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Sample records for groundwater bacterial community

  1. Bacterial communities in tetrachloroethene-polluted groundwaters: a case study.

    Science.gov (United States)

    Kotik, Michael; Davidová, Anna; Voříšková, Jana; Baldrian, Petr

    2013-06-01

    The compositions of bacterial groundwater communities of three sites contaminated with chlorinated ethenes were analyzed by pyrosequencing their 16S rRNA genes. For each location, the entire and the active bacterial populations were characterized by independent molecular analysis of the community DNA and RNA. The sites were selected to cover a broad range of different environmental conditions and contamination levels, with tetrachloroethene (PCE) and trichloroethene (TCE) being the primary contaminants. Before sampling the biomass, a long-term monitoring of the polluted locations revealed high concentrations of cis-1,2-dichloroethene (cDCE) and vinyl chloride (VC), which are toxic by-products of the incomplete bacterial degradation of PCE and TCE. The applied pyrosequencing technique enabled known dechlorinators to be identified at a very low detection level (study revealed that only a few species dominated the bacterial communities, with Albidiferax ferrireducens being the only highly prominent member found at all three sites. Only a limited number of OTUs with abundances of up to 1% and high sequence identities to known dechlorinating microorganisms were retrieved from the RNA pools of the two highly contaminated sites. The dechlorinating consortium was likely to be comprised of cDCE-assimilating bacteria (Polaromonas spp.), anaerobic organohalide respirers (mainly Geobacter spp.), and Burkholderia spp. involved in cometabolic dechlorination processes, together with methylotrophs (Methylobacter spp.). The deep sequencing results suggest that the indigenous dechlorinating consortia present at the investigated sites can be used as a starting point for future bioremediation activities by stimulating their anaerobic and aerobic chloroethene degradation capacities (i.e. reductive dechlorination, and metabolic and cometabolic oxidation).

  2. Arsenic release from shallow aquifers of the Hetao basin, Inner Mongolia: evidence from bacterial community in aquifer sediments and groundwater.

    Science.gov (United States)

    Li, Yuan; Guo, Huaming; Hao, Chunbo

    2014-12-01

    Indigenous microbes play crucial roles in arsenic mobilization in high arsenic groundwater systems. Databases concerning the presence and the activity of microbial communities are very useful in evaluating the potential of microbe-mediated arsenic mobilization in shallow aquifers hosting high arsenic groundwater. This study characterized microbial communities in groundwaters at different depths with different arsenic concentrations by DGGE and one sediment by 16S rRNA gene clone library, and evaluated arsenic mobilization in microcosm batches with the presence of indigenous bacteria. DGGE fingerprints revealed that the community structure changed substantially with depth at the same location. It indicated that a relatively higher bacterial diversity was present in the groundwater sample with lower arsenic concentration. Sequence analysis of 16S rRNA gene demonstrated that the sediment bacteria mainly belonged to Pseudomonas, Dietzia and Rhodococcus, which have been widely found in aquifer systems. Additionally, NO3(-)-reducing bacteria Pseudomonas sp. was the largest group, followed by Fe(III)-reducing, SO4(2-)-reducing and As(V)-reducing bacteria in the sediment sample. These anaerobic bacteria used the specific oxyanions as electron acceptor and played a significant role in reductive dissolution of Fe oxide minerals, reduction of As(V), and release of arsenic from sediments into groundwater. Microcosm experiments, using intact aquifer sediments, showed that arsenic release and Fe(III) reduction were microbially mediated in the presence of indigenous bacteria. High arsenic concentration was also observed in the batch without amendment of organic carbon, demonstrating that the natural organic matter in sediments was the potential electron donor for microbially mediated arsenic release from these aquifer sediments.

  3. Natural Attenuation model and degrading bacterial community of 1,1,1-Trichloroethane contaminant in Shallow Groundwater in Shanghai

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    Qiang eLu

    2015-08-01

    Full Text Available Natural attenuation is an effective and feasible technology for controlling groundwater contamination. This study investigated the potential effectiveness and mechanisms of natural attenuation of 1,1,1-trichloroethane (TCA contaminants in in Shallow Groundwater in Shanghai by using a column simulation experiment, reactive transport model, and 16S rRNA gene clone library. The results indicated that the majority of the contaminant mass was present at 2-6 m in depth, the contaminated area was approximately 1000 m2, and natural attenuation processes were occurring at the site. The effluent breakthrough curves from the column experiments demonstrated that the effectiveness of TCA natural attenuation in the groundwater accorded with the advection-dispersion-reaction equation. The kinetic parameter of adsorption and biotic dehydrochlorination of TCA was 0.068 m3/kg and 0.0045 d-1. The contamination plume was predicted to diminish and the maximum concentration of TCA decreased to 280 μg/L. The bacterial community in situ groundwater belonged to Trichococcus, Geobacteraceae, Geobacter, Mucilaginibacter and Arthrobacter.

  4. Spatial and temporal changes in sulphate-reducing groundwater bacterial community structure in response to Managed Aquifer Recharge.

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    Reed, D A; Toze, S; Chang, B

    2008-01-01

    The population dynamics of bacterial able to be cultured under sulphate reducing condition was studied in conjunction with changes in aquifer geochemistry using multivariate statistics for two contrasting Managed Aquifer Recharge (MAR) techniques at two different geographical locations (Perth, Western Australia and Adelaide, South Australia). Principal component analysis (PCA) was used to investigate spatial and temporal changes in the overall chemical signature of the aquifers using an array of chemical analytes which demonstrated a migrating geochemical plume. Denaturing Gradient Gel Electrophoresis (DGGE) using DNA from sulphate-reducing bacteria cultures was used to detect spatial and temporal changes in population dynamics. Bacterial and geochemical evidence suggested that groundwater at greatest distance from the nutrient source was least affected by treated effluent recharge. The results suggested that bacterial populations that were able to be cultured in sulphate reducing media responded to the migrating chemical gradient and to the changes in aquifer geochemistry. Most noticeably, sulphate-reducing bacterial populations associated with the infiltration galleries were stable in community structure over time. Additionally, the biodiversity of these culturable bacteria was restored when aquifer geochemistry returned to ambient conditions during the recovery phase at the Adelaide Aquifer Storage and Recovery site.

  5. The patterns of bacterial community and relationships between sulfate-reducing bacteria and hydrochemistry in sulfate-polluted groundwater of Baogang rare earth tailings.

    Science.gov (United States)

    An, Xinli; Baker, Paul; Li, Hu; Su, Jianqiang; Yu, Changping; Cai, Chao

    2016-11-01

    Microorganisms are the primary agents responsible for the modification, degradation, and/or detoxification of pollutants, and thus, they play a major role in their natural attenuation; yet, little is known about the structure and diversity of the subsurface community and relationships between microbial community and groundwater hydrochemistry. In this study, denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) allowed a comparative microbial community analysis of sulfate-contaminated groundwater samples from nine different wells in the region of Baogang rare earth tailings. Using real-time PCR, the abundance of total bacteria and the sulfate-reducing genes of aprA and dsrB were quantified. Statistical analyses showed a clear distinction of the microbial community diversity between the contaminated and uncontaminated samples, with Proteobacteria being the most dominant members of the microbial community. SO4(2-) concentrations exerted a significant effect on the variation of the bacterial community (P groundwater. The uncontaminated groundwater with low sulfate concentration harbored higher abundance of SRB than that in the polluted samples, while no significant correlation was observed between sulfate concentrations and SRB abundances in this study, suggesting other environmental factors possibly contributed to different distributions and abundances of SRB in the different sites. The results should facilitate expanded studies to identify robust microbe-environment interactions and provide a strong foundation for qualitative exploration of the bacterial diversity in rare earth tailings groundwater that might ultimately be incorporated into the remediation of environmental contamination.

  6. Efficacy of acetate-amended biostimulation for uranium sequestration: Combined analysis of sediment/groundwater geochemistry and bacterial community structure

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Jie; Veeramani, Harish; Qafoku, Nikolla; Singh, Gargi; Riquelme Breazeal, Maria V.; Pruden, Amy; Kukkadapu, Ravi K.; Gartman, Brandy N.; Hochella, Michael F.

    2017-03-01

    Systematic flow-through column experiments were conducted using sediments and ground water collected from different subsurface localities at the U.S. Department of Energy’s Integrated Field Research Challenge site in Rifle, Colorado. The principal purpose of this study is to gain a better understanding of the interactive effects of groundwater geochemistry, sediment mineralogy, and indigenous bacterial community structures on the efficacy of uranium removal from the groundwater with/without acetate amendment. Overall, we find that the subtle variations in the sediments’ mineralogy, particle size, redox conditions, as well as contents of metal(loid) co-contaminants showed a pronounced effect on the associated bacterial population and composition, which mainly determines the system’s performance with respect to uranium removal. Positive relationship was identified between the abundance of dissimilatory sulfate-reduction genes (i.e., drsA), markers of sulfate-reducing bacteria, and the sediments’ propensity to sequester aqueous uranium. In contrast, no obvious connections were observed between the abundance of common iron-reducing bacteria, e.g., Geobacter spp., and the sediments’ ability to sequester uranium. In the sediments with low bacterial biomass and the absence of sulfate-reducing conditions, abiotic adsorption onto mineral surfaces such as phyllosilicates likely played a relatively major role in the attenuation of aqueous uranium; however, in these scenarios, acetate amendment induced detectable rebounds in the effluent uranium concentrations. The results of this study suggest that reductive immobilization of uranium can be achieved under predominantly sulfate-reducing conditions, and provide insight into the integrated roles of various biogeochemical components in long-term uranium sequestration.

  7. Groundwater: A Community Action Guide.

    Science.gov (United States)

    Boyd, Susan, Ed.; And Others

    Designed to be a guide for community action, this booklet examines issues and trends related to groundwater contamination. Basic concepts about groundwater and information about problems affecting it are covered under the categories of (1) what is groundwater? (2) availability and depletion; (3) quality and contamination; (4) public health…

  8. Groundwater: A Community Action Guide.

    Science.gov (United States)

    Boyd, Susan, Ed.; And Others

    Designed to be a guide for community action, this booklet examines issues and trends related to groundwater contamination. Basic concepts about groundwater and information about problems affecting it are covered under the categories of (1) what is groundwater? (2) availability and depletion; (3) quality and contamination; (4) public health…

  9. Aerobic biodegradation of trichloroethylene and phenol co-contaminants in groundwater by a bacterial community using hydrogen peroxide as the sole oxygen source.

    Science.gov (United States)

    Li, Hui; Zhang, Shi-yang; Wang, Xiao-li; Yang, Jie; Gu, Ji-dong; Zhu, Rui-li; Wang, Ping; Lin, Kuang-fei; Liu, Yong-di

    2015-01-01

    Trichloroethylene (TCE) and phenol were often found together as co-contaminants in the groundwater of industrial contaminated sites. An effective method to remove TCE was aerobic biodegradation by co-metabolism using phenol as growth substrates. However, the aerobic biodegradation process was easily limited by low concentration of dissolved oxygen (DO) in groundwater, and DO was improved by air blast technique with difficulty. This study enriched a bacterial community using hydrogen peroxide (H2O2) as the sole oxygen source to aerobically degrade TCE by co-metabolism with phenol in groundwater. The enriched cultures were acclimatized to 2-8 mM H2O2 which induced catalase, superoxide dismutase and peroxidase to decompose H2O2 to release O2 and reduce the toxicity. The bacterial community could degrade 120 mg/L TCE within 12 days by using 8 mM H2O2 as the optimum concentration, and the TCE degradation efficiency reached up to 80.6%. 16S rRNA gene cloning and sequencing showed that Bordetella, Stenotrophomonas sp., Sinorhizobium sp., Variovorax sp. and Sphingobium sp. were the dominant species in the enrichments, which were clustered in three phyla: Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. Polymerase chain reaction detection proved that phenol hydroxylase (Lph) gene was involved in the co-metabolic degradation of phenol and TCE, which indicated that hydroxylase might catalyse the epoxidation of TCE to form the unstable molecule TCE-epoxide. The findings are significant for understanding the mechanism of biodegradation of TCE and phenol co-contamination and helpful for the potential applications of an aerobic bioremediation in situ the contaminated sites.

  10. Linking bacterial diversity and geochemistry of uranium-contaminated groundwater.

    Science.gov (United States)

    Cho, Kelly; Zholi, Alma; Frabutt, Dylan; Flood, Matthew; Floyd, Dalton; Tiquia, Sonia M

    2012-01-01

    To understand the link between bacterial diversity and geochemistry in uranium-contaminated groundwater, microbial communities were assessed based on clone libraries of 16S rDNA genes from the USDOE Oak Ridge Field Research Centre (FRC) site. Four groundwater wells (GW835, GW836, FW113-47 and FW215-49) with a wide range of pH (3 to 7), nitrate (44 to 23,400 mg L(-1)), uranium (0.73 to 60.36 mg L(-1)) and other metal contamination, were investigated. Results indicated that bacterial diversity correlated with the geochemistry of the groundwater. Microbial diversity decreased in relation to the contamination levels of the wells. The highly contaminated well (FW113-47) had lower gene diversity than less contaminated wells (FW215-49, GW835 and GW836). The high concentrations of contaminants present in well FW113-47 stimulated the growth of organisms capable of reducing uranium (Shewanella and Pseudomonas), nitrate (Pseudomonas, Rhodanobacter and Xanthomonas) and iron (Stenotrophomonas), and which were unique to this well. The clone libraries consisted primarily of sequences closely related to the phylum Proteobacteria, with FW-113-47 almost exclusively containing this phylum. Metal-reducing bacteria were present in all four wells, which may suggest that there is potential for successful bioremediation of the groundwater at the Oak Ridge FRC. The microbial community information gained from this study and previous studies at the site can be used to develop predictive multivariate and geographical information system (GIS) based models for microbial populations at the Oak Ridge FRC. This will allow for a better understanding of what organisms are likely to occur where and when, based on geochemistry, and how these organisms relate to bioremediation processes at the site.

  11. Bacterial Communities: Interactions to Scale

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    Reed M. Stubbendieck

    2016-08-01

    Full Text Available In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities.

  12. Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater

    Energy Technology Data Exchange (ETDEWEB)

    Mouser, P.J.; N' Guessan, A.L.; Elifantz, H.; Holmes, D.E.; Williams, K.H.; Wilkins, M.J.; Long, P.E.; Lovley, D.R.

    2009-04-01

    The impact of ammonium availability on microbial community structure and the physiological status and activity of Geobacter species during in situ bioremediation of uranium-contaminated groundwater was evaluated. Ammonium concentrations varied by as much as two orders of magnitude (<4 to 400 {micro}M) across the study site. Analysis of 16S rRNA gene sequences suggested that ammonium influenced the composition of the microbial community prior to acetate addition with Rhodoferax species predominating over Geobacter species at the site with the highest ammonium, and Dechloromonas species dominating at sites with lowest ammonium. However, once acetate was added, and dissimilatory metal reduction was stimulated, Geobacter species became the predominant organisms at all locations. Rates of U(VI) reduction appeared to be more related to the concentration of acetate that was delivered to each location rather than the amount of ammonium available in the groundwater. In situ mRNA transcript abundance of the nitrogen fixation gene, nifD, and the ammonium importer gene, amtB, in Geobacter species indicated that ammonium was the primary source of nitrogen during in situ uranium reduction, and that the abundance of amtB transcripts was inversely correlated to ammonium levels across all sites examined. These results suggest that nifD and amtB expression by subsurface Geobacter species are closely regulated in response to ammonium availability to ensure an adequate supply of nitrogen while conserving cell resources. Thus, quantifying nifD and amtB expression appears to be a useful approach for monitoring the nitrogen-related physiological status of Geobacter species in subsurface environments during bioremediation. This study also emphasizes the need for more detailed analysis of geochemical/physiological interactions at the field scale, in order to adequately model subsurface microbial processes.

  13. Pyrosequencing analysis of the bacterial community in drinking water wells.

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    Navarro-Noya, Yendi E; Suárez-Arriaga, Mayra C; Rojas-Valdes, Aketzally; Montoya-Ciriaco, Nina M; Gómez-Acata, Selene; Fernández-Luqueño, Fabián; Dendooven, Luc

    2013-07-01

    Wells used for drinking water often have a large biomass and a high bacterial diversity. Current technologies are not always able to reduce the bacterial population, and the threat of pathogen proliferation in drinking water sources is omnipresent. The environmental conditions that shape the microbial communities in drinking water sources have to be elucidated, so that pathogen proliferation can be foreseen. In this work, the bacterial community in nine water wells of a groundwater aquifer in Northern Mexico were characterized and correlated to environmental characteristics that might control them. Although a large variation was observed between the water samples, temperature and iron concentration were the characteristics that affected the bacterial community structure and composition in groundwater wells. Small increases in the concentration of iron in water modified the bacterial communities and promoted the growth of the iron-oxidizing bacteria Acidovorax. The abundance of the genera Flavobacterium and Duganella was correlated positively with temperature and the Acidobacteria Gp4 and Gp1, and the genus Acidovorax with iron concentrations in the well water. Large percentages of Flavobacterium and Pseudomonas bacteria were found, and this is of special concern as bacteria belonging to both genera are often biofilm developers, where pathogens survival increases.

  14. Forensic identification using skin bacterial communities

    OpenAIRE

    FIERER Noah; Lauber, Christian L.; Zhou, Nick; McDonald, Daniel; Costello, Elizabeth K.; Knight, Rob

    2010-01-01

    Recent work has demonstrated that the diversity of skin-associated bacterial communities is far higher than previously recognized, with a high degree of interindividual variability in the composition of bacterial communities. Given that skin bacterial communities are personalized, we hypothesized that we could use the residual skin bacteria left on objects for forensic identification, matching the bacteria on the object to the skin-associated bacteria of the individual who touched the object....

  15. Metatranscriptomic Analysis of Groundwater Reveals an Active Anammox Bacterial Population

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    Jewell, T. N. M.; Karaoz, U.; Thomas, B. C.; Banfield, J. F.; Brodie, E.; Williams, K. H.; Beller, H. R.

    2014-12-01

    Groundwater is a major natural resource, yet little is known about the contribution of microbial anaerobic ammonium oxidation (anammox) activity to subsurface nitrogen cycling. During anammox, energy is generated as ammonium is oxidized under anaerobic conditions to dinitrogen gas, using nitrite as the final electron acceptor. This process is a global sink for fixed nitrogen. Only a narrow range of monophyletic bacteria within the Planctomycetes carries out anammox, and the full extent of their metabolism, and subsequent impact on nitrogen cycling and microbial community structure, is still unknown. Here, we employ a metatranscriptomic analysis on enriched mRNA to identify the abundance and activity of a population of anammox bacteria within an aquifer at Rifle, CO. Planktonic biomass was collected over a two-month period after injection of up to 1.5 mM nitrate. Illumina-generated sequences were mapped to a phylogenetically binned Rifle metagenome database. We identified transcripts for genes with high protein sequence identities (81-98%) to those of anammox strain KSU-1 and to two of the five anammox bacteria genera, Brocadia and Kuenenia, suggesting an active, if not diverse, anammox population. Many of the most abundant anammox transcripts mapped to a single scaffold, indicative of a single dominant anammox species. Transcripts of the genes necessary for the anammox pathway were present, including an ammonium transporter (amtB), nitrite/formate transporter, nitrite reductase (nirK), and hydrazine oxidoreductase (hzoB). The form of nitrite reductase encoded by anammox is species-dependent, and we only identified nirK, with no evidence of anammox nirS. In addition to the anammox pathway we saw evidence of the anammox bacterial dissimilatory nitrate reduction to ammonium pathway (narH, putative nrfA, and nrfB), which provides an alternate means of generating substrates for anammox from nitrate, rather than relying on an external pool. Transcripts for hydroxylamine

  16. Flooding forested groundwater recharge areas modifies microbial communities from top soil to groundwater table.

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    Schütz, Kirsten; Nagel, Peter; Vetter, Walter; Kandeler, Ellen; Ruess, Liliane

    2009-01-01

    Subsurface microorganisms are crucial for contaminant degradation and maintenance of groundwater quality. This study investigates the microbial biomass and community composition [by phospholipid fatty acids (PLFAs)], as well as physical and chemical soil characteristics at woodland flooding sites of an artificial groundwater recharge system used for drinking water production. Vertical soil profiles to c. 4 m at two watered and one nonwatered site were analyzed. The microbial biomass was equal in watered and nonwatered sites, and considerable fractions (25-42%) were located in 40-340 cm depth. The microbial community structure differed significantly between watered and nonwatered sites, predominantly below 100 cm depth. Proportions of the bacterial PLFAs 16:1omega5, 16:1omega7, cy17:0 and 18:1omega9t, and the long-chained PLFAs 22:1omega9 and 24:1omega9 were more prominent at the watered sites, whereas branched, saturated PLFAs (iso/anteiso) dominated at the nonwatered site. PLFA community indices indicated stress response (trans/cis ratio), higher nutrient availability (unsaturation index) and changes in membrane fluidity (iso/anteiso ratio) due to flooding. In conclusion, water recharge processes led to nutrient input and altered environmental conditions, which resulted in a highly active and adapted microbial community residing in the vadose zone that effectively degraded organic compounds.

  17. Bacterial Diversity in Submarine Groundwater along the Coasts of the Yellow Sea

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    Qi eYe

    2016-01-01

    Full Text Available Submarine groundwater (SGD is one of the most significant pathways for the exchange of groundwater and/or source of nutrients, metals and carbon to the ocean, subsequently cause deleterious impacts on the coastal ecosystems. Microorganisms have been recognized as the important participators in the biogeochemical processes in the SGD. In this study, by utilizing 16S rRNA-based Illumina Miseq sequencing technology, we investigated bacterial diversity and distribution in both fresh well water and brackish recirculated porewater along the coasts in the Yellow Sea. The results showed that Actinobacteria and Betaproteobacteria, especially Comamonas spp. and Limnohabitans spp. were dominated in fresh well samples. Distinct patterns of bacterial communities were found among the porewater samples due to different locations, for examples, Cyanbacteria was the most abundant in the porewater samples far from the algal bloomed areas. The analysis of correlation between representative bacterial taxonomic groups and the contexture environmental parameters showed that fresh well water and brackish porewater might provide different nutrients to the coastal waters. Potential key bacterial groups such as Comamonas spp. may be excellent candidates for the bioremediation of the natural pollutants in the SGD. Our comprehensive understanding of bacterial diversity in the SGD along the coasts of the Yellow Sea will create a basis for designing the effective clean-up approach in-situ, and provide valuable information for the coastal management.

  18. Response of the microbial community to seasonal groundwater level fluctuations in petroleum hydrocarbon-contaminated groundwater.

