the structured biofilm under simple nutrient conditions (acetate) showed a lower internal resistance with AHL addition, indicating that the microbial communities were altered to enhance electron transfer between the biofilm and electrode. The change in the cathodic microbial structure with more electrochemically active bacteria and fewer hydrogen scavengers could contribute to a higher electron recovery and hydrogen yield with AHL addition. The regulation of the microbial community structure by AHLs represents a potential strategy to enhance electron transfer and hydrogen generation in

  16. Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in urban streams

    Science.gov (United States)

    Ledford, S. H.; Price, J. R.; Ryan, M. O.; Toran, L.; Sales, C. M.

    2017-12-01

    New technologies are allowing for intense scrutiny of the impact of land use on microbial communities in stream networks. We used a combination of analytical chemistry, real-time polymerase chain reaction (qPCR) and targeted amplicon sequencing for a preliminary study on the impact of wastewater treatment plant effluent discharge on urban streams. Samples were collected on two dates above and below treatment plants on the Wissahickon Creek, and its tributary, Sandy Run, in Montgomery County, PA, USA. As expected, effluent was observed to be a significant source of nutrients and human and non-specific fecal associated taxa. There was an observed increase in the alpha diversity at locations immediately below effluent outflows, which contributed many taxa involved in wastewater treatment processes and nutrient cycling to the stream's microbial community. Unexpectedly, modeling of microbial community shifts along the stream was not controlled by concentrations of measured nutrients. Furthermore, partial recovery, in the form of decreasing abundances of bacteria and nutrients associated with wastewater treatment plant processes, nutrient cycling bacteria, and taxa associated with fecal and sewage sources, was observed between effluent sources. Antecedent moisture conditions impacted overall microbial community diversity, with higher diversity occurring after rainfall. These findings hint at resilience in stream microbial communities to recover from wastewater treatment plant effluent and are vital to understanding the impacts of urbanization on microbial stream communities.

  17. Thermophillic and thermotolerant fungi isolated from the thermal effluent of nuclear power generating reactors

    International Nuclear Information System (INIS)

    Rippon, J.W.; Gerhold, R.; Heath, M.

    1980-01-01

    Over a period of a year, samples of water, foam, microbial mat, soil and air were obtained from areas associated with the cooling canal of a nuclear power station. The seventeen sample sites included water in the cooling canal that was thermally enriched and soil and water adjacent to, up-stream, downstream and at a distance from the generator. Air samples were taken at the plant and at various disstances from the plant. Fifty-two species of thermotolerant and thermophilic fungi were isolated. Of these, eleven species are grouped as opportunistic Mucorales or opportunistic Aspergillus sp. One veterinary pathogen was also isolated (Dactylaria gallopara). The opportunistic/pathogenic fungi were found primarily in the intake bay, the discharge bay and the cooling canal. Smaller numbers were obtained at both upstream and downstream locations. Soil samples near the cooling canal reflected an enrichment of thermophilous organisms, the previously mentioned opportunistic Mucorales and Aspergillus spp. Their numbers were found to be greater than that usually encountered in a mesophilic environment. However, air and soil samples taken at various distances from the power station indicated no greater abundance of these thermophilous fungi than would be expected from a thermal enriched environment. Our results indicate that there was no significant dissemination of thermophilous fungi from the thermal enriched effluents to the adjacent environment. These findings are consistent with the results of other investigators. (orig.)

  18. Survival of a microbial soil community under Martian conditions

    Science.gov (United States)

    Hansen, A. A.; Noernberg, P.; Merrison, J.; Lomstein, B. Aa.; Finster, K. W.

    2003-04-01

    Because of the similarities between Earth and Mars early history the hypothesis was forwarded that Mars is a site where extraterrestrial life might have and/or may still occur(red). Sample-return missions are planned by NASA and ESA to test this hypothesis. The enormous economic costs and the logistic challenges of these missions make earth-based model facilities inevitable. The Mars simulation system at University of Aarhus, Denmark allows microbiological experiments under Mars analogue conditions. Thus detailed studies on the effect of Mars environmental conditions on the survival and the activity of a natural microbial soil community were carried out. Changes in the soil community were determined with a suite of different approaches: 1) total microbial respiration activity was investigated with 14C-glucose, 2) the physiological profile was investigated by the EcoLog-system, 3) colony forming units were determined by plate counts and 4) the microbial diversity on the molecular level was accessed with Denaturing Gradient Gel Electrophoresis. The simulation experiments showed that a part of the bacterial community survived Martian conditions corresponding to 9 Sol. These and future simulation experiments will contribute to our understanding of the possibility for extraterrestrial and terrestrial life on Mars.

  19. Soil microbial community response to aboveground vegetation and ...

    African Journals Online (AJOL)

    lenovo

    2011-11-21

    Nov 21, 2011 ... magnitude, activity, structure and function of soil microbial community may .... CaO were quantified by inductively coupled plasmaatomic emission spectroscopy ...... Validation of signature polarlipid fatty acid biomarkers for ...

  20. Cellular content of biomolecules in sub-seafloor microbial communities

    DEFF Research Database (Denmark)

    Braun, Stefan; Morono, Yuki; Becker, Kevin W.

    2016-01-01

    the lifetime of their microbial sources. Here we provide for the first time measurements of the cellular content of biomolecules in sedimentary microbial cells. We separated intact cells from sediment matrices in samples from surficial, deeply buried, organic-rich, and organic-lean marine sediments by density...... content. We find that the cellular content of biomolecules in the marine subsurface is up to four times lower than previous estimates. Our approach will facilitate and improve the use of biomolecules as proxies for microbial abundance in environmental samples and ultimately provide better global estimates......Microbial biomolecules, typically from the cell envelope, can provide crucial information about distribution, activity, and adaptations of sub-seafloor microbial communities. However, when cells die these molecules can be preserved in the sediment on timescales that are likely longer than...

  1. Inactivation of Clostridium difficile in sewage sludge by anaerobic thermophilic digestion.

    Science.gov (United States)

    Xu, Changyun; Salsali, Hamidreza; Weese, Scott; Warriner, Keith

    2016-01-01

    There has been an increase in community-associated Clostridium difficile infections with biosolids derived from wastewater treatment being identified as one potential source. The current study evaluated the efficacy of thermophilic digestion in decreasing levels of C. difficile ribotype 078 associated with sewage sludge. Five isolates of C. difficile 078 were introduced (final density of 5 log CFU/g) into digested sludge and subjected to anaerobic digestion at mesophilic (36 or 42 °C) or thermophilic (55 °C) temperatures for up to 60 days. It was found that mesophilic digestion at 36 °C did not result in a significant reduction in C. difficile spore levels. In contrast, thermophilic sludge digestion reduced endospore levels at a rate of 0.19-2.68 log CFU/day, depending on the strain tested. The mechanism of lethality was indirect - by stimulating germination then inactivating the resultant vegetative cells. Acidification of sludge by adding acetic acid (6 g/L) inhibited the germination of spores regardless of the sludge digestion temperature. In conclusion, thermophilic digestion can be applied to reduce C. difficile in biosolids, thereby reducing the environmental burden of the enteric pathogen.

  2. Different substrates and starter inocula govern microbial community structures in biogas reactors.

    Science.gov (United States)

    Satpathy, Preseela; Steinigeweg, Sven; Cypionka, Heribert; Engelen, Bert

    2016-01-01

    The influence of different starter inocula on the microbial communities in biogas batch reactors fed with fresh maize and maize silage as substrates was investigated. Molecular biological analysis by Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rRNA gene fragments showed that each inoculum bore specific microbial communities with varying predominant phylotypes. Both, bacterial and archaeal DGGE profiles displayed three distinct communities that developed depending on the type of inoculum. Although maize and silage are similar substrates, different communities dominated the lactate-rich silage compared to lactate-free fresh maize. Cluster analysis of DGGE gels showed the communities of the same substrates to be stable with their respective inoculum. Bacteria-specific DGGE analysis revealed a rich diversity with Firmicutes being predominant. The other abundant phylotypes were Bacteroidetes and Synergistetes. Archaea-specific DGGE analysis displayed less diverse community structures, identifying members of the Methanosarcinales as the dominant methanogens present in all the three biogas digesters. In general, the source of inoculum played a significant role in shaping microbial communities. Adaptability of the inoculum to the substrates fed also influenced community compositions which further impacted the rates of biogas production.

  3. Improved Access To Aging Ocean Basement Biosphere For Microbial Geochemical Studies

    Science.gov (United States)

    Cowen, J. P.; Glazer, B.; Rappe, M.; Kenig, F.; Fisher, A.; Copson, D.; Harris, D.; Jolly, J.; Nuzzio, D.

    2005-12-01

    CORK observatories affixed to Integrated Ocean Drilling Program (IODP) boreholes offer an unprecedented opportunity to study biogeochemical properties and microbial diversity in circulating fluids from sediment-buried ocean basement. Preliminary 16S rRNA gene sequence data from 65 degrees C fluids escaping from the top of the over-pressured ODP borehole 1026B, on the flanks of the Juan de Fuca Ridge indicated the presence of diverse Bacteria and Archaea, including gene clones with varying degrees of relatedness to known dissimilatory nitrate reducers (with ammonia production), thermophilic sulfate reducers, and thermophilic fermentative heterotrophs, consistent with fluid chemistry measurements. However, questions remain regarding microbial community structure, key metabolic pathways and rates, and redox chemistry of the basement fluids, along with concerns for contamination issues. We describe ongoing developments intended to address key in situ analytical and sampling challenges including: 1) The new generation CORKs' dedicated microbiological/geochemical fluid delivery system specifically designed to minimize chemical contamination and surface biofouling; and 2) Development of a seafloor instrument sled for coupling to the CORK's bio-fluid delivery system for acquisition of real-time, in situ electrochemical (voltammetry) redox chemistry data on basement fluids, in addition to in situ particle filtration of basement fluids for molecular genetics, culturing and biogeochemical studies. Results of the first deployment of this instrument sled to new CORK observatory 1301A in Cascadia Basin, on the flanks of the Juan de Fuca Ridge, will be described.

  4. Distinctive tropical forest variants have unique soil microbial communities, but not always low microbial diversity

    Directory of Open Access Journals (Sweden)

    Binu M Tripathi

    2016-04-01

    Full Text Available There has been little study of whether different variants of tropical rainforest have distinct soil microbial communities and levels of diversity. We compared bacterial and fungal community composition and diversity between primary mixed dipterocarp, secondary mixed dipterocarp, white sand heath, inland heath, and peat swamp forests in Brunei Darussalam, northwest Borneo by analyzing Illumina Miseq sequence data of 16S rRNA gene and ITS1 region. We hypothesized that white sand heath, inland heath and peat swamp forests would show lower microbial diversity and relatively distinct microbial communities (compared to MDF primary and secondary forests due to their distinctive environments. We found that soil properties together with bacterial and fungal communities varied significantly between forest types. Alpha and beta-diversity of bacteria was highest in secondary dipterocarp and white sand heath forests. Also, bacterial alpha diversity was strongly structured by pH, adding another instance of this widespread pattern in nature. The alpha diversity of fungi was equally high in all forest types except peat swamp forest, although fungal beta-diversity was highest in primary and secondary mixed dipterocarp forests. The relative abundance of ectomycorrhizal (EcM fungi varied significantly between forest types, with highest relative abundance observed in MDF primary forest. Overall, our results suggest that the soil bacterial and fungal communities in these forest types are to a certain extent predictable and structured by soil properties, but that diversity is not determined by how distinctive the conditions are. This contrasts with the diversity patterns seen in rainforest trees, where distinctive soil conditions have consistently lower tree diversity.

  5. Relating Anaerobic Digestion Microbial Community and Process Function : Supplementary Issue: Water Microbiology

    Directory of Open Access Journals (Sweden)

    Kaushik Venkiteshwaran

    2015-01-01

    Full Text Available Anaerobic digestion (AD involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1 hydrolysis rate, (2 direct interspecies electron transfer to methanogens, (3 community structure–function relationships of methanogens, (4 methanogenesis via acetate oxidation, and (5 bioaugmentation to study community–activity relationships or improve engineered bioprocesses.

  6. Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy.

    Science.gov (United States)

    Rittmann, Bruce E; Krajmalnik-Brown, Rosa; Halden, Rolf U

    2008-08-01

    Microorganisms can produce renewable energy in large quantities and without damaging the environment or disrupting food supply. The microbial communities must be robust and self-stabilizing, and their essential syntrophies must be managed. Pre-genomic, genomic and post-genomic tools can provide crucial information about the structure and function of these microbial communities. Applying these tools will help accelerate the rate at which microbial bioenergy processes move from intriguing science to real-world practice.

  7. Soil inoculation with microbial communities - can this become a useful tool in soil remediation?

    Science.gov (United States)

    Krug, Angelika; Wang, Fang; Dörfler, Ulrike; Munch, Jean Charles; Schroll, Reiner

    2010-05-01

    We artificially loaded different type of agricultural soils with model 14C-labelled chemicals, and we inoculated such soils with different microbial communities as well as isolated strains to enhance the mineralization of such chemicals. Inocula were introduced by different approaches: (i) soil inocula, (ii) application of isolated strain as well as microbial community via media, (iii) isolated strain as well as microbial community attached to a carrier material. Most of the inoculation experiments were conducted in laboratory but we also tested one of these approaches under real environmental conditions in lysimeters and we could show that the approach was successful. We already could show that inoculating soils with microbial communities attached on a specific carrier material shows the highest mineralization effectiveness and also the highest sustainability. Microbes attached on clay particles preserved their function over a long time period even if the specific microbial substrate was already degraded or at least not detectable any more. Additionally we already could show that in specific cases some soil parameters might reduce the effectiveness of such an approach. Results on isoproturon as a model for phenylurea-herbicides and 1,2,4-trichlorobenzene as an example for an industrially used chemical as well as the corresponding chemicals` degrading microbial communities and isolated strain will be presented.

  8. Soil microbial community responses to antibiotic-contaminated manure under different soil moisture regimes.

    Science.gov (United States)

    Reichel, Rüdiger; Radl, Viviane; Rosendahl, Ingrid; Albert, Andreas; Amelung, Wulf; Schloter, Michael; Thiele-Bruhn, Sören

    2014-01-01

    Sulfadiazine (SDZ) is an antibiotic frequently administered to livestock, and it alters microbial communities when entering soils with animal manure, but understanding the interactions of these effects to the prevailing climatic regime has eluded researchers. A climatic factor that strongly controls microbial activity is soil moisture. Here, we hypothesized that the effects of SDZ on soil microbial communities will be modulated depending on the soil moisture conditions. To test this hypothesis, we performed a 49-day fully controlled climate chamber pot experiments with soil grown with Dactylis glomerata (L.). Manure-amended pots without or with SDZ contamination were incubated under a dynamic moisture regime (DMR) with repeated drying and rewetting changes of >20 % maximum water holding capacity (WHCmax) in comparison to a control moisture regime (CMR) at an average soil moisture of 38 % WHCmax. We then monitored changes in SDZ concentration as well as in the phenotypic phospholipid fatty acid and genotypic 16S rRNA gene fragment patterns of the microbial community after 7, 20, 27, 34, and 49 days of incubation. The results showed that strongly changing water supply made SDZ accessible to mild extraction in the short term. As a result, and despite rather small SDZ effects on community structures, the PLFA-derived microbial biomass was suppressed in the SDZ-contaminated DMR soils relative to the CMR ones, indicating that dynamic moisture changes accelerate the susceptibility of the soil microbial community to antibiotics.

  9. Discovery of Microorganisms and Enzymes Involved in High-Solids Decomposition of Rice Straw Using Metagenomic Analyses

    Science.gov (United States)

    D’haeseleer, Patrik; Khudyakov, Jane; Burd, Helcio; Hadi, Masood; Simmons, Blake A.; Singer, Steven W.; Thelen, Michael P.; VanderGheynst, Jean S.

    2013-01-01

    High-solids incubations were performed to enrich for microbial communities and enzymes that decompose rice straw under mesophilic (35°C) and thermophilic (55°C) conditions. Thermophilic enrichments yielded a community that was 7.5 times more metabolically active on rice straw than mesophilic enrichments. Extracted xylanase and endoglucanse activities were also 2.6 and 13.4 times greater, respectively, for thermophilic enrichments. Metagenome sequencing was performed on enriched communities to determine community composition and mine for genes encoding lignocellulolytic enzymes. Proteobacteria were found to dominate the mesophilic community while Actinobacteria were most abundant in the thermophilic community. Analysis of protein family representation in each metagenome indicated that cellobiohydrolases containing carbohydrate binding module 2 (CBM2) were significantly overrepresented in the thermophilic community. Micromonospora, a member of Actinobacteria, primarily housed these genes in the thermophilic community. In light of these findings, Micromonospora and other closely related Actinobacteria genera appear to be promising sources of thermophilic lignocellulolytic enzymes for rice straw deconstruction under high-solids conditions. Furthermore, these discoveries warrant future research to determine if exoglucanases with CBM2 represent thermostable enzymes tolerant to the process conditions expected to be encountered during industrial biofuel production. PMID:24205054

  10. Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses.

    Directory of Open Access Journals (Sweden)

    Amitha P Reddy

    Full Text Available High-solids incubations were performed to enrich for microbial communities and enzymes that decompose rice straw under mesophilic (35°C and thermophilic (55°C conditions. Thermophilic enrichments yielded a community that was 7.5 times more metabolically active on rice straw than mesophilic enrichments. Extracted xylanase and endoglucanse activities were also 2.6 and 13.4 times greater, respectively, for thermophilic enrichments. Metagenome sequencing was performed on enriched communities to determine community composition and mine for genes encoding lignocellulolytic enzymes. Proteobacteria were found to dominate the mesophilic community while Actinobacteria were most abundant in the thermophilic community. Analysis of protein family representation in each metagenome indicated that cellobiohydrolases containing carbohydrate binding module 2 (CBM2 were significantly overrepresented in the thermophilic community. Micromonospora, a member of Actinobacteria, primarily housed these genes in the thermophilic community. In light of these findings, Micromonospora and other closely related Actinobacteria genera appear to be promising sources of thermophilic lignocellulolytic enzymes for rice straw deconstruction under high-solids conditions. Furthermore, these discoveries warrant future research to determine if exoglucanases with CBM2 represent thermostable enzymes tolerant to the process conditions expected to be encountered during industrial biofuel production.

  11. Elevated temperature alters carbon cycling in a model microbial community

    Science.gov (United States)

    Mosier, A.; Li, Z.; Thomas, B. C.; Hettich, R. L.; Pan, C.; Banfield, J. F.

    2013-12-01

    Earth's climate is regulated by biogeochemical carbon exchanges between the land, oceans and atmosphere that are chiefly driven by microorganisms. Microbial communities are therefore indispensible to the study of carbon cycling and its impacts on the global climate system. In spite of the critical role of microbial communities in carbon cycling processes, microbial activity is currently minimally represented or altogether absent from most Earth System Models. Method development and hypothesis-driven experimentation on tractable model ecosystems of reduced complexity, as presented here, are essential for building molecularly resolved, benchmarked carbon-climate models. Here, we use chemoautotropic acid mine drainage biofilms as a model community to determine how elevated temperature, a key parameter of global climate change, regulates the flow of carbon through microbial-based ecosystems. This study represents the first community proteomics analysis using tandem mass tags (TMT), which enable accurate, precise, and reproducible quantification of proteins. We compare protein expression levels of biofilms growing over a narrow temperature range expected to occur with predicted climate changes. We show that elevated temperature leads to up-regulation of proteins involved in amino acid metabolism and protein modification, and down-regulation of proteins involved in growth and reproduction. Closely related bacterial genotypes differ in their response to temperature: Elevated temperature represses carbon fixation by two Leptospirillum genotypes, whereas carbon fixation is significantly up-regulated at higher temperature by a third closely related genotypic group. Leptospirillum group III bacteria are more susceptible to viral stress at elevated temperature, which may lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, this proteogenomics approach revealed the effects of climate change on carbon cycling pathways and other

  12. Analysis of stability to cheaters in models of antibiotic degrading microbial communities.

    Science.gov (United States)

    Szilágyi, András; Boza, Gergely; Scheuring, István

    2017-06-21

    Antibiotic resistance carried out by antibiotic degradation has been suggested recently as a new mechanism to maintain coexistence of microbial species competing on a single limiting resource, even in well-mixed homogeneous environments. Species diversity and community stability, however, critically depend on resistance against social cheaters, mutants that do not invest in production, but still enjoy the benefits provided by others. Here we investigate how different mutant cheaters affect the stability of antibiotic producing and degrading microbial communities. We consider two cheater types, production and degradation cheaters. We generalize the mixed inhibition-zone and chemostat models introduced previously [Kelsic, E. D., Zhao, J., Vetsigian, K., Kishony, R., 2015. Counteraction of an tibiotic production and degradation stabilizes microbial communities. Nature521, 516-519.] to study the population dynamics of microbial communities in well-mixed environment, and analyze the invasion of different cheaters in these models. We show that production cheaters, mutants that cease producing antibiotics, always destroy coexistence whenever there is a cost of producing these antibiotics. Degradation cheaters, mutants that loose their function of producing extracellular antibiotic degrading molecules, induce community collapse only if the cost of producing the degradation factors is above a critical level. Our analytical studies, supported by numerical simulations, highlight the sensitivity of antibiotic producing and degrading communities to loss-of-function mutants. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature.

    Science.gov (United States)

    Gajigan, Andrian P; Diaz, Leomir A; Conaco, Cecilia

    2017-08-01

    The coral is a holobiont formed by the close interaction between the coral animal and a diverse community of microorganisms, including dinoflagellates, bacteria, archaea, fungi, and viruses. The prokaryotic symbionts of corals are important for host fitness but are also highly sensitive to changes in the environment. In this study, we used 16S ribosomal RNA (rRNA) sequencing to examine the response of the microbial community associated with the coral, Acropora digitifera, to elevated temperature. The A. digitifera microbial community is dominated by operational taxonomic unit (OTUs) affiliated with classes Alphaproteobacteria and Gammaproteobacteria. The prokaryotic community in the coral tissue is distinct from that of the mucus and the surrounding seawater. Remarkably, the overall microbial community structure of A. digitifera remained stable for 10 days of continuous exptosure at 32°C compared to corals maintained at 27°C. However, the elevated temperature regime resulted in a decrease in the abundance of OTUs affiliated with certain groups of bacteria, such as order Rhodobacterales. On the other hand, some OTUs affiliated with the orders Alteromonadales, Vibrionales, and Flavobacteriales, which are often associated with diseased and stressed corals, increased in abundance. Thus, while the A. digitifera bacterial community structure appears resilient to higher temperature, prolonged exposure and intensified stress results in changes in the abundance of specific microbial community members that may affect the overall metabolic state and health of the coral holobiont. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  14. Establishment of thermophilic anaerobic terephthalic acid degradation system through one-step temperature increase startup strategy - Revealed by Illumina Miseq Sequencing.

    Science.gov (United States)

    Ma, Kai-Li; Li, Xiang-Kun; Wang, Ke; Meng, Ling-Wei; Liu, Gai-Ge; Zhang, Jie

    2017-10-01

    Over recent years, thermophilic digestion was constantly focused owing to its various advantage over mesophilic digestion. Notably, the startup approach of thermophilic digester needs to be seriously considered as unsuitable startup ways may result in system inefficiency. In this study, one-step temperature increase startup strategy from 37 °C to 55 °C was applied to establish a thermophilic anaerobic system treating terephthalic acid (TA) contained wastewater, meanwhile, the archaeal and bacterial community compositions at steady periods of 37 °C and 55 °C during the experimental process was also compared using Illumina Miseq Sequencing. The process operation demonstrated that the thermophilic TA degradation system was successfully established at 55 °C with over 95% COD reduction. For archaea community, the elevation of operational temperature from 37 °C to 55 °C accordingly increase the enrichment of hydrogenotrophic methanogens but decrease the abundance of the acetotrophic ones. While for bacterial community, the taxonomic analysis suggested that Syntrophorhabdus (27.40%) was the dominant genus promoting the efficient TA degradation under mesophilic condition, whereas OPB95 (24.99%) and TA06 (14.01%) related populations were largely observed and probably take some crucial role in TA degradation under thermophilic condition. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Methanogenesis in Thermophilic Biogas Reactors

    DEFF Research Database (Denmark)

    Ahring, Birgitte Kiær

    1995-01-01

    Methanogenesis in thermophilic biogas reactors fed with different wastes is examined. The specific methanogenic activity with acetate or hydrogen as substrate reflected the organic loading of the specific reactor examined. Increasing the loading of thermophilic reactors stabilized the process as ....... Experiments using biogas reactors fed with cow manure showed that the same biogas yield found at 550 C could be obtained at 610 C after a long adaptation period. However, propionate degradation was inhibited by increasing the temperature.......Methanogenesis in thermophilic biogas reactors fed with different wastes is examined. The specific methanogenic activity with acetate or hydrogen as substrate reflected the organic loading of the specific reactor examined. Increasing the loading of thermophilic reactors stabilized the process...... as indicated by a lower concentration of volatile fatty acids in the effluent from the reactors. The specific methanogenic activity in a thermophilic pilot-plant biogas reactor fed with a mixture of cow and pig manure reflected the stability of the reactor. The numbers of methanogens counted by the most...