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    Zhou, Ai-xia; Zhang, Yu-ling; Dong, Tian-zi; Lin, Xue-yu; Su, Xiao-si

    2015-07-01

    The effects of seasonal groundwater level fluctuations on the contamination characteristics of total petroleum hydrocarbons (TPH) in soils, groundwater, and the microbial community were investigated at a typical petrochemical site in northern China. The measurements of groundwater and soil at different depths showed that significant TPH residue was present in the soil in this study area, especially in the vicinity of the pollution source, where TPH concentrations were up to 2600 mg kg(-1). The TPH concentration in the groundwater fluctuated seasonally, and the maximum variation was 0.8 mg L(-1). The highest TPH concentrations were detected in the silty clay layer and lied in the groundwater level fluctuation zones. The groundwater could reach previously contaminated areas in the soil, leading to higher groundwater TPH concentrations as TPH leaches into the groundwater. The coincident variation of the electron acceptors and TPH concentration with groundwater-table fluctuations affected the microbial communities in groundwater. The microbial community structure was significantly different between the wet and dry seasons. The canonical correspondence analysis (CCA) results showed that in the wet season, TPH, NO3(-), Fe(2+), TMn, S(2-), and HCO3(-) were the major factors correlating the microbial community. A significant increase in abundance of operational taxonomic unit J1 (97% similar to Dechloromonas aromatica sp.) was also observed in wet season conditions, indicating an intense denitrifying activity in the wet season environment. In the dry season, due to weak groundwater level fluctuations and low temperature of groundwater, the microbial activity was weak. But iron and sulfate-reducing were also detected in dry season at this site. As a whole, groundwater-table fluctuations would affect the distribution, transport, and biodegradation of the contaminants. These results may be valuable for the control and remediation of soil and groundwater pollution at this site

  19. Antibiotics promote aggregation within aquatic bacterial communities

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    Gianluca eCorno

    2014-07-01

    Full Text Available The release of antibiotics (AB into the environment poses several threats for human health due to potential development of ABresistant natural bacteria. Even though the use of low-dose antibiotics has been promoted in health care and farming, significant amounts of AB are observed in aquatic environments. Knowledge on the impact of AB on natural bacterial communities is missing both in terms of spread and evolution of resistance mechanisms, and of modifications of community composition and productivity. New approaches are required to study the response of microbial communities rather than individual resistance genes. In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses. Bacterial abundance rapidly decreased by 75% in the presence of AB, independently of their concentration, and remained constant until the end of the experiment. The bacterial community was mainly dominated by Aeromonas hydrophila and Brevundimonas intermedia while the other two strains, Micrococcus luteus and Rhodococcus sp. never exceed 10%. Interestingly, the bacterial strains, which were isolated at the end of the experiment, were not AB-resistant, while reassembled communities composed of the 4 strains, isolated from treatments under AB stress, significantly raised their performance (growth rate, abundance in the presence of AB compared to the communities reassembled with strains isolated from the treatment without AB. By investigating the phenotypic adaptations of the communities subjected to the different treatments, we found that the presence of AB significantly increased co-aggregation by 5-6 fold.These results represent the first observation of co-aggregation as a successful strategy of AB resistance based on phenotype in aquatic bacterial communities, and can represent a fundamental step in the understanding of

  20. Investigation on bacterial community and diversity in the multilayer aquifer-aquitard system of the Pearl River Delta, China.

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    Liu, Kun; Jiao, Jiu Jimmy; Gu, Ji-Dong

    2014-12-01

    Bacteria play an important role in groundwater chemistry. The groundwater resource in the Pearl River Delta (PRD) is responsible for 50 million people's water requirement. High amount of ammonium, arsenic and methane had been reported in groundwater of the PRD, which was considered as the result of intensive bacterial metabolism in the multilayer aquifer-aquitard system. To investigate bacterial community in this system and its relation with groundwater chemistry, sediment and groundwater samples were taken from representative locations in the PRD at different lithological units. Bacterial 16S rRNA gene clone libraries were constructed for microbial identifications and community structures in different strata. Canonical correlation analysis between bacterial linages and environment variables (Cl(-), PO4(3-), SO4(2-), NH4(+)) showed that community structures were significantly modified by geological conditions. Higher bacterial diversity was observed in samples from the Holocene aquitard M1 and aquifer T1, while in the older aquitard M2 and basal aquifer T2, bacterial diversity was much lower. Chloroflexi, γ-proteobacteria and δ-proteobacteria were the dominant phyla in the aquitard sediment. β-proteobacteria was the dominant phylum in sediment which was strongly influenced by fresh water. The results of this study demonstrated that bacterial community contains information of geological events such as sea transgression and deltaic evolution, and microbes in the aquitards have great potential in dominating groundwater quality in aquifers.

  1. Bacterial communities associated with the lichen symbiosis.

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    Bates, Scott T; Cropsey, Garrett W G; Caporaso, J Gregory; Knight, Rob; Fierer, Noah

    2011-02-01

    Lichens are commonly described as a mutualistic symbiosis between fungi and "algae" (Chlorophyta or Cyanobacteria); however, they also have internal bacterial communities. Recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. However, we still have a limited understanding of the phylogenetic structure of these communities and their variability across lichen species. To address these knowledge gaps, we used bar-coded pyrosequencing to survey the bacterial communities associated with lichens. Bacterial sequences obtained from four lichen species at multiple locations on rock outcrops suggested that each lichen species harbored a distinct community and that all communities were dominated by Alphaproteobacteria. Across all samples, we recovered numerous bacterial phylotypes that were closely related to sequences isolated from lichens in prior investigations, including those from a lichen-associated Rhizobiales lineage (LAR1; putative N(2) fixers). LAR1-related phylotypes were relatively abundant and were found in all four lichen species, and many sequences closely related to other known N(2) fixers (e.g., Azospirillum, Bradyrhizobium, and Frankia) were recovered. Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses.

  2. Forensic identification using skin bacterial communities.

    Science.gov (United States)

    Fierer, Noah; Lauber, Christian L; Zhou, Nick; McDonald, Daniel; Costello, Elizabeth K; Knight, Rob

    2010-04-06

    Recent work has demonstrated that the diversity of skin-associated bacterial communities is far higher than previously recognized, with a high degree of interindividual variability in the composition of bacterial communities. Given that skin bacterial communities are personalized, we hypothesized that we could use the residual skin bacteria left on objects for forensic identification, matching the bacteria on the object to the skin-associated bacteria of the individual who touched the object. Here we describe a series of studies de-monstrating the validity of this approach. We show that skin-associated bacteria can be readily recovered from surfaces (including single computer keys and computer mice) and that the structure of these communities can be used to differentiate objects handled by different individuals, even if those objects have been left untouched for up to 2 weeks at room temperature. Furthermore, we demonstrate that we can use a high-throughput pyrosequencing-based ap-proach to quantitatively compare the bacterial communities on objects and skin to match the object to the individual with a high degree of certainty. Although additional work is needed to further establish the utility of this approach, this series of studies introduces a forensics approach that could eventually be used to independently evaluate results obtained using more traditional forensic practices.

  3. Jellyfish modulate bacterial dynamic and community structure.

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    Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina

    2012-01-01

    Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in

  4. Jellyfish modulate bacterial dynamic and community structure.

    Directory of Open Access Journals (Sweden)

    Tinkara Tinta

    Full Text Available Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into

  5. Urban greenness influences airborne bacterial community composition.

    Science.gov (United States)

    Mhuireach, Gwynne; Johnson, Bart R; Altrichter, Adam E; Ladau, Joshua; Meadow, James F; Pollard, Katherine S; Green, Jessica L

    2016-11-15

    Urban green space provides health benefits for city dwellers, and new evidence suggests that microorganisms associated with soil and vegetation could play a role. While airborne microorganisms are ubiquitous in urban areas, the influence of nearby vegetation on airborne microbial communities remains poorly understood. We examined airborne microbial communities in parks and parking lots in Eugene, Oregon, using high-throughput sequencing of the bacterial 16S rRNA gene on the Illumina MiSeq platform to identify bacterial taxa, and GIS to measure vegetation cover in buffer zones of different diameters. Our goal was to explore variation among highly vegetated (parks) versus non-vegetated (parking lots) urban environments. A secondary objective was to evaluate passive versus active collection methods for outdoor airborne microbial sampling. Airborne bacterial communities from five parks were different from those of five parking lots (p=0.023), although alpha diversity was similar. Direct gradient analysis showed that the proportion of vegetated area within a 50m radius of the sampling station explained 15% of the variation in bacterial community composition. A number of key taxa, including several Acidobacteriaceae were substantially more abundant in parks, while parking lots had higher relative abundance of Acetobacteraceae. Parks had greater beta diversity than parking lots, i.e. individual parks were characterized by unique bacterial signatures, whereas parking lot communities tended to be similar to each other. Although parks and parking lots were selected to form pairs of nearby sites, spatial proximity did not appear to affect compositional similarity. Our results also showed that passive and active collection methods gave comparable results, indicating the "settling dish" method is effective for outdoor airborne sampling. This work sets a foundation for understanding how urban vegetation may impact microbial communities, with potential implications for designing

  6. Characterization of Olkiluoto bacterial and archaeal communities by 454 pyrosequencing

    Energy Technology Data Exchange (ETDEWEB)

    Bomberg, M.; Nyyssoenen, M.; Itaevaara, M. [VTT Technical Research Centre of Finland, Espoo (Finland)

    2012-06-15

    Recent advancement in sequencing technologies, 'Next Generation Sequencing', such as FLX 454 pyrosequencing has made it possible to obtain large amounts of sequence data where previously only few sequences could be obtained. This technique is especially useful for the study of community composition of uncultured microbial populations in environmental samples. In this project, the FLX 454 pyrosequencing technique was used to obtain up to 20 000 16S rRNA sequences or 10 000 mRNA sequences from each sample for identification of the microbial species composition as well as for comparison of the microbial communities between different samples. This project focused on the characterization of active microbial communities in the groundwater at the final disposal site of high radioactive wastes in Olkiluoto by FLX 454 pyrosequencing of the bacterial and archaeal ribosomal RNA as well as of the mRNA transcripts of the dsrB gene and mcrA gene of sulphate reducing bacteria and methanogenic archaea, respectively. Specific emphasis was put on studying the relationship of active and latent sulphate reducers and methanogens by qPCR due to their important roles in deep geobiochemical processes connected to copper corrosion. Seven packered boreholes were sampled anaerobically in Olkiluoto during 2009-2010. Groundwater was pumped from specific depths and the microbial cells werecollected by filtration on a membrane. Active microbial communities were studied based on RNA extracted from the membranes and translated to copy DNA, followed by sequencing by 454 Tag pyrosequencing. A total of 27 different bacterial and 17 archaeal taxonomic groups were detected.

  7. Enhanced detection of groundwater contamination from a leaking waste disposal site by microbial community profiles

    Science.gov (United States)

    Mouser, Paula J.; Rizzo, Donna M.; Druschel, Gregory K.; Morales, Sergio E.; Hayden, Nancy; O'Grady, Patrick; Stevens, Lori

    2010-12-01

    Groundwater biogeochemistry is adversely impacted when municipal solid waste leachate, rich in nutrients and anthropogenic compounds, percolates into the subsurface from leaking landfills. Detecting leachate contamination using statistical techniques is challenging because well strategies or analytical techniques may be insufficient for detecting low levels of groundwater contamination. We sampled profiles of the microbial community from monitoring wells surrounding a leaking landfill using terminal restriction fragment length polymorphism (T-RFLP) targeting the 16S rRNA gene. Results show in situ monitoring of bacteria, archaea, and the family Geobacteraceae improves characterization of groundwater quality. Bacterial T-RFLP profiles showed shifts correlated to known gradients of leachate and effectively detected changes along plume fringes that were not detected using hydrochemical data. Experimental sediment microcosms exposed to leachate-contaminated groundwater revealed a shift from a β-Proteobacteria and Actinobacteria dominated community to one dominated by Firmicutes and δ-Proteobacteria. This shift is consistent with the transition from oxic conditions to an anoxic, iron-reducing environment as a result of landfill leachate-derived contaminants and associated redox conditions. We suggest microbial communities are more sensitive than hydrochemistry data for characterizing low levels of groundwater contamination and thus provide a novel source of information for optimizing detection and long-term monitoring strategies at landfill sites.

  8. Monitoring the Perturbation of Soil and Groundwater Microbial Communities Due to Pig Production Activities

    KAUST Repository

    Hong, Pei-Ying

    2013-02-08

    This study aimed to determine if biotic contaminants originating from pig production farms are disseminated into soil and groundwater microbial communities. A spatial and temporal sampling of soil and groundwater in proximity to pig production farms was conducted, and quantitative PCR (Q-PCR) was utilized to determine the abundances of tetracycline resistance genes (i.e., tetQ and tetZ) and integrase genes (i.e., intI1 and intI2). We observed that the abundances of tetZ, tetQ, intI1, and intI2 in the soils increased at least 6-fold after manure application, and their abundances remained elevated above the background for up to 16 months. Q-PCR further determined total abundances of up to 5.88 × 109 copies/ng DNA for tetZ, tetQ, intI1, and intI2 in some of the groundwater wells that were situated next to the manure lagoon and in the facility well used to supply water for one of the farms. We further utilized 16S rRNA-based pyrosequencing to assess the microbial communities, and our comparative analyses suggest that most of the soil samples collected before and after manure application did not change significantly, sharing a high Bray-Curtis similarity of 78.5%. In contrast, an increase in Bacteroidetes and sulfur-oxidizing bacterial populations was observed in the groundwaters collected from lagoon-associated groundwater wells. Genera associated with opportunistic human and animal pathogens, such as Acinetobacter, Arcobacter, Yersinia, and Coxiella, were detected in some of the manure-treated soils and affected groundwater wells. Feces-associated bacteria such as Streptococcus, Erysipelothrix, and Bacteroides were detected in the manure, soil, and groundwater ecosystems, suggesting a perturbation of the soil and groundwater environments by invader species from pig production activities.

  9. Microbial Community Succession During Lactate Amendment of Chromium Contaminated Groundwater Reveals a Predominance of Pelosinus spp.

    Energy Technology Data Exchange (ETDEWEB)

    Mosher, Jennifer J [ORNL; Phelps, Tommy Joe [ORNL; Drake, Meghan M [ORNL; Campbell, James H [ORNL; Moberly, James G [ORNL; Schadt, Christopher Warren [ORNL; Podar, Mircea [ORNL; Brown, Steven D [ORNL; Hazen, Terry [Lawrence Berkeley National Laboratory (LBNL); Arkin, Adam [Lawrence Berkeley National Laboratory (LBNL); Palumbo, Anthony Vito [ORNL; Faybishenko, Boris A [Lawrence Berkeley National Laboratory (LBNL); Elias, Dwayne A [ORNL

    2012-01-01

    Microbial community structure and metabolism in contaminated ecosystems are potentially controlled not only by the different populations within the community, but a myriad of dynamic physicochemical parameters as well. The goal of the current work was to determine the impact of organic acid enrichment, in this case lactate, on the succession of the native microbial community from a contaminated groundwater aquifer. Triplicate anaerobic, continuous-flow glass reactors were inoculated with Hanford 100-H groundwater and incubated for 95 days to obtain a stable, enriched community. The microbial community experienced a shift in the population dynamics over time to eventually form a community with far less diversity than the original. The final community was dominated by Pelosinus spp. and to a lesser degree, Acetobacterium spp. with small amounts of other bacteria and archaea including methanogens. The resultant diversity was far decreased from 63 genera within 12 phyla to 11 bacterial genera (from three phyla) and 2 archaeal genera (from one phylum). Isolation efforts were successful in attaining new species of Pelosinus and known members of Methanosarcina barkerii along with several sulfate- and Fe(III)- reducing consortia members. The continuous-flow reactors allowed for testing physiochemical factors with microbial community dynamics on a smaller, replicable, scale while also facilitating the isolation of several previously uncultured community members. These lab-scale simulations will presumably allow for a deeper understanding of the community metabolism with specific carbon amendments that can inform future in situ efforts.

  10. Soil bacterial community responses to global changes

    DEFF Research Database (Denmark)

    Bergmark, Lasse

    /change the microbial community towards a higher fungal dominance. That could lead to a change in the carbon and nutrient flow in soil. In Manuscript 2 the impact of climate change manipulations and the seasonal dynamics of soil fungi and bacterial communities are investigated. Our results show that the soil fungal......Soil bacteria and archaea are essential for ecosystem functioning and plant growth through their degradation of organic matter and turnover of nutrients. But since the majority of soil bacteria and archaea are unclassified and “nonculturable” the functionality of the microbial community and its...... overall importance for ecosystem function in soil is poorly understood. Global change factors may affect the diversity and functioning of soil prokaryotes and thereby ecosystem functioning. To gain a better understanding of the effects of global changes it is of fundamental importance to classify...

  11. Patterning bacterial communities on epithelial cells.

    Directory of Open Access Journals (Sweden)

    Mohammed Dwidar

    Full Text Available Micropatterning of bacteria using aqueous two phase system (ATPS enables the localized culture and formation of physically separated bacterial communities on human epithelial cell sheets. This method was used to compare the effects of Escherichia coli strain MG1655 and an isogenic invasive counterpart that expresses the invasin (inv gene from Yersinia pseudotuberculosis on the underlying epithelial cell layer. Large portions of the cell layer beneath the invasive strain were killed or detached while the non-invasive E. coli had no apparent effect on the epithelial cell layer over a 24 h observation period. In addition, simultaneous testing of the localized effects of three different bacterial species; E. coli MG1655, Shigella boydii KACC 10792 and Pseudomonas sp DSM 50906 on an epithelial cell layer is also demonstrated. The paper further shows the ability to use a bacterial predator, Bdellovibriobacteriovorus HD 100, to selectively remove the E. coli, S. boydii and P. sp communities from this bacteria-patterned epithelial cell layer. Importantly, predation and removal of the P. Sp was critical for maintaining viability of the underlying epithelial cells. Although this paper focuses on a few specific cell types, the technique should be broadly applicable to understand a variety of bacteria-epithelial cell interactions.

  12. Bacterial community reconstruction using compressed sensing.

    Science.gov (United States)

    Amir, Amnon; Zuk, Or

    2011-11-01

    Bacteria are the unseen majority on our planet, with millions of species and comprising most of the living protoplasm. We propose a novel approach for reconstruction of the composition of an unknown mixture of bacteria using a single Sanger-sequencing reaction of the mixture. Our method is based on compressive sensing theory, which deals with reconstruction of a sparse signal using a small number of measurements. Utilizing the fact that in many cases each bacterial community is comprised of a small subset of all known bacterial species, we show the feasibility of this approach for determining the composition of a bacterial mixture. Using simulations, we show that sequencing a few hundred base-pairs of the 16S rRNA gene sequence may provide enough information for reconstruction of mixtures containing tens of species, out of tens of thousands, even in the presence of realistic measurement noise. Finally, we show initial promising results when applying our method for the reconstruction of a toy experimental mixture with five species. Our approach may have a potential for a simple and efficient way for identifying bacterial species compositions in biological samples. All supplementary data and the MATLAB code are available at www.broadinstitute.org/?orzuk/publications/BCS/.

  13. Diversity of arsenite oxidizing bacterial communities in arsenic-rich deltaic aquifers in West Bengal, India

    Directory of Open Access Journals (Sweden)

    Devanita eGhosh

    2014-11-01

    Full Text Available High arsenic (As concentration in groundwater has affected human health, particularly in South-East Asia putting millions of people at risk. Biogeochemical cycling of As carried out by different bacterial groups are suggested to control the As fluxes in aquifers. A functional diversity approach in link with As precipitation was adopted to study bacterial community structures and their variation within the As contaminated Bengal Delta Plain (BDP aquifers of India. Groundwater samples collected from two shallow aquifers in Karimpur II (West Bengal, India, during years 2010 and 2011, were investigated to trace the effects of inter-annual variability in precipitation on community structure and diversity of bacterial assemblages. The study focused on amplification, clone library generation and sequencing of the arsenite oxidase large sub-unit gene aioA and 16S rRNA marker, with respect to changes in elemental concentrations. New set of primers were designed to amplify the aioA gene as a phylogenetic marker to study taxonomically diverse arsenite oxidizing bacterial groups in these aquifers. Overall narrow distribution of bacterial communities based on aioA and 16S rRNA sequences observed was due to poor nutrient status and anoxic conditions in these As contaminated aquifers. Proteobacteria was the dominant phylum detected, within which Acidovorax, Hydrogenophaga, Albidiferax, Bosea and Polymorphum were the major arsenite oxidizing bacterial genera. The structure of bacterial assemblages including those of arsenite oxidizing bacteria were affected by an increase in major elemental concentrations (e.g., As, iron, sulfur, and silica within two sampling sessions, which was supported by PCA analysis. One of the significant findings of this study is detection of novel lineages of 16S rRNA-like bacterial sequences indicating presence of indigenous bacterial communities across both wells of BDP that can play important role in biogeochemical cycling of

  14. Distinctive Sediment and Adjacent Groundwater Microbial Communities in Bangladesh Aquifers Suggested Through Microbial Lipid Distribution and δ13C Analysis

    Science.gov (United States)

    Martin, K. J. W.; van Geen, A.; Bostick, B. C.; Mailloux, B. J.; Ahmed, K. M.; Choudhury, I.; Slater, G.

    2016-12-01

    Arsenic groundwater contamination throughout shallow aquifer sediments in Southern Asia has resulted in a large-scale human health crisis. There is a strong consensus that microbial iron reduction coupled to organic carbon oxidation is the predominant mechanism driving this arsenic release. However, limited research has examined the composition and functioning of the indigenous microbial communities. Further, such research has varied between studies targeting microbial communities associated with groundwater versus those associated with sediments. The overall aim of this research study was to use microbial lipid biomarkers of bacterial and micro-eukaryal (phospholipid fatty acids (PLFA)) and archaea (di- and tetra- bound ether lipids) distributions and δ13C analysis to compare the indigenous sedimentary-associated microbial communities with the groundwater-associated microbial communities in Bangladesh aquifers. Field sampling was carried out at four locations (Site B, F, SAM and CAT) in the Araihazar Upazila, Bangladesh in 2013 and 2015. A significant difference (parsenic release in these systems.

  15. Novel bacterial isolate from Permian groundwater, capable of aggregating potential biofuel-producing microalga Nannochloropsis oceanica IMET1.

    Science.gov (United States)

    Wang, Hui; Laughinghouse, Haywood D; Anderson, Matthew A; Chen, Feng; Willliams, Ernest; Place, Allen R; Zmora, Odi; Zohar, Yonathan; Zheng, Tianling; Hill, Russell T

    2012-03-01

    Increasing petroleum costs and climate change have resulted in microalgae receiving attention as potential biofuel producers. Little information is available on the diversity and functions of bacterial communities associated with biofuel-producing algae. A potential biofuel-producing microalgal strain, Nannochloropsis oceanica IMET1, was grown in Permian groundwater. Changes in the bacterial community structure at three temperatures were monitored by two culture-independent methods, and culturable bacteria were characterized. After 9 days of incubation, N. oceanica IMET1 began to aggregate and precipitate in cultures grown at 30°C, whereas cells remained uniformly distributed at 15°C and 25°C. The bacterial communities in cultures at 30°C changed markedly. Some bacteria isolated only at 30°C were tested for their potential for aggregating microalgae. A novel bacterium designated HW001 showed a remarkable ability to aggregate N. oceanica IMET1, causing microalgal cells to aggregate after 3 days of incubation, while the total lipid content of the microalgal cells was not affected. Direct interaction of HW001 and N. oceanica is necessary for aggregation. HW001 can also aggregate the microalgae N. oceanica CT-1, Tetraselmis suecica, and T. chuii as well as the cyanobacterium Synechococcus WH8007. 16S rRNA gene sequence comparisons indicated the great novelty of this strain, which exhibited only 89% sequence similarity with any previously cultured bacteria. Specific primers targeted to HW001 revealed that the strain originated from the Permian groundwater. This study of the bacterial communities associated with potential biofuel-producing microalgae addresses a little-investigated area of microalgal biofuel research and provides a novel approach to harvest biofuel-producing microalgae by using the novel bacterium strain HW001.

  16. Carbon, metals and grain size correlate with bacterial community composition in sediments of a high arsenic aquifer

    Directory of Open Access Journals (Sweden)

    Teresa eLegg

    2012-03-01

    Full Text Available Bacterial communities can exert significant influence on the biogeochemical cycling of arsenic (As. This has globally important implications since As toxicity in drinking water affects the health of millions of people worldwide, including in the Ganges-Brahmaputra Delta region of Bangladesh where geogenic groundwater arsenic concentrations can be more than 10 times the World Health Organization’s limit. Thus, the goal of this research was to investigate patterns in bacterial community composition across environmental gradients in an aquifer with elevated groundwater As concentrations in Araihazar, Bangladesh. We characterized the bacterial community by pyrosequencing 16S rRNA genes from aquifer sediment samples collected at three locations along a groundwater flowpath, at a range of depths between 1.5 and 15 m. We identified significant shifts in bacterial community composition along the groundwater flowpath in the aquifer. In addition, we found that bacterial community structure was significantly related to sediment grain size, and sediment carbon (C, manganese (Mn, and iron (Fe concentrations. Deltaproteobacteria and Chloroflexi were more abundant in silty sediments with higher concentrations of C, Fe, and Mn. By contrast, Alphaproteobacteria and Betaproteobacteria were more abundant in sediments with higher concentrations of sand and Si, and lower concentrations of C and metals. Based on the phylogenetic affiliations of these taxa, these results may indicate a shift to more Fe-, Mn-, and humic substance- reducers in the high C and metal sediments. It is well-documented that C, Mn and Fe may influence the mobility of groundwater arsenic, and it is intriguing that these constituents may also structure the bacterial community.

  17. Biogeographic Congruency among Bacterial Communities from Terrestrial Sulfidic Springs

    Directory of Open Access Journals (Sweden)

    Brendan eHeadd

    2014-09-01

    Full Text Available Terrestrial sulfidic springs support diverse microbial communities by serving as stable conduits for geochemically diverse and nutrient-rich subsurface waters. Microorganisms that colonize terrestrial springs likely originate from groundwater, but may also be sourced from the surface. As such, the biogeographic distribution of microbial communities inhabiting sulfidic springs should be controlled by a combination of spring geochemistry and surface and subsurface transport mechanisms, and not necessarily geographic proximity to other springs. We examined the bacterial diversity of seven springs to test the hypothesis that occurrence of taxonomically similar microbes, important to the sulfur cycle, at each spring is controlled by geochemistry. Complementary Sanger sequencing and 454 pyrosequencing of 16S rRNA genes retrieved five proteobacterial classes, and Bacteroidetes, Chlorobi, Chloroflexi, and Firmicutes phyla from all springs, which suggested the potential for a core sulfidic spring microbiome. Among the putative sulfide-oxidizing groups (Epsilonproteobacteria and Gammaproteobacteria, up to 83% of the sequences from geochemically similar springs clustered together. Abundant populations of Hydrogenimonas-like or Sulfurovum-like spp. (Epsilonproteobacteria occurred with abundant Thiothrix and Thiofaba spp. (Gammaproteobacteria, but Arcobacter-like and Sulfurimonas spp. (Epsilonproteobacteria occurred with less abundant gammaproteobacterial populations. These distribution patterns confirmed that geochemistry rather than biogeography regulates bacterial dominance at each spring. Potential biogeographic controls were related to paleogeologic sedimentation patterns that could control long-term microbial transport mechanisms that link surface and subsurface environments. Knowing the composition of a core sulfidic spring microbial community could provide a way to monitor diversity changes if a system is threatened by anthropogenic processes or

  18. Biogas production using anaerobic groundwater containing a subterranean microbial community associated with the accretionary prism.

    Science.gov (United States)

    Baito, Kyohei; Imai, Satomi; Matsushita, Makoto; Otani, Miku; Sato, Yu; Kimura, Hiroyuki

    2015-09-01

    In a deep aquifer associated with an accretionary prism, significant methane (CH₄) is produced by a subterranean microbial community. Here, we developed bioreactors for producing CH₄ and hydrogen (H₂) using anaerobic groundwater collected from the deep aquifer. To generate CH₄, the anaerobic groundwater amended with organic substrates was incubated in the bioreactor. At first, H₂ was detected and accumulated in the gas phase of the bioreactor. After the H₂ decreased, rapid CH₄ production was observed. Phylogenetic analysis targeting 16S rRNA genes revealed that the H₂ -producing fermentative bacterium and hydrogenotrophic methanogen were predominant in the reactor. The results suggested that syntrophic biodegradation of organic substrates by the H₂ -producing fermentative bacterium and the hydrogenotrophic methanogen contributed to the CH₄ production. For H₂ production, the anaerobic groundwater, amended with organic substrates and an inhibitor of methanogens (2-bromoethanesulfonate), was incubated in a bioreactor. After incubation for 24 h, H₂ was detected from the gas phase of the bioreactor and accumulated. Bacterial 16S rRNA gene analysis suggested the dominance of the H₂ -producing fermentative bacterium in the reactor. Our study demonstrated a simple and rapid CH4 and H2 production utilizing anaerobic groundwater containing an active subterranean microbial community.

  19. Bacterial community development in experimental gingivitis.

    Science.gov (United States)

    Kistler, James O; Booth, Veronica; Bradshaw, David J; Wade, William G

    2013-01-01

    Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. This study used 454-pyrosequencing of the V1-V3 region of 16S rRNA genes (approximately 500 bp), and bacterial culture, to characterize the composition of plaque during the transition from periodontal health to gingivitis. A total of 20 healthy volunteers abstained from oral hygiene for two weeks, allowing plaque to accumulate and gingivitis to develop. Plaque samples were analyzed at baseline, and after one and two weeks. In addition, plaque samples from 20 chronic periodontitis patients were analyzed for cross-sectional comparison to the experimental gingivitis cohort. All of the healthy volunteers developed gingivitis after two weeks. Pyrosequencing yielded a final total of 344,267 sequences after filtering, with a mean length of 354 bases, that were clustered into an average of 299 species-level Operational Taxonomic Units (OTUs) per sample. Principal coordinates analysis (PCoA) plots revealed significant shifts in the bacterial community structure of plaque as gingivitis was induced, and community diversity increased significantly after two weeks. Changes in the relative abundance of OTUs during the transition from health to gingivitis were correlated to bleeding on probing (BoP) scores and resulted in the identification of new health- and gingivitis-associated taxa. Comparison of the healthy volunteers to the periodontitis patients also confirmed the association of a number of putative periodontal pathogens with chronic periodontitis. Taxa associated with gingivitis included Fusobacterium nucleatum subsp. polymorphum, Lachnospiraceae [G-2] sp. HOT100, Lautropia sp. HOTA94, and Prevotella oulorum, whilst Rothia dentocariosa was associated with periodontal health. Further study of these taxa is warranted and may lead to new therapeutic approaches

  20. Pyrene effects on rhizoplane bacterial communities.

    Science.gov (United States)

    Balcom, Ian N; Crowley, David E

    2009-09-01

    Certain plant species promote biodegradation of polycyclic aromatic hydrocarbons (PAHs), but few studies have examined the microbial populations that are associated with the rhizoplane of these plants. In this study, the bacterial composition of the rhizoplane were characterized for four plant species during in soils with different histories of exposure to PAH and in the presence or absence of a pyrene spike at 100 mg kg(-1) pyrene. Three of the plant species including Andropogon gerrardii, Panicum coloratum and Melilotus officinalis were known to stimulate PAH degradation. Wheat (Triticum aestivum) was used as a reference species. Results showed that after 90 days, approximately 45% of the pyrene spike disappeared from soil without plants. In contrast, cultivation of plants resulted in 95% disappearance of pyrene. There were no significant differences in the extent of pyrene disappearance for different plants. In all cases, 16S rRNA gene profiles of the rhizoplane were less complex in the pyrene-spiked soils, suggesting that richness and evenness of the predominant bacteria were reduced. Our results show that pyrene contamination results in significant shifts in the composition of rhizosphere bacterial communities that are still further influenced by the plant species and prior exposure history to PAH contamination.

  1. Interaction between resource identity and bacterial community composition regulates bacterial respiration in aquatic ecosystems

    Directory of Open Access Journals (Sweden)

    A. P. F. Pires

    Full Text Available Abstract Resource identity and composition structure bacterial community, which in turn determines the magnitude of bacterial processes and ecological services. However, the complex interaction between resource identity and bacterial community composition (BCC has been poorly understood so far. Using aquatic microcosms, we tested whether and how resource identity interacts with BCC in regulating bacterial respiration and bacterial functional diversity. Different aquatic macrophyte leachates were used as different carbon resources while BCC was manipulated through successional changes of bacterial populations in batch cultures. We observed that the same BCC treatment respired differently on each carbon resource; these resources also supported different amounts of bacterial functional diversity. There was no clear linear pattern of bacterial respiration in relation to time succession of bacterial communities in all leachates, i.e. differences on bacterial respiration between different BCC were rather idiosyncratic. Resource identity regulated the magnitude of respiration of each BCC, e.g. Ultricularia foliosa leachate sustained the greatest bacterial functional diversity and lowest rates of bacterial respiration in all BCC. We conclude that both resource identity and the BCC interact affecting the pattern and the magnitude of bacterial respiration in aquatic ecosystems.

  2. Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla

    OpenAIRE

    2014-01-01

    Agricultural practices affect the soil ecosystem in multiple ways and the soil microbial communities represent an integrated and dynamic measure of soil status. Our aim was to test whether the soil bacterial community and the relative abundance of major bacterial phyla responded predictably to long-term organic amendments representing different carbon qualities (peat and straw) in combination with nitrogen fertilization levels and if certain bacterial groups were indicative of specific treatm...

  3. Bacterial community succession in pine-wood decomposition

    Directory of Open Access Journals (Sweden)

    Anna eKielak

    2016-03-01

    Full Text Available Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

  4. The Influence of Pumping on Observed Bacterial Counts in Groundwater Samples: Implications for Sampling Protocol and Water Quality Interpretation

    Science.gov (United States)

    Kozuskanich, J.; Novakowski, K.; Anderson, B.

    2008-12-01

    Drinking water quality has become an important issue in Ontario following the events in Walkerton in 2000. Many rural communities are reliant on private groundwater wells for drinking water, and it is the responsibility of the owner to have the water tested to make sure it is safe for human consumption. Homeowners can usually take a sample to the local health unit for total coliform and E. Coli analysis at no charge to determine if the water supply is being tainted by surface water or fecal matter, both of which could indicate the potential for negative impacts on human health. However, is the sample coming out of the tap representative of what is going on the aquifer? The goal of this study is to observe how bacterial counts may vary during the course of well pumping, and how those changing results influence the assessment of water quality. Multiple tests were conducted in bedrock monitoring wells to examine the influence of pumping rate and pumped volume on observed counts of total coliform, E. Coli, fecal streptococcus, fecal coliform and heterotrophic plate count. Bacterial samples were collected frequently during the course of continuous purging events lasting up to 8 hours. Typical field parameters (temperature, salinity, pH, dissolved oxygen and ORP) were also continuously monitored during the course of each test. Common practice in groundwater studies is to wait until these parameters have stabilized or three well volumes have been removed prior to sampling, to ensure the sample is taken from new water entering the well from the aquifer, rather than the original water stored in the borehole prior to the test. In general, most bacterial counts were low, but did go above the drinking water standard of 0 counts/100mL (total coliform and E. Coli) at times during the tests. Results show the greatest variability in the observed bacterial counts at the onset of pumping prior to the removal of three well volumes. Samples taken after the removal of three well

  5. Spatial structuring of bacterial communities within individual Ginkgo biloba trees.

    Science.gov (United States)

    Leff, Jonathan W; Del Tredici, Peter; Friedman, William E; Fierer, Noah

    2015-07-01

    Plant-associated microorganisms affect the health of their hosts in diverse ways, yet the distribution of these organisms within individual plants remains poorly understood. To address this knowledge gap, we assessed the spatial variability in bacterial community diversity and composition found on and in aboveground tissues of individual Ginkgo biloba trees. We sampled bacterial communities from > 100 locations per tree, including leaf, branch and trunk samples and used high-throughput sequencing of the 16S rRNA gene to determine the diversity and composition of these communities. Bacterial community structure differed strongly between bark and leaf samples, with bark samples harbouring much greater bacterial diversity and a community composition distinct from leaves. Within sample types, we observed clear spatial patterns in bacterial diversity and community composition that corresponded to the samples' proximity to the exterior of the tree. The composition of the bacterial communities found on trees is highly variable, but this variability is predictable and dependent on sampling location. Moreover, this work highlights the importance of carefully considering plant spatial structure when characterizing the microbial communities associated with plants and their impacts on plant hosts.

  6. Enhancement of bacterial denitrification for nitrate removal in groundwater with electrical stimulation from microbial fuel cells

    Science.gov (United States)

    Zhang, Baogang; Liu, Ye; Tong, Shuang; Zheng, Maosheng; Zhao, Yinxin; Tian, Caixing; Liu, Hengyuan; Feng, Chuanping

    2014-12-01

    Electricity generated from the microbial fuel cell (MFC) is applied to the bioelectrical reactor (BER) directly as electrical stimulation means for enhancement of bacterial denitrification to remove nitrate effectively from groundwater. With maximum power density of 502.5 mW m-2 and voltage outputs ranging from 500 mV to 700 mV, the nitrate removal is accelerated, with less intermediates accumulation, compared with control sets without electrical stimulation. Denitrification bacteria proliferations and activities are promoted as its number and Adenosine-5'-triphosphate (ATP) concentration increased one order of magnitude (3.5 × 107 in per milliliter biofilm solution) and about 1.5 folds, respectively. Effects of electricity from MFCs on enhancement of bacterial behaviors are demonstrated for the first time. These results indicate that MFCs can be applied in the in-situ bioremediation of nitrate polluted groundwater for efficiency improvement.

  7. Effect of cell physicochemical characteristics and motility on bacterial transport in groundwater

    Science.gov (United States)

    Becker, M.W.; Collins, S.A.; Metge, D.W.; Harvey, R.W.; Shapiro, A.M.

    2004-01-01

    The influence of physicochemical characteristics and motility on bacterial transport in groundwater were examined in flow-through columns. Four strains of bacteria isolated from a crystalline rock groundwater system were investigated, with carboxylate-modified and amidine-modified latex microspheres and bromide as reference tracers. The bacterial isolates included a gram-positive rod (ML1), a gram-negative motile rod (ML2), a nonmotile mutant of ML2 (ML2m), and a gram-positive coccoid (ML3). Experiments were repeated at two flow velocities, in a glass column packed with glass beads, and in another packed with iron-oxyhydroxide coated glass beads. Bacteria breakthrough curves were interpreted using a transport equation that incorporates a sorption model from microscopic observation of bacterial deposition in flow-cell experiments. The model predicts that bacterial desorption rate will decrease exponentially with the amount of time the cell is attached to the solid surface. Desorption kinetics appeared to influence transport at the lower flow rate, but were not discernable at the higher flow rate. Iron-oxyhydroxide coatings had a lower-than-expected effect on bacterial breakthrough and no effect on the microsphere recovery in the column experiments. Cell wall type and shape also had minor effects on breakthrough. Motility tended to increase the adsorption rate, and decrease the desorption rate. The transport model predicts that at field scale, desorption rate kinetics may be important to the prediction of bacteria transport rates. ?? 2003 Elsevier B.V. All rights reserved.

  8. Dynamics of seawater bacterial communities in a shellfish hatchery.

    Science.gov (United States)

    Powell, S M; Chapman, C C; Bermudes, M; Tamplin, M L

    2013-08-01

    Bacterial disease is a significant issue for larviculture of several species of shellfish, including oysters. One source of bacteria is the seawater used throughout the hatchery. In this study carried out at a commercial oyster hatchery in Tasmania, Australia, the diversity of the bacterial community and its relationship with larval production outcomes were studied over a 2-year period using terminal restriction fragment length polymorphism and tag-encoded pyrosequencing. The bacterial communities were very diverse, dominated by the Alphaproteobacteria, Gammaproteobacteria, Flavobacteria and Cyanobacteria. The communities were highly variable on scales of days, weeks and seasons. The difference between the intake seawater and treated clean seawater used in the hatchery was smaller than the observed temporal differences in the seawater throughout the year. No clear correlation was observed between production outcomes and the overall bacterial community structure. However, one group of Cyanobacterial sequences was more abundant when mass mortality events occurred than when healthy spat were produced although they were always present.

  9. Influence of technological treatments on bacterial communities in ...

    African Journals Online (AJOL)

    J. Maïworé

    2012-04-26

    Apr 26, 2012 ... DGGE), bacterial community, technological treatments. INTRODUCTION ... containing a linear gradient like formamide and urea at ..... mexican pozol, a fermented maize dough, demonstrated the need for cultivation- ...

  10. Dynamics of Bacterial Community Composition in the Malaria Mosquito's Epithelia.

    Science.gov (United States)

    Tchioffo, Majoline T; Boissière, Anne; Abate, Luc; Nsango, Sandrine E; Bayibéki, Albert N; Awono-Ambéné, Parfait H; Christen, Richard; Gimonneau, Geoffrey; Morlais, Isabelle

    2015-01-01

    The Anopheles midgut hosts diverse bacterial communities and represents a complex ecosystem. Several evidences indicate that mosquito midgut microbiota interferes with malaria parasite transmission. However, the bacterial composition of salivary glands and ovaries, two other biologically important tissues, has not been described so far. In this study, we investigated the dynamics of the bacterial communities in the mosquito tissues from emerging mosquitoes until 8 days after a blood meal containing Plasmodium falciparum gametocytes and described the temporal colonization of the mosquito epithelia. Bacterial communities were identified in the midgut, ovaries, and salivary glands of individual mosquitoes using pyrosequencing of the 16S rRNA gene. We found that the mosquito epithelia share a core microbiota, but some bacteria taxa were more associated with one or another tissue at a particular time point. The bacterial composition in the tissues of emerging mosquitoes varied according to the breeding site, indicating that some bacteria are acquired from the environment. Our results revealed temporal variations in the bacterial community structure, possibly as a result of the mosquito physiological changes. The abundance of Serratia significantly correlated with P. falciparum infection both in the midgut and salivary glands of malaria challenged mosquitoes, which suggests that interactions occur between microbes and parasites. These bacteria may represent promising targets for vector control strategies. Overall, this study points out the importance of characterizing bacterial communities in malaria mosquito vectors.

  11. Adaptations in bacterial and fungal communities to termite fungiculture

    DEFF Research Database (Denmark)

    Otani, Saria

    . We therefore propose that division of labour extends beyond the termites to their gut bacterial communities. We also show that Termitomyces-fed cockroaches undergo compositional changes in their gut microbiotas. A step-wise gradient pattern in gut bacterial community that correlated with an increase...... in the proportion of fungal material provided to the cockroaches. However, gut microbiotas remained distinct from those of termites after Termitomyces-feeding, indicating that a fungal diet can play a role in structuring gut community composition, but at the same time exemplifies how original community compositions...

  12. Determinants of bacterial communities in Canadian agroforestry systems.

    Science.gov (United States)

    Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N; Bissett, Andrew; Richardson, Alan E; Siddique, Tariq; Bork, Edward W; Chang, Scott X

    2016-06-01

    Land-use change is one of the most important factors influencing soil microbial communities, which play a pivotal role in most biogeochemical and ecological processes. Using agroforestry systems as a model, this study examined the effects of land uses and edaphic properties on bacterial communities in three agroforestry types covering a 270 km soil-climate gradient in Alberta, Canada. Our results demonstrate that land-use patterns exert stronger effects on soil bacterial communities than soil zones in these agroforestry systems. Plots with trees in agroforestry systems promoted greater bacterial abundance and to some extent species richness, which was associated with more nutrient-rich soil resources. While Acidobacteria, Actinobacteria and Alphaproteobacteria were the dominant bacterial phyla and subphyla across land uses, Arthrobacter, Acidobacteria_Gp16, Burkholderia, Rhodanobacter and Rhizobium were the keystone taxa in these agroforestry systems. Soil pH and carbon contents emerged as the major determinants of bacterial community characteristics. We found non-random co-occurrence and modular patterns of soil bacterial communities, and these patterns were controlled by edaphic factors and not their taxonomy. Overall, this study highlights the drivers and co-occurrence patterns of soil microbial communities in agroforestry systems.

  13. Molecular characterization of microbial communities in deep coal seam groundwater of northern Japan

    Energy Technology Data Exchange (ETDEWEB)

    Shimizu, S.; Akiyama, M.; Naganuma, T.; Fujioka, M.; Nako, M.; Ishijima, Y. [Northern Advancement Center for Science and Technology, Hokkaido (Japan)

    2007-12-15

    We investigated microbial methanogenesis and community structure based on 16S rRNA gene sequences from a coal seam aquifer located 843-907 m below ground level in northern Japan; additionally, we studied the {delta}{sup 13}C and {delta} {sup 2}H ({delta}D) of coal-bed gases and other physicochemical parameters. Although isotopic analysis suggested a thermocatalytic origin for the gases, the microbial activity and community structure strongly implied the existence of methanogenic microbial communities in situ. Methane was generated in the enrichment cultures of the hydrogenotrophic and methylotrophic microorganisms obtained from coal seam groundwater. Methanogen clones dominated the archaeal 16S rRNA gene libraries and were mostly related to the hydrogenotrophic genus Methanoculleus and the methylotrophic genus Methanolobus. Bacterial 16S rRNA gene libraries were dominated by the clones related to the genera Acetobacterium and Syntrophus which have a symbiotic association with methanogens. LIBSHUFF analysis revealed that N{sub 2} gas injected into the coal seam (for enhanced methane production) does not affect the coverage of archaeal and bacterial populations. However, AMOVA analysis does provide evidence for a change in the genetic diversity of archaeal populations that are dominated by methanogens. Therefore, N{sub 2} injection into the coal seam might affect the cycling of matter by methanogens in situ.

  14. Elevation gradient of soil bacterial communities in bamboo plantations.

    Science.gov (United States)

    Lin, Yu-Te; Chiu, Chih-Yu

    2016-12-01

    Elevation trends of macro organisms have long been well studied. However, whether microbes also exhibit such patterns of elevation change is unknown. Here, we investigated the changes in bamboo forest soil bacterial communities along six elevation gradients, from 600 to 1800 m a.s.l. in Mt. Da-an, a subtropical montane area in Nantou county at central Taiwan. Data from 16S rRNA gene clone libraries revealed that more than 70 % of the six communities contained Acidobacteria and Proteobacteria, although the relative abundance differed. Nonmetric multidimensional scaling analysis of the distribution of operational taxonomic units showed differences in bamboo soil bacterial communities across gradients. The bacterial communities at 1000 and 1200 m showed greater diversity than the communities at both lower (600 and 800 m) and higher (1400 and 1800 m) elevations. In contrast to the bacterial community trend, soil C and N and microbial biomass properties increased linearly with elevation. The bamboo soil bacterial community could interact with multiple factors such as soil organic matter content and temperature, for differences in composition and diversity with change in elevation.

  15. Bacterial community diversity and variation in spray water sources and the tomato fruit surface

    Directory of Open Access Journals (Sweden)

    Ottesen Andrea R

    2011-04-01

    Full Text Available Abstract Background Tomato (Solanum lycopersicum consumption has been one of the most common causes of produce-associated salmonellosis in the United States. Contamination may originate from animal waste, insects, soil or water. Current guidelines for fresh tomato production recommend the use of potable water for applications coming in direct contact with the fruit, but due to high demand, water from other sources is frequently used. We sought to describe the overall bacterial diversity on the surface of tomato fruit and the effect of two different water sources (ground and surface water when used for direct crop applications by generating a 454-pyrosequencing 16S rRNA dataset of these different environments. This study represents the first in depth characterization of bacterial communities in the tomato fruit surface and the water sources commonly used in commercial vegetable production. Results The two water sources tested had a significantly different bacterial composition. Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia. The fruit surface bacterial communities on tomatoes sprayed with both water sources could not be differentiated using various statistical methods. Both fruit surface environments had a high representation of Gammaproteobacteria, and within this class the genera Pantoea and Enterobacter were the most abundant. Conclusions Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface. This study has provided the first next-generation sequencing database describing the bacterial communities living in the fruit surface of a tomato crop under two different spray water regimes, and therefore represents an

  16. Bacterial Community Succession During in situ Uranium Bioremediation: Spatial Similarities Along Controlled Flow Paths

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Chiachi; Wu, Weimin; Gentry, Terry J.; Carley, Jack; Corbin, Gail A.; Carroll, Sue L.; Watson, David B.; Jardine, Phil M.; Zhou, Jizhong; Criddle, Craig S.; Fields, Matthew W.