  16. Novel assay to measure the plasmid mobilizing potential of mixed microbial communities

    DEFF Research Database (Denmark)

    Klümper, Uli; Droumpali, Ariadni; Dechesne, Arnaud

    2014-01-01

    Mobilizable plasmids lack necessary genes for complete conjugation and are therefore non-self-transmissible. Instead, they rely on the conjugation system of conjugal plasmids to be horizontally transferred to new recipients. While community permissiveness, the fraction of a mixed microbial...... community that can receive self-transmissible conjugal plasmids, has been studied, the intrinsic ability of a community to mobilize plasmids that lack conjugation systems is unexplored. Here, we present a novel framework and experimental method to estimate the mobilization potential of mixed communities. We...... of the donors receiving the conjugal plasmid in the first step. Further work is needed to establish how plasmid mobilization potential varies within and across microbial communities....

  17. Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Fan; Zhang, Xiao-Tao; Hou, Du-Jie [China Univ. of Geosciences, Beijing (China). The Key Lab. of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism; She, Yue-Hui [Yangtze Univ., Jingzhou, Hubei (China). College of Chemistry and Environmental Engineering; Huazhong Univ. of Science and Technology, Wuhan (China). College of Life Science and Technology; Li, Hua-Min [Beijing Bioscience Research Center (China); Shu, Fu-Chang; Wang, Zheng-Liang [Yangtze Univ., Jingzhou, Hubei (China). College of Chemistry and Environmental Engineering; Yu, Long-Jiang [Huazhong Univ. of Science and Technology, Wuhan (China). College of Life Science and Technology

    2012-08-15

    Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes. (orig.)

  18. Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir.

    Science.gov (United States)

    Zhang, Fan; She, Yue-Hui; Li, Hua-Min; Zhang, Xiao-Tao; Shu, Fu-Chang; Wang, Zheng-Liang; Yu, Long-Jiang; Hou, Du-Jie

    2012-08-01

    Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes.

  19. Seasonal Analysis of Microbial Communities in Precipitation in the Greater Tokyo Area, Japan

    Directory of Open Access Journals (Sweden)

    Satoshi Hiraoka

    2017-08-01

    Full Text Available The presence of microbes in the atmosphere and their transport over long distances across the Earth's surface was recently shown. Precipitation is likely a major path by which aerial microbes fall to the ground surface, affecting its microbial ecosystems and introducing pathogenic microbes. Understanding microbial communities in precipitation is of multidisciplinary interest from the perspectives of microbial ecology and public health; however, community-wide and seasonal analyses have not been conducted. Here, we carried out 16S rRNA amplicon sequencing of 30 precipitation samples that were aseptically collected over 1 year in the Greater Tokyo Area, Japan. The precipitation microbial communities were dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria and were overall consistent with those previously reported in atmospheric aerosols and cloud water. Seasonal variations in composition were observed; specifically, Proteobacteria abundance significantly decreased from summer to winter. Notably, estimated ordinary habitats of precipitation microbes were dominated by animal-associated, soil-related, and marine-related environments, and reasonably consistent with estimated air mass backward trajectories. To our knowledge, this is the first amplicon-sequencing study investigating precipitation microbial communities involving sampling over the duration of a year.

  20. Mapping the ecological networks of microbial communities.

    Science.gov (United States)

    Xiao, Yandong; Angulo, Marco Tulio; Friedman, Jonathan; Waldor, Matthew K; Weiss, Scott T; Liu, Yang-Yu

    2017-12-11

    Mapping the ecological networks of microbial communities is a necessary step toward understanding their assembly rules and predicting their temporal behavior. However, existing methods require assuming a particular population dynamics model, which is not known a priori. Moreover, those methods require fitting longitudinal abundance data, which are often not informative enough for reliable inference. To overcome these limitations, here we develop a new method based on steady-state abundance data. Our method can infer the network topology and inter-taxa interaction types without assuming any particular population dynamics model. Additionally, when the population dynamics is assumed to follow the classic Generalized Lotka-Volterra model, our method can infer the inter-taxa interaction strengths and intrinsic growth rates. We systematically validate our method using simulated data, and then apply it to four experimental data sets. Our method represents a key step towards reliable modeling of complex, real-world microbial communities, such as the human gut microbiota.

  1. Microbial community composition is unaffected by anode potential

    KAUST Repository

    Zhu, Xiuping

    2014-01-21

    There is great controversy on how different set anode potentials affect the performance of a bioelectrochemical system (BES). It is often reported that more positive potentials improve acclimation and performance of exoelectrogenic biofilms, and alter microbial community structure, while in other studies relatively more negative potentials were needed to achieve higher current densities. To address this issue, the biomass, electroactivity, and community structure of anodic biofilms were examined over a wide range of set anode potentials (-0.25, -0.09, 0.21, 0.51, and 0.81 V vs a standard hydrogen electrode, SHE) in single-chamber microbial electrolysis cells. Maximum currents produced using a wastewater inoculum increased with anode potentials in the range of -0.25 to 0.21 V, but decreased at 0.51 and 0.81 V. The maximum currents were positively correlated with increasing biofilm biomass. Pyrosequencing indicated biofilm communities were all similar and dominated by bacteria most similar to Geobacter sulfurreducens. Differences in anode performance with various set potentials suggest that the exoelectrogenic communities self-regulate their exocellular electron transfer pathways to adapt to different anode potentials. © 2013 American Chemical Society.

  2. Microbial community composition is unaffected by anode potential

    KAUST Repository

    Zhu, Xiuping; Yates, Matthew D.; Hatzell, Marta C.; Rao, Hari Ananda; Saikaly, Pascal; Logan, Bruce E.

    2014-01-01

    There is great controversy on how different set anode potentials affect the performance of a bioelectrochemical system (BES). It is often reported that more positive potentials improve acclimation and performance of exoelectrogenic biofilms, and alter microbial community structure, while in other studies relatively more negative potentials were needed to achieve higher current densities. To address this issue, the biomass, electroactivity, and community structure of anodic biofilms were examined over a wide range of set anode potentials (-0.25, -0.09, 0.21, 0.51, and 0.81 V vs a standard hydrogen electrode, SHE) in single-chamber microbial electrolysis cells. Maximum currents produced using a wastewater inoculum increased with anode potentials in the range of -0.25 to 0.21 V, but decreased at 0.51 and 0.81 V. The maximum currents were positively correlated with increasing biofilm biomass. Pyrosequencing indicated biofilm communities were all similar and dominated by bacteria most similar to Geobacter sulfurreducens. Differences in anode performance with various set potentials suggest that the exoelectrogenic communities self-regulate their exocellular electron transfer pathways to adapt to different anode potentials. © 2013 American Chemical Society.

  3. Effects of a ciliate protozoa predator on microbial communities in pitcher plant (Sarracenia purpurea leaves.

    Directory of Open Access Journals (Sweden)

    Taylor K Paisie

    Full Text Available The aquatic communities found within the water filled leaves of the pitcher plant, Sarracenia purpurea, have a simple trophic structure providing an ideal system to study microscale interactions between protozoan predators and their bacterial prey. In this study, replicate communities were maintained with and without the presence of the bactivorous protozoan, Colpoda steinii, to determine the effects of grazing on microbial communities. Changes in microbial (Archaea and Bacteria community structure were assessed using iTag sequencing of 16S rRNA genes. The microbial communities were similar with and without the protozoan predator, with>1000 species. Of these species, Archaea were negligible, with Bacteria comprising 99.99% of the microbial community. The Proteobacteria and Bacteroidetes were the most dominant phyla. The addition of a protozoan predator did not have a significant effect on microbial evenness nor richness. However, the presence of the protozoan did cause a significant shift in the relative abundances of a number of bacterial species. This suggested that bactivorous protozoan may target specific bacterial species and/or that certain bacterial species have innate mechanisms by which they evade predators. These findings help to elucidate the effect that trophic structure perturbations have on predator prey interactions in microbial systems.

  4. In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study

    Directory of Open Access Journals (Sweden)

    Mallette Natasha

    2009-12-01

    Full Text Available Abstract Background Three methods were developed for the application of stoichiometry-based network analysis approaches including elementary mode analysis to the study of mass and energy flows in microbial communities. Each has distinct advantages and disadvantages suitable for analyzing systems with different degrees of complexity and a priori knowledge. These approaches were tested and compared using data from the thermophilic, phototrophic mat communities from Octopus and Mushroom Springs in Yellowstone National Park (USA. The models were based on three distinct microbial guilds: oxygenic phototrophs, filamentous anoxygenic phototrophs, and sulfate-reducing bacteria. Two phases, day and night, were modeled to account for differences in the sources of mass and energy and the routes available for their exchange. Results The in silico models were used to explore fundamental questions in ecology including the prediction of and explanation for measured relative abundances of primary producers in the mat, theoretical tradeoffs between overall productivity and the generation of toxic by-products, and the relative robustness of various guild interactions. Conclusion The three modeling approaches represent a flexible toolbox for creating cellular metabolic networks to study microbial communities on scales ranging from cells to ecosystems. A comparison of the three methods highlights considerations for selecting the one most appropriate for a given microbial system. For instance, communities represented only by metagenomic data can be modeled using the pooled method which analyzes a community's total metabolic potential without attempting to partition enzymes to different organisms. Systems with extensive a priori information on microbial guilds can be represented using the compartmentalized technique, employing distinct control volumes to separate guild-appropriate enzymes and metabolites. If the complexity of a compartmentalized network creates an

  5. Cutaneous Microbial Community Variation across Populations of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis

    Directory of Open Access Journals (Sweden)

    Obed Hernández-Gómez

    2017-07-01

    Full Text Available Multicellular hosts maintain complex associations with microbial communities. While microbial communities often serve important functional roles for their hosts, our understanding of the local and regional processes that structure these communities remains limited. Metacommunity analyses provide a promising tool for investigating mechanisms shaping microbiome heterogeneity, which is essential for predicting functional variation between hosts. Using a metacommunity framework, we examined heterogeneity in the skin microbiome of the eastern hellbender (Cryptobranchus alleganiensis alleganiensis. Hellbenders are broadly distributed throughout river systems in the eastern United States, but are present in specific environmental locations throughout their range. The large range of the species and history of population fragmentation suggest that local and regional processes contribute to the distribution of cutaneous symbiont diversity. Therefore, we characterized the skin and environmental bacterial communities at eight rivers throughout the range of the species. We observed variation among hellbender populations in skin microbial community diversity and proportion of shared operational taxonomic units (OTUs between animal and river water communities. Among populations sampled, we noted significant clumped OTU turnover (i.e., Clementsian structure resulting in unique cutaneous communities. In addition, we observed a significant positive correlation between skin community divergence and hellbender population genetic divergence. Host-population skin community dissimilarity did not correlate strongly with distance between sampling locations, indicating a weak spatial effect on the distribution of symbionts. These results suggest that species sorting mechanisms (i.e., local processes structure local skin microbial communities in hellbenders. The variation in skin community composition observed among host populations foreshadows a similar pattern in

  6. Quantitative comparison of the in situ microbial communities in different biomes

    Energy Technology Data Exchange (ETDEWEB)

    White, D.C. [Tennessee Univ., Knoxville, TN (United States)]|[Oak Ridge National Lab., TN (United States); Ringelberg, D.B.; Palmer, R.J. [Tennessee Univ., Knoxville, TN (United States). Center for Environmental Biotechnology

    1995-12-31

    A system to define microbial communities in different biomes requires the application of non-traditional methodology. Classical microbiological methods have severe limitations for the analysis of environmental samples. Pure-culture isolation, biochemical testing, and/or enumeration by direct microscopic counting are not well suited for the estimation of total biomass or the assessment of community composition within environmental samples. Such methods provide little insight into the in situ phenotypic activity of the extant microbiota since these techniques are dependent on microbial growth and thus select against many environmental microorganisms which are non- culturable under a wide range of conditions. It has been repeatedly documented in the literature that viable counts or direct counts of bacteria attached to sediment grains are difficult to quantitative and may grossly underestimate the extent of the existing community. The traditional tests provide little indication of the in situ nutritional status or for evidence of toxicity within the microbial community. A more recent development (MIDI Microbial Identification System), measure free and ester-linked fatty acids from isolated microorganisms. Bacterial isolates are identified by comparing their fatty acid profiles to the MIKI database which contains over 8000 entries. The application of the MIKI system to the analysis of environmental samples however, has significant drawbacks. The MIDI system was developed to identify clinical microorganisms and requires their isolation and culture on trypticase soy agar at 27{degrees}C. Since many isolates are unable to grow at these restrictive growth conditions, the system does not lend itself to identification of some environmental organisms. A more applicable methodology for environmental microbial analysis is based on the liquid extrication and separation of microbial lipids from environmental samples, followed by quantitative analysis using gas chromatography/

  7. Growing Rocks: Implications of Lithification for Microbial Communities and Nutrient Cycling

    Science.gov (United States)

    Corman, J. R.; Poret-Peterson, A. T.; Elser, J. J.

    2014-12-01

    Lithifying microbial communities ("microbialites") have left their signature on Earth's rock record for over 3.4 billion years and are regarded as important players in paleo-biogeochemical cycles. In this project, we study extant microbialites to understand the interactions between lithification and resource availability. All microbes need nutrients and energy for growth; indeed, nutrients are often a factor limiting microbial growth. We hypothesize that calcium carbonate deposition can sequester bioavailable phosphorus (P) and expect the growth of microbialites to be P-limited. To test our hypothesis, we first compared nutrient limitation in lithifying and non-lithifying microbial communities in Río Mesquites, Cuatro Ciénegas. Then, we experimentally manipulated calcification rates in the Río Mesquites microbialites. Our results suggest that lithifying microbialites are indeed P-limited, while non-lithifying, benthic microbial communities tend towards co-limitation by nitrogen (N) and P. Indeed, in microbialites, photosynthesis and aerobic respiration responded positively to P additions (Pbacterial community composition based on analysis of 16S rRNA genes. Unexpectedly, calcification rates increased with OC additions (P<0.05), but not with P additions, suggesting that sulfate reduction may be an important pathway for calcification. Experimental reductions in calcification rates caused changes to microbial biomass OC and P concentrations (P<0.01 and P<0.001, respectively), although shifts depended on whether calcification was decreased abiotically or biotically. These results show that resource availability does influence microbialite formation and that lithification may promote phosphorus limitation; however, further investigation is required to understand the mechanism by which the later occurs.

  8. Effects of application of corn straw on soil microbial community structure during the maize growing season.

    Science.gov (United States)

    Lu, Ping; Lin, Yin-Hua; Yang, Zhong-Qi; Xu, Yan-Peng; Tan, Fei; Jia, Xu-Dong; Wang, Miao; Xu, De-Rong; Wang, Xi-Zhuo

    2015-01-01

    This study investigated the influence of corn straw application on soil microbial communities and the relationship between such communities and soil properties in black soil. The crop used in this study was maize (Zea mays L.). The five treatments consisted of applying a gradient (50, 100, 150, and 200%) of shattered corn straw residue to the soil. Soil samples were taken from May through September during the 2012 maize growing season. The microbial community structure was determined using phospholipid fatty acid (PLFA) analysis. Our results revealed that the application of corn straw influenced the soil properties and increased the soil organic carbon and total nitrogen. Applying corn straw to fields also influenced the variation in soil microbial biomass and community composition, which is consistent with the variations found in soil total nitrogen (TN) and soil respiration (SR). However, the soil carbon-to-nitrogen ratio had no effect on soil microbial communities. The abundance of PLFAs, TN, and SR was higher in C1.5 than those in other treatments, suggesting that the soil properties and soil microbial community composition were affected positively by the application of corn straw to black soil. A Principal Component Analysis indicated that soil microbial communities were different in the straw decomposition processes. Moreover, the soil microbial communities from C1.5 were significantly different from those of CK (p soil and significant variations in the ratio of monounsaturated-to-branched fatty acids with different straw treatments that correlated with SR (p soil properties and soil microbial communities and that these properties affect these communities. The individual PLFA signatures were sensitive indicators that reflected the changes in the soil environment condition. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Microbial communities in acid water environments of two mines, China

    Energy Technology Data Exchange (ETDEWEB)

    Shengmu, Xiao; Xuehui, Xie [College of Environmental Science and Engineering, Donghua University, Shanghai (China); Jianshe, Liu [College of Environmental Science and Engineering, Donghua University, Shanghai (China); School of Resources Processing and Bioengineering, Central South University, Changsha (China)], E-mail: xiaoshengmu@gmail.com

    2009-03-15

    To understand the compositions and structures of microbial communities in different acid-aqueous environments, a PCR-based cloning approach was used. A total of five samples were collected from two mines in China. Two samples, named as G1 and G2, were acid mine drainage (AMD) samples and from Yunfu sulfide mine in Guangdong province, China. The rest of the three samples named as D1, DY and D3, were from three sites undertaking bioleaching in Yinshan lead-zinc mine in Jiangxi province, China. Phylogenetic analysis revealed that bacteria in the five samples fell into six putative divisions, which were {alpha}-Proteobacteria, {beta}-Proteobacteria, {gamma}-Proteobacteria, Firmicutes, Actinobacteria and Nitrospira. Archaea was only detected in the three samples from Yinshan lead-zinc mine, which fell into two phylogenentic divisions, Thermoplsma and Ferroplasma. In addition, the results of principal component analysis (PCA) suggested that more similar the geochemical properties in samples were, more similar microbial community structures in samples were. - Microbial community compositions in acid-aqueous environments from Chinese mines were studied, and the relationship with geochemical properties was obtained.

  10. Microbial communities in acid water environments of two mines, China

    International Nuclear Information System (INIS)

    Xiao Shengmu; Xie Xuehui; Liu Jianshe

    2009-01-01

    To understand the compositions and structures of microbial communities in different acid-aqueous environments, a PCR-based cloning approach was used. A total of five samples were collected from two mines in China. Two samples, named as G1 and G2, were acid mine drainage (AMD) samples and from Yunfu sulfide mine in Guangdong province, China. The rest of the three samples named as D1, DY and D3, were from three sites undertaking bioleaching in Yinshan lead-zinc mine in Jiangxi province, China. Phylogenetic analysis revealed that bacteria in the five samples fell into six putative divisions, which were α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Firmicutes, Actinobacteria and Nitrospira. Archaea was only detected in the three samples from Yinshan lead-zinc mine, which fell into two phylogenentic divisions, Thermoplsma and Ferroplasma. In addition, the results of principal component analysis (PCA) suggested that more similar the geochemical properties in samples were, more similar microbial community structures in samples were. - Microbial community compositions in acid-aqueous environments from Chinese mines were studied, and the relationship with geochemical properties was obtained

  11. Growth and element flux at fine taxonomic resolution in natural microbial communities

    Science.gov (United States)

    Hungate, Bruce; Mau, Rebecca; Schwartz, Egbert; Caporaso, J. Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J.; Liu, Cindy M.; McHugh, Theresa; Marks, Jane C.; Morrissey, Ember; Price, Lance B.

    2015-04-01

    Microorganisms are the engines of global biogeochemical cycles, driving half of all photosynthesis and nearly all decomposition. Yet, quantifying the rates at which uncultured microbial taxa grow and transform elements in intact and highly diverse natural communities in the environment remains among the most pressing challenges in microbial ecology today. Here, we show how shifts in the density of DNA caused by stable isotope incorporation can be used to estimate the growth rates of individual bacterial taxa in intact soil communities. We found that the distribution of growth rates followed the familiar lognormal distribution observed for the abundances, biomasses, and traits of many organisms. Growth rates of most bacterial taxa increased in response to glucose amendment, though the increase in growth observed for many taxa was larger than could be explained by direct utilization of the added glucose for growth, illustrating that glucose addition indirectly stimulated the utilization of other substrates. Variation in growth rates and phylogenetic distances were quantitatively related, connecting evolutionary history and biogeochemical function in intact soil microbial communities. Our approach has the potential to identify biogeochemically significant taxa in the microbial community and quantify their contributions to element transformations and ecosystem processes.

  12. Enrichment of extremophilic exoelectrogens in microbial electrolysis cells using Red Sea brine pools as inocula

    KAUST Repository

    Chehab, Noura A.

    2017-05-03

    Applying microbial electrochemical technologies for the treatment of highly saline or thermophilic solutions is challenging due to the lack of proper inocula to enrich for efficient exoelectrogens. Brine pools from three different locations (Valdivia, Atlantis II and Kebrit) in the Red Sea were investigated as potential inocula sources for enriching exoelectrogens in microbial electrolysis cells (MECs) under thermophilic (70°C) and hypersaline (25% salinity) conditions. Of these, only the Valdivia brine pool produced high and consistent current 6.8 ± 2.1 A/m2-anode in MECs operated at a set anode potential of +0.2 V vs. Ag/AgCl (+0.405 V vs. standard hydrogen electrode). These results show that exoelectrogens are present in these extreme environments and can be used to startup MEC under thermophilic and hypersaline conditions. Bacteroides was enriched on the anode of the Valdivia MEC, but it was not detected in the open circuit voltage reactor seeded with the Valdivia brine pool.

  13. Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years

    DEFF Research Database (Denmark)

    Rezende, Julia Rosa de; Kjeldsen, Kasper Urup; Hubert, Casey RJ

    2013-01-01

    S rRNA and of the dissimilatory (bi)sulfite reductase (dsrAB) genes within the endospore-forming SRB genus Desulfotomaculum. The thermophilic Desulfotomaculum community in Aarhus Bay sediments consisted of at least 23 species-level 16S rRNA sequence phylotypes. In two cases, pairs of identical 16S r......RNA and dsrAB sequences in Arctic surface sediment 3000km away showed that the same phylotypes are present in both locations. Radiotracer-enhanced most probable number analysis revealed that the abundance of endospores of thermophilic SRB in Aarhus Bay sediment was ca. 104 per cm3 at the surface and decreased...... in water masses preceding sedimentation. The sources of these thermophiles remain enigmatic, but at least one source may be common to both Aarhus Bay and Arctic sediments....

  14. Magnetic Separation for the Direct Observation of Mineral-Associated Microbial Diversity

    Science.gov (United States)

    Harrison, B. K.; Orphan, V.

    2006-12-01

    Previous studies have demonstrated that microorganisms may selectively colonize mineral surfaces in diverse environments. Mineral substrates may serve as an important source of limiting nutrients or provide electron acceptors and donors for dissimilatory reactions. This work presents a new method for characterizing the microbial diversity associated with specific components in environmental samples. Minerals are concentrated from the bulk sample according to magnetic susceptibility, resulting in compositionally distinct partitions. The microbial communities associated with these partitions are subsequently characterized using molecular techniques. Initial testing of samples from active and dormant hydrothermal chimney structures from the Lau and Fiji Basins show that mineral components may be concentrated from bulk samples without concealing pre-existing patterns of selective colonization. 16S gene surveys from environmental clone libraries reveal distinct colonization patterns for thermophilic archaea and bacteria between sulfide mineral partitions. This method offers a unique tool discerning the role of mineral composition in surface-associated diversity.

  15. Effects of uranium concentration on microbial community structure and functional potential.

    Science.gov (United States)

    Sutcliffe, Brodie; Chariton, Anthony A; Harford, Andrew J; Hose, Grant C; Greenfield, Paul; Elbourne, Liam D H; Oytam, Yalchin; Stephenson, Sarah; Midgley, David J; Paulsen, Ian T

    2017-08-01

    Located in the Northern Territory of Australia, Ranger uranium mine is directly adjacent to the UNESCO World Heritage listed Kakadu National Park, with rehabilitation targets needed to ensure the site can be incorporated into the park following the mine's closure in 2026. This study aimed to understand the impact of uranium concentration on microbial communities, in order to identify and describe potential breakpoints in microbial ecosystem services. This is the first study to report in situ deployment of uranium-spiked sediments along a concentration gradient (0-4000 mg U kg -1 ), with the study design maximising the advantages of both field surveys and laboratory manipulative studies. Changes to microbial communities were characterised through the use of amplicon and shotgun metagenomic next-generation sequencing. Significant changes to taxonomic and functional community assembly occurred at a concentration of 1500 mg U kg -1 sediment and above. At uranium concentrations of ≥ 1500 mg U kg -1 , genes associated with methanogenic consortia and processes increased in relative abundance, while numerous significant changes were also seen in the relative abundances of genes involved in nitrogen cycling. Such alterations in carbon and nitrogen cycling pathways suggest that taxonomic and functional changes to microbial communities may result in changes in ecosystem processes and resilience. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  16. Soil microbial community responses to acid exposure and neutralization treatment.