    2009-05-22

    Bacterial community succession was investigated in a field-scale subsurface reactor formed by a series of wells that received weekly ethanol additions to re-circulating groundwater. Ethanol additions stimulated denitrification, metal reduction, sulfate reduction, and U(VI) reduction to sparingly soluble U(IV). Clone libraries of SSU rRNA gene sequences from groundwater samples enabled tracking of spatial and temporal changes over a 1.5 y period. Analyses showed that the communities changed in a manner consistent with geochemical variations that occurred along temporal and spatial scales. Canonical correspondence analysis revealed that the levels of nitrate, uranium, sulfide, sulfate, and ethanol strongly correlated with particular bacterial populations. As sulfate and U(VI) levels declined, sequences representative of sulfate-reducers and metal-reducers were detected at high levels. Ultimately, sequences associated with sulfate-reducing populations predominated, and sulfate levels declined as U(VI) remained at low levels. When engineering controls were compared to the population variation via canonical ordination, changes could be related to dissolved oxygen control and ethanol addition. The data also indicated that the indigenous populations responded differently to stimulation for bio-reduction; however, the two bio-stimulated communities became more similar after different transitions in an idiosyncratic manner. The strong associations between particular environmental variables and certain populations provide insight into the establishment of practical and successful remediation strategies in radionuclide-contaminated environments with respect to engineering controls and microbial ecology.

  17. Hydrocarbon pollutants shape bacterial community assembly of harbor sediments

    KAUST Repository

    Barbato, Marta

    2016-02-02

    Petroleum pollution results in co-contamination by different classes of molecules, entailing the occurrence of marine sediments difficult to remediate, as in the case of the Ancona harbor (Mediterranean Sea, Italy). Autochthonous bioaugmentation (ABA), by exploiting the indigenous microbes of the environment to be treated, could represent a successful bioremediation strategy. In this perspective we aimed to i) identify the main drivers of the bacterial communities\\' richness in the sediments, ii) establish enrichment cultures with different hydrocarbon pollutants evaluating their effects on the bacterial communities\\' composition, and iii) obtain a collection of hydrocarbon degrading bacteria potentially exploitable in ABA. The correlation between the selection of different specialized bacterial populations and the type of pollutants was demonstrated by culture-independent analyses, and by establishing a collection of bacteria with different hydrocarbon degradation traits. Our observations indicate that pollution dictates the diversity of sediment bacterial communities and shapes the ABA potential in harbor sediments.

  18. Metamorphosis of a butterfly-associated bacterial community.

    Science.gov (United States)

    Hammer, Tobin J; McMillan, W Owen; Fierer, Noah

    2014-01-01

    Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies.

  19. Do honeybees shape the bacterial community composition in floral nectar?

    Directory of Open Access Journals (Sweden)

    Yana Aizenberg-Gershtein

    Full Text Available Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers. Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers' nectar, but not from those in the uncovered flowers' nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves.

  20. Groundwater.

    Science.gov (United States)

    Braids, Olin C.; Gillies, Nola P.

    1978-01-01

    Presents a literature review of groundwater quality covering publications of 1977. This review includes: (1) sources of groundwater contamination; and (2) management of groundwater. A list of 59 references is also presented. (HM)

  1. Supraglacial bacterial community structures vary across the Greenland ice sheet

    DEFF Research Database (Denmark)

    Cameron, Karen A.; Stibal, Marek; Zarsky, Jakub D.;

    2016-01-01

    The composition and spatial variability of microbial communities that reside within the extensive (>200 000 km(2)) biologically active area encompassing the Greenland ice sheet (GrIS) is hypothesized to be variable. We examined bacterial communities from cryoconite debris and surface ice across...

  2. Molecular analysis of microbial community in a groundwater sample polluted by landfill leachate and seawater

    Institute of Scientific and Technical Information of China (English)

    TIAN Yang-jie; YANG Hong; WU Xiu-juan; LI Dao-tang

    2005-01-01

    Seashore landfill aquifers are environments of special physicochemical conditions (high organic load and high salinity), and microbes in leachate-polluted aquifers play a significant role for intrinsic bioremediation. In order to characterize microbial diversity and look for clues on the relationship between microbial community structure and hydrochemistry, a culture-independent examination of a typical groundwater sample obtained from a seashore landfill was conducted by sequence analysis of 16S rDNA clone library. Two sets of universal 16S rDNA primers were used to amplify DNA extracted from the groundwater so that problems arising from primer efficiency and specificity could be reduced. Of 74 clones randomly selected from the libraries, 30 contained unique sequences whose analysis showed that the majority of them belonged to bacteria (95.9%), with Proteobacteria (63.5%) being the dominant division. One archaeal sequence and one eukaryotic sequence were found as well. Bacterial sequences belonging to the following phylogenic groups were identified: Bacteroidetes (20.3%), β, γ, δ and ε-subdivisions of Proteobacteria (47.3%, 9.5%, 5.4% and 1.3%, respectively), Firmicutes (1.4%), Actinobacteria (2.7%), Cyanobacteria (2.7%). The percentages of Proteobacteria and Bacteroides in seawater were greater than those in the groundwater from a non-seashore landfill, indicating a possible influence of seawater. Quite a few sequences had close relatives in marine or hypersaline environments. Many sequences showed affiliations with microbes involved in anaerobic fermentation. The remarkable abundance of sequences related to (per)chlorate-reducing bacteria (C1RB) in the groundwater was significant and worthy of further study.

  3. The development of permafrost bacterial communities under submarine conditions

    Science.gov (United States)

    Mitzscherling, Julia; Winkel, Matthias; Winterfeld, Maria; Horn, Fabian; Yang, Sizhong; Grigoriev, Mikhail N.; Wagner, Dirk; Overduin, Pier P.; Liebner, Susanne

    2017-07-01

    Submarine permafrost is more vulnerable to thawing than permafrost on land. Besides increased heat transfer from the ocean water, the penetration of salt lowers the freezing temperature and accelerates permafrost degradation. Microbial communities in thawing permafrost are expected to be stimulated by warming, but how they develop under submarine conditions is completely unknown. We used the unique records of two submarine permafrost cores from the Laptev Sea on the East Siberian Arctic Shelf, inundated about 540 and 2500 years ago, to trace how bacterial communities develop depending on duration of the marine influence and pore water chemistry. Combined with geochemical analysis, we quantified total cell numbers and bacterial gene copies and determined the community structure of bacteria using deep sequencing of the bacterial 16S rRNA gene. We show that submarine permafrost is an extreme habitat for microbial life deep below the seafloor with changing thermal and chemical conditions. Pore water chemistry revealed different pore water units reflecting the degree of marine influence and stages of permafrost thaw. Millennia after inundation by seawater, bacteria stratify into communities in permafrost, marine-affected permafrost, and seabed sediments. In contrast to pore water chemistry, the development of bacterial community structure, diversity, and abundance in submarine permafrost appears site specific, showing that both sedimentation and permafrost thaw histories strongly affect bacteria. Finally, highest microbial abundance was observed in the ice-bonded seawater unaffected but warmed permafrost of the longer inundated core, suggesting that permafrost bacterial communities exposed to submarine conditions start to proliferate millennia after warming.

  4. Bacterial diversity and community structure of a sub-surface aquifer exposed to realistic low herbicide concentrations

    DEFF Research Database (Denmark)

    Lipthay, Julia R. de; Johnsen, Kaare; Albrechtsen, H.-J.;

    2004-01-01

    contaminants. We examined the effect of in situ exposure to realistic low concentrations of herbicides on the microbial diversity and community structure of sub-surface sediments from a shallow aquifer near Vejen (Denmark). Three different community analyses were performed: colony morphology typing, sole......-surface aquifers to realistic low concentrations of herbicides may alter the overall structure of a natural bacterial community, although significant effects on the genetic diversity and carbon substrate usage cannot be detected. The observed impact was probably due to indirect effects. In future investigations......An increasing number of herbicides are found in our groundwater environments. This underlines the need for examining the effects of herbicide exposure on the indigenous groundwater microbial communities, as microbial degradation is the major process responsible for the complete removal of most...

  5. Impact of disinfection on drinking water biofilm bacterial community.

    Science.gov (United States)

    Mi, Zilong; Dai, Yu; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

    2015-11-01

    Disinfectants are commonly applied to control the growth of microorganisms in drinking water distribution systems. However, the effect of disinfection on drinking water microbial community remains poorly understood. The present study investigated the impacts of different disinfectants (chlorine and chloramine) and dosages on biofilm bacterial community in bench-scale pipe section reactors. Illumina MiSeq sequencing illustrated that disinfection strategy could affect both bacterial diversity and community structure of drinking water biofilm. Proteobacteria tended to predominate in chloraminated drinking water biofilms, while Firmicutes in chlorinated and unchlorinated biofilms. The major proteobacterial groups were influenced by both disinfectant type and dosage. In addition, chloramination had a more profound impact on bacterial community than chlorination.

  6. Endophytic bacterial community of a Mediterranean marine angiosperm (Posidonia oceanica

    Directory of Open Access Journals (Sweden)

    Neus eGarcias-Bonet

    2012-09-01

    Full Text Available Bacterial endophytes are crucial for the survival of many terrestrial plants, but little is known about the presence and importance of bacterial endophytes of marine plants. We conducted a survey of the endophytic bacterial community of the long-living Mediterranean marine angiosperm Posidonia oceanica in surface-sterilized tissues (roots, rhizomes and leaves by DGGE. A total of 26 Posidonia oceanica meadows around the Balearic Islands were sampled, and the band patterns obtained for each meadow were compared for the three sampled tissues. Endophytic bacterial sequences were detected in most of the samples analyzed. A total of 34 OTUs (Operational Taxonomic Units were detected. The main OTUs of endophytic bacteria present in P. oceanica tissues belonged primarily to Proteobacteria (α, γ and δ subclasses and Bacteroidetes. The OTUs found in roots significantly differed from those of rhizomes and leaves. Moreover, some OTUs were found to be associated to each type of tissue. Bipartite network analysis revealed differences in the bacterial endophyte communities present on different islands. The results of this study provide a pioneering step toward the characterization of the endophytic bacterial community associated with tissues of a marine angiosperm and reveal the presence of bacterial endophytes that differed among locations and tissue types.

  7. Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

    Directory of Open Access Journals (Sweden)

    Lidianne L. Rocha

    2016-01-01

    Full Text Available We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1 to habitats covered by Avicennia schaueriana (S2 and Rhizophora mangle (S3. Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.

  8. Toxicity of zero-valent iron nanoparticles to a trichloroethylene-degrading groundwater microbial community.

    Science.gov (United States)

    Zabetakis, Kara M; Niño de Guzmán, Gabriela T; Torrents, Alba; Yarwood, Stephanie

    2015-01-01

    The microbiological impact of zero-valent iron used in the remediation of groundwater was investigated by exposing a trichloroethylene-degrading anaerobic microbial community to two types of iron nanoparticles. Changes in total bacterial and archaeal population numbers were analyzed using qPCR and were compared to results from a blank and negative control to assess for microbial toxicity. Additionally, the results were compared to those of samples exposed to silver nanoparticles and iron filings in an attempt to discern the source of toxicity. Statistical analysis revealed that the three different iron treatments were equally toxic to the total bacteria and archaea populations, as compared with the controls. Conversely, the silver nanoparticles had a limited statistical impact when compared to the controls and increased the microbial populations in some instances. Therefore, the findings suggest that zero-valent iron toxicity does not result from a unique nanoparticle-based effect.

  9. Bacterial community associated with ensilage process of wilted guinea grass.

    Science.gov (United States)

    Parvin, S; Nishino, N

    2009-12-01

    To determine the effects of wilting, storage period and bacterial inoculant on the bacterial community and ensiling fermentation of guinea grass silage. Fermentation products, colony counts and denaturing gradient gel electrophoresis (DGGE) profiles were determined. There was more lactic acid than acetic acid in all silages, but the lactic acid to acetic acid ratio decreased with storage time. This shift from lactic to acetic acid was not prevented even with a combination of wilting and bacterial inoculant. The DGGE analyses suggest that facultatively heterofermentative lactic acid bacteria (Lactobacillus plantarum, Lactobacillus brevis and Lactobacillus pentosus) were involved in the shift to acetic acid fermentation. Lactic acid can dominate the fermentation in tropical grass silage with sufficient wilting prior to ensiling. Prolonged storage may lead to high levels of acetic acid without distinctive changes in the bacterial community. The bacterial community looks stable compared to fermentation products over the course of long storage periods in tropical grass silage. Acetic acid fermentation in tropical grass silage can be a result of the changes in bacterial metabolism rather than community structure.

  10. 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.

  11. 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.

  12. Changes in soil bacterial community structure with increasing disturbance frequency.

    Science.gov (United States)

    Kim, Mincheol; Heo, Eunjung; Kang, Hojeong; Adams, Jonathan

    2013-07-01

    Little is known of the responsiveness of soil bacterial community structure to disturbance. In this study, we subjected a soil microcosm to physical disturbance, sterilizing 90 % of the soil volume each time, at a range of frequencies. We analysed the bacterial community structure using 454 pyrosequencing of the 16S rRNA gene. Bacterial diversity was found to decline with the increasing disturbance frequencies. Total bacterial abundance was, however, higher at intermediate and high disturbance frequencies, compared to low and no-disturbance treatments. Changing disturbance frequency also led to changes in community composition, with changes in overall species composition and some groups becoming abundant at the expense of others. Some phylogenetic groups were found to be relatively more disturbance-sensitive or tolerant than others. With increasing disturbance frequency, phylogenetic species variability (an index of community composition) itself became more variable from one sample to another, suggesting a greater role of chance in community composition. Compared to the tightly clustered community of the original undisturbed soil, in all the aged disturbed soils the lists of most abundant operational taxonomic units (OTUs) in each replicate were very different, suggesting a possible role of stochasticity in resource colonization and exploitation in the aged and disturbed soils. For example, colonization may be affected by whichever localized concentrations of bacterial populations happen to survive the last disturbance and be reincorporated in abundance into each pot. Overall, it appears that the soil bacterial community is very sensitive to physical disturbance, losing diversity, and that certain groups have identifiable 'high disturbance' vs. 'low disturbance' niches.

  13. Soil bacterial community shifts associated with sugarcane straw removal

    Science.gov (United States)

    Pimentel, Laisa; Gumiere, Thiago; Andreote, Fernando; Cerri, Carlos

    2017-04-01

    In Brazil, the adoption of the mechanical unburned sugarcane harvest potentially increase the quantity of residue left in the field after harvesting. Economically, this material has a high potential for second generation ethanol (2G) production. However, crop residues have an essential role in diverse properties and processes in the soil. The greater part of the uncertainties about straw removal for 2G ethanol production is based on its effects in soil microbial community. In this sense, it is important to identify the main impacts of sugarcane straw removal on soil microbial community. Therefore, we conducted a field study, during one year, in Valparaíso (São Paulo state - Brazil) to evaluate the effects of straw decomposition on soil bacterial community. Specifically, we wanted: i) to compare the rates of straw removal and ii) to evaluate the effects of straw decomposition on soil bacterial groups over one year. The experiment was in a randomized block design with treatments arranged in strip plot. The treatments are different rates of sugarcane straw removal, namely: no removal, 50, 75 and 100% of straw removal. Soil sampling was carried out at 0, 4, 8 and 12 months after the sugarcane harvest (August 2015). Total DNA was extracted from soil using the PowersoilTM DNA Isolation kit. And the abundance of bacterial in each soil sample was estimated via quantification of 16S rRNA gene. The composition of the bacterial communities was estimated via terminal restriction fragment length polymorphism (T-RFLP) analysis, and the T-RF sizes were performed on a 3500 Genetic Analyzer. Finally, the results were examined with GeneMapper 4.1 software. There was bacterial community shifts through the time and among the rates of sugarcane straw removal. Bacterial community was firstly determined by the time scale, which explained 29.16% of total variation. Rates of straw removal explained 11.55% of shifts on bacterial community. Distribution through the time is an important

  14. Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland

    Science.gov (United States)

    Bomberg, Malin; Lamminmäki, Tiina; Itävaara, Merja

    2016-11-01

    The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is high, but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798 m by high throughput amplicon sequencing using the Illumina HiSeq platform. Between 1.7 × 104 and 1.2 × 106 bacterial or archaeal sequence reads per sample were obtained. These sequences revealed that up to 95 and 99 % of the bacterial and archaeal sequences obtained from the 12 samples, respectively, belonged to only a few common species, i.e. the core microbiome. However, the remaining rare microbiome contained over 3- and 6-fold more bacterial and archaeal taxa. The metabolic properties of the microbial communities were predicted using PICRUSt. The approximate estimation showed that the metabolic pathways commonly included fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation, and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle, and the Wood-Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier environmental conditions, but could also be induced again if changes in their living conditions occur.

  15. 3D printing of microscopic bacterial communities

    Science.gov (United States)

    Connell, Jodi L.; Ritschdorff, Eric T.; Whiteley, Marvin; Shear, Jason B.

    2013-01-01

    Bacteria communicate via short-range physical and chemical signals, interactions known to mediate quorum sensing, sporulation, and other adaptive phenotypes. Although most in vitro studies examine bacterial properties averaged over large populations, the levels of key molecular determinants of bacterial fitness and pathogenicity (e.g., oxygen, quorum-sensing signals) may vary over micrometer scales within small, dense cellular aggregates believed to play key roles in disease transmission. A detailed understanding of how cell–cell interactions contribute to pathogenicity in natural, complex environments will require a new level of control in constructing more relevant cellular models for assessing bacterial phenotypes. Here, we describe a microscopic three-dimensional (3D) printing strategy that enables multiple populations of bacteria to be organized within essentially any 3D geometry, including adjacent, nested, and free-floating colonies. In this laser-based lithographic technique, microscopic containers are formed around selected bacteria suspended in gelatin via focal cross-linking of polypeptide molecules. After excess reagent is removed, trapped bacteria are localized within sealed cavities formed by the cross-linked gelatin, a highly porous material that supports rapid growth of fully enclosed cellular populations and readily transmits numerous biologically active species, including polypeptides, antibiotics, and quorum-sensing signals. Using this approach, we show that a picoliter-volume aggregate of Staphylococcus aureus can display substantial resistance to β-lactam antibiotics by enclosure within a shell composed of Pseudomonas aeruginosa. PMID:24101503

  16. Bacterial Communities Associated with Different Anthurium andraeanum L. Plant Tissues

    OpenAIRE

    Sarria-Guzmán, Yohanna; Chávez-Romero, Yosef; Gómez-Acata, Selene; Montes-Molina, Joaquín Adolfo; Morales-Salazar, Eleacin; Dendooven,Luc; Yendi E. Navarro-Noya

    2016-01-01

    Plant-associated microbes have specific beneficial functions and are considered key drivers for plant health. The bacterial community structure of healthy Anthurium andraeanum L. plants was studied by 16S rRNA gene pyrosequencing associated with different plant parts and the rhizosphere. A limited number of bacterial taxa, i.e., Sinorhizobium, Fimbriimonadales, and Gammaproteobacteria HTCC2089 were enriched in the A. andraeanum rhizosphere. Endophytes were more diverse in the roots than in th...

  17. Plasmids spread very fast in heterogeneous bacterial communities.

    Science.gov (United States)

    Dionisio, Francisco; Matic, Ivan; Radman, Miroslav; Rodrigues, Olivia R; Taddei, François

    2002-01-01

    Conjugative plasmids can mediate gene transfer between bacterial taxa in diverse environments. The ability to donate the F-type conjugative plasmid R1 greatly varies among enteric bacteria due to the interaction of the system that represses sex-pili formations (products of finOP) of plasmids already harbored by a bacterial strain with those of the R1 plasmid. The presence of efficient donors in heterogeneous bacterial populations can accelerate plasmid transfer and can spread by several orders of magnitude. Such donors allow millions of other bacteria to acquire the plasmid in a matter of days whereas, in the absence of such strains, plasmid dissemination would take years. This "amplification effect" could have an impact on the evolution of bacterial pathogens that exist in heterogeneous bacterial communities because conjugative plasmids can carry virulence or antibiotic-resistance genes. PMID:12524329

  18. Bacterial community analysis of drinking water biofilms in southern Sweden.

    Science.gov (United States)

    Lührig, Katharina; Canbäck, Björn; Paul, Catherine J; Johansson, Tomas; Persson, Kenneth M; Rådström, Peter

    2015-01-01

    Next-generation sequencing of the V1-V2 and V3 variable regions of the 16S rRNA gene generated a total of 674,116 reads that described six distinct bacterial biofilm communities from both water meters and pipes. A high degree of reproducibility was demonstrated for the experimental and analytical work-flow by analyzing the communities present in parallel water meters, the rare occurrence of biological replicates within a working drinking water distribution system. The communities observed in water meters from households that did not complain about their drinking water were defined by sequences representing Proteobacteria (82-87%), with 22-40% of all sequences being classified as Sphingomonadaceae. However, a water meter biofilm community from a household with consumer reports of red water and flowing water containing elevated levels of iron and manganese had fewer sequences representing Proteobacteria (44%); only 0.6% of all sequences were classified as Sphingomonadaceae; and, in contrast to the other water meter communities, markedly more sequences represented Nitrospira and Pedomicrobium. The biofilm communities in pipes were distinct from those in water meters, and contained sequences that were identified as Mycobacterium, Nocardia, Desulfovibrio, and Sulfuricurvum. The approach employed in the present study resolved the bacterial diversity present in these biofilm communities as well as the differences that occurred in biofilms within a single distribution system, and suggests that next-generation sequencing of 16S rRNA amplicons can show changes in bacterial biofilm communities associated with different water qualities.

  19. Bacterial community development in experimental gingivitis

    National Research Council Canada - National Science Library

    Kistler, James O; Booth, Veronica; Bradshaw, David J; Wade, William G

    2013-01-01

    Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities...

  20. Architectural design drives the biogeography of indoor bacterial communities.

    Science.gov (United States)

    Kembel, Steven W; Meadow, James F; O'Connor, Timothy K; Mhuireach, Gwynne; Northcutt, Dale; Kline, Jeff; Moriyama, Maxwell; Brown, G Z; Bohannan, Brendan J M; Green, Jessica L

    2014-01-01

    Architectural design has the potential to influence the microbiology of the built environment, with implications for human health and well-being, but the impact of design on the microbial biogeography of buildings remains poorly understood. In this study we combined microbiological data with information on the function, form, and organization of spaces from a classroom and office building to understand how design choices influence the biogeography of the built environment microbiome. Sequencing of the bacterial 16S gene from dust samples revealed that indoor bacterial communities were extremely diverse, containing more than 32,750 OTUs (operational taxonomic units, 97% sequence similarity cutoff), but most communities were dominated by Proteobacteria, Firmicutes, and Deinococci. Architectural design characteristics related to space type, building arrangement, human use and movement, and ventilation source had a large influence on the structure of bacterial communities. Restrooms contained bacterial communities that were highly distinct from all other rooms, and spaces with high human occupant diversity and a high degree of connectedness to other spaces via ventilation or human movement contained a distinct set of bacterial taxa when compared to spaces with low occupant diversity and low connectedness. Within offices, the source of ventilation air had the greatest effect on bacterial community structure. Our study indicates that humans have a guiding impact on the microbial biodiversity in buildings, both indirectly through the effects of architectural design on microbial community structure, and more directly through the effects of human occupancy and use patterns on the microbes found in different spaces and space types. The impact of design decisions in structuring the indoor microbiome offers the possibility to use ecological knowledge to shape our buildings in a way that will select for an indoor microbiome that promotes our health and well-being.

  1. Microbial community response to addition of polylactate compounds to stimulate hexavalent chromium reduction in groundwater.

    Science.gov (United States)

    Brodie, Eoin L; Joyner, Dominique C; Faybishenko, Boris; Conrad, Mark E; Rios-Velazquez, Carlos; Malave, Josue; Martinez, Ramon; Mork, Benjamin; Willett, Anna; Koenigsberg, Steven; Herman, Donald J; Firestone, Mary K; Hazen, Terry C

    2011-10-01

    To evaluate the efficacy of bioimmobilization of Cr(VI) in groundwater at the Department of Energy Hanford site, we conducted a series of microcosm experiments using a range of commercial electron donors with varying degrees of lactate polymerization (polylactate). These experiments were conducted using Hanford Formation sediments (coarse sand and gravel) immersed in Hanford groundwater, which were amended with Cr(VI) and several types of lactate-based electron donors (Hydrogen Release Compound, HRC; primer-HRC, pHRC; extended release HRC) and the polylactate-cysteine form (Metal Remediation Compound, MRC). The results showed that polylactate compounds stimulated an increase in bacterial biomass and activity to a greater extent than sodium lactate when applied at equivalent carbon concentrations. At the same time, concentrations of headspace hydrogen and methane increased and correlated with changes in the microbial community structure. Enrichment of Pseudomonas spp. occurred with all lactate additions, and enrichment of sulfate-reducing Desulfosporosinus spp. occurred with almost complete sulfate reduction. The results of these experiments demonstrate that amendment with the pHRC and MRC forms result in effective removal of Cr(VI) from solution most likely by both direct (enzymatic) and indirect (microbially generated reductant) mechanisms.

  2. Supraglacial bacterial community structures vary across the Greenland ice sheet.

    Science.gov (United States)

    Cameron, Karen A; Stibal, Marek; Zarsky, Jakub D; Gözdereliler, Erkin; Schostag, Morten; Jacobsen, Carsten S

    2016-02-01

    The composition and spatial variability of microbial communities that reside within the extensive (>200 000 km(2)) biologically active area encompassing the Greenland ice sheet (GrIS) is hypothesized to be variable. We examined bacterial communities from cryoconite debris and surface ice across the GrIS, using sequence analysis and quantitative PCR of 16S rRNA genes from co-extracted DNA and RNA. Communities were found to differ across the ice sheet, with 82.8% of the total calculated variation attributed to spatial distribution on a scale of tens of kilometers separation. Amplicons related to Sphingobacteriaceae, Pseudanabaenaceae and WPS-2 accounted for the greatest portion of calculated dissimilarities. The bacterial communities of ice and cryoconite were moderately similar (global R = 0.360, P = 0.002) and the sampled surface type (ice versus cryoconite) did not contribute heavily towards community dissimilarities (2.3% of total variability calculated). The majority of dissimilarities found between cryoconite 16S rRNA gene amplicons from DNA and RNA was calculated to be the result of changes in three taxa, Pseudanabaenaceae, Sphingobacteriaceae and WPS-2, which together contributed towards 80.8 ± 12.6% of dissimilarities between samples. Bacterial communities across the GrIS are spatially variable active communities that are likely influenced by localized biological inputs and physicochemical conditions.

  3. Pigment profiles and bacterial communities from Thailand thermal mats.

    Science.gov (United States)

    Portillo, M C; Sririn, V; Kanoksilapatham, W; Gonzalez, J M

    2009-11-01

    Differently colored layers of freshwater hot spring mats at Boekleung (Western Thailand) were studied. Temperatures ranged from over 50 up to 57 degrees C. Two mats were characterized: a laminated mat with a green and a red layers, and a monolayer, greenish-yellow mat. Bacterial communities in green, red, and yellow layers were investigated using molecular, culturing and pigment analysis methods. Pigment profiles covered a wide spectrum from chlorophylls to carotenoids. A green mat layer showed higher relative content of chlorophyll than yellow and red layers which presented higher proportion of carotenoids. Cyanobacterial isolates grow up to 55-56 degrees C and their pigment profiles showed a relatively high content of chlorophylls suggesting the importance of other bacterial groups in the mat pigment profiles. Bacterial communities were analyzed by 16S rDNA surveys showing Cyanobacteria and Chloroflexi as the mayor components of the community. Other significant members were Candidate Division OP10, Bacteroidetes, Planctomycetes and Actinobacteria. These results highlight a major participation of Cyanobacteria and Chloroflexi in thermal mat communities, and the preferential presence of Candidate Division OP10 in green mat layers. Differently colored mat layers showed characteristic bacterial communities which could be discriminated from pigment profiles and molecular surveys.

  4. The bacterial community of entomophilic nematodes and host beetles.

    Science.gov (United States)

    Koneru, Sneha L; Salinas, Heilly; Flores, Gilberto E; Hong, Ray L

    2016-05-01

    Insects form the most species-rich lineage of Eukaryotes and each is a potential host for organisms from multiple phyla, including fungi, protozoa, mites, bacteria and nematodes. In particular, beetles are known to be associated with distinct bacterial communities and entomophilic nematodes. While entomopathogenic nematodes require symbiotic bacteria to kill and reproduce inside their insect hosts, the microbial ecology that facilitates other types of nematode-insect associations is largely unknown. To illuminate detailed patterns of the tritrophic beetle-nematode-bacteria relationship, we surveyed the nematode infestation profiles of scarab beetles in the greater Los Angeles area over a five-year period and found distinct nematode infestation patterns for certain beetle hosts. Over a single season, we characterized the bacterial communities of beetles and their associated nematodes using high-throughput sequencing of the 16S rRNA gene. We found significant differences in bacterial community composition among the five prevalent beetle host species, independent of geographical origin. Anaerobes Synergistaceae and sulphate-reducing Desulfovibrionaceae were most abundant in Amblonoxia beetles, while Enterobacteriaceae and Lachnospiraceae were common in Cyclocephala beetles. Unlike entomopathogenic nematodes that carry bacterial symbionts, insect-associated nematodes do not alter the beetles' native bacterial communities, nor do their microbiomes differ according to nematode or beetle host species. The conservation of Diplogastrid nematodes associations with Melolonthinae beetles and sulphate-reducing bacteria suggests a possible link between beetle-bacterial communities and their associated nematodes. Our results establish a starting point towards understanding the dynamic interactions between soil macroinvertebrates and their microbiota in a highly accessible urban environment.

  5. Canopy soil bacterial communities altered by severing host tree limbs

    Directory of Open Access Journals (Sweden)

    Cody R. Dangerfield

    2017-09-01

    Full Text Available Trees of temperate rainforests host a large biomass of epiphytic plants, which are associated with soils formed in the forest canopy. Falling of epiphytic material results in the transfer of carbon and nutrients from the canopy to the forest floor. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different operational taxonomic units. A field experiment was conducted with epiphytic material from six Acer macrophyllum trees in Olympic National Park, Washington, USA to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, the unique nature of canopy soil bacteria is determined in part by the host tree and not only by the physical environmental conditions associated with the canopy. Connection to the living tree appears to be a key feature of the canopy habitat. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities.

  6. Distribution of Archaeal and Bacterial communities in a subtropical reservoir

    Directory of Open Access Journals (Sweden)

    Laís Américo Soares

    2015-12-01

    Full Text Available Abstract Aim: Microbial communities play a central role in environmental process such as organic matter mineralization and the nutrient cycling process in aquatic ecosystems. Despite their ecological importance, variability of the structure of archaeal and bacterial communities in freshwater remains understudied. Methods In the present study we investigated the richness and density of archaea and bacteria in the water column and sediments of the Itupararanga Reservoir. We also evaluated the relationship between the communities and the biotic and abiotic characteristics. Samples were taken at five depths in the water column next to the dam and three depths next to the reservoir entrance. Results PCR-DGGE evaluation of the archaeal and bacterial communities showed that both were present in the water column, even in oxygenated conditions. Conclusions The density of the bacteria (qPCR was greater than that of the archaea, a result of the higher metabolic plasticity of bacteria compared with archaea.

  7. Microbial Community of High Arsenic Groundwater in Agricultural Irrigation Area of Hetao Plain, Inner Mongolia.

    Science.gov (United States)

    Wang, Yanhong; Li, Ping; Jiang, Zhou; Sinkkonen, Aki; Wang, Shi; Tu, Jin; Wei, Dazhun; Dong, Hailiang; Wang, Yanxin

    2016-01-01

    Microbial communities can play important role in arsenic release in groundwater aquifers. To investigate the microbial communities in high arsenic groundwater aquifers in agricultural irrigation area, 17 groundwater samples with different arsenic concentrations were collected along the agricultural drainage channels of Hangjinhouqi County, Inner Mongolia and examined by illumina MiSeq sequencing approach targeting the V4 region of the 16S rRNA genes. Both principal component analysis and hierarchical clustering results indicated that these samples were divided into two groups (high and low arsenic groups) according to the variation of geochemical characteristics. Arsenic concentrations showed strongly positive correlations with [Formula: see text] and total organic carbon (TOC). Sequencing results revealed that a total of 329-2823 operational taxonomic units (OTUs) were observed at the 97% OTU level. Microbial richness and diversity of high arsenic groundwater samples along the drainage channels were lower than those of low arsenic groundwater samples but higher than those of high arsenic groundwaters from strongly reducing areas. The microbial community structure in groundwater along the drainage channels was different from those in strongly reducing arsenic-rich aquifers of Hetao Plain and other high arsenic groundwater aquifers including Bangladesh, West Bengal, and Vietnam. Acinetobacter and Pseudomonas dominated with high percentages in both high and low arsenic groundwaters. Alishewanella, Psychrobacter, Methylotenera, and Crenothrix showed relatively high abundances in high arsenic groundwater, while Rheinheimera and the unidentified OP3 were predominant populations in low arsenic groundwater. Archaeal populations displayed a low occurrence and mainly dominated by methanogens such as Methanocorpusculum and Methanospirillum. Microbial community compositions were different between high and low arsenic groundwater samples based on the results of principal

  8. Microbial Community of High Arsenic Groundwater in Agricultural Irrigation Area of Hetao Plain, Inner Mongolia

    Science.gov (United States)

    Wang, Yanhong; Li, Ping; Jiang, Zhou; Sinkkonen, Aki; Wang, Shi; Tu, Jin; Wei, Dazhun; Dong, Hailiang; Wang, Yanxin

    2016-01-01

    Microbial communities can play important role in arsenic release in groundwater aquifers. To investigate the microbial communities in high arsenic groundwater aquifers in agricultural irrigation area, 17 groundwater samples with different arsenic concentrations were collected along the agricultural drainage channels of Hangjinhouqi County, Inner Mongolia and examined by illumina MiSeq sequencing approach targeting the V4 region of the 16S rRNA genes. Both principal component analysis and hierarchical clustering results indicated that these samples were divided into two groups (high and low arsenic groups) according to the variation of geochemical characteristics. Arsenic concentrations showed strongly positive correlations with NH4+ and total organic carbon (TOC). Sequencing results revealed that a total of 329–2823 operational taxonomic units (OTUs) were observed at the 97% OTU level. Microbial richness and diversity of high arsenic groundwater samples along the drainage channels were lower than those of low arsenic groundwater samples but higher than those of high arsenic groundwaters from strongly reducing areas. The microbial community structure in groundwater along the drainage channels was different from those in strongly reducing arsenic-rich aquifers of Hetao Plain and other high arsenic groundwater aquifers including Bangladesh, West Bengal, and Vietnam. Acinetobacter and Pseudomonas dominated with high percentages in both high and low arsenic groundwaters. Alishewanella, Psychrobacter, Methylotenera, and Crenothrix showed relatively high abundances in high arsenic groundwater, while Rheinheimera and the unidentified OP3 were predominant populations in low arsenic groundwater. Archaeal populations displayed a low occurrence and mainly dominated by methanogens such as Methanocorpusculum and Methanospirillum. Microbial community compositions were different between high and low arsenic groundwater samples based on the results of principal coordinate

  9. Panamanian frog species host unique skin bacterial communities

    Directory of Open Access Journals (Sweden)

    Lisa K. Belden

    2015-10-01

    Full Text Available Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd, that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26% were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in

  10. Effects of sulfadiazine on soil bacterial communities

    DEFF Research Database (Denmark)

    Hangler, Martin

    as fertilizers on agricultural lands they represent a route for antibiotics into the soil environment where they may persist and affect levels of antibiotic resistance in soil microbial communities over time. In this work the level of tolerance to the antibiotic sulfadiazine (SDZ) was studied in a number...... of soils applying the pollution-induced community tolerance (PICT)-approach. As SDZ is amphoteric and thus exist on either neutral, anionic or cationic form soil pH is likely to influence the toxicity and bioavailability of SDZ to soil bacteria. In manuscript I the aim was to set a baseline, a PICT...... designed to test effects on soil quality of a range of different fertilizers in agriculture. In manuscript II extracted bacteria from soil samples representing a broad range of natural soil pH values were tested for their toxicity response to SDZ when amended at different assay pH. Toxicity clearly...

  11. Sediment Bacterial Communities Reflect the History of a Sea Basin

    Science.gov (United States)

    Lyra, Christina; Sinkko, Hanna; Rantanen, Matias; Paulin, Lars; Kotilainen, Aarno

    2013-01-01

    How entire microbial communities are structured across stratified sediments from the historical standpoint is unknown. The Baltic Sea is an ideal research object for historical reconstruction, since it has experienced many fresh- and brackish water periods and is depleted of dissolved oxygen, which increases the sediment's preservation potential. We investigated the bacterial communities, chemical elements (e.g. Cr, Pb Na, P, Sr and U) and sediment composition in a stratified sediment core dated by radiocarbon and spanning 8000 years of Baltic Sea history, using up-to-date multivariate statistics. The communities were analysed by 16S rRNA gene terminal restriction fragment length polymorphism. The communities of the deep Early Litorina and surface Late Litorina Sea laminae were separated from the communities of the middle Litorina Sea laminae, which were associated with elevated concentrations of U and Sr trace elements, palaeo-oxygen and palaeosalinity proxies. Thus, the Litorina Sea laminae were characterized by past oxygen deficiency and salinity increase. The communities of the laminae, bioturbated and homogeneous sediments were differentiated, based on the same historical sea phases, with correct classifications of 90%. Palaeosalinity was one of the major parameters that separated the bacterial communities of the stratified sediments. A discontinuous spatial structure with a surprising increase in community heterogeneity was detected in Litorina Sea sediments from 388 to 422 cm deep, which suggests that a salinity maximum occurred in the central Gulf of Finland app. 6200–6600 years ago. The community heterogeneity decreased from the surface down to 306 cm, which reflected downcore mineralization. The plateau of the decrease was in the app. 2000-year-old sediment layers. Bacterial community data may be used as an additional tool in ocean-drilling projects, in which it is important to detect mineralization plateaus both to determine historically comparable

  12. The Role of the Bacterial Community of an Agroecosystem in Simazine Degradation

    Directory of Open Access Journals (Sweden)

    Anna Barra Caracciolo

    Full Text Available The use of pesticides and fertilizers in agricultural practice is the main source of soil and groundwater contamination. S-Triazines are among the most used herbicides in the world for selective weed control in several types of crops. The homeostatic capability of an agroecosystem to remove a triazinic herbicide, simazine, was assessed in microcosms treated with the herbicide in presence/absence of urea fertilizer. The latter, as well as a fertilizer, is also one of the last by-products before simazine mineralization. The biodegradation, in terms of disappearance of 50% of the initial concentration (DT50, was compared to the degradation and metabolite formation occurring in sterilized soil. Moreover, the bacterial community response was assessed in terms of abundance and community structure by the epifluorescence direct count method and fluorescence in situ hybridization. The results show that the microbial community has a primary role in simazine degradation and that this process is due to the presence of a microbial pool working in succession and of which the metabolism may be modulated by exogenous sources of nitrogen, like urea. The latter influences the degradative pathway with a greater formation and accumulation of the desethyl-simazine metabolite, which is a hazardous contaminant of soil and groundwater ecosystems, as well as its parent compound.

  13. The Role of the Bacterial Community of an Agroecosystem in Simazine Degradation

    Directory of Open Access Journals (Sweden)

    Roberto Ciccoli

    2011-02-01

    Full Text Available The use of pesticides and fertilizers in agricultural practice is the main source of soil and groundwater contamination. S-Triazines are among the most used herbicides in the world for selective weed control in several types of crops. The homeostatic capability of an agroecosystem to remove a triazinic herbicide, simazine, was assessed in microcosms treated with the herbicide in presence/absence of urea fertilizer. The latter, as well as a fertilizer, is also one of the last by-products before simazine mineralization. The biodegradation, in terms of disappearance of 50% of the initial concentration (DT50, was compared to the degradation and metabolite formation occurring in sterilized soil. Moreover, the bacterial community response was assessed in terms of abundance and community structure by the epifluorescence direct count method and fluorescence in situ hybridization. The results show that the microbial community has a primary role in simazine degradation and that this process is due to the presence of a microbial pool working in succession and of which the metabolism may be modulated by exogenous sources of nitrogen, like urea. The latter influences the degradative pathway with a greater formation and accumulation of the desethyl-simazine metabolite, which is a hazardous contaminant of soil and groundwater ecosystems, as well as its parent compound.

  14. 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.

  15. Hydrocephalus in adults with community-acquired bacterial meningitis

    NARCIS (Netherlands)

    E. Soemirien Kasanmoentalib; M.C. Brouwer; A. van der Ende; D. van de Beek

    2010-01-01

    Objective: To evaluate the occurrence, treatment, and outcome of hydrocephalus complicating community-acquired bacterial meningitis in adults. Methods: Case series from a prospective nationwide cohort study from Dutch hospitals from 2006 to 2009. Results: Hydrocephalus was diagnosed in 26 of 577 epi

  16. Marine bacterial communities are resistant to elevated carbon dioxide levels.

    Science.gov (United States)

    Oliver, Anna E; Newbold, Lindsay K; Whiteley, Andrew S; van der Gast, Christopher J

    2014-12-01

    It is well established that the release of anthropogenic-derived CO2 into the atmosphere will be mainly absorbed by the oceans, with a concomitant drop in pH, a process termed ocean acidification. As such, there is considerable interest in how changes in increased CO2 and lower pH will affect marine biota, such as bacteria, which play central roles in oceanic biogeochemical processes. Set within an ecological framework, we investigated the direct effects of elevated CO2, contrasted with ambient conditions on the resistance and resilience of marine bacterial communities in a replicated temporal seawater mesocosm experiment. The results of the study strongly indicate that marine bacterial communities are highly resistant to the elevated CO2 and lower pH conditions imposed, as demonstrated from measures of turnover using taxa–time relationships and distance–decay relationships. In addition, no significant differences in community abundance, structure or composition were observed. Our results suggest that there are no direct effects on marine bacterial communities and that the bacterial fraction of microbial plankton holds enough flexibility and evolutionary capacity to withstand predicted future changes from elevated CO2 and subsequent ocean acidification.

  17. Functional recovery of biofilm bacterial communities after copper exposure.

    NARCIS (Netherlands)

    Boivin, Marie-Elène Y; Massieux, Boris; Breure, Anton M; Greve, Gerdit D; Rutgers, Michiel; Admiraal, Wim

    2006-01-01

    Potential of bacterial communities in biofilms to recover after copper exposure was investigated. Biofilms grown outdoor in shallow water on glass dishes were exposed in the laboratory to 0.6, 2.1, 6.8 micromol/l copper amended surface water and a reference and subsequently to un-amended surface wat

  18. Bacterial community succession in pine-wood decomposition

    NARCIS (Netherlands)

    Kielak, Anna; Scheublin, Tanja; Mendes, L.W.; Van Veen, Johannes A; Kuramae, Eiko Eurya

    2016-01-01

    BACKGROUND: Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance a

  19. Bacterial community profiles in low microbial abundance sponges.

    Science.gov (United States)

    Giles, Emily C; Kamke, Janine; Moitinho-Silva, Lucas; Taylor, Michael W; Hentschel, Ute; Ravasi, Timothy; Schmitt, Susanne

    2013-01-01

    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.

  20. Comparative survey of bacterial and archaeal communities in high arsenic shallow aquifers using 454 pyrosequencing and traditional methods.

    Science.gov (United States)

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

    2014-12-01

    A survey of bacterial and archaeal community structure was carried out in 10 shallow tube wells in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia by 16S rRNA gene based two-step nested PCR-DGGE, clone libraries and 454 pyrosequencing. 12 bacterial and 18 archaeal DGGE bands and 26-136 species-level OTUs were detected for all the samples. 299 bacterial and 283 archaeal 16S rRNA gene clones for two typical samples were identified by phylogenetic analysis. Most of the results from these different methods were consistent with the dominant bacterial populations. But the proportions of the microbial populations were mostly different and the bacterial communities in most of these samples from pyrosequencing were both more abundant and more diverse than those from the traditional methods. Even after quality filtering, pyrosequencing revealed some populations including Alishewanella, Sulfuricurvum, Arthrobacter, Sporosarcina and Algoriphagus which were not detected with traditional techniques. The most dominant bacterial populations in these samples identified as some arsenic, iron, nitrogen and sulfur reducing and oxidizing related populations including Acinetobacter, Pseudomonas, Flavobacterium, Brevundimonas, Massilia, Planococcus, and Aquabacterium and archaeal communities Nitrosophaera and Methanosaeta. Acinetobacter and Pseudomonas were distinctly abundant in most of these samples. Methanogens were found as the dominant archeal population with three methods. From the results of traditional methods, the dominant archaeal populations apparently changed from phylum Thaumarchaeota to Euryarchaeota with the arsenic concentrations increasing. But this structure dynamic change was not revealed with pyrosequencing. Our results imply that an integrated approach combining the traditional methods and next generation sequencing approaches to characterize the microbial communities in high arsenic groundwater is recommended.

  1. Bacterial community diversity in municipal waste landfill sites.

    Science.gov (United States)

    Song, Liyan; Wang, Yangqing; Tang, Wei; Lei, Yu

    2015-09-01

    Little is known about the bacterial diversity of landfills and how environmental factors impact the diversity. In this study, PCR-based 454 pyrosequencing was used to investigate the bacterial communities of ten landfill leachate samples from five landfill sites in China. A total of 137 K useable sequences from the V3-V6 regions of the 16S rRNA gene were retrieved from 205 K reads. These sequences revealed the presence of a large number of operational taxonomic units (OTUs) in the landfills (709-1599 OTUs per sample). The most predominant bacterial representatives in the landfills investigated, regardless of geographic area, included Gammaproteobacteria, Firmicutes, and Bacteroidetes. The phyla Fusobacteria and Tenericutes were also found for the first time to be predominant in the landfills. The phylum Fusobacteria predominated (51.5 and 48.8%) in two semi-arid landfills, and the phylum Tenericutes dominated (30.6%) at one humid, subtropical landfill. Further, a large number of Pseudomonas was detected in most samples, comprising the dominant group and accounting for 40.9 to 92.4% of the total abundance. Principal component analysis (PCA) and cluster analysis based on OTU abundance showed that the abundant taxa separated the bacterial community. Canonical correlation analysis (CCA) suggested that precipitation and landfilling age significantly impact on the bacterial community structure. The bacterial community function (e.g., cellulolytic bacteria, sulfate-reducing bacteria (SRB), sulfate-oxidizing bacteria, and xenobiotic organic compound (XOC)-degrading bacteria) was also diverse, but the pattern is unclear.

  2. Bacterial communities of two ubiquitous Great Barrier Reef corals reveals both site- and species-specificity of common bacterial associates.