    Science.gov (United States)

    Shin, Doyun; Lee, Yunho; Park, Jeonghyun; Moon, Hee Sun; Hyun, Sung Pil

    2017-12-15

    Changes in microbial community induced by acid shock were studied in the context of potential release of acids to the environment due to chemical accidents. The responses of microbial communities in three different soils to the exposure to sulfuric or hydrofluoric acid and to the subsequent neutralization treatment were investigated as functions of acid concentration and exposure time by using 16S-rRNA gene based pyrosequencing and DGGE (Denaturing Gradient Gel Electrophoresis). Measurements of soil pH and dissolved ion concentrations revealed that the added acids were neutralized to different degrees, depending on the mineral composition and soil texture. Hydrofluoric acid was more effectively neutralized by the soils, compared with sulfuric acid at the same normality. Gram-negative ß-Proteobacteria were shown to be the most acid-sensitive bacterial strains, while spore-forming Gram-positive Bacilli were the most acid-tolerant. The results of this study suggest that the Gram-positive to Gram-negative bacterial ratio may serve as an effective bio-indicator in assessing the impact of the acid shock on the microbial community. Neutralization treatments helped recover the ratio closer to their original values. The findings of this study show that microbial community changes as well as geochemical changes such as pH and dissolved ion concentrations need to be considered in estimating the impact of an acid spill, in selecting an optimal remediation strategy, and in deciding when to end remedial actions at the acid spill impacted site. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Applying functional metagenomics to search for novel lignocellulosic enzymes in a microbial consortium derived from a thermophilic composting phase of sugarcane bagasse and cow manure.

    Science.gov (United States)

    Colombo, Lívia Tavares; de Oliveira, Marcelo Nagem Valério; Carneiro, Deisy Guimarães; de Souza, Robson Assis; Alvim, Mariana Caroline Tocantins; Dos Santos, Josenilda Carlos; da Silva, Cynthia Canêdo; Vidigal, Pedro Marcus Pereira; da Silveira, Wendel Batista; Passos, Flávia Maria Lopes

    2016-09-01

    Environments where lignocellulosic biomass is naturally decomposed are sources for discovery of new hydrolytic enzymes that can reduce the high cost of enzymatic cocktails for second-generation ethanol production. Metagenomic analysis was applied to discover genes coding carbohydrate-depleting enzymes from a microbial laboratory subculture using a mix of sugarcane bagasse and cow manure in the thermophilic composting phase. From a fosmid library, 182 clones had the ability to hydrolyse carbohydrate. Sequencing of 30 fosmids resulted in 12 contigs encoding 34 putative carbohydrate-active enzymes belonging to 17 glycosyl hydrolase (GH) families. One third of the putative proteins belong to the GH3 family, which includes β-glucosidase enzymes known to be important in the cellulose-deconstruction process but present with low activity in commercial enzyme preparations. Phylogenetic analysis of the amino acid sequences of seven selected proteins, including three β-glucosidases, showed low relatedness with protein sequences deposited in databases. These findings highlight microbial consortia obtained from a mixture of decomposing biomass residues, such as sugar cane bagasse and cow manure, as a rich resource of novel enzymes potentially useful in biotechnology for saccharification of lignocellulosic substrate.

  18. Peatland Microbial Communities and Decomposition Processes in the James Bay Lowlands, Canada

    Science.gov (United States)

    Preston, Michael D.; Smemo, Kurt A.; McLaughlin, James W.; Basiliko, Nathan

    2012-01-01

    Northern peatlands are a large repository of atmospheric carbon due to an imbalance between primary production by plants and microbial decomposition. The James Bay Lowlands (JBL) of northern Ontario are a large peatland-complex but remain relatively unstudied. Climate change models predict the region will experience warmer and drier conditions, potentially altering plant community composition, and shifting the region from a long-term carbon sink to a source. We collected a peat core from two geographically separated (ca. 200 km) ombrotrophic peatlands (Victor and Kinoje Bogs) and one minerotrophic peatland (Victor Fen) located near Victor Bog within the JBL. We characterized (i) archaeal, bacterial, and fungal community structure with terminal restriction fragment length polymorphism of ribosomal DNA, (ii) estimated microbial activity using community level physiological profiling and extracellular enzymes activities, and (iii) the aeration and temperature dependence of carbon mineralization at three depths (0–10, 50–60, and 100–110 cm) from each site. Similar dominant microbial taxa were observed at all three peatlands despite differences in nutrient content and substrate quality. In contrast, we observed differences in basal respiration, enzyme activity, and the magnitude of substrate utilization, which were all generally higher at Victor Fen and similar between the two bogs. However, there was no preferential mineralization of carbon substrates between the bogs and fens. Microbial community composition did not correlate with measures of microbial activity but pH was a strong predictor of activity across all sites and depths. Increased peat temperature and aeration stimulated CO2 production but this did not correlate with a change in enzyme activities. Potential microbial activity in the JBL appears to be influenced by the quality of the peat substrate and the presence of microbial inhibitors, which suggests the existing peat substrate will have a large

  19. Investigation of the microbial communities colonizing prepainted steel used for roofing and walling.

    Science.gov (United States)

    Huynh, Tran T; Jamil, Ili; Pianegonda, Nicole A; Blanksby, Stephen J; Barker, Philip J; Manefield, Mike; Rice, Scott A

    2017-04-01

    Microbial colonization of prepainted steel, commonly used in roofing applications, impacts their aesthetics, durability, and functionality. Understanding the relevant organisms and the mechanisms by which colonization occurs would provide valuable information that can be subsequently used to design fouling prevention strategies. Here, next-generation sequencing and microbial community finger printing (T-RFLP) were used to study the community composition of microbes colonizing prepainted steel roofing materials at Burrawang, Australia and Kapar, Malaysia over a 52-week period. Community diversity was low and was dominated by Bacillus spp., cyanobacteria, actinobacteria, Cladosporium sp., Epicoccum nigrum, and Teratosphaeriaceae sp. Cultivation-based methods isolated approximately 20 different fungi and bacteria, some of which, such as E. nigrum and Cladosporium sp., were represented in the community sequence data. Fluorescence in situ hybridization imaging showed that fungi were the most dominant organisms present. Analysis of the sequence and T-RFLP data indicated that the microbial communities differed significantly between locations and changed significantly over time. The study demonstrates the utility of molecular ecology tools to identify and characterize microbial communities associated with the fouling of painted steel surfaces and ultimately can enable the targeted development of control strategies based on the dominant species responsible for fouling. © 2016 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  20. Emergent biosynthetic capacity in simple microbial communities.

    Directory of Open Access Journals (Sweden)

    Hsuan-Chao Chiu

    2014-07-01

    Full Text Available Microbes have an astonishing capacity to transform their environments. Yet, the metabolic capacity of a single species is limited and the vast majority of microorganisms form complex communities and join forces to exhibit capabilities far exceeding those achieved by any single species. Such enhanced metabolic capacities represent a promising route to many medical, environmental, and industrial applications and call for the development of a predictive, systems-level understanding of synergistic microbial capacity. Here we present a comprehensive computational framework, integrating high-quality metabolic models of multiple species, temporal dynamics, and flux variability analysis, to study the metabolic capacity and dynamics of simple two-species microbial ecosystems. We specifically focus on detecting emergent biosynthetic capacity--instances in which a community growing on some medium produces and secretes metabolites that are not secreted by any member species when growing in isolation on that same medium. Using this framework to model a large collection of two-species communities on multiple media, we demonstrate that emergent biosynthetic capacity is highly prevalent. We identify commonly observed emergent metabolites and metabolic reprogramming patterns, characterizing typical mechanisms of emergent capacity. We further find that emergent secretion tends to occur in two waves, the first as soon as the two organisms are introduced, and the second when the medium is depleted and nutrients become limited. Finally, aiming to identify global community determinants of emergent capacity, we find a marked association between the level of emergent biosynthetic capacity and the functional/phylogenetic distance between community members. Specifically, we demonstrate a "Goldilocks" principle, where high levels of emergent capacity are observed when the species comprising the community are functionally neither too close, nor too distant. Taken together

  1. Nanomodification of the electrodes in microbial fuel cell: impact of nanoparticle density on electricity production and microbial community

    DEFF Research Database (Denmark)

    Al Atraktchi, Fatima Al-Zahraa; Zhang, Yifeng; Angelidaki, Irini

    2014-01-01

    The nano-decoration of electrode with nanoparticles is one effective way to enhance power output of microbial fuel cells (MFCs). However, the amount of nanoparticles used for decoration has not been optimized yet, and how it affects the microbial community is still unknown. In this study, differe...

  2. Lineage-specific responses of microbial communities to environmental change.

    Science.gov (United States)

    Youngblut, Nicholas D; Shade, Ashley; Read, Jordan S; McMahon, Katherine D; Whitaker, Rachel J

    2013-01-01

    A great challenge facing microbial ecology is how to define ecologically relevant taxonomic units. To address this challenge, we investigated how changing the definition of operational taxonomic units (OTUs) influences the perception of ecological patterns in microbial communities as they respond to a dramatic environmental change. We used pyrosequenced tags of the bacterial V2 16S rRNA region, as well as clone libraries constructed from the cytochrome oxidase C gene ccoN, to provide additional taxonomic resolution for the common freshwater genus Polynucleobacter. At the most highly resolved taxonomic scale, we show that distinct genotypes associated with the abundant Polynucleobacter lineages exhibit divergent spatial patterns and dramatic changes over time, while the also abundant Actinobacteria OTUs are highly coherent. This clearly demonstrates that different bacterial lineages demand different taxonomic definitions to capture ecological patterns. Based on the temporal distribution of highly resolved taxa in the hypolimnion, we demonstrate that change in the population structure of a single genotype can provide additional insight into the mechanisms of community-level responses. These results highlight the importance and feasibility of examining ecological change in microbial communities across taxonomic scales while also providing valuable insight into the ecological characteristics of ecologically coherent groups in this system.

  3. Exogenous Nitrogen Addition Reduced the Temperature Sensitivity of Microbial Respiration without Altering the Microbial Community Composition

    Directory of Open Access Journals (Sweden)

    Hui Wei

    2017-12-01

    Full Text Available Atmospheric nitrogen (N deposition is changing in both load quantity and chemical composition. The load effects have been studied extensively, whereas the composition effects remain poorly understood. We conducted a microcosm experiment to study how N chemistry affected the soil microbial community composition characterized by phospholipid fatty acids (PLFAs and activity indicated by microbial CO2 release. Surface and subsurface soils collected from an old-growth subtropical forest were supplemented with three N-containing materials (ammonium, nitrate, and urea at the current regional deposition load (50 kg ha-1 yr-1 and incubated at three temperatures (10, 20, and 30°C to detect the interactive effects of N deposition and temperature. The results showed that the additions of N, regardless of form, did not alter the microbial PLFAs at any of the three temperatures. However, the addition of urea significantly stimulated soil CO2 release in the early incubation stage. Compared with the control, N addition consistently reduced the temperature dependency of microbial respiration, implying that N deposition could potentially weaken the positive feedback of the warming-stimulated soil CO2 release to the atmosphere. The consistent N effects for the surface and subsurface soils suggest that the effects of N on soil microbial communities may be independent of soil chemical contents and stoichiometry.

  4. Thermophilic prokaryotic communities inhabiting the biofilm and well water of a thermal karst system located in Budapest (Hungary).

    Science.gov (United States)

    Anda, Dóra; Makk, Judit; Krett, Gergely; Jurecska, Laura; Márialigeti, Károly; Mádl-Szőnyi, Judit; Borsodi, Andrea K

    2015-07-01

    In this study, scanning electron microscopy (SEM) and 16S rRNA gene-based phylogenetic approach were applied to reveal the morphological structure and genetic diversity of thermophilic prokaryotic communities of a thermal karst well located in Budapest (Hungary). Bacterial and archaeal diversity of the well water (73.7 °C) and the biofilm developed on the inner surface of an outflow pipeline of the well were studied by molecular cloning method. According to the SEM images calcium carbonate minerals serve as a surface for colonization of bacterial aggregates. The vast majority of the bacterial and archaeal clones showed the highest sequence similarities to chemolithoautotrophic species. The bacterial clone libraries were dominated by sulfur oxidizer Thiobacillus (Betaproteobacteria) in the water and Sulfurihydrogenibium (Aquificae) in the biofilm. A relatively high proportion of molecular clones represented genera Thermus and Bellilinea in the biofilm library. The most abundant phylotypes both in water and biofilm archaeal clone libraries were closely related to thermophilic ammonia oxidizer Nitrosocaldus and Nitrososphaera but phylotypes belonging to methanogens were also detected. The results show that in addition to the bacterial sulfur and hydrogen oxidation, mainly archaeal ammonia oxidation may play a decisive role in the studied thermal karst system.

  5. Impact of temperature and substrate concentration on degradation rates of acetate, propionate and hydrogen and their links to microbial community structure.

    Science.gov (United States)

    Zhao, Jing; Westerholm, Maria; Qiao, Wei; Yin, Dongmin; Bi, Shaojie; Jiang, Mengmeng; Dong, Renjie

    2018-05-01

    The present study investigates the conversion of acetate, propionate and hydrogen consumption linked to the microbial community structure and related to temperature and substrate concentration. Biogas reactors were continuously fed with coffee powder (20 g-COD/L) or acetate (20, 40, and 60 g-COD/L) and operated for 193 days at 37 °C or 55 °C conditions. Starting HRT was 23 days which was then reduced to 7 days. The kinetics of acetate and propionate degradation and hydrogen consumption rates were measured in batch assays. At HRT 7 days, the degradation rate of propionate was higher in thermophilic batches, while acetate degradation rate was higher at mesophilic conditions. The gaseous hydrogen consumption in acetate reactors increased proportionally with temperature and substrate concentration, while the dissolved hydrogen was not affected. The relative high abundance of hydrogentrophic methanogens indicated that the methanogenesis was directed towards the syntrophic acetate oxidation pathway at high acetate concentration and high temperature. Copyright © 2018 Elsevier Ltd. All rights reserved.

  6. Particle size variations of activated carbon on biofilm formation in thermophilic biohydrogen production from palm oil mill effluent

    International Nuclear Information System (INIS)

    Jamali, Nur Syakina; Jahim, Jamaliah Md; Isahak, Wan Nor Roslam Wan; Abdul, Peer Mohamed

    2017-01-01

    Highlights: • Biofilm was developed on GAC by self-attachment immobilisation. • Effect of various micropore size of GAC was evaluated in H_2 production. • Capability of attached-biofilm to degrade cellulosic fibre in POME was evaluated. • Microbial community colonized on GAC was characterised. - Abstract: In this study, we examined the formation of thermophilic microbial biofilm by self-attachment on microbial carrier of granular activated carbon (GAC) in five different micro-pore volumes 0.31, 0.41, 0.44, 0.48, and 0.50 cm"3/g. It was found that the highest hydrogen production rate of 100.8 ± 3.7 mmol H_2/l.d and yield of 1.01 ± 0.07 mol H_2/mol sugar were obtained at 0.44 cm"3/g volume size of GAC. The cellulolytic activity of attached-biofilm was further investigated using POME as a feedstock. The results showed that in all diluted POME substrate, the total sugar consumed by the microbes was found higher than that the amount of soluble monomeric sugar present in the POME medium. It is believe that the microbial biofilm was able to hydrolyse polymeric sugar of cellulosic fibre in the POME by performing enzymatic hydrolysis into simple monomeric sugar. The isolated biofilm bacteria that subjected to 16S rRNA gene analysis presented 99% high homology to the species of Thermoanaerobacterium thermosaccharolyticum which were guaranteed to perform a cellulosic degradation activity.

  7. Non-destructive sampling of rock-dwelling microbial communities using sterile adhesive tape.

    Science.gov (United States)

    Cutler, Nick A; Oliver, Anna E; Viles, Heather A; Whiteley, Andrew S

    2012-12-01

    Building stone provides a habitat for an array of microorganisms, many of which have been demonstrated to have a deleterious effect on the appearance and/or structural integrity of stone masonry. It is essential to understand the composition and structure of stone-dwelling (lithobiontic) microbial communities if successful stone conservation strategies are to be applied, particularly in the face of global environmental change. Ideally, the techniques used to sample such assemblages should be non-destructive due to the sensitive conservation status of many stone buildings. This paper quantitatively assesses the performance of sterile adhesive tape as a non-destructive sampling technique and compares the results of tape sampling with an alternative, destructive, sampling method. We used DNA fingerprinting (TRFLP) to characterise the algal, fungal and bacterial communities living on a stone slab. Our results demonstrate that tape sampling may be used to collect viable quantities of microbial DNA from environmental samples. This technique is ideally suited to the sampling of microbial biofilms, particularly when these communities are dominated by green algae. It provides a good approximation of total community diversity (i.e. the aggregate diversity of epilithic and endolithic communities). Tape sampling is straightforward, rapid and cost effective. When combined with molecular analytical techniques, this sampling method has the potential to make a major contribution to efforts to understand the structure of lithobiontic microbial communities and our ability to predict the response of such communities to future environmental change. Copyright © 2012 Elsevier B.V. All rights reserved.

  8. Termite hindguts and the ecology of microbial communities in the sequencing age.

    Science.gov (United States)

    Tai, Vera; Keeling, Patrick J

    2013-01-01

    Advances in high-throughput nucleic acid sequencing have improved our understanding of microbial communities in a number of ways. Deeper sequence coverage provides the means to assess diversity at the resolution necessary to recover ecological and biogeographic patterns, and at the same time single-cell genomics provides detailed information about the interactions between members of a microbial community. Given the vastness and complexity of microbial ecosystems, such analyses remain challenging for most environments, so greater insight can also be drawn from analysing less dynamic ecosystems. Here, we outline the advantages of one such environment, the wood-digesting hindgut communities of termites and cockroaches, and how it is a model to examine and compare both protist and bacterial communities. Beyond the analysis of diversity, our understanding of protist community ecology will depend on using statistically sound sampling regimes at biologically relevant scales, transitioning from discovery-based to experimental ecology, incorporating single-cell microbiology and other data sources, and continued development of analytical tools. © 2013 The Author(s) Journal of Eukaryotic Microbiology © 2013 International Society of Protistologists.

  9. Metagenomic Insights into Evolution of a Heavy Metal-Contaminated Groundwater Microbial Community

    Energy Technology Data Exchange (ETDEWEB)

    Hemme, Christopher L.; Deng, Ye; Gentry, Terry J.; Fields, Matthew W.; Wu, Liyou; Barua, Soumitra; Barry, Kerrie; Tringe, Susannah G.; Watson, David B.; He, Zhili; Hazen, Terry C.; Tiedje, James M.; Rubin, Edward M.; Zhou, Jizhong

    2010-02-15

    Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents (~;;50 years) have resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying ?- and ?-proteobacterial populations. The resulting community is over-abundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could be a key mechanism in rapidly responding and adapting to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

  10. Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge

    OpenAIRE

    Dahle, H?kon; ?kland, Ingeborg; Thorseth, Ingunn H; Pederesen, Rolf B; Steen, Ida H

    2015-01-01

    Methods developed in geochemical modelling combined with recent advances in molecular microbial ecology provide new opportunities to explore how microbial communities are shaped by their chemical surroundings. Here, we present a framework for analyses of how chemical energy availability shape chemotrophic microbial communities in hydrothermal systems through an investigation of two geochemically different basalt-hosted hydrothermal systems on the Arctic Mid-Ocean Ridge: the Soria Moria Vent f...

  11. Dissolved nitrogen transformations and microbial community structure in the organic layer of forest soils in Olkiluoto in 2006

    International Nuclear Information System (INIS)

    Potila, H.; Sarjala, T.; Aro, L.

    2007-02-01

    Carbon (C) and nitrogen (N) cycles in the ecosystem are strongly coupled. Biomass, structure and activity of the bacterial and fungal community are the key factors influencing C and N cycles. Changes in the function of soil microbial community can be a signal of plant responses to environmental changes. Dissolved N compounds, microbial biomass, microbial activity, fungal community structure and functional diversity of microbial communities were measured in September 2006 from five monitoring plots on Olkiluoto to assess information about soil microbial community structure and activity. High within and between variation in the studied plots were detected. However, in this study the values and their variation in the level of N mineralisation, dissolved N compounds, fungal biomass and microbial community structure in the studied plots were within a normal range in comparison with other published data of similar forest types in Finland. (orig.)

  12. Diversity and Function of Microbial Community in Chinese Strong-Flavor Baijiu Ecosystem: A Review

    Directory of Open Access Journals (Sweden)

    Wei Zou

    2018-04-01

    Full Text Available Strong flavor baijiu (SFB, also called Luzhou-flavor liquor, is the most popular Chinese baijiu. It is manufactured via solid fermentation, with daqu as the starter. Microbial diversity of the SFB ecosystem and the synergistic effects of the enzymes and compounds produced by them are responsible for the special flavor and mouthfeel of SFB. The present review covers research studies focused on microbial community analysis of the SFB ecosystem, including the culturable microorganisms, their metabolic functions, microbial community diversity and their interactions. The review specifically emphasizes on the most recently conducted culture-independent analysis of SFB microbial community diversity. Furthermore, the possible application of systems biology approaches for elucidating the molecular mechanisms of SFB production were also reviewed and prospected.

  13. The microbial community of the cystic fibrosis airway is disrupted in early life.

    Directory of Open Access Journals (Sweden)

    Julie Renwick

    Full Text Available Molecular techniques have uncovered vast numbers of organisms in the cystic fibrosis (CF airways, the clinical significance of which is yet to be determined. The aim of this study was to describe and compare the microbial communities of the lower airway of clinically stable children with CF and children without CF.Bronchoalveolar lavage (BAL fluid and paired oropharyngeal swabs from clinically stable children with CF (n = 13 and BAL from children without CF (n = 9 were collected. DNA was isolated, the 16S rRNA regions amplified, fragmented, biotinylated and hybridised to a 16S rRNA microarray. Patient medical and demographic information was recorded and standard microbiological culture was performed.A diverse bacterial community was detected in the lower airways of children with CF and children without CF. The airway microbiome of clinically stable children with CF and children without CF were significantly different as measured by Shannon's Diversity Indices (p = 0.001; t test and Principle coordinate analysis (p = 0.01; Adonis test. Overall the CF airway microbial community was more variable and had a less even distribution than the microbial community in the airways of children without CF. We highlighted several bacteria of interest, particularly Prevotella veroralis, CW040 and a Corynebacterium, which were of significantly differential abundance between the CF and non-CF lower airways. Both Pseudomonas aeruginosa and Streptococcus pneumoniae culture abundance were found to be associated with CF airway microbial community structure. The CF upper and lower airways were found to have a broadly similar microbial milieu.The microbial communities in the lower airways of stable children with CF and children without CF show significant differences in overall diversity. These discrepancies indicate a disruption of the airway microflora occurring early in life in children with CF.

  14. Bar-coded pyrosequencing reveals the responses of PBDE-degrading microbial communities to electron donor amendments.

    Directory of Open Access Journals (Sweden)

    Meiying Xu

    Full Text Available Polybrominated diphenyl ethers (PBDEs can be reductively degraded by microorganisms under anaerobic conditions. However, little is known about the effect of electron donors on microbial communities involved in PBDEs degradation. Here we employed 454 Titanium pyrosequencing to examine the phylogenetic diversity, composition, structure and dynamics of microbial communities from microcosms under the conditions of different electron donor amendments. The community structures in each of the five alternate electron donor enrichments were significantly shifted in comparison with those of the control microcosm. Commonly existing OTUs between the treatment and control consortia increased from 5 to 17 and more than 50% of OTUs increased around 13.7 to 186 times at least in one of the microcosms after 90-days enrichment. Although the microbial communities at different taxonomic levels were significantly changed by different environmental variable groups in redundancy analysis, significant correlations were observed between the microbial communities and PBDE congener profiles. The lesser-brominated PBDE congeners, tri-BDE congener (BDE-32 and hexa-BDE, were identified as the key factors shaping the microbial community structures at OTU level. Some rare populations, including the known dechlorinating bacterium, Dehalobacter, showed significant positive-correlation with the amounts of PBDE congeners in the consortia. The same results were also observed on some unclassified bacteria. These results suggest that PBDEs-degrading microbial communities can be successfully enriched, and their structures and compositions can be manipulated through adjusting the environmental parameters.

  15. Microbial community analysis of shallow subsurface samples with PCR-DGGE

    Energy Technology Data Exchange (ETDEWEB)

    Itaevaara, M.; Suihko, M. -L.; Kapanen, A.; Piskonen, R.; Juvonen, R. [VTT Biotechnology, Espoo (Finland)

    2005-11-15

    This work is part of the site investigations for the disposal of spent nuclear fuel in Olkiluoto bedrock. The purpose of the research was to study the suitability of PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) method for monitoring of hydrogeomicrobiology of Olkiluoto repository site. PCR-DGGE method has been applied for monitoring microbial processes in several applications. The benefit of the method is that microorganisms are not cultivated but the presence of microbial communities can be monitored by direct DNA extractions from the environmental samples. Partial 16SrDNA gene sequence is specifically amplified by PCR (polymerase chain reaction) which detect bacteria as a group. The gene sequences are separated in DGGE, and the nucleotide bands are then cut out, extracted, sequenced and identified by the genelibraries by e.g. Blast program. PCR-DGGE method can be used to detect microorganisms which are present abundantly in the microbial communities because small quantities of genes cannot be separated reliably. However, generally the microorganisms involved in several environmental processes are naturally enriched and present as major population. This makes it possible to utilize PCRDGGE as a monitoring method. In this study, we studied the structure of microbial communities in ten ground water samples originating from Olkiluoto. Two universal bacterial primer sets were compared which amplified two different regions of the 16SrDNA gene. The longer sequence amplified resulted in fewer bands in DGGE, in addition there were problems with purification of the sequences after DGGE. The shorter sequence gave more bands in DGGE and more clear results without any amplification problems. Comparison of the sequences from the gene-libraries resulted in the detection of the same species by both primer sets, in addition some different species were detected. Several species were anaerobic bacteria, such as acetogenic and sulphate reducing

  16. Microbial community analysis of shallow subsurface samples with PCR-DGGE

    International Nuclear Information System (INIS)

    Itaevaara, M.; Suihko, M.-L.; Kapanen, A.; Piskonen, R.; Juvonen, R.

    2005-11-01

    This work is part of the site investigations for the disposal of spent nuclear fuel in Olkiluoto bedrock. The purpose of the research was to study the suitability of PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) method for monitoring of hydrogeomicrobiology of Olkiluoto repository site. PCR-DGGE method has been applied for monitoring microbial processes in several applications. The benefit of the method is that microorganisms are not cultivated but the presence of microbial communities can be monitored by direct DNA extractions from the environmental samples. Partial 16SrDNA gene sequence is specifically amplified by PCR (polymerase chain reaction) which detect bacteria as a group. The gene sequences are separated in DGGE, and the nucleotide bands are then cut out, extracted, sequenced and identified by the genelibraries by e.g. Blast program. PCR-DGGE method can be used to detect microorganisms which are present abundantly in the microbial communities because small quantities of genes cannot be separated reliably. However, generally the microorganisms involved in several environmental processes are naturally enriched and present as major population. This makes it possible to utilize PCRDGGE as a monitoring method. In this study, we studied the structure of microbial communities in ten ground water samples originating from Olkiluoto. Two universal bacterial primer sets were compared which amplified two different regions of the 16SrDNA gene. The longer sequence amplified resulted in fewer bands in DGGE, in addition there were problems with purification of the sequences after DGGE. The shorter sequence gave more bands in DGGE and more clear results without any amplification problems. Comparison of the sequences from the gene-libraries resulted in the detection of the same species by both primer sets, in addition some different species were detected. Several species were anaerobic bacteria, such as acetogenic and sulphate reducing

  17. Deciphering Diversity Indices for a Better Understanding of Microbial Communities.

    Science.gov (United States)

    Kim, Bo-Ra; Shin, Jiwon; Guevarra, Robin; Lee, Jun Hyung; Kim, Doo Wan; Seol, Kuk-Hwan; Lee, Ju-Hoon; Kim, Hyeun Bum; Isaacson, Richard

    2017-12-28

    The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using cultureindependent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate large-scale data sets that describe the microbial composition of a certain niche. Consequently, understanding microbial diversity becomes of greater importance when investigating the composition, function, and dynamics of the microbiota associated with health and diseases. Even though there is no general agreement on which diversity index is the best to use, diversity indices have been used to compare the diversity among samples and between treatments with controls. Tools such as the Shannon- Weaver index and Simpson index can be used to describe population diversity in samples. The purpose of this review is to explain the principles of diversity indices, such as Shannon- Weaver and Simpson, to aid general microbiologists in better understanding bacterial communities. In this review, important questions concerning microbial diversity are addressed. Information from this review should facilitate evidence-based strategies to explore microbial communities.

  18. Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers

    Science.gov (United States)

    Cobaugh, Kelly L.; Schaeffer, Sean M.; DeBruyn, Jennifer M.

    2015-01-01

    The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession

  19. Interactions between plant and rhizosphere microbial communities in a metalliferous soil

    International Nuclear Information System (INIS)

    Epelde, Lur; Becerril, Jose M.; Barrutia, Oihana; Gonzalez-Oreja, Jose A.; Garbisu, Carlos

    2010-01-01

    In the present work, the relationships between plant consortia, consisting of 1-4 metallicolous pseudometallophytes with different metal-tolerance strategies (Thlaspi caerulescens: hyperaccumulator; Jasione montana: accumulator; Rumex acetosa: indicator; Festuca rubra: excluder), and their rhizosphere microbial communities were studied in a mine soil polluted with high levels of Cd, Pb and Zn. Physiological response and phytoremediation potential of the studied pseudometallophytes were also investigated. The studied metallicolous populations are tolerant to metal pollution and offer potential for the development of phytoextraction and phytostabilization technologies. T. caerulescens appears very tolerant to metal stress and most suitable for metal phytoextraction; the other three species enhance soil functionality. Soil microbial properties had a stronger effect on plant biomass rather than the other way around (35.2% versus 14.9%). An ecological understanding of how contaminants, ecosystem functions and biological communities interact in the long-term is needed for proper management of these fragile metalliferous ecosystems. - Rhizosphere microbial communities in highly polluted mine soils are determinant for the growth of pseudometallophytes.

  20. Modeling microbial community structure and functional diversity across time and space.

    Science.gov (United States)

    Larsen, Peter E; Gibbons, Sean M; Gilbert, Jack A

    2012-07-01

    Microbial communities exhibit exquisitely complex structure. Many aspects of this complexity, from the number of species to the total number of interactions, are currently very difficult to examine directly. However, extraordinary efforts are being made to make these systems accessible to scientific investigation. While recent advances in high-throughput sequencing technologies have improved accessibility to the taxonomic and functional diversity of complex communities, monitoring the dynamics of these systems over time and space - using appropriate experimental design - is still expensive. Fortunately, modeling can be used as a lens to focus low-resolution observations of community dynamics to enable mathematical abstractions of functional and taxonomic dynamics across space and time. Here, we review the approaches for modeling bacterial diversity at both the very large and the very small scales at which microbial systems interact with their environments. We show that modeling can help to connect biogeochemical processes to specific microbial metabolic pathways. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  1. Interactions between plant and rhizosphere microbial communities in a metalliferous soil

    Energy Technology Data Exchange (ETDEWEB)

    Epelde, Lur [NEIKER-Tecnalia, Department of Ecosystems, c/Berreaga 1, E-48160 Derio (Spain); Becerril, Jose M.; Barrutia, Oihana [Department of Plant Biology and Ecology, University of the Basque Country, UPV/EHU, P.O. Box 644, E-48080 Bilbao (Spain); Gonzalez-Oreja, Jose A. [NEIKER-Tecnalia, Department of Ecosystems, c/Berreaga 1, E-48160 Derio (Spain); Garbisu, Carlos, E-mail: cgarbisu@neiker.ne [NEIKER-Tecnalia, Department of Ecosystems, c/Berreaga 1, E-48160 Derio (Spain)

    2010-05-15

    In the present work, the relationships between plant consortia, consisting of 1-4 metallicolous pseudometallophytes with different metal-tolerance strategies (Thlaspi caerulescens: hyperaccumulator; Jasione montana: accumulator; Rumex acetosa: indicator; Festuca rubra: excluder), and their rhizosphere microbial communities were studied in a mine soil polluted with high levels of Cd, Pb and Zn. Physiological response and phytoremediation potential of the studied pseudometallophytes were also investigated. The studied metallicolous populations are tolerant to metal pollution and offer potential for the development of phytoextraction and phytostabilization technologies. T. caerulescens appears very tolerant to metal stress and most suitable for metal phytoextraction; the other three species enhance soil functionality. Soil microbial properties had a stronger effect on plant biomass rather than the other way around (35.2% versus 14.9%). An ecological understanding of how contaminants, ecosystem functions and biological communities interact in the long-term is needed for proper management of these fragile metalliferous ecosystems. - Rhizosphere microbial communities in highly polluted mine soils are determinant for the growth of pseudometallophytes.

  2. Soil biochar amendment shapes the composition of N_2O-reducing microbial communities

    International Nuclear Information System (INIS)

    Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H.; Kappler, Andreas; Behrens, Sebastian

    2016-01-01

    Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N_2O) emissions. N_2O is a potent greenhouse gas. The main sources of N_2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N_2O emission mitigation and the abundance and activity of N_2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described ‘atypical’ nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N_2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N_2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N_2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. - Highlights: • Biochar promoted anaerobic, alkalinity-adapted, and polymer-degrading microbial taxa. • Biochar fostered the development of distinct N_2O-reducing microbial taxa. • Taxonomic shifts among N_2O-reducing microbes might explain lower N_2O emissions.

  3. Aerobic carbon-cycle related microbial communities in boreal peatlands: responses to water-level drawdown

    Energy Technology Data Exchange (ETDEWEB)

    Peltoniemi, K

    2010-07-01

    Boreal peatlands represent a considerable portion of the global carbon (C) pool. Water-level drawdown (WLD) causes peatland drying and induces a vegetation change, which affects the decomposition of soil organic matter and the release of greenhouse gases (CO{sub 2} and CH{sub 4}). The objective of this thesis was to study the microbial communities related to the C cycle and their response to WLD in two boreal peatlands. Both sampling depth and site type had a strong impact on all microbial communities. In general, bacteria dominated the deeper layers of the nutrient-rich fen and the wettest surfaces of the nutrient-poor bog sites, whereas fungi seemed more abundant in the drier surfaces of the bog. WLD clearly affected the microbial communities but the effect was dependent on site type. The fungal and methane-oxidizing bacteria (MOB) community composition changed at all sites but the actinobacterial community response was apparent only in the fen after WLD. Microbial communities became more similar among sites after long-term WLD. Litter quality had a large impact on community composition, whereas the effects of site type and WLD were relatively minor. The decomposition rate of fresh organic matter was influenced slightly by actinobacteria, but not at all by fungi. Field respiration measurements in the northern fen indicated that WLD accelerates the decomposition of soil organic matter. In addition, a correlation between activity and certain fungal sequences indicated that community composition affects the decomposition of older organic matter in deeper peat layers. WLD had a negative impact on CH{sub 4} oxidation, especially in the oligotrophic fen. Fungal sequences were matched to taxa capable of utilizing a broad range of substrates. Most of the actinobacterial sequences could not be matched to characterized taxa in reference databases. This thesis represents the first investigation of microbial communities and their response to WLD among a variety of boreal

  4. Genome-wide association study of Arabidopsis thaliana leaf microbial community.

    Science.gov (United States)

    Horton, Matthew W; Bodenhausen, Natacha; Beilsmith, Kathleen; Meng, Dazhe; Muegge, Brian D; Subramanian, Sathish; Vetter, M Madlen; Vilhjálmsson, Bjarni J; Nordborg, Magnus; Gordon, Jeffrey I; Bergelson, Joy

    2014-11-10

    Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the fungi and bacteria that colonize its leaves and the host loci that influence the microbe numbers. The composition of this community differs among accessions of A. thaliana. Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community. Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.

  5. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    Directory of Open Access Journals (Sweden)

    Yao Zhang

    Full Text Available To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4 concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4 was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4 concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  6. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    Science.gov (United States)

    Zhang, Yao; Zhao, Zihao; Chen, Chen-Tung Arthur; Tang, Kai; Su, Jianqiang; Jiao, Nianzhi

    2012-01-01

    To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4)) concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4) was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4) concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  7. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients.

    Science.gov (United States)

    Fierer, Noah; Lauber, Christian L; Ramirez, Kelly S; Zaneveld, Jesse; Bradford, Mark A; Knight, Rob

    2012-05-01

    Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.

  8. The impact of zero-valent iron nanoparticles upon soil microbial communities is context dependent.

    Science.gov (United States)

    Pawlett, Mark; Ritz, Karl; Dorey, Robert A; Rocks, Sophie; Ramsden, Jeremy; Harris, Jim A

    2013-02-01

    Nanosized zero-valent iron (nZVI) is an effective land remediation tool, but there remains little information regarding its impact upon and interactions with the soil microbial community. nZVI stabilised with sodium carboxymethyl cellulose was applied to soils of three contrasting textures and organic matter contents to determine impacts on soil microbial biomass, phenotypic (phospholipid fatty acid (PLFA)), and functional (multiple substrate-induced respiration (MSIR)) profiles. The nZVI significantly reduced microbial biomass by 29 % but only where soil was amended with 5 % straw. Effects of nZVI on MSIR profiles were only evident in the clay soils and were independent of organic matter content. PLFA profiling indicated that the soil microbial community structure in sandy soils were apparently the most, and clay soils the least, vulnerable to nZVI suggesting a protective effect imparted by clays. Evidence of nZVI bactericidal effects on Gram-negative bacteria and a potential reduction of arbuscular mycorrhizal fungi are presented. Data imply that the impact of nZVI on soil microbial communities is dependent on organic matter content and soil mineral type. Thereby, evaluations of nZVI toxicity on soil microbial communities should consider context. The reduction of AM fungi following nZVI application may have implications for land remediation.

  9. Microbial activity and community structure in two drained fen soils in the Ljubljana Marsh

    NARCIS (Netherlands)

    Kraigher, Barbara; Stres, Blaz; Hacin, Janez; Ausec, Luka; Mahne, Ivan; van Elsas, Jan D.; Mandic-Mulec, Ines

    Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is a general lack of knowledge about the microbial communities that abound in these systems. We examined the microbial activity and community structure in two fen soils differing in SOC content sampled

  10. Soil microbial community of abandoned sand fields

    Czech Academy of Sciences Publication Activity Database

    Elhottová, Dana; Szili-Kovács, T.; Tříska, Jan

    2002-01-01

    Roč. 47, č. 4 (2002), s. 435-440 ISSN 0015-5632 R&D Projects: GA ČR GA526/99/P033 Grant - others:OTKA(HU) T25739 Institutional research plan: CEZ:AV0Z6066911 Keywords : microbial community * abandoned fields Subject RIV: EH - Ecology, Behaviour Impact factor: 0.979, year: 2002

  11. Monitoring the microbial community during solid-state acetic acid fermentation of Zhenjiang aromatic vinegar.

    Science.gov (United States)

    Xu, Wei; Huang, Zhiyong; Zhang, Xiaojun; Li, Qi; Lu, Zhenming; Shi, Jinsong; Xu, Zhenghong; Ma, Yanhe

    2011-09-01

    Zhenjiang aromatic vinegar is one of the most famous Chinese traditional vinegars. In this study, change of the microbial community during its fermentation process was investigated. DGGE results showed that microbial community was comparatively stable, and the diversity has a disciplinary series of changes during the fermentation process. It was suggested that domestication of microbes and unique cycle-inoculation style used in the fermentation of Zhenjiang aromatic vinegar were responsible for comparatively stable of the microbial community. Furthermore, two clone libraries were constructed. The results showed that bacteria presented in the fermentation belonged to genus Lactobacillus, Acetobacter, Gluconacetobacter, Staphylococcus, Enterobacter, Pseudomonas, Flavobacterium and Sinorhizobium, while the fungi were genus Saccharomyces. DGGE combined with clone library analysis was an effective and credible technique for analyzing the microbial community during the fermentation process of Zhenjiang aromatic vinegar. Real-time PCR results suggested that the biomass showed a "system microbes self-domestication" process in the first 5 days, then reached a higher level at the 7th day before gradually decreasing until the fermentation ended at the 20th day. This is the first report to study the changes of microbial community during fermentation process of Chinese traditional solid-state fermentation of vinegar. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs

    Directory of Open Access Journals (Sweden)

    Ping Hu

    2016-01-01

    Full Text Available Oil reservoirs are major sites of methane production and carbon turnover, processes with significant impacts on energy resources and global biogeochemical cycles. We applied a cultivation-independent genomic approach to define microbial community membership and predict roles for specific organisms in biogeochemical transformations in Alaska North Slope oil fields. Produced water samples were collected from six locations between 1,128 m (24 to 27°C and 2,743 m (80 to 83°C below the surface. Microbial community complexity decreased with increasing temperature, and the potential to degrade hydrocarbon compounds was most prevalent in the lower-temperature reservoirs. Sulfate availability, rather than sulfate reduction potential, seems to be the limiting factor for sulfide production in some of the reservoirs under investigation. Most microorganisms in the intermediate- and higher-temperature samples were related to previously studied methanogenic and nonmethanogenic archaea and thermophilic bacteria, but one candidate phylum bacterium, a member of the Acetothermia (OP1, was present in Kuparuk sample K3. The greatest numbers of candidate phyla were recovered from the mesothermic reservoir samples SB1 and SB2. We reconstructed a nearly complete genome for an organism from the candidate phylum Parcubacteria (OD1 that was abundant in sample SB1. Consistent with prior findings for members of this lineage, the OD1 genome is small, and metabolic predictions support an obligately anaerobic, fermentation-based lifestyle. At moderate abundance in samples SB1 and SB2 were members of bacteria from other candidate phyla, including Microgenomates (OP11, Atribacteria (OP9, candidate phyla TA06 and WS6, and Marinimicrobia (SAR406. The results presented here elucidate potential roles of organisms in oil reservoir biological processes.

  13. Silver Sulfidation in Thermophilic Anaerobic Digesters and Effects on Antibiotic Resistance Genes

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Bojeong; Miller, Jennifer H.; Monsegue, Niven; Levard, Clément; Hong, Yanjuan; Hull, Matthew S.; Murayama, Mitsuhiro; Brown, Gordon E.; Vikesland, Peter J.; Knocke, William R.; Pruden, Amy; Hochella, Michael F.

    2015-12-15

    Physical and chemical transformations and biological responses of silver nanoparticles (AgNPs) in wastewater treatment systems are of particular interest because of the extensive existing and continually growing uses of AgNPs in consumer products. In this study, we investigated the transformation of AgNPs and AgNO3 during thermophilic anaerobic digestion and effects on selection or transfer of antibiotic resistance genes (ARGs). Ag2S-NPs, sulfidation products of both AgNPs and AgNO3, were recovered from raw and digested sludges and were analyzed by analytical transmission electron microscopy (TEM) and X-ray absorption spectroscopy (XAS). TEM and XAS revealed rapid (≤20 min) Ag sulfidation for both Ag treatments. Once transformed, Ag2S-NPs (as individual NPs or an NP aggregate) persisted for the duration of the batch digestion. The digestion process produced Ag2S-NPs that were strongly associated with sludge organics and/or other inorganic precipitates. Ag treatments (up to 1,000 mg Ag/kg) did not have an impact on the performance of thermophilic anaerobic digesters or ARG response, as indicated by quantitative polymerase chain reaction measurements of sul1, tet(W), and tet(O) and also intI1, an indicator of horizontal gene transfer of ARGs. Thus, rapid Ag sulfidation and stabilization with organics effectively sequester Ag and prevent biological interactions with the digester microbial community that could induce horizontal gene transfer or adversely impact digester performance through antimicrobial activity. This finding suggests that sulfide-rich anaerobic environments, such as digesters, likely have a high buffer capacity to mitigate the biological effects of AgNPs.

  14. Changes in coral-associated microbial communities during a bleaching event.

    Science.gov (United States)

    Bourne, David; Iida, Yuki; Uthicke, Sven; Smith-Keune, Carolyn

    2008-04-01

    Environmental stressors such as increased sea surface temperatures are well-known for contributing to coral bleaching; however, the effect of increased temperatures and subsequent bleaching on coral-associated microbial communities is poorly understood. Colonies of the hard coral Acropora millepora were tagged on a reef flat off Magnetic Island (Great Barrier Reef) and surveyed over 2.5 years, which included a severe bleaching event in January/February 2002. Daily average water temperatures exceeded the previous 10-year average by more than 1 degrees C for extended periods with field-based visual surveys recording all tagged colonies displaying signs of bleaching. During the bleaching period, direct counts of coral zooxanthellae densities decreased by approximately 64%, before recovery to pre-bleaching levels after the thermal stress event. A subset of three tagged coral colonies were sampled through the bleaching event and changes in the microbial community elucidated. Denaturing gradient gel electrophoresis (DGGE) analysis demonstrated conserved bacterial banding profiles between the three coral colonies, confirming previous studies highlighting specific microbial associations. As coral colonies bleached, the microbial community shifted and redundancy analysis (RDA) of DGGE banding patterns revealed a correlation of increasing temperature with the appearance of Vibrio-affiliated sequences. Interestingly, this shift to a Vibrio-dominated community commenced prior to visual signs of bleaching. Clone libraries hybridized with Vibrio-specific oligonucleotide probes confirmed an increase in the fraction of Vibrio-affiliated clones during the bleaching period. Post bleaching, the coral microbial associations again shifted, returning to a profile similar to the fingerprints prior to bleaching. This provided further evidence for corals selecting and shaping their microbial partners. For non-bleached samples, a close association with Spongiobacter-related sequences were

  15. Influence of cotton crop development and level of irrigation of microbial community structure

    Science.gov (United States)

    Soil microbial population densities can easily reach one billion cells per gram of soil;and soil microbial diversity has been shown to exceed fifty thousand individual species per gram of soil. Soil type and underlying soil structure are considered primary determinants of microbial community structu...

  16. Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities

    Science.gov (United States)

    Avera, Bethany; Badgley, Brian; Barrett, John E.; Franklin, Josh; Knowlton, Katharine F.; Ray, Partha P.; Smitherman, Crystal

    2017-01-01

    Intensifying livestock production to meet the demands of a growing global population coincides with increases in both the administration of veterinary antibiotics and manure inputs to soils. These trends have the potential to increase antibiotic resistance in soil microbial communities. The effect of maintaining increased antibiotic resistance on soil microbial communities and the ecosystem processes they regulate is unknown. We compare soil microbial communities from paired reference and dairy manure-exposed sites across the USA. Given that manure exposure has been shown to elicit increased antibiotic resistance in soil microbial communities, we expect that manure-exposed sites will exhibit (i) compositionally different soil microbial communities, with shifts toward taxa known to exhibit resistance; (ii) greater abundance of antibiotic resistance genes; and (iii) corresponding maintenance of antibiotic resistance would lead to decreased microbial efficiency. We found that bacterial and fungal communities differed between reference and manure-exposed sites. Additionally, the β-lactam resistance gene ampC was 5.2-fold greater under manure exposure, potentially due to the use of cephalosporin antibiotics in dairy herds. Finally, ampC abundance was positively correlated with indicators of microbial stress, and microbial mass-specific respiration, which increased 2.1-fold under manure exposure. These findings demonstrate that the maintenance of antibiotic resistance associated with manure inputs alters soil microbial communities and ecosystem function. PMID:28356447

  17. Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities.