    Directory of Open Access Journals (Sweden)

    E Charlotte E Kvennefors

    Full Text Available BACKGROUND: Coral-associated bacteria are increasingly considered to be important in coral health, and altered bacterial community structures have been linked to both coral disease and bleaching. Despite this, assessments of bacterial communities on corals rarely apply sufficient replication to adequately describe the natural variability. Replicated data such as these are crucial in determining potential roles of bacteria on coral. METHODOLOGY/PRINCIPAL FINDINGS: Denaturing Gradient Gel Electrophoresis (DGGE of the V3 region of the 16S ribosomal DNA was used in a highly replicated approach to analyse bacterial communities on both healthy and diseased corals. Although site-specific variations in the bacterial communities of healthy corals were present, host species-specific bacterial associates within a distinct cluster of gamma-proteobacteria could be identified, which are potentially linked to coral health. Corals affected by "White Syndrome" (WS underwent pronounced changes in their bacterial communities in comparison to healthy colonies. However, the community structure and bacterial ribotypes identified in diseased corals did not support the previously suggested theory of a bacterial pathogen as the causative agent of the syndrome. CONCLUSIONS/SIGNIFICANCE: This is the first study to employ large numbers of replicated samples to assess the bacterial communities of healthy and diseased corals, and the first culture-independent assessment of bacterial communities on WS affected Acroporid corals on the GBR. Results indicate that a minimum of 6 replicate samples are required in order to draw inferences on species, spatial or health-related changes in community composition, as a set of clearly distinct bacterial community profiles exist in healthy corals. Coral bacterial communities may be both site and species specific. Furthermore, a cluster of gamma-proteobacterial ribotypes may represent a group of specific common coral and marine

  3. Assessment of Changes in Biodiversity when a Community of Ultramicrobacteria Isolated from Groundwater Is Stimulated to Form a Biofilm.

    Science.gov (United States)

    Ross, N.; Villemur, R.; Marcandella, E.; Deschênes, L.

    2001-07-01

    The stimulation of groundwater bacteria to form biofilms, for the remediation of polluted aquifers, is subjected to environmental regulations that include measurement of effects on microbial biodiversity. Groundwater microorganisms contain a proportion of unidentified and uncharacterized ultramicrobacteria (UMB) that might play a major role in the bioclogging of geological materials. This study aimed to assess the changes in genetic and metabolic biodiversity when a community of UMB, isolated from groundwater, is stimulated to form biofilms on a ceramic surface. UMB were stimulated with aerobic conditions and injection of molasses, in reactors reproducing groundwater composition and temperature. Concentration of planktonic viable UMB, secretion of extracellular polymeric substances (EPS), and biofilm thickness were monitored. The assessment of changes in biodiversity was achieved by comparing the initial UMB community to the biofilm community, using the single strand conformational polymorphism (SSCP) method, the cloning and sequencing of 16S rRNA gene (16S rDNA) sequences, and the Biolog microplate system. The hypothesis stating that indigenous UMB would play a significant role of in the biofilm development was corroborated. Within 13 days of stimulation, the UMB produced 700 mg L?1 of planktonic EPS and formed a biofilm up to a thickness of 1100 mm. This stimulation led to a decrease in genetic diversity and an increase in metabolic diversity. The decrease in genetic diversity was shown by a reduced number of single strand DNA fragments in the SSCP profiles. As such, 16S rDNA sequences from the biofilm revealed the predominance of four bacterial groups: Zoogloea, Bacillus/Paenibacillus, Enterobacteriaceae, and Pseudomonads. A significant increase in metabolic diversity was shown by a highest substrate richness profile and a lower substrate evenness profile of the biofilm bacterial population (p = 0.0 and p = 0.09, respectively). This higher metabolic diversity

  4. Soil bacterial community responses to global changes

    DEFF Research Database (Denmark)

    Bergmark, Lasse

    ’ of climate change manipulations on soil microorganisms and nutrient availability in a Danish heathland, where the samples were taken shortly after a prolonged pre-summer drought. The major findings in the study are that warming increased measures of fungi and bacteria and drought might shift......Soil bacteria and archaea are essential for ecosystem functioning and plant growth through their degradation of organic matter and turnover of nutrients. But since the majority of soil bacteria and archaea are unclassified and “nonculturable” the functionality of the microbial community and its...... overall importance for ecosystem function in soil is poorly understood. Global change factors may affect the diversity and functioning of soil prokaryotes and thereby ecosystem functioning. To gain a better understanding of the effects of global changes it is of fundamental importance to classify...

  5. Effects of sulfadiazine on soil bacterial communities

    DEFF Research Database (Denmark)

    Hangler, Martin

    as fertilizers on agricultural lands they represent a route for antibiotics into the soil environment where they may persist and affect levels of antibiotic resistance in soil microbial communities over time. In this work the level of tolerance to the antibiotic sulfadiazine (SDZ) was studied in a number......-threshold, of a non-contaminated soil environment at various pH of which to compare other soils. Soil samples representing a broad range of natural pH were collected from the pH gradient at the Hoosfield acid strip, part of the long-term field experiment at the Rothamstead Research Station (UK) and exposed...... and transport of SDZ at the interphase between dewatered SDZ-amended sewage sludge and soil. SDZ was not mineralized within sludge aggregates and travelled more than 10 mm into the surrounding soil. The strongest PICT response was observed in soils fertilized with organic fertilizers or inorganic NPK fertilizer...

  6. Dominance of sphingomonads in a copper-exposed biofilm community for groundwater treatment.

    Science.gov (United States)

    Vílchez, R; Pozo, C; Gómez, M A; Rodelas, B; González-López, J

    2007-02-01

    The structure, biological activity and microbial biodiversity of a biofilm used for the removal of copper from groundwater were studied and compared with those of a biofilm grown under copper-free conditions. A laboratory-scale submerged fixed biofilter was fed with groundwater (2.3 l h(-1)) artificially polluted with Cu(II) (15 mg l(-1)) and amended with sucrose (150 mg l(-1)) as carbon source. Between 73 and 90 % of the Cu(II) was removed from water during long-term operation (over 200 days). The biofilm was a complex ecosystem, consisting of eukaryotic and prokaryotic micro-organisms. Scanning electron microscopy revealed marked structural changes in the biofilm induced by Cu(II), compared to the biofilm grown in absence of the heavy metal. Analysis of cell-bound extracellular polymeric substances (EPS) demonstrated a significant modification of the composition of cell envelopes in response to Cu(II). Transmission electron microscopy and energy-dispersive X-ray microanalysis (EDX) showed that copper bioaccumulated in the EPS matrix by becoming bound to phosphates and/or silicates, whereas copper accumulated only intracytoplasmically in cells of eukaryotic microbes. Cu(II) also decreased sucrose consumption, ATP content and alkaline phosphatase activity of the biofilm. A detailed study of the bacterial community composition was conducted by 16S rRNA-based temperature gradient gel electrophoresis (TGGE) profiling, which showed spatial and temporal stability of the species diversity of copper-exposed biofilms during biofilter operation. PCR reamplification and sequencing of 14 TGGE bands showed the prevalence of alphaproteobacteria, with most sequences (78 %) affiliated to the Sphingomonadaceae. The major cultivable colony type in plate counts of the copper-exposed biofilm was also identified as that of Sphingomonas sp. These data confirm a major role of these organisms in the composition of the Cu(II)-removing community.

  7. Bacterial community survey of sediments at Naracoorte Caves, Australia

    Directory of Open Access Journals (Sweden)

    Ball Andrew S.

    2012-07-01

    Full Text Available Bacterial diversity in sediments at UNESCO World Heritage listed Naracoorte Caves was surveyed as part of an investigation carried out in a larger study on assessing microbial communities in caves. Cave selection was based on tourist accessibility; Stick Tomato and Alexandra Cave (> 15000 annual visits and Strawhaven Cave was used as control (no tourist access. Microbial analysis showed that Bacillus was the most commonly detected microbial genus by culture dependent and independent survey of tourist accessible and inaccessible areas of show (tourist accessible and control caves. Other detected sediment bacterial groups were assigned to the Firmicutes, Actinobacteria and Proteobacteria. The survey also showed differences in bacterial diversity in caves with human access compared to the control cave with the control cave having unique microbial sequences (Acinetobacter, Agromyces, Micrococcus and Streptomyces. The show caves had higher bacterial counts, different 16S rDNA based DGGE cluster patterns and principal component groupings compared to Strawhaven. Different factors such as human access, cave use and configurations could have been responsible for the differences observed in the bacterial community cluster patterns (tourist accessible and inaccessible areas of these caves. Cave sediments can therefore act as reservoirs of microorganisms. This might have some implications on cave conservation activities especially if these sediments harbor rock art degrading microorganisms in caves with rock art.

  8. Influence of hexavalent chromium on lactate-enriched Hanford groundwater microbial communities.

    Energy Technology Data Exchange (ETDEWEB)

    Somenahally, Anil C [ORNL; Mosher, Jennifer J [ORNL; Yuan, Tong [University of Oklahoma; Podar, Mircea [ORNL; Phelps, Tommy Joe [ORNL; Brown, Steven D [ORNL; Yang, Zamin Koo [ORNL; Hazen, Terry C [ORNL; Arkin, Adam [Lawrence Berkeley National Laboratory (LBNL); Palumbo, Anthony Vito [ORNL; Zhou, Jizhong [University of Oklahoma; Elias, Dwayne A [ORNL

    2013-01-01

    Microbial reduction and immobilization of chromate (Cr(VI)) is a plausible bioremediation strategy. However, higher Cr(VI) concentrations may impose stress on native Cr-reducing communities. We sought to determine if Cr(VI) would influence the lactate enriched native microbial community structure and function in groundwater from the Cr contaminated site at Hanford, WA. Steady state continuous flow bioreactors were amended with lactate and Cr(VI) (0.0, 0.1 and 3.0 mg/L). Microbial growth, metabolites, Cr(VI) concentrations, 16S rRNA gene sequences and GeoChip based functional gene composition in bioreactors were monitored for 15 weeks. Temporal trends and some differences in growth, metabolite profiles, and community composition were observed, largely between Low-Cr and High-Cr bioreactors. In both High-Cr and Low-Cr bioreactors, Cr(VI) was reduced in the bioreactors. With lactate enrichment, the native communities did not significantly differ between Cr concentrations. Native bacterial communities were diverse, whereas after lactate enrichment, Pelosinus spp., and Sporotalea spp., were the most predominant groups in all bioreactors. Similarly, the Archaea diversity significantly decreased from Methanosaeta (35%), Methanosarcina (17%), Halobacteriales (12%), Methanoregula (8%) and others, to mostly Methanosarcina spp. (95%) after lactate enrichment. Composition of several key functional genes was distinct in Low-Cr bioreactors compared to High-Cr. Among the Cr resistant probes (chrA), Burkholderia vietnamiensis, Comamonas testosterone and Ralstonia pickettii proliferated in Cr amended bioreactors. In-situ fermentative conditions facilitated Cr(VI) reduction, and as a result the 3.0 mg/L Cr(VI) did not appear to give chromate reducing strains a competitive advantage for proliferation or for increasing Cr-reduction.

  9. Experimental warming effects on the bacterial community structure and diversity

    Science.gov (United States)

    Kim, W.; Han, S.; Adams, J.; Son, Y.

    2014-12-01

    The objective of this study is to investigate the responses of soil bacterial community to future temperature increase by conducting open-field warming experiment. We conducted an open-field experimental warming system using infra-red heater in 2011 and regulated the temperature of warmed plots by 3oC higher than that of control plots constantly. The seeds of Pinus densiflora, Abies holophylla, Abies koreana, Betula costata, Quercus variabilis, Fraxinus rhynchophylla, and Zelkova serrata were planted in each 1 m × 1 m plot (n=3) in April, 2012. We collected soil samples from the rhizosphere of 7 tree species. DNA was extracted and PCR-amplified for the bacterial 16S gene targeting V1-V3 region. The paired-end sequencing was performed at Beijing Genome Institute (BGI, Hong Kong, China) using 2× 100 bp Hiseq2000 (Illumina). This study aimed to answer the following prediction/hypothesis: 1) Experimental warming will change the structure of soil bacterial community, 2) There will be distinct 'indicator group' which response to warming treatment relatively more sensitive than other groups. 3) Warming treatment will enhance the microbial activity in terms of soil respiration. 4) The rhizoplane bacterial communities for each of 7 tree species will show different response pattern to warming treatment. Since the sequence data does not arrive before the submission deadline, therefore, we would like to present the results and discussions on December 2014, AGU Fall Meeting.

  10. Microbial Community Dynamics of Lactate Enriched Hanford Groundwaters

    Energy Technology Data Exchange (ETDEWEB)

    Mosher, Jennifer J.; Drake, Meghan M.; Carroll, Susan L.; Yang, Zamin K.; Schadt, Christopher W.; Brown, Stephen D.; Podar, Mircea; Hazen, Terry C.; Arkin, Adam P.; Phelps, Tommy J.; Palumbo, Anthony V.; Faybishenko, Boris A.; Elias, Dwayne A.

    2010-05-01

    The Department of Energy site at Hanford, WA, has been historically impacted by U and Cr from the nuclear weapons industry. In an attempt to stimulate microbial remediation of these metals, in-situ lactate enrichment experiments are ongoing. In order to bridge the gap from the laboratory to the field, we inoculated triplicate anaerobic, continuous-flow glass reactors with groundwater collected from well Hanford 100-H in order to obtain a stable, enriched community while selecting for metal-reducing bacteria. Each reactor was fed from a single carboy containing defined media with 30 mM lactate at a rate of 0.223 ml/min under continuous nitrogen flow at 9 ml/min. Cell counts, organic acids, gDNA (for qPCR and pyrosequencing) and gases were sampled during the experiment. Cell counts remained low (less than 1x107 cells/ml) during the first two weeks of the experiment, but by day 20, had reached a density greater than 1x108 cells/ml. Metabolite analysis showed a decrease in the lactate concentrations over time. Pyruvate concentrations ranged from 20-40 uM the first week of the experiment then was undetectable after day 10. Likewise, formate appeared in the reactors during the first week with concentrations of 1.48-1.65 mM at day 7 then the concentrations decreased to 0.69-0.95 on day 10 and were undetectable on day 15. Acetate was present in low amounts on day 3 (0.15-0.33 mM) and steadily increased to 3.35-5.22 mM over time. Similarly, carbon dioxide was present in low concentrations early on and increased to 0.28-0.35 mM as the experiment progressed. We also were able to detect low amounts of methane (10-20 uM) during the first week of the experiment, but by day 10 the methane was undetectable. From these results and pyrosequencing analysis, we conclude that a shift in the microbial community dynamics occurred over time to eventually form a stable and enriched microbial community. Comprehensive investigations such as these allow for the examination of not only which

  11. Polyphasic analysis of an Azoarcus-Leptothrix-dominated bacterial biofilm developed on stainless steel surface in a gasoline-contaminated hypoxic groundwater.

    Science.gov (United States)

    Benedek, Tibor; Táncsics, András; Szabó, István; Farkas, Milán; Szoboszlay, Sándor; Fábián, Krisztina; Maróti, Gergely; Kriszt, Balázs

    2016-05-01

    Pump and treat systems are widely used for hydrocarbon-contaminated groundwater remediation. Although biofouling (formation of clogging biofilms on pump surfaces) is a common problem in these systems, scarce information is available regarding the phylogenetic and functional complexity of such biofilms. Extensive information about the taxa and species as well as metabolic potential of a bacterial biofilm developed on the stainless steel surface of a pump submerged in a gasoline-contaminated hypoxic groundwater is presented. Results shed light on a complex network of interconnected hydrocarbon-degrading chemoorganotrophic and chemolitotrophic bacteria. It was found that besides the well-known hydrocarbon-degrading aerobic/facultative anaerobic biofilm-forming organisms (e.g., Azoarcus, Leptothrix, Acidovorax, Thauera, Pseudomonas, etc.), representatives of Fe(2+)-and Mn(2+)-oxidizing (Thiobacillus, Sideroxydans, Gallionella, Rhodopseudomonas, etc.) as well as of Fe(3+)- and Mn(4+)-respiring (Rhodoferax, Geobacter, Magnetospirillum, Sulfurimonas, etc.) bacteria were present in the biofilm. The predominance of β-Proteobacteria within the biofilm bacterial community in phylogenetic and functional point of view was revealed. Investigation of meta-cleavage dioxygenase and benzylsuccinate synthase (bssA) genes indicated that within the biofilm, Azoarcus, Leptothrix, Zoogloea, and Thauera species are most probably involved in intrinsic biodegradation of aromatic hydrocarbons. Polyphasic analysis of the biofilm shed light on the fact that subsurface microbial accretions might be reservoirs of novel putatively hydrocarbon-degrading bacterial species. Moreover, clogging biofilms besides their detrimental effects might supplement the efficiency of pump and treat systems.

  12. Foliar bacterial communities of trembling aspen in a common garden.

    Science.gov (United States)

    Mason, Charles J; Pfammatter, Jesse A; Holeski, Liza M; Raffa, Kenneth F

    2015-02-01

    Microbial associations with plants are widely distributed and are structured by a number of biotic and physical factors. Among biotic factors, the host plant genotype may be integral to these plant-microbe interactions. Trees in the genus Populus have become models for studies in scaling effects of host plant genetics and in plant-microbe interactions. Using 454 pyrosequencing of the 16S rRNA gene, we assessed the foliar bacterial community of 7 genotypes of mature trembling aspen trees (Populus tremuloides Michx.) grown in a common garden. Trees were selected based on prior analyses showing clonal variation in their concentration of chemicals conferring resistance against insect herbivores. At broad taxonomic designations, the bacterial community of trembling aspen was similar across all plant genotypes. At a finer taxonomic scale, the foliage of these trees varied in their community composition, but there was no distinct pattern to colonization or abundance related to plant genotype. The most abundant operational taxonomic units (OTUs) were classified as Ralstonia, Bradyrhizobium, Pseudomonas, and Brucella. These OTUs varied across the common garden, but there was no significant effect of host plant genotype or spatial position on the abundance of these members. Our results suggest that aspen genotype is less important in the structuring of its foliar bacterial communities than are other, poorly understood processes.

  13. Groundwater Isolation Governs Chemistry and Microbial Community Structure along Hydrologic Flowpaths

    Science.gov (United States)

    Ben Maamar, Sarah; Aquilina, Luc; Quaiser, Achim; Pauwels, Hélène; Michon-Coudouel, Sophie; Vergnaud-Ayraud, Virginie; Labasque, Thierry; Roques, Clément; Abbott, Benjamin W.; Dufresne, Alexis

    2015-01-01

    This study deals with the effects of hydrodynamic functioning of hard-rock aquifers on microbial communities. In hard-rock aquifers, the heterogeneous hydrologic circulation strongly constrains groundwater residence time, hydrochemistry, and nutrient supply. Here, residence time and a wide range of environmental factors were used to test the influence of groundwater circulation on active microbial community composition, assessed by high throughput sequencing of 16S rRNA. Groundwater of different ages was sampled along hydrogeologic paths or loops, in three contrasting hard-rock aquifers in Brittany (France). Microbial community composition was driven by groundwater residence time and hydrogeologic loop position. In recent groundwater, in the upper section of the aquifers or in their recharge zone, surface water inputs caused high nitrate concentration and the predominance of putative denitrifiers. Although denitrification does not seem to fully decrease nitrate concentrations due to low dissolved organic carbon concentrations, nitrate input has a major effect on microbial communities. The occurrence of taxa possibly associated with the application of organic fertilizers was also noticed. In ancient isolated groundwater, an ecosystem based on Fe(II)/Fe(III) and S/SO4 redox cycling was observed down to several 100 of meters below the surface. In this depth section, microbial communities were dominated by iron oxidizing bacteria belonging to Gallionellaceae. The latter were associated to old groundwater with high Fe concentrations mixed to a small but not null percentage of recent groundwater inducing oxygen concentrations below 2.5 mg/L. These two types of microbial community were observed in the three sites, independently of site geology and aquifer geometry, indicating hydrogeologic circulation exercises a major control on microbial communities. PMID:26733990

  14. Ecology and biogeography of bacterial communities associated with chloroethene-contaminated aquifers

    Directory of Open Access Journals (Sweden)

    Pierre eRossi

    2012-07-01

    Full Text Available Massive usage, along with careless handling, storage, spills and leakages made chloroethenes (CEs one of the most abundant classes of groundwater contaminants. Anaerobic organohalide-respiring bacteria (OHRB can couple reductive dechlorination of CEs with energy conservation, a central microbial process in (enhanced natural attenuation of CE-contaminated aquifers. Spatial variability of OHRB guild members present in contaminated sites has not yet been investigated in detail and it is not known whether the spatial localization of contaminated sites could impact differentially remediation capacities. The goal of this study was to investigate how spatially-distant microbial communities responded to the presence of CEs. Bacterial communities associated with five geographically distant European CEs-contaminated aquifers were analyzed with terminal-restriction fragment length polymorphism. Numerical ecology tools were used to assess the separate and combined effects on the communities of their spatial localization, their local environmental conditions and their contaminant concentrations. Three spatial scales were used for the assessment of the structuration of the communities as a function of geographical distances, namely at the aquifer scale, at medium (50 km and long (ca. 1000 km distances between aquifers. As a result, bacterial communities were structured with an almost identical contribution by both the geographical position of the aquifer and local environmental variables, especially electron donors and acceptors. The impact of environmental factors decreased with distance between aquifers, with the concomitant increase in importance of a geographical factor. Contrastingly, CEs contributed at a low extent at the medium scale and became important only when all aquifers were considered together, at a large geographical scale, suggesting that distant communities were structured partially by a common niche specialization in organohalide

  15. Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater

    Science.gov (United States)

    Applegate, Olin; Li, Xunde; Kliegman, Joseph I.; Langelier, Charles; Atwill, Edward R.; Harter, Thomas; DeRisi, Joseph L.

    2017-01-01

    Background Climate change produces extremes in both temperature and precipitation causing increased drought severity and increased reliance on groundwater resources. Agricultural practices, which rely on groundwater, are sensitive to but also sources of contaminants, including nitrate. How agricultural contamination drives groundwater geochemistry through microbial metabolism is poorly understood. Methods On an active cow dairy in the Central Valley of California, we sampled groundwater from three wells at depths of 4.3 m (two wells) and 100 m (one well) below ground surface (bgs) as well as an effluent surface water lagoon that fertilizes surrounding corn fields. We analyzed the samples for concentrations of solutes, heavy metals, and USDA pathogenic bacteria of the Escherichia coli and Enterococcus groups as part of a long term groundwater monitoring study. Whole metagenome shotgun sequencing and assembly revealed taxonomic composition and metabolic potential of the community. Results Elevated nitrate and dissolved organic carbon occurred at 4.3m but not at 100m bgs. Metagenomics confirmed chemical observations and revealed several Planctomycete genomes, including a new Brocadiaceae lineage and a likely Planctomycetes OM190, as well novel diversity and high abundance of nano-prokaryotes from the Candidate Phyla Radiation (CPR), the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea (DPANN) and the Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota (TACK) superphyla. Pathway analysis suggests community interactions based on complimentary primary metabolic pathways and abundant secondary metabolite operons encoding antimicrobials and quorum sensing systems. Conclusions The metagenomes show strong resemblance to activated sludge communities from a nitrogen removal reactor at a wastewater treatment plant, suggesting that natural bioremediation occurs through microbial metabolism. Elevated nitrate and rich secondary metabolite

  16. Influence of groundwater depth on species composition and community structure in the transition zone of Cele oasis

    Institute of Scientific and Technical Information of China (English)

    Frank; M.; THOMAS

    2010-01-01

    The paper analyzes the hypothesis that the distribution of dominant plant species and characteristics of plant communities are related to groundwater depth. The results showed that variations of groundwater depth impacted distributions and characteristics of dominant plant communities. However, besides groundwater depth, the community composition and species diversity were also influenced by physiognomy of the habitat. Based on the similarity coefficient, the differences between dominant plant communities were significant at different groundwater depths. Compared with other results relating to desert vegetation and groundwater depth, variations of community distribution were similar at the large spatial scale. However, in this extremely arid region, there were significant differences in community type and community succession when compared with other arid regions, especially in relationship to deep groundwater depth. With groundwater depth from deep to shallow, communities transformed with the sequence of Alhagi communities, Tamarix spp. communities, Populus communities, Phragmites communities, and Sophora communities. At groundwater depth of less than 6.0 m, the community type and composition changed, and the species diversity increased. Among these dominant species, Tamarix exhibited the biggest efficiency in resource utilization according to niche breadth, which means it possessed the best adaptability to environmental conditions at the oasis margins.