    Science.gov (United States)

    Wepking, Carl; Avera, Bethany; Badgley, Brian; Barrett, John E; Franklin, Josh; Knowlton, Katharine F; Ray, Partha P; Smitherman, Crystal; Strickland, Michael S

    2017-03-29

    Intensifying livestock production to meet the demands of a growing global population coincides with increases in both the administration of veterinary antibiotics and manure inputs to soils. These trends have the potential to increase antibiotic resistance in soil microbial communities. The effect of maintaining increased antibiotic resistance on soil microbial communities and the ecosystem processes they regulate is unknown. We compare soil microbial communities from paired reference and dairy manure-exposed sites across the USA. Given that manure exposure has been shown to elicit increased antibiotic resistance in soil microbial communities, we expect that manure-exposed sites will exhibit (i) compositionally different soil microbial communities, with shifts toward taxa known to exhibit resistance; (ii) greater abundance of antibiotic resistance genes; and (iii) corresponding maintenance of antibiotic resistance would lead to decreased microbial efficiency. We found that bacterial and fungal communities differed between reference and manure-exposed sites. Additionally, the β-lactam resistance gene ampC was 5.2-fold greater under manure exposure, potentially due to the use of cephalosporin antibiotics in dairy herds. Finally, ampC abundance was positively correlated with indicators of microbial stress, and microbial mass-specific respiration, which increased 2.1-fold under manure exposure. These findings demonstrate that the maintenance of antibiotic resistance associated with manure inputs alters soil microbial communities and ecosystem function. © 2017 The Author(s).

  18. Common Hydraulic Fracturing Fluid Additives Alter the Structure and Function of Anaerobic Microbial Communities.

    Science.gov (United States)

    Mumford, Adam C; Akob, Denise M; Klinges, J Grace; Cozzarelli, Isabelle M

    2018-04-15

    The development of unconventional oil and gas (UOG) resources results in the production of large volumes of wastewater containing a complex mixture of hydraulic fracturing chemical additives and components from the formation. The release of these wastewaters into the environment poses potential risks that are poorly understood. Microbial communities in stream sediments form the base of the food chain and may serve as sentinels for changes in stream health. Iron-reducing organisms have been shown to play a role in the biodegradation of a wide range of organic compounds, and so to evaluate their response to UOG wastewater, we enriched anaerobic microbial communities from sediments collected upstream (background) and downstream (impacted) of an UOG wastewater injection disposal facility in the presence of hydraulic fracturing fluid (HFF) additives: guar gum, ethylene glycol, and two biocides, 2,2-dibromo-3-nitrilopropionamide (DBNPA) and bronopol (C 3 H 6 BrNO 4 ). Iron reduction was significantly inhibited early in the incubations with the addition of biocides, whereas amendment with guar gum and ethylene glycol stimulated iron reduction relative to levels in the unamended controls. Changes in the microbial community structure were observed across all treatments, indicating the potential for even small amounts of UOG wastewater components to influence natural microbial processes. The microbial community structure differed between enrichments with background and impacted sediments, suggesting that impacted sediments may have been preconditioned by exposure to wastewater. These experiments demonstrated the potential for biocides to significantly decrease iron reduction rates immediately following a spill and demonstrated how microbial communities previously exposed to UOG wastewater may be more resilient to additional spills. IMPORTANCE Organic components of UOG wastewater can alter microbial communities and biogeochemical processes, which could alter the rates of

  19. Microbial Communities in Different Tissues of Atta sexdens rubropilosa Leaf-cutting Ants.

    Science.gov (United States)

    Vieira, Alexsandro S; Ramalho, Manuela O; Martins, Cintia; Martins, Vanderlei G; Bueno, Odair C

    2017-10-01

    Bacterial endosymbionts are common in all insects, and symbiosis has played an integral role in ant evolution. Atta sexdens rubropilosa leaf-cutting ants cultivate their symbiotic fungus using fresh leaves. They need to defend themselves and their brood against diseases, but they also need to defend their obligate fungus gardens, their primary food source, from infection, parasitism, and usurpation by competitors. This study aimed to characterize the microbial communities in whole workers and different tissues of A. sexdens rubropilosa queens using Ion Torrent NGS. Our results showed that the microbial community in the midgut differs in abundance and diversity from the communities in the postpharyngeal gland of the queen and in whole workers. The main microbial orders in whole workers were Lactobacillales, Clostridiales, Enterobacteriales, Actinomycetales, Burkholderiales, and Bacillales. In the tissues of the queens, the main orders were Burkholderiales, Clostridiales, Syntrophobacterales, Lactobacillales, Bacillales, and Actinomycetales (midgut) and Entomoplasmatales, unclassified γ-proteobacteria, and Actinomycetales (postpharyngeal glands). The high abundance of Entomoplasmatales in the postpharyngeal glands (77%) of the queens was an unprecedented finding. We discuss the role of microbial communities in different tissues and castes. Bacteria are likely to play a role in nutrition and immune defense as well as helping antimicrobial defense in this ant species.

  20. An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease

    Science.gov (United States)

    Yang, Hongwu; Li, Juan; Xiao, Yunhua; Gu, Yabing; Liu, Hongwei; Liang, Yili; Liu, Xueduan; Hu, Jin; Meng, Delong; Yin, Huaqun

    2017-01-01

    The soil microbial communities play an important role in plant health, however, the relationship between the below-ground microbiome and above-ground plant health remains unclear. To reveal such a relationship, we analyzed soil microbial communities through sequencing of 16S rRNA gene amplicons from 15 different tobacco fields with different levels of wilt disease in the central south part of China. We found that plant health was related to the soil microbial diversity as plants may benefit from the diverse microbial communities. Also, those 15 fields were grouped into ‘healthy’ and ‘infected’ samples based upon soil microbial community composition analyses such as unweighted paired-group method with arithmetic means (UPGMA) and principle component analysis, and furthermore, molecular ecological network analysis indicated that some potential plant-beneficial microbial groups, e.g., Bacillus and Actinobacteria could act as network key taxa, thus reducing the chance of plant soil-borne pathogen invasion. In addition, we propose that a more complex soil ecology network may help suppress tobacco wilt, which was also consistent with highly diversity and composition with plant-beneficial microbial groups. This study provides new insights into our understanding the relationship between the soil microbiome and plant health. PMID:29163453

  1. Ability of industrial anaerobic ecosystems to produce methane from ethanol in psychrophilic, mesophilic and thermophilic conditions

    International Nuclear Information System (INIS)

    Mabala, Jojo Charlie

    2012-01-01

    potential for adaptation depended on the presence of very specific methanogenic Archaea populations. When placing the adapted ecosystems in temperatures different from the original temperature, only mesophilic ecosystems adapted to psychrophilic temperatures. As expected, specific methanogenic activity was always obtained at the original temperature of the ecosystem. Analysis of bacterial and archaeal communities at the end of the acclimation period revealed that acclimation of thermophilic and mesophilic ecosystems to lower temperatures only modified slightly the structure of microbial communities. On the other hand, more significant changes were obtained when the incubation temperature was increased in comparison to the original temperature of the ecosystem. In summary, the study of the effect of incubation temperature (5 deg. C to 55 deg. C) on the fermentation activity and microbial population structure is a good model for laboratory study to understand the impact of abiotic factor on the structural and functional dynamics of a complex microbial community. (author) [fr

  2. Microbial community dynamics and biogas production from manure fractions in sludge bed anaerobic digestion.

    Science.gov (United States)

    Nordgård, A S R; Bergland, W H; Bakke, R; Vadstein, O; Østgaard, K; Bakke, I

    2015-12-01

    To elucidate how granular sludge inoculum and particle-rich organic loading affect the structure of the microbial communities and process performance in upflow anaerobic sludge bed (UASB) reactors. We investigated four reactors run on dairy manure filtrate and four on pig manure supernatant for three months achieving similar methane yields. The reactors fed with less particle rich pig manure stabilized faster and had highest capacity. Microbial community dynamics analysed by a PCR/denaturing gradient gel electrophoresis approach showed that influent was a major determinant for the composition of the reactor communities. Comparisons of pre- and non-adapted inoculum in the reactors run on pig manure supernatant showed that the community structure of the nonadapted inoculum adapted in approximately two months. Microbiota variance partitioning analysis revealed that running time, organic loading rate and inoculum together explained 26 and 31% of the variance in bacterial and archaeal communities respectively. The microbial communities of UASBs adapted to the reactor conditions in treatment of particle rich manure fractions, obtaining high capacity, especially on pig manure supernatant. These findings provide relevant insight into the microbial community dynamics in startup and operation of sludge bed reactors for methane production from slurry fractions, a major potential source of biogas. © 2015 The Society for Applied Microbiology.

  3. The Arsenite Oxidation Potential of Native Microbial Communities from Arsenic-Rich Freshwaters.

    Science.gov (United States)

    Fazi, Stefano; Crognale, Simona; Casentini, Barbara; Amalfitano, Stefano; Lotti, Francesca; Rossetti, Simona

    2016-07-01

    Microorganisms play an important role in speciation and mobility of arsenic in the environment, by mediating redox transformations of both inorganic and organic species. Since arsenite [As(III)] is more toxic than arsenate [As(V)] to the biota, the microbial driven processes of As(V) reduction and As(III) oxidation may play a prominent role in mediating the environmental impact of arsenic contamination. However, little is known about the ecology and dynamics of As(III)-oxidizing populations within native microbial communities exposed to natural high levels of As. In this study, two techniques for single cell quantification (i.e., flow cytometry, CARD-FISH) were used to analyze the structure of aquatic microbial communities across a gradient of arsenic (As) contamination in different freshwater environments (i.e., groundwaters, surface and thermal waters). Moreover, we followed the structural evolution of these communities and their capacity to oxidize arsenite, when experimentally exposed to high As(III) concentrations in experimental microcosms. Betaproteobacteria and Deltaproteobacteria were the main groups retrieved in groundwaters and surface waters, while Beta and Gammaproteobacteria dominated the bacteria community in thermal waters. At the end of microcosm incubations, the communities were able to oxidize up to 95 % of arsenite, with an increase of Alphaproteobacteria in most of the experimental conditions. Finally, heterotrophic As(III)-oxidizing strains (one Alphaproteobacteria and two Gammaproteobacteria) were isolated from As rich waters. Our findings underlined that native microbial communities from different arsenic-contaminated freshwaters can efficiently perform arsenite oxidation, thus contributing to reduce the overall As toxicity to the aquatic biota.

  4. Microbial Community Assessment in Wetlands for Water Pollution Control: Past, Present, and Future Outlook

    Directory of Open Access Journals (Sweden)

    Kela P. Weber

    2016-11-01

    Full Text Available The field of treatment wetlands (TWs is rapidly expanding and, arguably, is tasked with studying and understanding one of the most complex water treatment systems available. Microbial communities are generally considered to be responsible for the majority of wastewater constituent degradation in TWs. However, they are also known to be spatially heterogeneous, temporally dynamic, as well as structurally and functionally diverse. Presented here is a meta-analysis of all peer reviewed TW journal articles which utilized a microbial community assessment methodology over the period of 1988 to July 2016. A total of 1101 papers were reviewed, 512 from 1988 to 2012, 215 of which included a microbial community assessment aspect and were subsequently classified as representing past research, and 589 from 2013 to July 2016, 196 of which were classified as representing current TW microbial community research. In general, TW microbial community research has increased over time, with a marked surge in the past four years. Microbial community structure is currently the most commonly used methodological type followed by activity, enumeration and function, respectively. Areas of research focus included nitrogen transformations (156, organic degradation (33, and emerging contaminants (32, with general characterization studies also accounting for a significant proportion (243. Microbial communities from a range of TW systems have been investigated over the last four years with meso-scale (10–1000 L being the most commonly studied system size followed by large-scale (>100,000 L, micro-scale (<10 L, and pilot-scale (1000–100,000 L. Free water surface flow (SF, horizontal subsurface flow (HF, and vertical flow (VF systems are being studied in approximately equal proportions with the majority of studies focused on gaining fixed media/biofilm samples for analysis (rather than from the rhizosphere or interstitial water. Looking at efforts from a regional perspective

  5. Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition.

    Science.gov (United States)

    Wang, Cheng; Dong, Da; Wang, Haoshu; Müller, Karin; Qin, Yong; Wang, Hailong; Wu, Weixiang

    2016-01-01

    Compost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are thus important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. Studies have revealed substantial diversity in compost microbiomes, yet how this diversity relates to functions and even to the genes encoding lignocellulolytic enzymes remains obscure. Here, we used a metagenomic analysis of the rice straw-adapted (RSA) microbial consortia enriched from compost ecosystems to decipher the systematic and functional contexts within such a distinctive microbiome. Analyses of the 16S pyrotag library and 5 Gbp of metagenomic sequence showed that the phylum Actinobacteria was the predominant group among the Bacteria in the RSA consortia, followed by Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes. The CAZymes profile revealed that CAZyme genes in the RSA consortia were also widely distributed within these bacterial phyla. Strikingly, about 46.1 % of CAZyme genes were from actinomycetal communities, which harbored a substantially expanded catalog of the cellobiohydrolase, β-glucosidase, acetyl xylan esterase, arabinofuranosidase, pectin lyase, and ligninase genes. Among these communities, a variety of previously unrecognized species was found, which reveals a greater ecological functional diversity of thermophilic Actinobacteria than previously assumed. These data underline the pivotal role of thermophilic Actinobacteria in lignocellulose biodegradation processes in the compost habitat. Besides revealing a new benchmark for microbial enzymatic deconstruction of lignocelluloses, the results suggest that actinomycetes found in compost ecosystems are potential candidates for mining efficient lignocellulosic enzymes in the biofuel industry.

  6. Effect of environmental conditions on the fatty acid fingerprint of microbial communities

    Science.gov (United States)

    Biryukov, Mikhail; Dippold, Michaela; Kuzyakov, Yakov

    2014-05-01

    Lipid biomarkers, especially phospholipids, are routinely used to characterize microbial community structure in environmental samples. Interpretations of these fingerprints mainly depend on rare results of pure cultures which were cultivated under standardized batch conditions. However, membrane lipids (e.g. phopholipid biomarker) build up the interface between microorganisms and their environment and consequently are prone to be adapted according to the environmental conditions. We cultivated several bacteria, isolated from soil (gram-positive and gram-negative) under various conditions e.g. C supply and temperature regimes. Effect of growth conditions on phospholipids fatty acid (PLFA) as well as neutral lipid fatty acids (NLFA) and glycolipid fatty acids (GLFA) was investigated by conventional method of extraction and derivatization, followed by assessments with gas chromatography mass spectrometry (GC-MS). In addition, phospholipids were measured as intact molecules by ultra high performance liquid chromatography - quadrupole - time of flight mass spectrometer (UHPLC-Q-ToF) to further assess the composition of headgroups with fatty acids residues and their response on changing environmental conditions. PLFA fingerprints revealed a strong effect of growth stage, C supply and temperature e.g. decrease of temperature increased the amount of branched and/or unsaturated fatty acids to maintain the membrane fluidity. This strongly changes the ratio of specific to unspecific fatty acids depending on environmental conditions. Therefore, amounts of specific fatty acids cannot be used to assess biomass of a functional microbial group in soil. Intracellular neutral lipids depended less on environmental conditions reflecting a more stable biomarker group but also showed less specific fatty acids then PLFA. Therefore, combination of several lipid classes is suggested as more powerful tool to assess amounts and functionality of environmental microbial communities. Further

  7. The gut microbial community of Midas cichlid fish in repeatedly evolved limnetic-benthic species pairs.

    Science.gov (United States)

    Franchini, Paolo; Fruciano, Carmelo; Frickey, Tancred; Jones, Julia C; Meyer, Axel

    2014-01-01

    Gut bacterial communities are now known to influence a range of fitness related aspects of organisms. But how different the microbial community is in closely related species, and if these differences can be interpreted as adaptive is still unclear. In this study we compared microbial communities in two sets of closely related sympatric crater lake cichlid fish species pairs that show similar adaptations along the limnetic-benthic axis. The gut microbial community composition differs in the species pair inhabiting the older of two crater lakes. One major difference, relative to other fish, is that in these cichlids that live in hypersaline crater lakes, the microbial community is largely made up of Oceanospirillales (52.28%) which are halotolerant or halophilic bacteria. This analysis opens up further avenues to identify candidate symbiotic or co-evolved bacteria playing a role in adaptation to similar diets and life-styles or even have a role in speciation. Future functional and phylosymbiotic analyses might help to address these issues.

  8. Hydration status and diurnal trophic interactions shape microbial community function in desert biocrusts

    Directory of Open Access Journals (Sweden)

    M. Kim

    2017-12-01

    Full Text Available Biological soil crusts (biocrusts are self-organised thin assemblies of microbes, lichens, and mosses that are ubiquitous in arid regions and serve as important ecological and biogeochemical hotspots. Biocrust ecological function is intricately shaped by strong gradients of water, light, oxygen, and dynamics in the abundance and spatial organisation of the microbial community within a few millimetres of the soil surface. We report a mechanistic model that links the biophysical and chemical processes that shape the functioning of biocrust representative microbial communities that interact trophically and respond dynamically to cycles of hydration, light, and temperature. The model captures key features of carbon and nitrogen cycling within biocrusts, such as microbial activity and distribution (during early stages of biocrust establishment under diurnal cycles and the associated dynamics of biogeochemical fluxes at different hydration conditions. The study offers new insights into the highly dynamic and localised processes performed by microbial communities within thin desert biocrusts.

  9. Hydration status and diurnal trophic interactions shape microbial community function in desert biocrusts

    Science.gov (United States)

    Kim, Minsu; Or, Dani

    2017-12-01

    Biological soil crusts (biocrusts) are self-organised thin assemblies of microbes, lichens, and mosses that are ubiquitous in arid regions and serve as important ecological and biogeochemical hotspots. Biocrust ecological function is intricately shaped by strong gradients of water, light, oxygen, and dynamics in the abundance and spatial organisation of the microbial community within a few millimetres of the soil surface. We report a mechanistic model that links the biophysical and chemical processes that shape the functioning of biocrust representative microbial communities that interact trophically and respond dynamically to cycles of hydration, light, and temperature. The model captures key features of carbon and nitrogen cycling within biocrusts, such as microbial activity and distribution (during early stages of biocrust establishment) under diurnal cycles and the associated dynamics of biogeochemical fluxes at different hydration conditions. The study offers new insights into the highly dynamic and localised processes performed by microbial communities within thin desert biocrusts.

  10. Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities.

    Science.gov (United States)

    Abraham, Paul E; Giannone, Richard J; Xiong, Weili; Hettich, Robert L

    2014-06-17

    Contemporary microbial ecology studies usually employ one or more "omics" approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other "meta-omic" approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool. Copyright © 2014 John Wiley & Sons, Inc.

  11. Opportunistic Pathogens and Microbial Communities and Their Associations with Sediment Physical Parameters in Drinking Water Storage Tank Sediments

    Science.gov (United States)

    Qin, Ke; Struewing, Ian; Domingo, Jorge Santo; Lytle, Darren

    2017-01-01

    The occurrence and densities of opportunistic pathogens (OPs), the microbial community structure, and their associations with sediment elements from eight water storage tanks in Ohio, West Virginia, and Texas were investigated. The elemental composition of sediments was measured through X-ray fluorescence (XRF) spectra. The occurrence and densities of OPs and amoeba hosts (i.e., Legionella spp. and L. pneumophila, Mycobacterium spp., P. aeruginosa, V. vermiformis, Acanthamoeba spp.) were determined using genus- or species-specific qPCR assays. Microbial community analysis was performed using next generation sequencing on the Illumina Miseq platform. Mycobacterium spp. were most frequently detected in the sediments and water samples (88% and 88%), followed by Legionella spp. (50% and 50%), Acanthamoeba spp. (63% and 13%), V. vermiformis (50% and 25%), and P. aeruginosa (0 and 50%) by qPCR method. Comamonadaceae (22.8%), Sphingomonadaceae (10.3%), and Oxalobacteraceae (10.1%) were the most dominant families by sequencing method. Microbial communities in water samples were mostly separated with those in sediment samples, suggesting differences of communities between two matrices even in the same location. There were associations of OPs with microbial communities. Both OPs and microbial community structures were positively associated with some elements (Al and K) in sediments mainly from pipe material corrosions. Opportunistic pathogens presented in both water and sediments, and the latter could act as a reservoir of microbial contamination. There appears to be an association between potential opportunistic pathogens and microbial community structures. These microbial communities may be influenced by constituents within storage tank sediments. The results imply that compositions of microbial community and elements may influence and indicate microbial water quality and pipeline corrosion, and that these constituents may be important for optimal storage tank management

  12. Profile Changes in the Soil Microbial Community When Desert Becomes Oasis.

    Directory of Open Access Journals (Sweden)

    Chen-hua Li

    Full Text Available The conversion of virgin desert into oasis farmland creates two contrasting types of land-cover. During oasis formation with irrigation and fertilizer application, however, the changes in the soil microbial population, which play critical roles in the ecosystem, remain poorly understood. We applied high-throughput pyrosequencing to investigate bacterial and archaeal communities throughout the profile (0-3 m in an experimental field, where irrigation and fertilization began in 1990 and cropped with winter wheat since then. To assess the effects of cultivation, the following treatments were compared with the virgin desert: CK (no fertilizer, PK, NK, NP, NPK, NPKR, and NPKM (R: straw residue; M: manure fertilizer. Irrigation had a greater impact on the overall microbial community than fertilizer application. The greatest impact occurred in topsoil (0-0.2 m, e.g., Cyanobacteria (25% total abundance were most abundant in desert soil, while Actinobacteria (26% were most abundant in oasis soil. The proportions of extremophilic and photosynthetic groups (e.g., Deinococcus-Thermus and Cyanobacteria decreased, while the proportions of R-strategy (e.g., Gammaproteobacteria including Xanthomonadales, nitrifying (e.g., Nitrospirae, and anaerobic bacteria (e.g., Anaerolineae increased throughout the oasis profile. Archaea occurred only in oasis soil. The impact of fertilizer application was mainly reflected in the non-dominant communities or finer taxonomic divisions. Oasis formation led to a dramatic shift in microbial community and enhanced soil enzyme activities. The rapidly increased soil moisture and decreased salt caused by irrigation were responsible for this shift. Furthermore, difference in fertilization and crop growth altered the organic carbon contents in the soil, which resulted in differences of microbial communities within oasis.

  13. Phylogenetic Evidence for the Existence of Novel Thermophilic Bacteria in Hot Spring Sulfur-Turf Microbial Mats in Japan

    Science.gov (United States)

    Yamamoto, Hiroyuki; Hiraishi, Akira; Kato, Kenji; Chiura, Hiroshi X.; Maki, Yonosuke; Shimizu, Akira

    1998-01-01

    So-called sulfur-turf microbial mats, which are macroscopic white filaments or bundles consisting of large sausage-shaped bacteria and elemental sulfur particles, occur in sulfide-containing hot springs in Japan. However, no thermophiles from sulfur-turf mats have yet been isolated as cultivable strains. This study was undertaken to determine the phylogenetic positions of the sausage-shaped bacteria in sulfur-turf mats by direct cloning and sequencing of 16S rRNA genes amplified from the bulk DNAs of the mats. Common clones with 16S rDNA sequences with similarity levels of 94.8 to 99% were isolated from sulfur-turf mat samples from two geographically remote hot springs. Phylogenetic analysis showed that the phylotypes of the common clones formed a major cluster with members of the Aquifex-Hydrogenobacter complex, which represents the most deeply branching lineage of the domain bacteria. Furthermore, the bacteria of the sulfur-turf mat phylotypes formed a clade distinguishable from that of other members of the Aquifex-Hydrogenobacter complex at the order or subclass level. In situ hybridization with clone-specific probes for 16S rRNA revealed that the common phylotype of sulfur-turf mat bacteria is that of the predominant sausage-shaped bacteria. PMID:9572936

  14. Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes.

    Science.gov (United States)

    Wang, Cheng; Dong, Da; Strong, P J; Zhu, Weijing; Ma, Zhuang; Qin, Yong; Wu, Weixiang

    2017-08-16

    Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases. In this study, changes of resistome expression were determined and related to active microbiome profiles during the dynamic composting process. This was achieved by integrating metagenomic and time series metatranscriptomic data for the evolving microbial community during composting. Composting noticeably reduced the aggregated expression level of the manure resistome, which primarily consisted of genes encoding for tetracycline, vancomycin, fluoroquinolone, beta-lactam, and aminoglycoside resistance, as well as efflux pumps. Furthermore, a varied transcriptional response of resistome to composting at the ARG levels was highlighted. The expression of tetracycline resistance genes (tetM-tetW-tetO-tetS) decreased during composting, where distinctive shifts in the four phases of composting were related to variations in antibiotic concentration. Composting had no effect on the expression of sulfonamide and fluoroquinolone resistance genes, which increased slightly during the thermophilic phase and then decreased to initial levels. As indigenous populations switched greatly throughout the dynamic composting, the core resistome persisted and their reservoir hosts' composition was significantly correlated with dynamic active microbial phylogenetic structure. Hosts for sulfonamide and fuoroquinolone resistance genes changed notably in phylognetic structure

  15. Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea

    Science.gov (United States)

    Graw, Michael F.; D'Angelo, Grace; Borchers, Matthew; Thurber, Andrew R.; Johnson, Joel E.; Zhang, Chuanlun; Liu, Haodong; Colwell, Frederick S.

    2018-01-01

    The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics. PMID:29696012

  16. Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms.

    Science.gov (United States)

    Simonin, Marie; Nunan, Naoise; Bloor, Juliette M G; Pouteau, Valérie; Niboyet, Audrey

    2017-05-01

    Nitrogen (N) addition is known to affect soil microbial communities, but the interactive effects of N addition with other drivers of global change remain unclear. The impacts of multiple global changes on the structure of microbial communities may be mediated by specific microbial groups with different life-history strategies. Here, we investigated the combined effects of elevated CO2 and N addition on soil microbial communities using PLFA profiling in a short-term grassland mesocosm experiment. We also examined the linkages between the relative abundance of r- and K-strategist microorganisms and resistance of the microbial community structure to experimental treatments. N addition had a significant effect on microbial community structure, likely driven by concurrent increases in plant biomass and in soil labile C and N. In contrast, microbial community structure did not change under elevated CO2 or show significant CO2 × N interactions. Resistance of soil microbial community structure decreased with increasing fungal/bacterial ratio, but showed a positive relationship with the Gram-positive/Gram-negative bacterial ratio. Our findings suggest that the Gram-positive/Gram-negative bacteria ratio may be a useful indicator of microbial community resistance and that K-strategist abundance may play a role in the short-term stability of microbial communities under global change. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. Epigeic earthworms exert a bottleneck effect on microbial communities through gut associated processes.

    Science.gov (United States)

    Gómez-Brandón, María; Aira, Manuel; Lores, Marta; Domínguez, Jorge

    2011-01-01

    Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet. To address these questions we determined the microbial community structure (phospholipid fatty acid profiles) and microbial activity (fluorescein diacetate hydrolysis) in the earthworm casts derived from three types of animal manure (cow, horse and pig manure), which differed in microbial composition. The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed. Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions within the decomposer food web influence on nutrient cycling.

  18. Epigeic earthworms exert a bottleneck effect on microbial communities through gut associated processes.

    Directory of Open Access Journals (Sweden)

    María Gómez-Brandón

    Full Text Available BACKGROUND: Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet. METHODOLOGY: To address these questions we determined the microbial community structure (phospholipid fatty acid profiles and microbial activity (fluorescein diacetate hydrolysis in the earthworm casts derived from three types of animal manure (cow, horse and pig manure, which differed in microbial composition. PRINCIPAL FINDINGS: The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed. CONCLUSIONS/SIGNIFICANCE: Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions

  19. Microbial Reduction of Fe(III) and SO42- and Associated Microbial Communities in the Alluvial Aquifer Groundwater and Sediments.

    Science.gov (United States)

    Lee, Ji-Hoon; Lee, Bong-Joo

    2017-11-25

    Agricultural demands continuously increased use of groundwater, causing drawdown of water table and need of artificial recharge using adjacent stream waters. River water intrusion into groundwater can alter the geochemical and microbiological characteristics in the aquifer and subsurface. In an effort to investigate the subsurface biogeochemical activities before operation of artificial recharge at the test site, established at the bank of Nakdong River, Changwon, South Korea, organic carbon transported from river water to groundwater was mimicked and the effect on the indigenous microbial communities was investigated with the microcosm incubations of the groundwater and subsurface sediments. Laboratory incubations indicated microbial reduction of Fe(III) and sulfate. Next-generation Illumina MiSeq sequences of V4 region of 16S rRNA gene provided that the shifts of microbial taxa to Fe(III)-reducing and/or sulfate-reducing microorganisms such as Geobacter, Albidiferax, Desulfocapsa, Desulfuromonas, and Desulfovibrio were in good correlation with the sequential flourishment of microbial reduction of Fe(III) and sulfate as the incubations progressed. This suggests the potential role of dissolved organic carbons migrated with the river water into groundwater in the managed aquifer recharge system on the indigenous microbial community composition and following alterations of subsurface biogeochemistry and microbial metabolic activities.

  20. Comparison of microbial communities associated with three Atlantic ultramafic hydrothermal systems.

    Science.gov (United States)

    Roussel, Erwan G; Konn, Cécile; Charlou, Jean-Luc; Donval, Jean-Pierre; Fouquet, Yves; Querellou, Joël; Prieur, Daniel; Bonavita, Marie-Anne Cambon

    2011-09-01

    The distribution of Archaea and methanogenic, methanotrophic and sulfate-reducing communities in three Atlantic ultramafic-hosted hydrothermal systems (Rainbow, Ashadze, Lost City) was compared using 16S rRNA gene and functional gene (mcrA, pmoA and dsrA) clone libraries. The overall archaeal community was diverse and heterogeneously distributed between the hydrothermal sites and the types of samples analyzed (seawater, hydrothermal fluid, chimney and sediment). The Lost City hydrothermal field, characterized by high alkaline warm fluids (pH>11; Tphylum and Methanopyrales order were also retrieved from the Rainbow and Ashadze hydrothermal fluids. However, the methanogenic Methanococcales was the most widely distributed hyper/thermophilic archaeal group among the hot and acidic ultramafic-hosted hydrothermal system environments. Most of the lineages detected are linked to methane and hydrogen cycling, suggesting that in ultramafic-hosted hydrothermal systems, large methanogenic and methanotrophic communities could be fuelled by hydrothermal fluids highly enriched in methane and hydrogen. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  1. Differences in microbial community composition between injection and production water samples of water flooding petroleum reservoirs

    Directory of Open Access Journals (Sweden)

    P. K. Gao

    2015-06-01

    Full Text Available Microbial communities in injected water are expected to have significant influence on those of reservoir strata in long-term water flooding petroleum reservoirs. To investigate the similarities and differences in microbial communities in injected water and reservoir strata, high-throughput sequencing of microbial partial 16S rRNA of the water samples collected from the wellhead and downhole of injection wells, and from production wells in a homogeneous sandstone reservoir and a heterogeneous conglomerate reservoir were performed. The results indicate that a small number of microbial populations are shared between the water samples from the injection and production wells in the sandstone reservoir, whereas a large number of microbial populations are shared in the conglomerate reservoir. The bacterial and archaeal communities in the reservoir strata have high concentrations, which are similar to those in the injected water. However, microbial population abundance exhibited large differences between the water samples from the injection and production wells. The number of shared populations reflects the influence of microbial communities in injected water on those in reservoir strata to some extent, and show strong association with the unique variation of reservoir environments.

  2. Microbial Community and Functional Gene Changes in Arctic Tundra Soils in a Microcosm Warming Experiment

    Directory of Open Access Journals (Sweden)

    Ziming Yang

    2017-09-01

    Full Text Available Microbial decomposition of soil organic carbon (SOC in thawing Arctic permafrost is important in determining greenhouse gas feedbacks of tundra ecosystems to climate. However, the changes in microbial community structure during SOC decomposition are poorly known. Here we examine these changes using frozen soils from Barrow, Alaska, USA, in anoxic microcosm incubation at −2 and 8°C for 122 days. The functional gene array GeoChip was used to determine microbial community structure and the functional genes associated with SOC degradation, methanogenesis, and Fe(III reduction. Results show that soil incubation after 122 days at 8°C significantly decreased functional gene abundance (P < 0.05 associated with SOC degradation, fermentation, methanogenesis, and iron cycling, particularly in organic-rich soil. These observations correspond well with decreases in labile SOC content (e.g., reducing sugar and ethanol, methane and CO2 production, and Fe(III reduction. In contrast, the community functional structure was largely unchanged in the −2°C incubation. Soil type (i.e., organic vs. mineral and the availability of labile SOC were among the most significant factors impacting microbial community structure. These results demonstrate the important roles of microbial community in SOC degradation and support previous findings that SOC in organic-rich Arctic tundra is highly vulnerable to microbial degradation under warming.

  3. Contrasting microbial community changes during mass extinctions at the Middle/Late Permian and Permian/Triassic boundaries

    Science.gov (United States)

    Xie, Shucheng; Algeo, Thomas J.; Zhou, Wenfeng; Ruan, Xiaoyan; Luo, Genming; Huang, Junhua; Yan, Jiaxin

    2017-02-01

    Microbial communities are known to expand as a result of environmental deterioration during mass extinctions, but differences in microbial community changes between extinction events and their underlying causes have received little study to date. Here, we present a systematic investigation of microbial lipid biomarkers spanning ∼20 Myr (Middle Permian to Early Triassic) at Shangsi, South China, to contrast microbial changes associated with the Guadalupian-Lopingian boundary (GLB) and Permian-Triassic boundary (PTB) mass extinctions. High-resolution analysis of the PTB crisis interval reveals a distinct succession of microbial communities based on secular variation in moretanes, 2-methylhopanes, aryl isoprenoids, steranes, n-alkyl cyclohexanes, and other biomarkers. The first episode of the PTB mass extinction (ME1) was associated with increases in red algae and nitrogen-fixing bacteria along with evidence for enhanced wildfires and elevated soil erosion, whereas the second episode was associated with expansions of green sulfur bacteria, nitrogen-fixing bacteria, and acritarchs coinciding with climatic hyperwarming, ocean stratification, and seawater acidification. This pattern of microbial community change suggests that marine environmental deterioration was greater during the second extinction episode (ME2). The GLB shows more limited changes in microbial community composition and more limited environmental deterioration than the PTB, consistent with differences in species-level extinction rates (∼71% vs. 90%, respectively). Microbial biomarker records have the potential to refine our understanding of the nature of these crises and to provide insights concerning possible outcomes of present-day anthropogenic stresses on Earth's ecosystems.

  4. New steady-state microbial community compositions and process performances in biogas reactors induced by temperature disturbances

    DEFF Research Database (Denmark)

    Luo, Gang; De Francisci, Davide; Kougias, Panagiotis

    2015-01-01

    that stochastic factors had a minor role in shaping the profile of the microbial community composition and activity in biogas reactors. On the contrary, temperature disturbance was found to play an important role in the microbial community composition as well as process performance for biogas reactors. Although...... three different temperature disturbances were applied to each biogas reactor, the increased methane yields (around 10% higher) and decreased volatile fatty acids (VFAs) concentrations at steady state were found in all three reactors after the temperature disturbances. After the temperature disturbance...... in shaping the profile of the microbial community composition and activity in biogas reactors. New steady-state microbial community profiles and reactor performances were observed in all the biogas reactors after the temperature disturbance....

  5. Microbial Fingerprints of Community Structure Correlate with Changes in Ecosystem Function Induced by Perturbing the Redox Environment

    Science.gov (United States)

    Mills, A. L.; Ford, R. M.; Vallino, J. J.; Herman, J. S.; Hornberger, G. M.

    2001-12-01

    Restoration of high-quality groundwater has been an elusive engineering goal. Consequently, natural microbially-mediated reactions are increasingly relied upon to degrade organic contaminants, including hydrocarbons and many synthetic compounds. Of concern is how the introduction of an organic chemical contaminant affects the indigenous microbial communities, the geochemistry of the aquifer, and the function of the ecosystem. The presence of functional redundancy in microbial communities suggests that recovery of the community after a disturbance such as a contamination event could easily result in a community that is similar in function to that which existed prior to the contamination, but which is compositionally quite different. To investigate the relationship between community structure and function we observed the response of a diverse microbial community obtained from raw sewage to a dynamic redox environment using an aerobic/anaerobic/aerobic cycle. To evaluate changes in community function CO2, pH, ammonium and nitrate levels were monitored. A phylogenetically-based DNA technique (tRFLP) was used to assess changes in microbial community structure. Principal component analysis of the tRFLP data revealed significant changes in the composition of the microbial community that correlated well with changes in community function. Results from our experiments will be discussed in the context of a metabolic model based the biogeochemistry of the system. The governing philosophy of this thermodynamically constrained metabolic model is that living systems synthesize and allocate cellular machinery in such a way as to "optimally" utilize available resources in the environment. The robustness of this optimization-based approach provides a powerful tool for studying relationships between microbial diversity and ecosystem function.

  6. Burning fire-prone Mediterranean shrublands: immediate changes in soil microbial community structure and ecosystem functions.

    Science.gov (United States)

    Goberna, M; García, C; Insam, H; Hernández, M T; Verdú, M

    2012-07-01

    Wildfires subject soil microbes to extreme temperatures and modify their physical and chemical habitat. This might immediately alter their community structure and ecosystem functions. We burned a fire-prone shrubland under controlled conditions to investigate (1) the fire-induced changes in the community structure of soil archaea, bacteria and fungi by analysing 16S or 18S rRNA gene amplicons separated through denaturing gradient gel electrophoresis; (2) the physical and chemical variables determining the immediate shifts in the microbial community structure; and (3) the microbial drivers of the change in ecosystem functions related to biogeochemical cycling. Prokaryotes and eukaryotes were structured by the local environment in pre-fire soils. Fire caused a significant shift in the microbial community structure, biomass C, respiration and soil hydrolases. One-day changes in bacterial and fungal community structure correlated to the rise in total organic C and NO(3)(-)-N caused by the combustion of plant residues. In the following week, bacterial communities shifted further forced by desiccation and increasing concentrations of macronutrients. Shifts in archaeal community structure were unrelated to any of the 18 environmental variables measured. Fire-induced changes in the community structure of bacteria, rather than archaea or fungi, were correlated to the enhanced microbial biomass, CO(2) production and hydrolysis of C and P organics. This is the first report on the combined effects of fire on the three biological domains in soils. We concluded that immediately after fire the biogeochemical cycling in Mediterranean shrublands becomes less conservative through the increased microbial biomass, activity and changes in the bacterial community structure.

  7. Microbial community responses to soil tillage and crop rotation in a corn/soybean agroecosystem.

    Science.gov (United States)

    Smith, Chris R; Blair, Peter L; Boyd, Charlie; Cody, Brianne; Hazel, Alexander; Hedrick, Ashley; Kathuria, Hitesh; Khurana, Parul; Kramer, Brent; Muterspaw, Kristin; Peck, Charles; Sells, Emily; Skinner, Jessica; Tegeler, Cara; Wolfe, Zoe

    2016-11-01

    The acreage planted in corn and soybean crops is vast, and these crops contribute substantially to the world economy. The agricultural practices employed for farming these crops have major effects on ecosystem health at a worldwide scale. The microbial communities living in agricultural soils significantly contribute to nutrient uptake and cycling and can have both positive and negative impacts on the crops growing with them. In this study, we examined the impact of the crop planted and soil tillage on nutrient levels, microbial communities, and the biochemical pathways present in the soil. We found that farming practice, that is conventional tillage versus no-till, had a much greater impact on nearly everything measured compared to the crop planted. No-till fields tended to have higher nutrient levels and distinct microbial communities. Moreover, no-till fields had more DNA sequences associated with key nitrogen cycle processes, suggesting that the microbial communities were more active in cycling nitrogen. Our results indicate that tilling of agricultural soil may magnify the degree of nutrient waste and runoff by altering nutrient cycles through changes to microbial communities. Currently, a minority of acreage is maintained without tillage despite clear benefits to soil nutrient levels, and a decrease in nutrient runoff-both of which have ecosystem-level effects and both direct and indirect effects on humans and other organisms.

  8. Influences of Different Halophyte Vegetation on Soil Microbial Community at Temperate Salt Marsh.

    Science.gov (United States)

    Chaudhary, Doongar R; Kim, Jinhyun; Kang, Hojeong

    2018-04-01

    Salt marshes are transitional zone between terrestrial and aquatic ecosystems, occupied mainly by halophytic vegetation which provides numerous ecological services to coastal ecosystem. Halophyte-associated microbial community plays an important role in the adaptation of plants to adverse condition and also affected habitat characteristics. To explore the relationship between halophytes and soil microbial community, we studied the soil enzyme activities, soil microbial community structure, and functional gene abundance in halophytes- (Carex scabrifolia, Phragmites australis, and Suaeda japonica) covered and un-vegetated (mud flat) soils at Suncheon Bay, South Korea. Higher concentrations of total, Gram-positive, Gram-negative, total bacterial, and actinomycetes PLFAs (phospholipid fatty acids) were observed in the soil underneath the halophytes compared with mud flat soil and were highest in Carex soil. Halophyte-covered soils had different microbial community composition due to higher abundance of Gram-negative bacteria than mud flat soil. Similar to PLFA concentrations, the increased activities of β-glucosidase, cellulase, phosphatase, and sulfatase enzymes were observed under halophyte soil compared to mud flat soil and Carex exhibited highest activities. The abundance of archaeal 16S rRNA, fungal ITS, and denitrifying genes (nirK, nirS, and nosZ) were not influenced by the halophytes. Abundance bacterial 16S rRNA and dissimilatory (bi)sulfite (dsrA) genes were highest in Carex-covered soil. The abundance of functional genes involved in methane cycle (mcrA and pmoA) was not affected by the halophytes. However, the ratios of mcrA/pmoA and mcrA/dsrA increased in halophyte-covered soils which indicate higher methanogenesis activities. The finding of the study also suggests that halophytes had increased the microbial and enzyme activities, and played a pivotal role in shaping microbial community structure.

  9. Soil biochar amendment shapes the composition of N2O-reducing microbial communities.

    Science.gov (United States)

    Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H; Kappler, Andreas; Behrens, Sebastian

    2016-08-15

    Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N2O) emissions. N2O is a potent greenhouse gas. The main sources of N2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N2O emission mitigation and the abundance and activity of N2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described 'atypical' nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Microbial community dynamics and transformation of vascular plant detritus in two wetland ecosystems

    International Nuclear Information System (INIS)

    Moran, M.A.

    1987-01-01

    The microbial ecology of two wetland ecosystems in southeastern Georgia, USA, was studied with respect to microbial community dynamics and microbially-mediated transformations of vascular plant detritus. In the Okefenokee Swamp, biomass of microorganisms in the water column and sediments was generally lower in winter months and higher during spring and summer. Biomass and activity (measured as 14 C-lignocellulose mineralization) differed significantly among five habitats within the Okefenokee, and also among locations within each habitat. Significant heterogeneity in the structure of Okefenokee microbial communities was found at scales from 30 cm to 150 m. In field and laboratory studies of vascular plant decomposition in the Okefenokee and a salt marsh on Sapelo Island, the mathematical model which best describes decomposition kinetics is the decaying coefficient model

  11. Diversity and distribution of autotrophic microbial community along environmental gradients in grassland soils on the Tibetan Plateau.

    Science.gov (United States)

    Guo, Guangxia; Kong, Weidong; Liu, Jinbo; Zhao, Jingxue; Du, Haodong; Zhang, Xianzhou; Xia, Pinhua

    2015-10-01

    Soil microbial autotrophs play a significant role in CO2 fixation in terrestrial ecosystem, particularly in vegetation-constrained ecosystems with environmental stresses, such as the Tibetan Plateau characterized by low temperature and high UV. However, soil microbial autotrophic communities and their driving factors remain less appreciated. We investigated the structure and shift of microbial autotrophic communities and their driving factors along an elevation gradient (4400-5100 m above sea level) in alpine grassland soils on the Tibetan Plateau. The autotrophic microbial communities were characterized by quantitative PCR, terminal restriction fragment length polymorphism (T-RFLP), and cloning/sequencing of cbbL genes, encoding the large subunit for the CO2 fixation protein ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). High cbbL gene abundance and high RubisCO enzyme activity were observed and both significantly increased with increasing elevations. Path analysis identified that soil RubisCO enzyme causally originated from microbial autotrophs, and its activity was indirectly driven by soil water content, temperature, and NH4 (+) content. Soil autotrophic microbial community structure dramatically shifted along the elevation and was jointly driven by soil temperature, water content, nutrients, and plant types. The autotrophic microbial communities were dominated by bacterial autotrophs, which were affiliated with Rhizobiales, Burkholderiales, and Actinomycetales. These autotrophs have been well documented to degrade organic matters; thus, metabolic versatility could be a key strategy for microbial autotrophs to survive in the harsh environments. Our results demonstrated high abundance of microbial autotrophs and high CO2 fixation potential in alpine grassland soils and provided a novel model to identify dominant drivers of soil microbial communities and their ecological functions.

  12. Continuous fermentative hydrogen production from cheese whey wastewater under thermophilic anaerobic conditions

    Energy Technology Data Exchange (ETDEWEB)

    Azbar, Nuri; Cetinkaya Dokgoez, F. Tuba; Keskin, Tugba; Korkmaz, Kemal S.; Syed, Hamid M. [Bioengineering Department, Faculty of Engineering, Ege University, EBILTEM, Bornova, 35100 Izmir (Turkey)

    2009-09-15

    Hydrogen (H{sub 2}) production from cheese processing wastewater via dark anaerobic fermentation was conducted using mixed microbial communities under thermophilic conditions. The effects of varying hydraulic retention time (HRT: 1, 2 and 3.5 days) and especially high organic load rates (OLR: 21, 35 and 47 g chemical oxygen demand (COD)/l/day) on biohydrogen production in a continuous stirred tank reactor were investigated. The biogas contained 5-82% (45% on average) hydrogen and the hydrogen production rate ranged from 0.3 to 7.9 l H{sub 2}/l/day (2.5 l/l/day on average). H{sub 2} yields of 22, 15 and 5 mmol/g COD (at a constant influent COD of 40 g/l) were achieved at HRT values of 3.5, 2, and 1 days, respectively. On the other hand, H{sub 2} yields were monitored to be 3, 9 and 6 mmol/g COD, for OLR values of 47, 35 and 21 g COD/l/day, when HRT was kept constant at 1 day. The total measurable volatile fatty acid concentration in the effluent (as a function of influent COD) ranged between 118 and 27,012 mg/l, which was mainly composed of acetic acid, iso-butyric acid, butyric acid, propionic acid, formate and lactate. Ethanol and acetone production was also monitored from time to time. To characterize the microbial community in the bioreactor at different HRTs, DNA in mixed liquor samples was extracted immediately for PCR amplification of 16S RNA gene using eubacterial primers corresponding to 8F and 518R. The PCR product was cloned and subjected to DNA sequencing. The sequencing results were analyzed by using MegaBlast available on NCBI website which showed 99% identity to uncultured Thermoanaerobacteriaceae bacterium. (author)

  13. Subgingival microbial communities in Leukocyte Adhesion Deficiency and their relationship with local immunopathology.

    Science.gov (United States)

    Moutsopoulos, Niki M; Chalmers, Natalia I; Barb, Jennifer J; Abusleme, Loreto; Greenwell-Wild, Teresa; Dutzan, Nicolas; Paster, Bruce J; Munson, Peter J; Fine, Daniel H; Uzel, Gulbu; Holland, Steven M

    2015-03-01

    Leukocyte Adhesion Deficiency I (LAD-I) is a primary immunodeficiency caused by single gene mutations in the CD18 subunit of β2 integrins which result in defective transmigration of neutrophils into the tissues. Affected patients suffer from recurrent life threatening infections and severe oral disease (periodontitis). Microbial communities in the local environment (subgingival plaque) are thought to be the triggers for inflammatory periodontitis, yet little is known regarding the microbial communities associated with LAD-I periodontitis. Here we present the first comprehensive characterization of the subgingival communities in LAD-I, using a 16S rRNA gene-based microarray, and investigate the relationship of this tooth adherent microbiome to the local immunopathology of periodontitis. We show that the LAD subgingival microbiome is distinct from that of health and Localized Aggressive Periodontitits. Select periodontitis-associated species in the LAD microbiome included Parvimonas micra, Porphyromonas endodontalis, Eubacterium brachy and Treponema species. Pseudomonas aeruginosa, a bacterium not typically found in subgingival plaque is detected in LAD-I. We suggest that microbial products from LAD-associated communities may have a role in stimulating the local inflammatory response. We demonstrate that bacterial LPS translocates into the lesions of LAD-periodontitis potentially triggering immunopathology. We also show in in vitro assays with human macrophages and in vivo in animal models that microbial products from LAD-associated subgingival plaque trigger IL-23-related immune responses, which have been shown to dominate in patient lesions. In conclusion, our current study characterizes the subgingival microbial communities in LAD-periodontitis and supports their role as triggers of disease pathogenesis.

  14. Subgingival microbial communities in Leukocyte Adhesion Deficiency and their relationship with local immunopathology.