  17. Influence of groundwater depth on species composition and community structure in the transition zone of Cele oasis

    Institute of Scientific and Technical Information of China (English)

    XiangYi LI; LiSha LIN; Qiang ZHAO; XiMing ZHANG; Frank M.THOMAS

    2010-01-01

    The paper analyzes the hypothesis that the distribution of dominant plant species and characteristics of plant communities are related to groundwater depth.The results showed that variations of groundwater depth impacted distributions and characteristics of dominant plant communities.However,besides groundwater depth,the community composition and species diversity were also influenced by physiognomy of the habitat.Based on the similarity coefficient,the differences between dominant plant communities were significant at different groundwater depths.Compared with other results relating to desert vegetation and groundwater depth,variations of community distribution were similar at the large spatial scale.However,in this extremely arid region,there were significant differences in community type and community succession when compared with other arid regions,especially in relationship to deep groundwater depth.With groundwater depth from deep to shallow,communities transformed with the sequence of Alhagi communities,Tamarix spp.communities,Populus communities,Phragmites communities,and Sophora communities.At groundwater depth of less than 6.0m,the community type and composition changed,and the species diversity increased.Among these dominant species,Tamarix exhibited the biggest efficiency in resource utilization according to niche breadth,which means it possessed the best adaptability to environmental conditions at the oasis margins.

  18. Bacterial communities associated with apical periodontitis and dental implant failure

    Directory of Open Access Journals (Sweden)

    Simon Dingsdag

    2016-11-01

    Full Text Available Background: Previously, we demonstrated that bacteria reside in apparently healed alveolar bone, using culture and Sanger sequencing techniques. Bacteria in apparently healed alveolar bone may have a role in peri-implantitis and dental implant failure. Objective: To compare bacterial communities associated with apical periodontitis, those colonising a failed implant and alveolar bone with reference biofilm samples from healthy teeth. Methods and results: The study consisted of 196 samples collected from 40 patients undergoing routine dental implant insertion or rehabilitation. The bacterial 16S ribosomal DNA sequences were amplified. Samples yielding sufficient polymerase chain reaction product for further molecular analyses were subjected to terminal restriction fragment length polymorphism (T-RFLP; 31 samples and next generation DNA sequencing (454 GS FLX Titanium; 8 samples. T-RFLP analysis revealed that the bacterial communities in diseased tissues were more similar to each other (p<0.049 than those from the healthy reference samples. Next generation sequencing detected 13 bacterial phyla and 373 putative bacterial species, revealing an increased abundance of Gram-negative [Prevotella, Fusobacterium (p<0.004, Treponema, Veillonellaceae, TG5 (Synergistetes] bacteria and a decreased abundance of Gram-positive [(Actinomyces, Corynebacterium (p<0.008] bacteria in the diseased tissue samples (n=5 relative to reference supragingival healthy samples (n=3. Conclusion: Increased abundances of Prevotella, Fusobacterium and TG5 (Synergistetes were associated with apical periodontitis and a failed implant. A larger sample set is needed to confirm these trends and to better define the processes of bacterial pathogenesis in implant failure and apical periodontitis. The application of combined culture-based, microscopic and molecular technique-based approaches is suggested for future studies.

  19. Mechanism of uranium (VI) removal by two anaerobic bacterial communities

    Energy Technology Data Exchange (ETDEWEB)

    Martins, Monica [Centro de Ciencias do Mar, Universidade do Algarve, FCT-DQF (edificio 8), Campus de Gambelas, 8005-139 Faro (Portugal); Faleiro, Maria Leonor [IBB - Centro de Biomedicina Molecular e Estrutural, Universidade do Algarve, FCT, Campus de Gambelas, 8005-139 Faro (Portugal); Costa, Ana M. Rosa da [Centro de Investigacao em Quimica do Algarve, Universidade do Algarve, FCT, DQF, Campus de Gambelas, 8005-139 Faro (Portugal); Chaves, Sandra; Tenreiro, Rogerio [Universidade de Lisboa, Faculdade de Ciencias, Centro de Biodiversidade, Genomica Integrativa e Funcional (BioFIG), Campus de FCUL, Campo Grande, 1749-016 Lisboa (Portugal); Matos, Antonio Pedro [Servico de Anatomia Patologica, Hospital Curry Cabral, Lisboa (Portugal); Costa, Maria Clara, E-mail: mcorada@ualg.pt [Centro de Ciencias do Mar, Universidade do Algarve, FCT-DQF (edificio 8), Campus de Gambelas, 8005-139 Faro (Portugal)

    2010-12-15

    The mechanism of uranium (VI) removal by two anaerobic bacterial consortia, recovered from an uncontaminated site (consortium A) and other from an uranium mine (consortium U), was investigated. The highest efficiency of U (VI) removal by both consortia (97%) occurred at room temperature and at pH 7.2. Furthermore, it was found that U (VI) removal by consortium A occurred by enzymatic reduction and bioaccumulation, while the enzymatic process was the only mechanism involved in metal removal by consortium U. FTIR analysis suggested that after U (VI) reduction, U (IV) could be bound to carboxyl, phosphate and amide groups of bacterial cells. Phylogenetic analysis of 16S rRNA showed that community A was mainly composed by bacteria closely related to Sporotalea genus and Rhodocyclaceae family, while community U was mainly composed by bacteria related to Clostridium genus and Rhodocyclaceae family.

  20. Bacteriocin-Mediated Competitive Interactions of Bacterial Populations and Communities

    Science.gov (United States)

    Riley, Margaret A.

    Explaining the coexistence of competing species is a major challenge in community ecology. In bacterial systems, competition is often driven by the production of bacteriocins; narrow spectrum proteinaceous toxins that serve to kill closely related species providing the producer better access to limited resources. Bacteriocin producers have been shown to competitively exclude sensitive, nonproducing strains. However, the interaction dynamics between bacteriocin producers, each lethal to its competitor, are largely unknown. Several recent studies have revealed some of the complexity of these interactions, employing a suite of in vitro, in vivo, and in silico bacterial model systems. This chapter describes the current state of knowledge regarding the population and community ecology of this potent family of toxins.

  1. Assessing the diversity of bacterial communities associated with plants

    Science.gov (United States)

    Andreote, Fernando Dini; Azevedo, João Lúcio; Araújo, Welington Luiz

    2009-01-01

    Plant–bacteria interactions result from reciprocal recognition between both species. These interactions are responsible for essential biological processes in plant development and health status. Here, we present a review of the methodologies applied to investigate shifts in bacterial communities associated with plants. A description of techniques is made from initial isolations to culture-independent approaches focusing on quantitative Polymerase Chain Reaction in real time (qPCR), Denaturing Gradient Gel Electrophoresis (DGGE), clone library construction and analysis, the application of multivariate analyses to microbial ecology data and the upcoming high throughput methodologies such as microarrays and pyrosequencing. This review supplies information about the development of traditional methods and a general overview about the new insights into bacterial communities associated with plants. PMID:24031382

  2. Bacterial communities in sediment of a Mediterranean marine protected area.

    Science.gov (United States)

    Catania, Valentina; Sarà, Gianluca; Settanni, Luca; Quatrini, Paola

    2017-04-01

    Biodiversity is crucial in preservation of ecosystems, and bacterial communities play an indispensable role for the functioning of marine ecosystems. The Mediterranean marine protected area (MPA) "Capo Gallo-Isola delle Femmine" was instituted to preserve marine biodiversity. The bacterial diversity associated with MPA sediment was compared with that from sediment of an adjacent harbour exposed to intense nautical traffic. The MPA sediment showed higher diversity with respect to the impacted site. A 16S rDNA clone library of the MPA sediment allowed the identification of 7 phyla: Proteobacteria (78%), Firmicutes (11%), Acidobacteria (3%), Actinobacteria (3%), Bacteroidetes (2%), Planctomycetes (2%), and Cyanobacteria (1%). Analysis of the hydrocarbon (HC)-degrading bacteria was performed using enrichment cultures. Most of the MPA sediment isolates were affiliated with Gram-positive G+C rich bacteria, whereas the majority of taxa in the harbour sediment clustered with Alpha- and Gammaproteobacteria; no Gram-positive HC degraders were isolated from the harbour sediment. Our results show that protection probably has an influence on bacterial diversity, and suggest the importance of monitoring the effects of protection at microbial level as well. This study creates a baseline of data that can be used to assess changes over time in bacterial communities associated with a Mediterranean MPA.

  3. Bacterial community profiles in low microbial abundance sponges

    OpenAIRE

    Giles, Emily C; Kamke, Janine; Moitinho-Silva, Lucas; Taylor, Michael W.; Hentschel, Ute; Ravasi, Timothy; Schmitt, Susanne

    2013-01-01

    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 bacteri...

  4. Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators.

    Directory of Open Access Journals (Sweden)

    Cindy H Wu

    Full Text Available BACKGROUND: Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. METHODOLOGY/PRINCIPAL FINDINGS: Using a high-density microarray (PhyloChip, we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and alpha-proteobacteria found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC:A from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. CONCLUSIONS/SIGNIFICANCE: This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.

  5. Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators

    Energy Technology Data Exchange (ETDEWEB)

    Wu, C.H.; Sercu, B.; Van De Werhorst, L.C.; Wong, J.; DeSantis, T.Z.; Brodie, E.L.; Hazen, T.C.; Holden, P.A.; Andersen, G.L.

    2010-03-01

    Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and a-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC:A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.

  6. Bacterial community of biofilms developed under different water supply conditions in a distribution system.

    Science.gov (United States)

    Sun, Huifang; Shi, Baoyou; Bai, Yaohui; Wang, Dongsheng

    2014-02-15

    In order to understand the bacterial community characteristics of biofilms developed under different finished water supply histories in drinking water distribution systems (DWDS), biofilm samples on different type of iron corrosion scales in a real DWDS were collected and systematically investigated using 454 pyrosequencing of 16S rRNA gene. The richness and diversity estimators showed that biofilms formed in DWDS transporting finished groundwater (GW) had the lowest level of bacterial diversity. From phylum to genus level, the dominant bacterial groups found in the biofilms under finished surface water (SW) and GW conditions were distinct. Proteobacteria was the dominant group in all biofilm samples (in the range of 40%-97%), but was relatively higher in biofilms with GW. The relative abundance of Firmicutes in biofilms with SW (28%-35%) was significantly higher (piron-reducing bacteria (mainly Bacillus) and iron-oxidizing bacteria (mainly Acidovorax) were relatively higher in biofilms with SW, which might contribute to the formation of much thicker or tubercle-formed corrosion scales under SW supply condition. Several potential opportunistic pathogens, such as Burkholderia fungorum, Mycobacterium neoaurum, Mycobacterium frederiksbergense were detected in the biofilms.

  7. Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis.

    Science.gov (United States)

    Oakley, Brian B; Fiedler, Tina L; Marrazzo, Jeanne M; Fredricks, David N

    2008-08-01

    Bacterial vaginosis (BV) is a common syndrome associated with numerous adverse health outcomes in women. Despite its medical importance, the etiology and microbial ecology of BV remain poorly understood. We used broad-range PCR to census the community structure of the healthy and BV-affected vaginal microbial ecosystems and synthesized current publicly available bacterial 16S rRNA gene sequence data from this environment. The community of vaginal bacteria detected in subjects with BV was much more taxon rich and diverse than in subjects without BV. At a 97% sequence similarity cutoff, the number of operational taxonomic units (OTUs) per patient in 28 subjects with BV was nearly three times greater than in 13 subjects without BV: 14.8 +/- 0.7 versus 5.2 +/- 0.75 (mean +/- standard error). OTU-based analyses revealed previously hidden diversity for many vaginal bacteria that are currently poorly represented in GenBank. Our sequencing efforts yielded many novel phylotypes (123 of our sequences represented 38 OTUs not previously found in the vaginal ecosystem), including several novel BV-associated OTUs, such as those belonging to the Prevotella species complex, which remain severely underrepresented in the current NCBI database. Community composition was highly variable among subjects at a fine taxonomic scale, but at the phylum level, Actinobacteria and Bacteroidetes were strongly associated with BV. Our data describe a previously unrecognized extent of bacterial diversity in the vaginal ecosystem. The human vagina hosts many bacteria that are only distantly related to known species, and subjects with BV harbor particularly taxon-rich and diverse bacterial communities.

  8. Diversity of Human Vaginal Bacterial Communities and Associations with Clinically Defined Bacterial Vaginosis▿ †

    Science.gov (United States)

    Oakley, Brian B.; Fiedler, Tina L.; Marrazzo, Jeanne M.; Fredricks, David N.

    2008-01-01

    Bacterial vaginosis (BV) is a common syndrome associated with numerous adverse health outcomes in women. Despite its medical importance, the etiology and microbial ecology of BV remain poorly understood. We used broad-range PCR to census the community structure of the healthy and BV-affected vaginal microbial ecosystems and synthesized current publicly available bacterial 16S rRNA gene sequence data from this environment. The community of vaginal bacteria detected in subjects with BV was much more taxon rich and diverse than in subjects without BV. At a 97% sequence similarity cutoff, the number of operational taxonomic units (OTUs) per patient in 28 subjects with BV was nearly three times greater than in 13 subjects without BV: 14.8 ± 0.7 versus 5.2 ± 0.75 (mean ± standard error). OTU-based analyses revealed previously hidden diversity for many vaginal bacteria that are currently poorly represented in GenBank. Our sequencing efforts yielded many novel phylotypes (123 of our sequences represented 38 OTUs not previously found in the vaginal ecosystem), including several novel BV-associated OTUs, such as those belonging to the Prevotella species complex, which remain severely underrepresented in the current NCBI database. Community composition was highly variable among subjects at a fine taxonomic scale, but at the phylum level, Actinobacteria and Bacteroidetes were strongly associated with BV. Our data describe a previously unrecognized extent of bacterial diversity in the vaginal ecosystem. The human vagina hosts many bacteria that are only distantly related to known species, and subjects with BV harbor particularly taxon-rich and diverse bacterial communities. PMID:18487399

  9. Using the Community Land Model to Assess Uncertainty in Basin Scale GRACE-Based Groundwater Estimates

    Science.gov (United States)

    Swenson, S. C.; Lawrence, D. M.

    2015-12-01

    One method for interpreting the variability in total water storage observed by GRACE is to partition the integrated GRACE measurement into its component storage reservoirs based on information provided by hydrological models. Such models, often designed to be used in couple Earth System models, simulate the stocks and fluxes of moisture through the land surface and subsurface. One application of this method attempts to isolate groundwater changes by removing modeled surface water, snow, and soil moisture changes from GRACE total water storage estimates. Human impacts on groundwater variability can be estimated by further removing model estimates of climate-driven groundwater changes. Errors in modeled water storage components directly affect the residual groundwater estimates. Here we examine the influence of model structure and process representation on soil moisture and groundwater uncertainty using the Community Land Model, with a particular focus on basins in the western U.S.

  10. Endosymbiont dominated bacterial communities in a dwarf spider.

    Directory of Open Access Journals (Sweden)

    Bram Vanthournout

    Full Text Available The microbial community of spiders is little known, with previous studies focussing primarily on the medical importance of spiders as vectors of pathogenic bacteria and on the screening of known cytoplasmic endosymbiont bacteria. These screening studies have been performed by means of specific primers that only amplify a selective set of endosymbionts, hampering the detection of unreported species in spiders. In order to have a more complete overview of the bacterial species that can be present in spiders, we applied a combination of a cloning assay, DGGE profiling and high-throughput sequencing on multiple individuals of the dwarf spider Oedothorax gibbosus. This revealed a co-infection of at least three known (Wolbachia, Rickettsia and Cardinium and the detection of a previously unreported endosymbiont bacterium (Rhabdochlamydia in spiders. 16S rRNA gene sequences of Rhabdochlamydia matched closely with those of Candidatus R. porcellionis, which is currently only reported as a pathogen from a woodlouse and with Candidatus R. crassificans reported from a cockroach. Remarkably, this bacterium appears to present in very high proportions in one of the two populations only, with all investigated females being infected. We also recovered Acinetobacter in high abundance in one individual. In total, more than 99% of approximately 4.5M high-throughput sequencing reads were restricted to these five bacterial species. In contrast to previously reported screening studies of terrestrial arthropods, our results suggest that the bacterial communities in this spider species are dominated by, or even restricted to endosymbiont bacteria. Given the high prevalence of endosymbiont species in spiders, this bacterial community pattern could be widespread in the Araneae order.

  11. Glyphosate effects on soil rhizosphere-associated bacterial communities.

    Science.gov (United States)

    Newman, Molli M; Hoilett, Nigel; Lorenz, Nicola; Dick, Richard P; Liles, Mark R; Ramsier, Cliff; Kloepper, Joseph W

    2016-02-01

    Glyphosate is one of the most widely used herbicides in agriculture with predictions that 1.35 million metric tons will be used annually by 2017. With the advent of glyphosate tolerant (GT) cropping more than 10 years ago, there is now concern for non-target effects on soil microbial communities that has potential to negatively affect soil functions, plant health, and crop productivity. Although extensive research has been done on short-term response to glyphosate, relatively little information is available on long-term effects. Therefore, the overall objective was to investigate shifts in the rhizosphere bacterial community following long-term glyphosate application on GT corn and soybean in the greenhouse. In this study, rhizosphere soil was sampled from rhizoboxes following 4 growth periods, and bacterial community composition was compared between glyphosate treated and untreated rhizospheres using next-generation barcoded sequencing. In the presence or absence of glyphosate, corn and soybean rhizospheres were dominated by members of the phyla Proteobacteria, Acidobacteria, and Actinobacteria. Proteobacteria (particularly gammaproteobacteria) increased in relative abundance for both crops following glyphosate exposure, and the relative abundance of Acidobacteria decreased in response to glyphosate exposure. Given that some members of the Acidobacteria are involved in biogeochemical processes, a decrease in their abundance could lead to significant changes in nutrient status of the rhizosphere. Our results also highlight the need for applying culture-independent approaches in studying the effects of pesticides on the soil and rhizosphere microbial community.

  12. Bacterial endophytic communities in the grapevine depend on pest management.

    Science.gov (United States)

    Campisano, Andrea; Antonielli, Livio; Pancher, Michael; Yousaf, Sohail; Pindo, Massimo; Pertot, Ilaria

    2014-01-01

    Microbial plant endophytes are receiving ever-increasing attention as a result of compelling evidence regarding functional interaction with the host plant. Microbial communities in plants were recently reported to be influenced by numerous environmental and anthropogenic factors, including soil and pest management. In this study we used automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and pyrosequencing of 16S rDNA to assess the effect of organic production and integrated pest management (IPM) on bacterial endophytic communities in two widespread grapevines cultivars (Merlot and Chardonnay). High levels of the dominant Ralstonia, Burkholderia and Pseudomonas genera were detected in all the samples We found differences in the composition of endophytic communities in grapevines cultivated using organic production and IPM. Operational taxonomic units (OTUs) assigned to the Mesorhizobium, Caulobacter and Staphylococcus genera were relatively more abundant in plants from organic vineyards, while Ralstonia, Burkholderia and Stenotrophomonas were more abundant in grapevines from IPM vineyards. Minor differences in bacterial endophytic communities were also found in the grapevines of the two cultivars.

  13. Survival of bacterial indicators and the functional diversity of native microbial communities in the Floridan aquifer system, south Florida

    Science.gov (United States)

    Lisle, John T.

    2014-01-01

    model than when exposed to groundwater from the APPZ (range: 0.540–0.684 h-1). The inactivation rates for the first phase of the models for P. aeruginosa were not significantly different between the UFA (range: 0.144–0.770 h-1) and APPZ (range: 0.159–0.772 h-1) aquifer zones. The inactivation rates for the second phase of the model for this P. aeruginosa were also similar between UFA (range: 0.003–0.008 h-1) and APPZ (0.004–0.005 h-1) zones, although significantly slower than the model’s first phase rates for this bacterial species. Geochemical data were used to determine which dissimilatory biogeochemical reactions were most likely to occur under the native conditions in the UFA and APPZ zones using thermodynamics principles to calculate free energy yields and other cell-related energetics data. The biogeochemical processes of acetotrophic and hydrogenotrophic sulfate reduction, methanogenesis and anaerobic oxidation of methane dominated in all six groundwater sites. A high throughput DNA microarray sequencing technology was used to characterize the diversity in the native aquifer bacterial communities (bacteria and archaea) and assign putative physiological capabilities to the members of those communities. The bacterial communities in both zones of the aquifer were shown to possess the capabilities for primary and secondary fermentation, acetogenesis, methanogenesis, anaerobic methane oxidation, syntrophy with methanogens, ammonification, and sulfate reduction. The data from this study provide the first determination of bacterial indicator survival during exposure to native geochemical conditions of the Floridan aquifer in south Florida. Additionally, the energetics and functional bacterial diversity characterizations are the first descriptions of native bacterial communities in this region of the Floridan aquifer and reveal how these communities persist under such extreme conditions. Collectively, these types of data can be used to develop and refine

  14. Bacterial Communities Associated with Different Anthurium andraeanum L. Plant Tissues

    Science.gov (United States)

    Sarria-Guzmán, Yohanna; Chávez-Romero, Yosef; Gómez-Acata, Selene; Montes-Molina, Joaquín Adolfo; Morales-Salazar, Eleacin; Dendooven, Luc; Navarro-Noya, Yendi E.

    2016-01-01

    Plant-associated microbes have specific beneficial functions and are considered key drivers for plant health. The bacterial community structure of healthy Anthurium andraeanum L. plants was studied by 16S rRNA gene pyrosequencing associated with different plant parts and the rhizosphere. A limited number of bacterial taxa, i.e., Sinorhizobium, Fimbriimonadales, and Gammaproteobacteria HTCC2089 were enriched in the A. andraeanum rhizosphere. Endophytes were more diverse in the roots than in the shoots, whereas all shoot endophytes were found in the roots. Streptomyces, Flavobacterium succinicans, and Asteroleplasma were only found in the roots, Variovorax paradoxus only in the stem, and Fimbriimonas 97%-OTUs only in the spathe, i.e., considered specialists, while Brevibacillus, Lachnospiraceae, Pseudomonas, and Pseudomonas pseudoalcaligenes were generalist and colonized all plant parts. The anaerobic diazotrophic bacteria Lachnospiraceae, Clostridium sp., and Clostridium bifermentans colonized the shoot system. Phylotypes belonging to Pseudomonas were detected in the rhizosphere and in the substrate (an equiproportional mixture of soil, cow manure, and peat), and dominated the endosphere. Pseudomonas included nine 97%-OTUs with different patterns of distribution and phylogenetic affiliations with different species. P. pseudoalcaligenes and P. putida dominated the shoots, but were also found in the roots and rhizosphere. P. fluorescens was present in all plant parts, while P. resinovorans, P. denitrificans, P. aeruginosa, and P. stutzeri were only detected in the substrate and rhizosphere. The composition of plant-associated bacterial communities is generally considered to be suitable as an indicator of plant health. PMID:27524305

  15. Bacterial Communities of Three Saline Meromictic Lakes in Central Asia.

    Science.gov (United States)

    Baatar, Bayanmunkh; Chiang, Pei-Wen; Rogozin, Denis Yu; Wu, Yu-Ting; Tseng, Ching-Hung; Yang, Cheng-Yu; Chiu, Hsiu-Hui; Oyuntsetseg, Bolormaa; Degermendzhy, Andrey G; Tang, Sen-Lin

    2016-01-01

    Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium) were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance), Lake Shunet (~27.1%) and Lake Oigon (~9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity) were associated (P< 0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches.