    Directory of Open Access Journals (Sweden)

    Niki M Moutsopoulos

    2015-03-01

    Full Text Available Leukocyte Adhesion Deficiency I (LAD-I is a primary immunodeficiency caused by single gene mutations in the CD18 subunit of β2 integrins which result in defective transmigration of neutrophils into the tissues. Affected patients suffer from recurrent life threatening infections and severe oral disease (periodontitis. Microbial communities in the local environment (subgingival plaque are thought to be the triggers for inflammatory periodontitis, yet little is known regarding the microbial communities associated with LAD-I periodontitis. Here we present the first comprehensive characterization of the subgingival communities in LAD-I, using a 16S rRNA gene-based microarray, and investigate the relationship of this tooth adherent microbiome to the local immunopathology of periodontitis. We show that the LAD subgingival microbiome is distinct from that of health and Localized Aggressive Periodontitits. Select periodontitis-associated species in the LAD microbiome included Parvimonas micra, Porphyromonas endodontalis, Eubacterium brachy and Treponema species. Pseudomonas aeruginosa, a bacterium not typically found in subgingival plaque is detected in LAD-I. We suggest that microbial products from LAD-associated communities may have a role in stimulating the local inflammatory response. We demonstrate that bacterial LPS translocates into the lesions of LAD-periodontitis potentially triggering immunopathology. We also show in in vitro assays with human macrophages and in vivo in animal models that microbial products from LAD-associated subgingival plaque trigger IL-23-related immune responses, which have been shown to dominate in patient lesions. In conclusion, our current study characterizes the subgingival microbial communities in LAD-periodontitis and supports their role as triggers of disease pathogenesis.

  15. Quantitative phylogenetic assessment of microbial communities indiverse environments

    Energy Technology Data Exchange (ETDEWEB)

    von Mering, C.; Hugenholtz, P.; Raes, J.; Tringe, S.G.; Doerks,T.; Jensen, L.J.; Ward, N.; Bork, P.

    2007-01-01

    The taxonomic composition of environmental communities is an important indicator of their ecology and function. Here, we use a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative and accurate picture of community composition than traditional rRNA-based approaches using polymerase chain reaction (PCR). By mapping marker genes from four diverse environmental data sets onto a reference species phylogeny, we show that certain communities evolve faster than others, determine preferred habitats for entire microbial clades, and provide evidence that such habitat preferences are often remarkably stable over time.

  16. Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

    Directory of Open Access Journals (Sweden)

    Chris L Dupont

    Full Text Available Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.

  17. The formation of illite from nontronite by mesophilic and thermophilic bacterial reaction

    Science.gov (United States)

    Jaisi, Deb P.; Eberl, Dennis D.; Dong, Hailiang; Kim, Jinwook

    2011-01-01

    The formation of illite through the smectite-to-illite (S-I) reaction is considered to be one of the most important mineral reactions occurring during diagenesis. In biologically catalyzed systems, however, this transformation has been suggested to be rapid and to bypass the high temperature and long time requirements. To understand the factors that promote the S-I reaction, the present study focused on the effects of pH, temperature, solution chemistry, and aging on the S-I reaction in microbially mediated systems. Fe(III)-reduction experiments were performed in both growth and non-growth media with two types of bacteria: mesophilic (Shewanella putrefaciens CN32) and thermophilic (Thermus scotoductus SA-01). Reductive dissolution of NAu-2 was observed and the formation of illite in treatment with thermophilic SA-01 was indicated by X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HRTEM). A basic pH (8.4) and high temperature (65°C) were the most favorable conditions for the formation of illite. A long incubation time was also found to enhance the formation of illite. K-nontronite (non-permanent fixation of K) was also detected and differentiated from the discrete illite in the XRD profiles. These results collectively suggested that the formation of illite associated with the biologically catalyzed smectite-to-illite reaction pathway may bypass the prolonged time and high temperature required for the S-I reaction in the absence of microbial activity.

  18. Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover.

    Science.gov (United States)

    You, Yeming; Wang, Juan; Huang, Xueman; Tang, Zuoxin; Liu, Shirong; Sun, Osbert J

    2014-03-01

    Forest soils store vast amounts of terrestrial carbon, but we are still limited in mechanistic understanding on how soil organic carbon (SOC) stabilization or turnover is controlled by biotic and abiotic factors in forest ecosystems. We used phospholipid fatty acids (PLFAs) as biomarker to study soil microbial community structure and measured activities of five extracellular enzymes involved in the degradation of cellulose (i.e., β-1,4-glucosidase and cellobiohydrolase), chitin (i.e., β-1,4-N-acetylglucosaminidase), and lignin (i.e., phenol oxidase and peroxidase) as indicators of soil microbial functioning in carbon transformation or turnover across varying biotic and abiotic conditions in a typical temperate forest ecosystem in central China. Redundancy analysis (RDA) was performed to determine the interrelationship between individual PFLAs and biotic and abiotic site factors as well as the linkage between soil microbial structure and function. Path analysis was further conducted to examine the controls of site factors on soil microbial community structure and the regulatory pathway of changes in SOC relating to microbial community structure and function. We found that soil microbial community structure is strongly influenced by water, temperature, SOC, fine root mass, clay content, and C/N ratio in soils and that the relative abundance of Gram-negative bacteria, saprophytic fungi, and actinomycetes explained most of the variations in the specific activities of soil enzymes involved in SOC transformation or turnover. The abundance of soil bacterial communities is strongly linked with the extracellular enzymes involved in carbon transformation, whereas the abundance of saprophytic fungi is associated with activities of extracellular enzymes driving carbon oxidation. Findings in this study demonstrate the complex interactions and linkage among plant traits, microenvironment, and soil physiochemical properties in affecting SOC via microbial regulations.

  19. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

    KAUST Repository

    Lee, Onon

    2010-11-18

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored. © 2011 International Society for Microbial Ecology All rights reserved.

  20. Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage.

    Science.gov (United States)

    Chen, Lin-xing; Hu, Min; Huang, Li-nan; Hua, Zheng-shuang; Kuang, Jia-liang; Li, Sheng-jin; Shu, Wen-sheng

    2015-07-01

    The microbial communities in acid mine drainage have been extensively studied to reveal their roles in acid generation and adaption to this environment. Lacking, however, are integrated community- and organism-wide comparative gene transcriptional analyses that could reveal the response and adaptation mechanisms of these extraordinary microorganisms to different environmental conditions. In this study, comparative metagenomics and metatranscriptomics were performed on microbial assemblages collected from four geochemically distinct acid mine drainage (AMD) sites. Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities. Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions. Organism-wide comparative analyses of the active taxa revealed environment-dependent gene transcriptional profiles, especially the distinct strategies used by Acidithiobacillus ferrivorans and Leptospirillum ferrodiazotrophum in nutrients assimilation and energy generation for survival under different conditions. Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.

  1. An assessment of microbial communities associated with surface mining-disturbed overburden.

    Science.gov (United States)

    Poncelet, Dominique M; Cavender, Nicole; Cutright, Teresa J; Senko, John M

    2014-03-01

    To assess the microbiological changes that occur during the maturation of overburden that has been disturbed by surface mining of coal, a surface mining-disturbed overburden unit in southeastern Ohio, USA was characterized. Overburden from the same unit that had been disturbed for 37 and 16 years were compared to undisturbed soil from the same region. Overburden and soil samples were collected as shallow subsurface cores from each subregion of the mined area (i.e., land 16 years and 37 years post-mining, and unmined land). Chemical and mineralogical characteristics of overburden samples were determined, as were microbial respiration rates. The composition of microbial communities associated with overburden and soil were determined using culture-independent, nucleic acid-based approaches. Chemical and mineralogical evaluation of overburden suggested that weathering of disturbed overburden gave rise to a setting with lower pH and more oxidized chemical constituents. Overburden-associated microbial biomass and respiration rates increased with time after overburden disturbance. Evaluation of 16S rRNA gene libraries that were produced by "next-generation" sequencing technology revealed that recently disturbed overburden contained an abundance of phylotypes attributable to sulfur-oxidizing Limnobacter spp., but with increasing time post-disturbance, overburden-associated microbial communities developed a structure similar to that of undisturbed soil, but retained characteristics of more recently disturbed overburden. Our results indicate that over time, the biogeochemical weathering of disturbed overburden leads to the development of geochemical conditions and microbial communities that approximate those of undisturbed soil, but that this transition is incomplete after 37 years of overburden maturation.

  2. Thermophilic Fungi: Their Physiology and Enzymes†

    Science.gov (United States)

    Maheshwari, Ramesh; Bharadwaj, Girish; Bhat, Mahalingeshwara K.

    2000-01-01

    Thermophilic fungi are a small assemblage in mycota that have a minimum temperature of growth at or above 20°C and a maximum temperature of growth extending up to 60 to 62°C. As the only representatives of eukaryotic organisms that can grow at temperatures above 45°C, the thermophilic fungi are valuable experimental systems for investigations of mechanisms that allow growth at moderately high temperature yet limit their growth beyond 60 to 62°C. Although widespread in terrestrial habitats, they have remained underexplored compared to thermophilic species of eubacteria and archaea. However, thermophilic fungi are potential sources of enzymes with scientific and commercial interests. This review, for the first time, compiles information on the physiology and enzymes of thermophilic fungi. Thermophilic fungi can be grown in minimal media with metabolic rates and growth yields comparable to those of mesophilic fungi. Studies of their growth kinetics, respiration, mixed-substrate utilization, nutrient uptake, and protein breakdown rate have provided some basic information not only on thermophilic fungi but also on filamentous fungi in general. Some species have the ability to grow at ambient temperatures if cultures are initiated with germinated spores or mycelial inoculum or if a nutritionally rich medium is used. Thermophilic fungi have a powerful ability to degrade polysaccharide constituents of biomass. The properties of their enzymes show differences not only among species but also among strains of the same species. Their extracellular enzymes display temperature optima for activity that are close to or above the optimum temperature for the growth of organism and, in general, are more heat stable than those of the mesophilic fungi. Some extracellular enzymes from thermophilic fungi are being produced commercially, and a few others have commercial prospects. Genes of thermophilic fungi encoding lipase, protease, xylanase, and cellulase have been cloned and

  3. Enrichment of extremophilic exoelectrogens in microbial electrolysis cells using Red Sea brine pools as inocula.

    Science.gov (United States)

    Shehab, Noura A; Ortiz-Medina, Juan F; Katuri, Krishna P; Hari, Ananda Rao; Amy, Gary; Logan, Bruce E; Saikaly, Pascal E

    2017-09-01

    Applying microbial electrochemical technologies for the treatment of highly saline or thermophilic solutions is challenging due to the lack of proper inocula to enrich for efficient exoelectrogens. Brine pools from three different locations (Valdivia, Atlantis II and Kebrit) in the Red Sea were investigated as potential inocula sources for enriching exoelectrogens in microbial electrolysis cells (MECs) under thermophilic (70°C) and hypersaline (25% salinity) conditions. Of these, only the Valdivia brine pool produced high and consistent current 6.8±2.1A/m 2 -anode in MECs operated at a set anode potential of +0.2V vs. Ag/AgCl (+0.405V vs. standard hydrogen electrode). These results show that exoelectrogens are present in these extreme environments and can be used to startup MEC under thermophilic and hypersaline conditions. Bacteroides was enriched on the anode of the Valdivia MEC, but it was not detected in the open circuit voltage reactor seeded with the Valdivia brine pool. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Forest soil microbial communities: Using metagenomic approaches to survey permanent plots

    Science.gov (United States)

    Amy L. Ross-Davis; Jane E. Stewart; John W. Hanna; John D. Shaw; Andrew T. Hudak; Theresa B. Jain; Robert J. Denner; Russell T. Graham; Deborah S. Page-Dumroese; Joanne M. Tirocke; Mee-Sook Kim; Ned B. Klopfenstein

    2014-01-01

    Forest soil ecosystems include some of the most complex microbial communities on Earth (Fierer et al. 2012). These assemblages of archaea, bacteria, fungi, and protists play essential roles in biogeochemical cycles (van der Heijden et al. 2008) and account for considerable terrestrial biomass (Nielsen et al. 2011). Yet, determining the microbial composition of forest...

  5. Hydrogen Production by Thermophilic Fermentation

    NARCIS (Netherlands)

    Niel, van E.W.J.; Willquist, K.; Zeidan, A.A.; Vrije, de T.; Mars, A.E.; Claassen, P.A.M.

    2012-01-01

    Of the many ways hydrogen can be produced, this chapter focuses on biological hydrogen production by thermophilic bacteria and archaea in dark fermentations. The thermophiles are held as promising candidates for a cost-effective fermentation process, because of their relatively high yields and broad

  6. Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea

    Directory of Open Access Journals (Sweden)

    Michael F. Graw

    2018-04-01

    Full Text Available The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics.

  7. The roles of host evolutionary relationships (genus: Nasonia) and development in structuring microbial communities.

    Science.gov (United States)

    Brucker, Robert M; Bordenstein, Seth R

    2012-02-01

    The comparative structure of bacterial communities among closely related host species remains relatively unexplored. For instance, as speciation events progress from incipient to complete stages, does divergence in the composition of the species' microbial communities parallel the divergence of host nuclear genes? To address this question, we used the recently diverged species of the parasitoid wasp genus Nasonia to test whether the evolutionary relationships of their bacterial microbiotas recapitulate the Nasonia phylogenetic history. We also assessed microbial diversity in Nasonia at different stages of development to determine the role that host age plays in microbiota structure. The results indicate that all three species of Nasonia share simple larval microbiotas dominated by the γ-proteobacteria class; however, bacterial species diversity increases as Nasonia develop into pupae and adults. Finally, under identical environmental conditions, the relationships of the microbial communities reflect the phylogeny of the Nasonia host species at multiple developmental stages, which suggests that the structure of an animal's microbial community is closely allied with divergence of host genes. These findings highlight the importance of host evolutionary relationships on microbiota composition and have broad implications for future studies of microbial symbiosis and animal speciation. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

  8. Soil biochar amendment shapes the composition of N{sub 2}O-reducing microbial communities

    Energy Technology Data Exchange (ETDEWEB)

    Harter, Johannes; Weigold, Pascal [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); El-Hadidi, Mohamed; Huson, Daniel H. [Algorithms in Bioinformatics, Center for Bioinformatics, University of Tuebingen, Sand 14, 72076 Tuebingen (Germany); Kappler, Andreas [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); Behrens, Sebastian, E-mail: sbehrens@umn.edu [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Drive S.E., Minneapolis, MN 55455-0116 (United States); BioTechnology Institute, 140 Gortner Labs, 1479 Gortner Avenue, St. Paul, MN 55108-6106 (United States)

    2016-08-15

    Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N{sub 2}O) emissions. N{sub 2}O is a potent greenhouse gas. The main sources of N{sub 2}O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N{sub 2}O emission mitigation and the abundance and activity of N{sub 2}O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described ‘atypical’ nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N{sub 2}O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N{sub 2}O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N{sub 2}O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. - Highlights: • Biochar promoted anaerobic, alkalinity-adapted, and polymer-degrading microbial taxa. • Biochar fostered the development of distinct N{sub 2}O-reducing microbial taxa. • Taxonomic shifts among N{sub 2}O-reducing microbes

  9. Impact of simulated acid rain on soil microbial community function in Masson pine seedlings

    Directory of Open Access Journals (Sweden)

    Lin Wang

    2014-09-01

    Conclusion: The results obtained indicated that the higher acid load decreased the soil microbial activity and no effects on soil microbial diversity assessed by Biolog of potted Masson pine seedlings. Simulated acid rain also changed the metabolic capability of the soil microbial community.

  10. Myceliophthora thermophila syn. Sporotrichum thermophile: a thermophilic mould of biotechnological potential.

    Science.gov (United States)

    Singh, Bijender

    2016-01-01

    Myceliophthora thermophila syn. Sporotrichum thermophile is a ubiquitous thermophilic mould with a strong ability to degrade organic matter during optimal growth at 45 °C. Both genome analysis and experimental data have suggested that the mould is capable of hydrolyzing all major polysaccharides found in biomass. The mould is able to secrete a large number of hydrolytic enzymes (cellulases, laccases, xylanases, pectinases, lipases, phytases and some other miscellaneous enzymes) employed in various biotechnological applications. Characterization of the biomass-hydrolyzing activity of wild and recombinant enzymes suggests that this mould is highly efficient in biomass decomposition at both moderate and high temperatures. The native enzymes produced by the mould are more efficient in activity than their mesophilic counterparts beside their low enzyme titers. The mould is able to synthesize various biomolecules, which are used in multifarious applications. Genome sequence data of M. thermophila also supported the physiological data. This review describes the biotechnological potential of thermophilic mould, M. thermophila supported by genomic and experimental evidences.

  11. Estimating the Transfer Range of Plasmids Encoding Antimicrobial Resistance in a Wastewater Treatment Plant Microbial Community

    DEFF Research Database (Denmark)

    Li, Liguan; Dechesne, Arnaud; He, Zhiming

    2018-01-01

    sludge microbial community was challenged in standardized filter matings with one of three multidrug resistance plasmids (pKJK5, pB10, and RP4) harbored by Escherichia coli or Pseudomonas putida. Different donor–plasmid combinations had distinct transfer frequencies, ranging from 3 to 50 conjugation...... events per 100000 cells of the WWTP microbial community. In addition, transfer was observed to a broad phylogenetic range of 13 bacterial phyla with several taxa containing potentially pathogenic species. Preferential transfer to taxa belonging to the predicted evolutionary host range of the plasmids...... ARG transmission. However, the contribution of microbial communities in WWTPs to ARG dissemination remains poorly understood. Here, we examined for the first time plasmid permissiveness of an activated sludge microbial community by utilizing an established fluorescent bioreporter system. The activated...

  12. The effect of alum addition on microbial communities in poultry litter.

    Science.gov (United States)

    Rothrock, M J; Cook, K L; Warren, J G; Sistani, K

    2008-08-01

    Alum [Al(2)(SO(4))(3).14H(2)O] is a common poultry litter amendment used to decrease water-soluble phosphorus or reduce ammonia volatilization, or both. Although the physiochemical effects of alum addition have been well researched, little attention has been given to the poultry litter microbial communities. The goal of this study was to use molecular biological methods [denaturing gradient gel electrophoresis (DGGE), community cloning, and quantitative real-time PCR] to characterize general, group-specific and pathogenic microbial communities in alum (10% wt/wt) and non-alum-treated litter. According to quantitative real-time PCR analyses, alum addition to the poultry litter resulted in significant reductions in both Campylobacter jejuni and Escherichia coli concentrations by the end of the first month of the experiment (3 log and 2 log, respectively). The concentrations of Salmonella spp. were below detection (Eubacterium and low %GC gram-positive groups in the alum-treated litters by the end of the first month, with no bands detectable for either group after 8 wk of incubation. Conversely, minimal effects of alum addition were observed in the Actinomycetes community. The most significant shift in the microbial community (based on DGGE analyses) occurred in the fungal population, with a large increase in diversity and abundance within 1 mo of alum addition (1 dominant band on d 0 to 9 dominant bands at 4 wk). Specifically, the incidence of Aspergillus spp. increased from 0 to 50% of the sequences in fungal clone libraries (n = 80) over the course of the experiment. This suggests that the addition of alum to poultry litter potentially shifts the microbial populations from bacterially dominated to dominated by fungi. The ramifications of this shift in dominance are still unknown, and future work will be aimed at characterizing these fungi and elucidating their role in the acidified litter environment.

  13. PHYLOGENETIC AND FUNCTIONAL DIVERSITY OF SEAGULL AND CANADIAN GEESE FECAL MICROBIAL COMMUNITIES

    Science.gov (United States)

    In spite of increasing public health concerns on the risks associated with swimming in waters contaminated with waterfowl feces, there is little information on the gut microbial communities of aquatic birds. To address the molecular microbial diversity of waterfowl, 16S rDNA and ...

  14. Thermophilic microorganisms in biomining.

    Science.gov (United States)

    Donati, Edgardo Rubén; Castro, Camila; Urbieta, María Sofía

    2016-11-01

    Biomining is an applied biotechnology for mineral processing and metal extraction from ores and concentrates. This alternative technology for recovering metals involves the hydrometallurgical processes known as bioleaching and biooxidation where the metal is directly solubilized or released from the matrix for further solubilization, respectively. Several commercial applications of biomining can be found around the world to recover mainly copper and gold but also other metals; most of them are operating at temperatures below 40-50 °C using mesophilic and moderate thermophilic microorganisms. Although biomining offers an economically viable and cleaner option, its share of the world´s production of metals has not grown as much as it was expected, mainly considering that due to environmental restrictions in many countries smelting and roasting technologies are being eliminated. The slow rate of biomining processes is for sure the main reason of their poor implementation. In this scenario the use of thermophiles could be advantageous because higher operational temperature would increase the rate of the process and in addition it would eliminate the energy input for cooling the system (bioleaching reactions are exothermic causing a serious temperature increase in bioreactors and inside heaps that adversely affects most of the mesophilic microorganisms) and it would decrease the passivation of mineral surfaces. In the last few years many thermophilic bacteria and archaea have been isolated, characterized, and even used for extracting metals. This paper reviews the current status of biomining using thermophiles, describes the main characteristics of thermophilic biominers and discusses the future for this biotechnology.

  15. Bioinformatic approaches reveal metagenomic characterization of soil microbial community.

    Directory of Open Access Journals (Sweden)

    Zhuofei Xu

    Full Text Available As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function.

  16. Degradation of oxytetracycline and its impacts on biogas-producing microbial community structure.

    Science.gov (United States)

    Coban, Halil; Ertekin, Emine; Ince, Orhan; Turker, Gokhan; Akyol, Çağrı; Ince, Bahar

    2016-07-01

    The effect of veterinary antibiotics in anaerobic digesters is a concern where methane production efficiency is highly dependent on microbial community structure. In this study, both anaerobic degradation of a common veterinary antibiotic, oxytetracycline (OTC), and its effects on an anaerobic digester microbial community were investigated. Qualitative and quantitative molecular tools were used to monitor changes in microbial community structure during a 60-day batch incubation period of cow manure with the addition of different concentrations of the antibiotic. Molecular data were interpreted by a further redundancy analysis as a multivariate statistics approach. At the end of the experiment, approximately 48, 33, and 17 % of the initially added 50, 100, and 200 mg l(-1) of OTC was still present in the serum bottles which reduced the biogas production via accumulation of some of the volatile fatty acids (VFAs). Biogas production was highly correlated with Methanobacteriales and Methanosarcinales gene copy numbers, and those parameters were negatively affected with oxytetracycline and VFA concentrations.

  17. Effect of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil.

    Science.gov (United States)

    Kim, Seong-Hye; Han, Hyo-Yeol; Lee, You-Jin; Kim, Chul Woong; Yang, Ji-Won

    2010-07-15

    Electrokinetic remediation has been successfully used to remove organic contaminants and heavy metals within soil. The electrokinetic process changes basic soil properties, but little is known about the impact of this remediation technology on indigenous soil microbial activities. This study reports on the effects of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil. The main removal mechanism of diesel was electroosmosis and most of the bacteria were transported by electroosmosis. After 25 days of electrokinetic remediation (0.63 mA cm(-2)), soil pH developed from pH 3.5 near the anode to pH 10.8 near the cathode. The soil pH change by electrokinetics reduced microbial cell number and microbial diversity. Especially the number of culturable bacteria decreased significantly and only Bacillus and strains in Bacillales were found as culturable bacteria. The use of EDTA as an electrolyte seemed to have detrimental effects on the soil microbial activity, particularly in the soil near the cathode. On the other hand, the soil dehydrogenase activity was enhanced close to the anode and the analysis of microbial community structure showed the increase of several microbial populations after electrokinetics. It is thought that the main causes of changes in microbial activities were soil pH and direct electric current. The results described here suggest that the application of electrokinetics can be a promising soil remediation technology if soil parameters, electric current, and electrolyte are suitably controlled based on the understanding of interaction between electrokinetics, contaminants, and indigenous microbial community. Copyright 2010 Elsevier B.V. All rights reserved.

  18. Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input.

    Science.gov (United States)

    Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P; Jansson, Janet K; Hopkins, David W; Aspray, Thomas J; Seely, Mary; Trindade, Marla I; Cowan, Don A

    2016-09-29

    The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO 2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

  19. Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P.; Jansson, Janet K.; Hopkins, David W.; Aspray, Thomas J.; Seely, Mary; Trindade, Marla I.; Cowan, Don A.

    2016-09-29

    The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

  20. Diversity and function of the microbial community on anodes of sediment microbial fuel cells fueled by root exudates

    Energy Technology Data Exchange (ETDEWEB)

    Cabezas da Rosa, Angela

    2010-11-26

    Anode microbial communities are essential for current production in microbial fuel cells. Anode reducing bacteria are capable of using the anode as final electron acceptor in their respiratory chain. The electrons delivered to the anode travel through a circuit to the cathode where they reduce oxygen to water generating an electric current. A novel type of sediment microbial fuel cell (SMFC) harvest energy from photosynthetically derived compounds released through the roots. Nothing is known about anode microbial communities of this type of microbial fuel cell. This work consists of three parts. The first part focuses on the study of bacterial and archaeal community compositions on anodes of SMFCs fueled by rice root exudates. By using terminal restriction fragment length polymorphism (T-RFLP), a profiling technique, and cloning / sequencing of 16S rRNA, we determined that the support type used for the plant (vermiculite, potting soil or rice field soil) is an important factor determining the composition of the microbial community. Finally, by comparing microbial communities of current producing anodes and non-current producing controls we determined that Desulfobulbus- and Geobacter-related populations were probably most important for current production in potting soil and rice field soil SMFCs, respectively. However, {delta}-proteobacterial Anaeromyxobacter spp., unclassified {delta}-proteobacteria and Anaerolineae were also part of the anode biofilm in rice field soil SMFCs and these populations might also play a role in current production. Moreover, distinct clusters of Geobacter and Anaeromyxobacter populations were stimulated by rice root exudates. Regarding Archaea, uncultured Euryarchaea were abundant on anodes of potting soil SMFCs indicating a potential role in current production. In both, rice field soil and potting soil SMFCs, a decrease of Methanosaeta, an acetotrophic methanogen, was detected on current producing anodes. In the second part we focused

  1. Alcohol dehydrogenases from thermophilic and hyperthermophilic archaea and bacteria.

    Science.gov (United States)

    Radianingtyas, Helia; Wright, Phillip C

    2003-12-01

    Many studies have been undertaken to characterise alcohol dehydrogenases (ADHs) from thermophiles and hyperthermophiles, mainly to better understand their activities and thermostability. To date, there are 20 thermophilic archaeal and 17 thermophilic bacterial strains known to have ADHs or similar enzymes, including the hypothetical proteins. Some of these thermophiles are found to have multiple ADHs, sometimes of different types. A rigid delineation of amino acid sequences amongst currently elucidated thermophilic ADHs and similar proteins is phylogenetically apparent. All are NAD(P)-dependent, with one exception that utilises the cofactor F(420) instead. Within the NAD(P)-dependent group, the thermophilic ADHs are orderly clustered as zinc-dependent ADHs, short-chain ADHs, and iron-containing/activated ADHs. Distance matrix calculations reveal that thermophilic ADHs within one type are homologous, with those derived from a single genus often showing high similarities. Elucidation of the enzyme activity and stability, coupled with structure analysis, provides excellent information to explain the relationship between them, and thermophilic ADHs diversity.

  2. Microbial community in high arsenic shallow groundwater aquifers in Hetao Basin of Inner Mongolia, China.

    Directory of Open Access Journals (Sweden)

    Ping Li

    Full Text Available A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12-267 operational taxonomic units (OTUs. Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO4(2-, SO4(2-/total sulfur ratio, and Fe(2+ were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia.

  3. Microbial community in high arsenic shallow groundwater aquifers in Hetao Basin of Inner Mongolia, China.

    Science.gov (United States)

    Li, Ping; Wang, Yanhong; Dai, Xinyue; Zhang, Rui; Jiang, Zhou; Jiang, Dawei; Wang, Shang; Jiang, Hongchen; Wang, Yanxin; Dong, Hailiang

    2015-01-01

    A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12-267 operational taxonomic units (OTUs). Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO4(2-), SO4(2-)/total sulfur ratio, and Fe(2+) were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia.

  4. Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Graham, Emily B.; Crump, Alex R.; Resch, Charles T.; Fansler, Sarah; Arntzen, Evan; Kennedy, David W.; Fredrickson, Jim K.; Stegen, James C.

    2016-12-16

    Community assembly processes govern shifts in species abundances in response to environmental change, yet our understanding of assembly remains largely decoupled from ecosystem function. Here, we test hypotheses regarding assembly and function across space and time using hyporheic microbial communities as a model system. We pair sampling of two habitat types through hydrologic fluctuation with null modeling and multivariate statistics. We demonstrate that dual selective pressures assimilate to generate compositional changes at distinct timescales among habitat types, resulting in contrasting associations of Betaproteobacteria and Thaumarchaeota with selection and with seasonal changes in aerobic metabolism. Our results culminate in a conceptual model in which selection from contrasting environments regulates taxon abundance and ecosystem function through time, with increases in function when oscillating selection opposes stable selective pressures. Our model is applicable within both macrobial and microbial ecology and presents an avenue for assimilating community assembly processes into predictions of ecosystem function.

  5. Detection of Metabolism Function of Microbial Community of Corpses by Biolog-Eco Method.

    Science.gov (United States)

    Jiang, X Y; Wang, J F; Zhu, G H; Ma, M Y; Lai, Y; Zhou, H

    2016-06-01

    To detect the changes of microbial community functional diversity of corpses with different postmortem interval (PMI) and to evaluate forensic application value for estimating PMI. The cultivation of microbial community from the anal swabs of a Sus scrofa and a human corpse placed in field environment from 0 to 240 h after death was performed using the Biolog-Eco Microplate and the variations of the absorbance values were also monitored. Combined with the technology of forensic pathology and flies succession, the metabolic characteristics and changes of microbial community on the decomposed corpse under natural environment were also observed. The diversity of microbial metabolism function was found to be negatively correlated with the number of maggots in the corpses. The freezing processing had the greatest impact on average well color development value at 0 h and the impact almost disappeared after 48 h. The diversity of microbial metabolism of the samples became relatively unstable after 192 h. The principal component analysis showed that 31 carbon sources could be consolidated for 5 principal components (accumulative contribution ratio >90%).The carbon source tsquare-analysis showed that N -acetyl- D -glucosamine and L -serine were the dominant carbon sources for estimating the PMI (0=240 h) of the Sus scrofa and human corpse. The Biolog-Eco method can be used to reveal the metabolic differences of the carbon resources utilization of the microbial community on the corpses during 0-240 h after death, which could provide a new basis for estimating the PMI. Copyright© by the Editorial Department of Journal of Forensic Medicine

  6. Functional gene diversity of soil microbial communities from five oil-contaminated fields in China.

    Science.gov (United States)

    Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

    2011-03-01

    To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

  7. Common hydraulic fracturing fluid additives alter the structure and function of anaerobic microbial communities

    Science.gov (United States)

    Mumford, Adam C.; Akob, Denise M.; Klinges, J. Grace; Cozzarelli, Isabelle M.

    2018-01-01

    The development of unconventional oil and gas (UOG) resources results in the production of large volumes of wastewater containing a complex mixture of hydraulic fracturing chemical additives and components from the formation. The release of these wastewaters into the environment poses potential risks that are poorly understood. Microbial communities in stream sediments form the base of the food chain and may serve as sentinels for changes in stream health. Iron-reducing organisms have been shown to play a role in the biodegradation of a wide range of organic compounds, and so to evaluate their response to UOG wastewater, we enriched anaerobic microbial communities from sediments collected upstream (background) and downstream (impacted) of an UOG wastewater injection disposal facility in the presence of hydraulic fracturing fluid (HFF) additives: guar gum, ethylene glycol, and two biocides, 2,2-dibromo-3-nitrilopropionamide (DBNPA) and bronopol (C3H6BrNO4). Iron reduction was significantly inhibited early in the incubations with the addition of biocides, whereas amendment with guar gum and ethylene glycol stimulated iron reduction relative to levels in the unamended controls. Changes in the microbial community structure were observed across all treatments, indicating the potential for even small amounts of UOG wastewater components to influence natural microbial processes. The microbial community structure differed between enrichments with background and impacted sediments, suggesting that impacted sediments may have been preconditioned by exposure to wastewater. These experiments demonstrated the potential for biocides to significantly decrease iron reduction rates immediately following a spill and demonstrated how microbial communities previously exposed to UOG wastewater may be more resilient to additional spills.

  8. Microbial community composition of transiently wetted Antarctic Dry Valley soils.

    Science.gov (United States)

    Niederberger, Thomas D; Sohm, Jill A; Gunderson, Troy E; Parker, Alexander E; Tirindelli, Joëlle; Capone, Douglas G; Carpenter, Edward J; Cary, Stephen C

    2015-01-01

    During the summer months, wet (hyporheic) soils associated with ephemeral streams and lake edges in the Antarctic Dry Valleys (DVs) become hotspots of biological activity and are hypothesized to be an important source of carbon and nitrogen for arid DV soils. Recent research in the DV has focused on the geochemistry and microbial ecology of lakes and arid soils, with substantially less information being available on hyporheic soils. Here, we determined the unique properties of hyporheic microbial communities, resolved their relationship to environmental parameters and compared them to archetypal arid DV soils. Generally, pH increased and chlorophyll a concentrations decreased along transects from wet to arid soils (9.0 to ~7.0 for pH and ~0.8 to ~5 μg/cm(3) for chlorophyll a, respectively). Soil water content decreased to below ~3% in the arid soils. Community fingerprinting-based principle component analyses revealed that bacterial communities formed distinct clusters specific to arid and wet soils; however, eukaryotic communities that clustered together did not have similar soil moisture content nor did they group together based on sampling location. Collectively, rRNA pyrosequencing indicated a considerably higher abundance of Cyanobacteria in wet soils and a higher abundance of Acidobacterial, Actinobacterial, Deinococcus/Thermus, Bacteroidetes, Firmicutes, Gemmatimonadetes, Nitrospira, and Planctomycetes in arid soils. The two most significant differences at the genus level were Gillisia signatures present in arid soils and chloroplast signatures related to Streptophyta that were common in wet soils. Fungal dominance was observed in arid soils and Viridiplantae were more common in wet soils. This research represents an in-depth characterization of microbial communities inhabiting wet DV soils. Results indicate that the repeated wetting of hyporheic zones has a profound impact on the bacterial and eukaryotic communities inhabiting in these areas.

  9. Biodiversity of thermophilic prokaryotes with hydrolytic activities in hot springs of Uzon Caldera, Kamchatka (Russia).

    Science.gov (United States)

    Kublanov, Ilya V; Perevalova, Anna A; Slobodkina, Galina B; Lebedinsky, Aleksander V; Bidzhieva, Salima K; Kolganova, Tatyana V; Kaliberda, Elena N; Rumsh, Lev D; Haertlé, Thomas; Bonch-Osmolovskaya, Elizaveta A

    2009-01-01

    Samples of water from the hot springs of Uzon Caldera with temperatures from 68 to 87 degrees C and pHs of 4.1 to 7.0, supplemented with proteinaceous (albumin, casein, or alpha- or beta-keratin) or carbohydrate (cellulose, carboxymethyl cellulose, chitin, or agarose) biological polymers, were filled with thermal water and incubated at the same sites, with the contents of the tubes freely accessible to the hydrothermal fluid. As a result, several enrichment cultures growing in situ on different polymeric substrates were obtained. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments obtained after PCR with Bacteria-specific primers showed that the bacterial communities developing on carbohydrates included the genera Caldicellulosiruptor and Dictyoglomus and that those developing on proteins contained members of the Thermotogales order. DGGE analysis performed after PCR with Archaea- and Crenarchaeota-specific primers showed that archaea related to uncultured environmental clones, particularly those of the Crenarchaeota phylum, were present in both carbohydrate- and protein-degrading communities. Five isolates obtained from in situ enrichments or corresponding natural samples of water and sediments represented the bacterial genera Dictyoglomus and Caldanaerobacter as well as new archaea of the Crenarchaeota phylum. Thus, in situ enrichment and consequent isolation showed the diversity of thermophilic prokaryotes competing for biopolymers in microbial communities of terrestrial hot springs.

  10. Microbially influenced corrosion communities associated with fuel-grade ethanol environments.

    Science.gov (United States)

    Williamson, Charles H D; Jain, Luke A; Mishra, Brajendra; Olson, David L; Spear, John R

    2015-08-01

    Microbially influenced corrosion (MIC) is a costly problem that impacts hydrocarbon production and processing equipment, water distribution systems, ships, railcars, and other types of metallic infrastructure. In particular, MIC is known to cause considerable damage to hydrocarbon fuel infrastructure including production, transportation, and storage systems, often times with catastrophic environmental contamination results. As the production and use of alternative fuels such as fuel-grade ethanol (FGE) increase, it is important to consider MIC of engineered materials exposed to these "newer fuels" as they enter existing infrastructure. Reports of suspected MIC in systems handling FGE and water prompted an investigation of the microbial diversity associated with these environments. Small subunit ribosomal RNA gene pyrosequencing surveys indicate that acetic-acid-producing bacteria (Acetobacter spp. and Gluconacetobacter spp.) are prevalent in environments exposed to FGE and water. Other microbes previously implicated in corrosion, such as sulfate-reducing bacteria and methanogens, were also identified. In addition, acetic-acid-producing microbes and sulfate-reducing microbes were cultivated from sampled environments containing FGE and water. Results indicate that complex microbial communities form in these FGE environments and could cause significant MIC-related damage that may be difficult to control. How to better manage these microbial communities will be a defining aspect of improving mitigation of global infrastructure corrosion.

  11. Microbial community changes along the active seepage site of one cold seep in the Red Sea.

    KAUST Repository

    Cao, Huiluo

    2015-07-21

    The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

  12. Microbial community changes along the active seepage site of one cold seep in the Red Sea.

    KAUST Repository

    Cao, Huiluo; Zhang, Weipeng; Wang, Yong; Qian, Pei-Yuan

    2015-01-01

    The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

  13. Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities.

    Science.gov (United States)

    Campbell, Barbara J; Polson, Shawn W; Zeigler Allen, Lisa; Williamson, Shannon J; Lee, Charles K; Wommack, K Eric; Cary, S Craig

    2013-01-01

    Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments.

  14. The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon

    Directory of Open Access Journals (Sweden)

    Wei Hui Xu

    2015-09-01

    Full Text Available The growth of watermelon is often threatened by Fusarium oxysporum f. sp. niveum (Fon in successively monocultured soil, which results in economic loss. The objective of this study was to investigate the effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon and to explore the relationship between the effect and the incidence of wilt caused by Fon. The results showed that the activities of soil polyphenol oxidase, urease and invertase were increased, the microbial biomass nitrogen (MBN and microbial biomass phosphorus (MBP were significantly increased, and the ratio of MBC/MBN was decreased (P<0.05. Real-time PCR analysis showed that the Fon population declined significantly in the watermelon/wheat companion system compared with the monoculture system (P<0.05. The analysis of microbial communities showed that the relative abundance of microbial communities was changed in the rhizosphere of watermelon. Compared with the monoculture system, the relative abundances of Alphaproteobacteria, Actinobacteria, Gemmatimonadetes and Sordariomycetes were increased, and the relative abundances of Gammaproteobacteria, Sphingobacteria, Cytophagia, Pezizomycetes, and Eurotiomycetes were decreased in the rhizosphere of watermelon in the watermelon/wheat companion system; importantly, the incidence of Fusarium wilt was also decreased in the watermelon/wheat companion system. In conclusion, this study indicated that D123 wheat as a companion crop increased soil enzyme activities and microbial biomass, decreased the Fon population, and changed the relative abundance of microbial communities in the rhizosphere of watermelon, which may be related to the reduction of Fusarium wilt in the watermelon/wheat companion system.

  15. Soil Rhizosphere Microbial Communities and Enzyme Activities under Organic Farming in Alabama

    Directory of Open Access Journals (Sweden)

    Zachary Senwo

    2011-07-01

    Full Text Available Evaluation of the soil rhizosphere has been limited by the lack of robust assessments that can explore the vast complex structure and diversity of soil microbial communities. Our objective was to combine fatty acid methyl ester (FAME and pyrosequencing techniques to evaluate soil microbial community structure and diversity. In addition, we evaluated biogeochemical functionality of the microbial communities via enzymatic activities of nutrient cycling. Samples were taken from a silt loam at 0–10 and 10–20 cm in an organic farm under lettuce (Lactuca sativa, potato (Solanum tuberosum, onion (Allium cepa L, broccoli (Brassica oleracea var. botrytis and Tall fescue pasture grass (Festuca arundinacea. Several FAMEs (a15:0, i15:0, i15:1, i16:0, a17:0, i17:0, 10Me17:0, cy17:0, 16:1ω5c and 18:1ω9c varied among the crop rhizospheres. FAME profiles of the soil microbial community under pasture showed a higher fungal:bacterial ratio compared to the soil under lettuce, potato, onion, and broccoli. Soil under potato showed higher sum of fungal FAME indicators compared to broccoli, onion and lettuce. Microbial biomass C and enzyme activities associated with pasture and potato were higher than the other rhizospheres. The lowest soil microbial biomass C and enzyme activities were found under onion. Pyrosequencing revealed significant differences regarding the maximum operational taxonomic units (OTU at 3% dissimilarity level (roughly corresponding to the bacterial species level at 0–10 cm (581.7–770.0 compared to 10–20 cm (563.3–727.7 soil depths. The lowest OTUs detected at 0–10 cm were under broccoli (581.7; whereas the lowest OTUs found at 10–20 cm were under potato (563.3. The predominant phyla (85% in this soil at both depths were Bacteroidetes (i.e., Flavobacteria, Sphingobacteria, and Proteobacteria. Flavobacteriaceae and Xanthomonadaceae were predominant under broccoli. Rhizobiaceae, Hyphomicrobiaceae, and Acidobacteriaceae were more

  16. Soil mineral assemblage influences on microbial communities and carbon cycling under fresh organic matter input

    Science.gov (United States)

    Finley, B. K.; Schwartz, E.; Koch, B.; Dijkstra, P.; Hungate, B. A.

    2017-12-01

    The interactions between soil mineral assemblages and microbial communities are important drivers of soil organic carbon (SOC) cycling and storage, although the mechanisms driving these interactions remain unclear. There is increasing evidence supporting the importance of associations with poorly crystalline, short-range order (SRO) minerals in protection of SOC from microbial utilization. However, how the microbial processing of SRO-associated SOC may be influenced by fresh organic matter inputs (priming) remains poorly understood. The influence on SRO minerals on soil microbial community dynamics is uncertain as well. Therefore, we conducted a priming incubation by adding either a simulated root exudate mixture or conifer needle litter to three soils from a mixed-conifer ecosystem. The parent material of the soils were andesite, basalt, and granite and decreased in SRO mineral content, respectively. We also conducted a parallel quantitative stable isotope probing incubation by adding 18O-labelled water to the soils to isotopically label microbial DNA in situ. This allowed us to characterize and identify the active bacterial and archaeal community and taxon-specific growth under fresh organic matter input. While the granite soil (lowest SRO content), had the largest total mineralization, the least priming occurred. The andesite and basalt soils (greater SRO content) had lower total respiration, but greater priming. Across all treatments, the granite soil, while having the lowest species richness of the entire community (249 taxa, both active and inactive), had a larger active community (90%) in response to new SOC input. The andesite and basalt soils, while having greater total species richness of the entire community at 333 and 325 taxa, respectively, had fewer active taxa in response to new C compared to the granite soil (30% and 49% taxa, respectively). These findings suggest that the soil mineral assemblage is an important driver on SOC cycling under fresh

  17. Multistage A-O Activated Sludge Process for Paraformaldehyde Wastewater Treatment and Microbial Community Structure Analysis

    Directory of Open Access Journals (Sweden)

    Danyang Zheng

    2016-01-01

    Full Text Available In recent years, the effect of formaldehyde on microorganisms and body had become a global public health issue. The multistage combination of anaerobic and aerobic process was adopted to treat paraformaldehyde wastewater. Microbial community structure in different reaction stages was analyzed through high-throughput sequencing. Results showed that multistage A-O activated sludge process positively influenced polyformaldehyde wastewater. The removal rates of formaldehyde were basically stable at more than 99% and those of COD were about 89%. Analysis of the microbial diversity index indicated that the microbial diversity of the reactor was high, and the treatment effect was good. Moreover, microbial community had certain similarity in the same system. Microbial communities in different units also showed typical representative characteristics affected by working conditions and influent concentrations. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant fungal genera in the phylum level of community composition. As to family and genus levels, Peptostreptococcaceae was distributed at various stages and the dominant in this system. This bacterium also played an important role in organic matter removal, particularly decomposition of the acidified middle metabolites. In addition, Rhodobacteraceae and Rhodocyclaceae were the formaldehyde-degrading bacteria found in the reactor.

  18. Plant stimulation of soil microbial community succession: how sequential expression mediates soil carbon stabilization and turnover

    Energy Technology Data Exchange (ETDEWEB)

    Firestone, Mary [Univ. of California, Berkeley, CA (United States)

    2015-03-31

    It is now understood that most plant C is utilized or transformed by soil microorganisms en route to stabilization. Hence the composition of microbial communities that mediate decomposition and transformation of root C is critical, as are the metabolic capabilities of these communities. The change in composition and function of the C-transforming microbial communities over time in effect defines the biological component of soil C stabilization. Our research was designed to test 2 general hypotheses; the first two hypotheses are discussed first; H1: Root-exudate interactions with soil microbial populations results in the expression of enzymatic capacities for macromolecular, complex carbon decomposition; and H2: Microbial communities surrounding roots undergo taxonomic succession linked to functional gene activities as roots grow, mature, and decompose in soil. Over the term of the project we made significant progress in 1) quantifying the temporal pattern of root interactions with the soil decomposing community and 2) characterizing the role of root exudates in mediating these interactions.

  19. Microbial community dynamics in the rhizosphere of a cadmium hyper-accumulator

    Science.gov (United States)

    Wood, J. L.; Zhang, C.; Mathews, E. R.; Tang, C.; Franks, A. E.

    2016-11-01

    Phytoextraction is influenced by the indigenous soil microbial communities during the remediation of heavy metal contaminated soils. Soil microbial communities can affect plant growth, metal availability and the performance of phytoextraction-assisting inocula. Understanding the basic ecology of indigenous soil communities associated with the phytoextraction process, including the interplay between selective pressures upon the communities, is an important step towards phytoextraction optimization. This study investigated the impact of cadmium (Cd), and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the structure of soil-bacterial and fungal communities using automated ribosomal intergenic spacer analysis (ARISA) and quantitative PCR (qPCR). Whilst Cd had no detectable influence upon fungal communities, bacterial communities underwent significant structural changes with no reduction in 16S rRNA copy number. The presence of C. rossii influenced the structure of all communities and increased ITS copy number. Suites of operational taxonomic units (OTUs) changed in abundance in response to either Cd or C. rossii, however we found little evidence to suggest that the two selective pressures were acting synergistically. The Cd-induced turnover in bacterial OTUs suggests that Cd alters competition dynamics within the community. Further work to understand how competition is altered could provide a deeper understanding of the microbiome-plant-environment and aid phytoextraction optimization.

  20. Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity.

    Directory of Open Access Journals (Sweden)

    Richard R Rodrigues

    Full Text Available The importance of plant-microbe associations for the invasion of plant species have not been often tested under field conditions. The research sought to determine patterns of change in microbial communities associated with the establishment of invasive plants with different taxonomic and phenetic traits. Three independent locations in Virginia, USA were selected. One site was invaded by a grass (Microstegium vimineum, another by a shrub (Rhamnus davurica, and the third by a tree (Ailanthus altissima. The native vegetation from these sites was used as reference. 16S rRNA and ITS regions were sequenced to study root-zone bacterial and fungal communities, respectively, in invaded and non-invaded samples and analyzed using Quantitative Insights Into Microbial Ecology (QIIME. Though root-zone microbial community structure initially differed across locations, plant invasion shifted communities in similar ways. Indicator species analysis revealed that Operational Taxonomic Units (OTUs closely related to Proteobacteria, Acidobacteria, Actinobacteria, and Ascomycota increased in abundance due to plant invasions. The Hyphomonadaceae family in the Rhodobacterales order and ammonia-oxidizing Nitrospirae phylum showed greater relative abundance in the invaded root-zone soils. Hyphomicrobiaceae, another bacterial family within the phyla Proteobacteria increased as a result of plant invasion, but the effect associated most strongly with root-zones of M. vimineum and R. davurica. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt showed bacteria responsible for nitrogen cycling in soil increased in relative abundance in association with plant invasion. In agreement with phylogenetic and functional analyses, greater turnover of ammonium and nitrate was associated with plant invasion. Overall, bacterial and fungal communities changed congruently across plant invaders, and support the hypothesis that