  16. Biogas production using anaerobic groundwater containing a subterranean microbial community associated with the accretionary prism

    OpenAIRE

    Baito, Kyohei; Imai, Satomi; Matsushita, Makoto; Otani, Miku; Sato, Yu; Kimura, Hiroyuki

    2014-01-01

    In a deep aquifer associated with an accretionary prism, significant methane (CH4) is produced by a subterranean microbial community. Here, we developed bioreactors for producing CH4 and hydrogen (H2) using anaerobic groundwater collected from the deep aquifer. To generate CH4, the anaerobic groundwater amended with organic substrates was incubated in the bioreactor. At first, H2 was detected and accumulated in the gas phase of the bioreactor. After the H2 decreased, rapid CH4 production was ...

  17. Bacterial communities vary between sinuses in chronic rhinosinusitis patients

    Directory of Open Access Journals (Sweden)

    Tom V Joss

    2016-01-01

    Full Text Available Chronic rhinosinusitis (CRS is a common and potentially debilitating disease characterized by inflammation of the sinus mucosa for longer than 12 weeks. Bacterial colonization of the sinuses and its role in the pathogenesis of this disease is an ongoing area of research. Recent advances in culture-independent molecular techniques for bacterial identification have the potential to provide a more accurate and complete assessment of the sinus microbiome, however there is little concordance in results between studies, possibly due to differences in the sampling location and techniques. This study aimed to determine whether the microbial communities from one sinus could be considered representative of all sinuses, and examine differences between two commonly used methods for sample collection, swabs and tissue biopsies. High-throughput DNA sequencing of the bacterial 16S rRNA gene was applied to both swab and tissue samples from multiple sinuses of 19 patients undergoing surgery for treatment of CRS. Results from swabs and tissue biopsies showed a high degree of similarity, indicating that swabbing is sufficient to recover the microbial community from the sinuses. Microbial communities from different sinuses within individual patients differed to varying degrees, demonstrating that it is possible for distinct microbiomes to exist simultaneously in different sinuses of the same patient. The sequencing results correlated well with culture-based pathogen identification conducted in parallel, although the culturing missed many species detected by sequencing. This finding has implications for future research into the sinus microbiome, which should take this heterogeneity into account by sampling patients from more than one sinus. It may also be of clinical importance, as determination of antibiotic sensitivities using culture of a swab from a single sinus could miss relevant pathogens that are localized to another sinus.

  18. Viral impacts on bacterial communities in Arctic cryoconite

    DEFF Research Database (Denmark)

    Bellas, Christopher M.; Anesio, Alexandre M.; Telling, Jon;

    2013-01-01

    The surfaces of glaciers are extreme ecosystems dominated by microbial communities. Viruses are found in abundance here, with a high frequency of bacteria displaying visible virus infection. In this study, viral and bacterial production was measured in Arctic cryoconite holes to address the control......, virus production was found to be high, up to 8.98 x 10(7) virus like particles g(-1) dry wt. h(-1) were produced, which is comparable to virus production in sediments around the globe. The virus burst size was assessed by transmission electron microscopy and found to be amongst the lowest recorded...

  19. Bacterial growth and biofilm formation in household-stored groundwater collected from public wells.

    Science.gov (United States)

    Burkowska-But, Aleksandra; Kalwasińska, Agnieszka; Swiontek Brzezinska, Maria

    2015-06-01

    The research was aimed at assessing changes in the number of bacteria and evaluating biofilm formation in groundwater collected from public wells, both aspects directly related to the methods of household storage. In the research, water collected from Cretaceous aquifer wells in Toruń (Poland) was stored in a refrigerator and at room temperature. Microbiological parameters of the water were measured immediately after the water collection, and then after 3 and 7 days of storage under specified conditions. The microbiological examination involved determining the number of heterotrophic bacteria capable of growth at 22 and 37 °C, the number of spore-forming bacteria, and the total number of bacteria on membrane filters. The storage may affect water quality to such an extent that the water, which initially met the microbiological criteria for water intended for human consumption, may pose a health risk. The repeated use of the same containers for water storage results in biofilm formation containing live and metabolically active bacterial cells.

  20. Predictors of inferior outcome in community acquired bacterial meningitis.

    Science.gov (United States)

    Streharova, A; Krcmery, V; Kisac, P; Kalavsky, E; Holeckova, K; Lesnakova, A; Luzinsky, L; Adamkovicova, E; Pavlikova, Z; Spilakova, N; Kacunova, B; Dovalova, V; Wiczmandyova, O; Spanik, S; Liskova, A; Chovancova, D; Kovac, M; Ondrusova, A; Bauer, F; Benca, J; Rudinsky, B; Sramka, M; Kralova, J; Krsakova, J; Krumpolcova, M; Findova, L; Svabova, V; Sladeckova, V; Seckova, S; Saniova, J; Pavlicova, B; Taziarova, M; Bukovinova, P; Kolenova, A; Horvathova, E; Hvizdak, F; Luzica, R; Rolnikova, B; Bocakova, A; Grey, E; Bielova, M; Huttova, M; Sabo, I; Jalili, N

    2007-11-01

    The aim of this study was to assess mortality and sequellae within cases from Nationwide survey of community acquired meningitis and identify risk factors for inferior outcome. Risk factors such as underlying disease (diabetes mellitus, cancer, trauma, neonatal age, splenectomy, alcoholism, sepsis, other infections), etiology, clinical symptoms and outcome (death, improvement and cured after modifications of ATB therapy, cured without change of therapy, cured with neurologic sequellae) were recorded and analysed with univariate analysis (chi2 or t test for trends, CDC Atlanta 2004). Analysing risk factors for inferior outcome (death or cured with neurologic sequellae), we compared patients who died or survived with neurologic sequellae to all patients with community acquired bacterial meningitis. Univariate analysis showed that trauma (palcohol abuse (pdiabetes, S. aureus (pdiabetes mellitus (palcoholism (palcohol abuse (p<0.05), craniocerbral trauma (p<0.05) and less common in meningitis with pneumococcal etiology (p<0.05).

  1. [Prolonged cultivation of an anaerobic bacterial community producing hydrogen].

    Science.gov (United States)

    Belokopytov, B F; Ryzhmanova, Ia V; Laurinavichius, K S; Shcherbakova, V A

    2012-01-01

    This paper studies various methods of long-term maintenance of the process of hydrogen evolution during the growth of an aerobic bacterial community on a starch-containing environment. When cultured in separable trip fermentation mode for 72 days, from 0.10 to 0.23 H2/l of medium/day was formed. The regime of regular reseeding lasted more than 100 days, forming an average of 0.81 1 H2/l of medium/day. The advantages and disadvantages of different methods of microbial hydrogen production during a dark starch fermentation process are presented. From the obtained H2 forming microbial communities, we isolated an anaerobic spore-forming bacterium (strain BF). Phylogenetic analysis of the 16S RNA gene sequence of the new strain showed that according to its genotype it belongs to the Clostridium butyricum species.

  2. Plant community and soil chemistry responses to long-term nitrogen inputs drive changes in alpine bacterial communities.

    Science.gov (United States)

    Yuan, Xia; Knelman, Joseph E; Gasarch, Eve; Wang, Deli; Nemergut, Diana R; Seastedt, Timothy R

    2016-06-01

    Bacterial community composition and diversity was studied in alpine tundra soils across a plant species and moisture gradient in 20 y-old experimental plots with four nutrient addition regimes (control, nitrogen (N), phosphorus (P) or both nutrients). Different bacterial communities inhabited different alpine meadows, reflecting differences in moisture, nutrients and plant species. Bacterial community alpha-diversity metrics were strongly correlated with plant richness and the production of forbs. After meadow type, N addition proved the strongest determinant of bacterial community structure. Structural Equation Modeling demonstrated that tundra bacterial community responses to N addition occur via changes in plant community composition and soil pH resulting from N inputs, thus disentangling the influence of direct (resource availability) vs. indirect (changes in plant community structure and soil pH) N effects that have remained unexplored in past work examining bacterial responses to long-term N inputs in these vulnerable environments. Across meadow types, the relative influence of these indirect N effects on bacterial community structure varied. In explicitly evaluating the relative importance of direct and indirect effects of long-term N addition on bacterial communities, this study provides new mechanistic understandings of the interaction between plant and microbial community responses to N inputs amidst environmental change.

  3. Phylogenetic comparisons of bacterial communities from serpentine and nonserpentine soils.

    Science.gov (United States)

    Oline, David K

    2006-11-01

    I present the results of a culture-independent survey of soil bacterial communities from serpentine soils and adjacent nonserpentine comparator soils using a variety of newly developed phylogenetically based statistical tools. The study design included site-based replication of the serpentine-to-nonserpentine community comparison over a regional scale ( approximately 100 km) in Northern California and Southern Oregon by producing 16S rRNA clone libraries from pairs of samples taken on either side of the serepentine-nonserpentine edaphic boundary at three geographical sites. At the division level, the serpentine and nonserpentine communities were similar to each other and to previous data from forest soils. Comparisons of both richness and Shannon diversity produced no significant differences between any of the libraries, but the vast majority of phylogenetically based tests were significant, even with only 50 sequences per library. These results suggest that most samples were distinct, consisting of a collection of lineages generally not found in other samples. The pattern of results showed that serpentine communities tended to be more similar to each other than they were to nonserpentine communities, and these differences were at a lower taxonomic scale. Comparisons of two nonserpentine communities generally showed differences, and some results suggest that the geographical site may control community composition as well. These results show the power of phylogenetic tests to discern differences between 16S rRNA libraries compared to tests that discard DNA data to bin sequences into operational taxonomic units, and they stress the importance of replication at larger scales for inferences regarding microbial biogeography.

  4. COMPOSITION AND ACTIVITY OF BACTERIAL COMMUNITY OF COAL TAILING

    Directory of Open Access Journals (Sweden)

    Blayda I. A.

    2014-10-01

    Full Text Available The aim of this research was to study the composition of aboriginal bacterial community of coal tailing and to evaluate lixiviation activity of different groups of microorganisms belonging to this community. Using standard microbiological techniques we obtained and quantified the saving cultures of microorganisms from different physiological groups — filamentous fungi, heterotrophic microorganisms, mesophilic and thermophilic moderately acidophilic sulfur-oxidizing chemolithotrophic bacteria. Their oxidative activity was also established. The optimal results were achieved for collective leaching of rare and heavy metals into the solution under thermophilic conditions, which are favorable for the growth and activity of Sulfobacillus and under mesophilic conditions with the usage of ferrous iron as an energy substrate. This confirms the leading role of A. ferrooxidans in the processes of bacterial leaching of metals. Comparing our results with the available literature data we made a conclusion that the qualitative composition of acidophilic chemolithotrophic bacteria living in technogenic waste did not differ from the microbiocenose structure of natural sulfide ores.

  5. Bacterial community dynamics during the ensilage of wilted grass.

    Science.gov (United States)

    McEniry, J; O'Kiely, P; Clipson, N J W; Forristal, P D; Doyle, E M

    2008-08-01

    Grass silage is the product formed by a natural lactic acid bacterial fermentation when grass is stored under anaerobic conditions, and represents an important ruminant feedstuff on farms during winter. Of the two commonly employed methods of ensiling forage, baled silage composition frequently differs from that of comparable precision-chop silage reflecting a different ensiling environment. The aim of this study was to investigate the dynamics of the silage fermentation in wilted grass and between ensiling systems. Fermentation dynamics were examined using traditional methods of silage analyses, including microbial enumeration and analysis of fermentation products, and culture-independent terminal restriction fragment length polymorphism (T-RFLP). A successful fermentation was achieved in both systems, with the fermentation (increase in lactic acid bacteria and lactic acid concentration, decrease in pH) proceeding rapidly once the herbage was ensiled. Under controlled conditions, little difference in silage quality and microbial composition were observed between ensiling systems and this was further reflected in the T-RFLP community analysis. T-RFLP proved a potentially useful tool to study the ensilage process and could provide valid support to traditional methods, or a viable alternative to these methods, for investigating the dynamics of the bacterial community over the course of the fermentation.

  6. Protozoa Drive the Dynamics of Culturable Biocontrol Bacterial Communities.

    Directory of Open Access Journals (Sweden)

    Maren Stella Müller

    Full Text Available Some soil bacteria protect plants against soil-borne diseases by producing toxic secondary metabolites. Such beneficial biocontrol bacteria can be used in agricultural systems as alternative to agrochemicals. The broad spectrum toxins responsible for plant protection also inhibit predation by protozoa and nematodes, the main consumers of bacteria in soil. Therefore, predation pressure may favour biocontrol bacteria and contribute to plant health. We analyzed the effect of Acanthamoeba castellanii on semi-natural soil bacterial communities in a microcosm experiment. We determined the frequency of culturable bacteria carrying genes responsible for the production of the antifungal compounds 2,4-diacetylphloroglucinol (DAPG, pyrrolnitrin (PRN and hydrogen cyanide (HCN in presence and absence of A. castellanii. We then measured if amoebae affected soil suppressiveness in a bioassay with sugar beet seedlings confronted to the fungal pathogen Rhizoctonia solani. Amoebae increased the frequency of both DAPG and HCN positive bacteria in later plant growth phases (2 and 3 weeks, as well as the average number of biocontrol genes per bacterium. The abundance of DAPG positive bacteria correlated with disease suppression, suggesting that their promotion by amoebae may enhance soil health. However, the net effect of amoebae on soil suppressiveness was neutral to slightly negative, possibly because amoebae slow down the establishment of biocontrol bacteria on the recently emerged seedlings used in the assay. The results indicate that microfaunal predators foster biocontrol bacterial communities. Understanding interactions between biocontrol bacteria and their predators may thus help developing environmentally friendly management practices of agricultural systems.

  7. The structure and functions of bacterial communities in an agrocenosis

    Science.gov (United States)

    Dobrovol'skaya, T. G.; Khusnetdinova, K. A.; Manucharova, N. A.; Balabko, P. N.

    2016-01-01

    The most significant factor responsible for the specific taxonomic composition of the bacterial communities in the agrocenosis studied was found to be a part or organ of plants (leaves, flowers, roots, fruits). A stage of plant ontogeny also determines changes of taxa. In the course of the plant growth, eccrisotrophic bacteria are replaced by hydrolytic ones that belong to the group of cellulose-decomposing bacteria. Representatives of the proteobacteria genera that are difficult to identify by phenotypic methods were determined using molecular-biological methods. They were revealed only on oat leaves in the moist period. As the vetch-oat mixture was fertilized with BIOUD-1 (foliar application) in the phyllosphere of both oats and vetch, on all the plant organs, representatives of the Rhodococcus genus as dominants were isolated. This fact was related to the capability of bacteria to decompose the complex aromatic compounds that are ingredients of the fertilizers applied. Another positive effect for plants of the bacterial communities forming in agrocenoses is the presence of bacteria that are antagonists of phytopathogenic bacteria. Thus, in agrocenoses, some interrelationships promoting the growth and reproduction of plants are formed in crop plants and bacteria.

  8. Protozoa Drive the Dynamics of Culturable Biocontrol Bacterial Communities.

    Science.gov (United States)

    Müller, Maren Stella; Scheu, Stefan; Jousset, Alexandre

    2013-01-01

    Some soil bacteria protect plants against soil-borne diseases by producing toxic secondary metabolites. Such beneficial biocontrol bacteria can be used in agricultural systems as alternative to agrochemicals. The broad spectrum toxins responsible for plant protection also inhibit predation by protozoa and nematodes, the main consumers of bacteria in soil. Therefore, predation pressure may favour biocontrol bacteria and contribute to plant health. We analyzed the effect of Acanthamoeba castellanii on semi-natural soil bacterial communities in a microcosm experiment. We determined the frequency of culturable bacteria carrying genes responsible for the production of the antifungal compounds 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin (PRN) and hydrogen cyanide (HCN) in presence and absence of A. castellanii. We then measured if amoebae affected soil suppressiveness in a bioassay with sugar beet seedlings confronted to the fungal pathogen Rhizoctonia solani. Amoebae increased the frequency of both DAPG and HCN positive bacteria in later plant growth phases (2 and 3 weeks), as well as the average number of biocontrol genes per bacterium. The abundance of DAPG positive bacteria correlated with disease suppression, suggesting that their promotion by amoebae may enhance soil health. However, the net effect of amoebae on soil suppressiveness was neutral to slightly negative, possibly because amoebae slow down the establishment of biocontrol bacteria on the recently emerged seedlings used in the assay. The results indicate that microfaunal predators foster biocontrol bacterial communities. Understanding interactions between biocontrol bacteria and their predators may thus help developing environmentally friendly management practices of agricultural systems.

  9. Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities.

    Directory of Open Access Journals (Sweden)

    Sebastian Germerodt

    2016-06-01

    Full Text Available Bacterial communities are taxonomically highly diverse, yet the mechanisms that maintain this diversity remain poorly understood. We hypothesized that an obligate and mutual exchange of metabolites, as is very common among bacterial cells, could stabilize different genotypes within microbial communities. To test this, we developed a cellular automaton to model interactions among six empirically characterized genotypes that differ in their ability and propensity to produce amino acids. By systematically varying intrinsic (i.e. benefit-to-cost ratio and extrinsic parameters (i.e. metabolite diffusion level, environmental amino acid availability, we show that obligate cross-feeding of essential metabolites is selected for under a broad range of conditions. In spatially structured environments, positive assortment among cross-feeders resulted in the formation of cooperative clusters, which limited exploitation by non-producing auxotrophs, yet allowed them to persist at the clusters' periphery. Strikingly, cross-feeding helped to maintain genotypic diversity within populations, while amino acid supplementation to the environment decoupled obligate interactions and favored auxotrophic cells that saved amino acid production costs over metabolically autonomous prototrophs. Together, our results suggest that spatially structured environments and limited nutrient availabilities should facilitate the evolution of metabolic interactions, which can help to maintain genotypic diversity within natural microbial populations.

  10. Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure

    Directory of Open Access Journals (Sweden)

    Wouter A. A. de Steenhuijsen Piters

    2016-03-01

    Full Text Available The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem—also called “microbiome”—is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1:e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting.

  11. Phylogenetically and Spatially Close Marine Sponges Harbour Divergent Bacterial Communities

    Science.gov (United States)

    Hardoim, Cristiane C. P.; Esteves, Ana I. S.; Pires, Francisco R.; Gonçalves, Jorge M. S.; Cox, Cymon J.; Xavier, Joana R.; Costa, Rodrigo

    2012-01-01

    Recent studies have unravelled the diversity of sponge-associated bacteria that may play essential roles in sponge health and metabolism. Nevertheless, our understanding of this microbiota remains limited to a few host species found in restricted geographical localities, and the extent to which the sponge host determines the composition of its own microbiome remains a matter of debate. We address bacterial abundance and diversity of two temperate marine sponges belonging to the Irciniidae family - Sarcotragus spinosulus and Ircinia variabilis – in the Northeast Atlantic. Epifluorescence microscopy revealed that S. spinosulus hosted significantly more prokaryotic cells than I. variabilis and that prokaryotic abundance in both species was about 4 orders of magnitude higher than in seawater. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) profiles of S. spinosulus and I. variabilis differed markedly from each other – with higher number of ribotypes observed in S. spinosulus – and from those of seawater. Four PCR-DGGE bands, two specific to S. spinosulus, one specific to I. variabilis, and one present in both sponge species, affiliated with an uncultured sponge-specific phylogenetic cluster in the order Acidimicrobiales (Actinobacteria). Two PCR-DGGE bands present exclusively in S. spinosulus fingerprints affiliated with one sponge-specific phylogenetic cluster in the phylum Chloroflexi and with sponge-derived sequences in the order Chromatiales (Gammaproteobacteria), respectively. One Alphaproteobacteria band specific to S. spinosulus was placed in an uncultured sponge-specific phylogenetic cluster with a close relationship to the genus Rhodovulum. Our results confirm the hypothesized host-specific composition of bacterial communities between phylogenetically and spatially close sponge species in the Irciniidae family, with S. spinosulus displaying higher bacterial community diversity and distinctiveness than I. variabilis. These

  12. Phylogenetically and spatially close marine sponges harbour divergent bacterial communities.

    Directory of Open Access Journals (Sweden)

    Cristiane C P Hardoim

    Full Text Available Recent studies have unravelled the diversity of sponge-associated bacteria that may play essential roles in sponge health and metabolism. Nevertheless, our understanding of this microbiota remains limited to a few host species found in restricted geographical localities, and the extent to which the sponge host determines the composition of its own microbiome remains a matter of debate. We address bacterial abundance and diversity of two temperate marine sponges belonging to the Irciniidae family--Sarcotragus spinosulus and Ircinia variabilis--in the Northeast Atlantic. Epifluorescence microscopy revealed that S. spinosulus hosted significantly more prokaryotic cells than I. variabilis and that prokaryotic abundance in both species was about 4 orders of magnitude higher than in seawater. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE profiles of S. spinosulus and I. variabilis differed markedly from each other--with higher number of ribotypes observed in S. spinosulus--and from those of seawater. Four PCR-DGGE bands, two specific to S. spinosulus, one specific to I. variabilis, and one present in both sponge species, affiliated with an uncultured sponge-specific phylogenetic cluster in the order Acidimicrobiales (Actinobacteria. Two PCR-DGGE bands present exclusively in S. spinosulus fingerprints affiliated with one sponge-specific phylogenetic cluster in the phylum Chloroflexi and with sponge-derived sequences in the order Chromatiales (Gammaproteobacteria, respectively. One Alphaproteobacteria band specific to S. spinosulus was placed in an uncultured sponge-specific phylogenetic cluster with a close relationship to the genus Rhodovulum. Our results confirm the hypothesized host-specific composition of bacterial communities between phylogenetically and spatially close sponge species in the Irciniidae family, with S. spinosulus displaying higher bacterial community diversity and distinctiveness than I. variabilis

  13. Understanding the bacterial communities of hard cheese with blowing defect.

    Science.gov (United States)

    Bassi, Daniela; Puglisi, Edoardo; Cocconcelli, Pier Sandro

    2015-12-01

    The environment of hard cheese encourages bacterial synergies and competitions along the ripening process, which might lead in defects such as clostridial blowing. In this study, Denaturing Gradient Gel Electrophoresis (DGGE), a quantitative Clostridium tyrobutyricum PCR and next-generation Illumina-based sequencing of 16S rRNA gene were applied to study 83 Grana Padano spoiled samples. The aim was to investigate the community of clostridia involved in spoilage, the ecological relationships with the other members of the cheese microbiota, and the effect of lysozyme. Three main genera were dominant in the analysed cheeses, Lactobacillus, Streptococcus and Clostridium, and the assignment at the species level was of 94.3% of 4,477,326 high quality sequences. C. tyrobutyricum and C. butyricum were the most prevalent clostridia. Hierarchical clustering based on the abundance of bacterial genera, revealed three main clusters: one characterized by the highest proportion of Clostridium, a second where Lactobacillus was predominant and the last, dominated by Streptococcus thermophilus. Ecological relationships among species were found: cheeses characterized by an high abundance of S. thermophilus and L. rhamnosus were spoiled by C. tyrobutyricum while, when L. delbrueckii was the most abundant Lactobacillus, C. butyricum was the dominant spoiling species. Lysozyme also shaped the bacterial community, reducing C. tyrobutyricum in favour of C. butyricum. Moreover, this preservative increased the proportion of L. delbrueckii and obligate heterofermentative lactobacilli and lowered L. helveticus and non-starter species, such as L. rhamnosus and L. casei.

  14. Bacterial symbionts in insects or the story of communities affecting communities.

    Science.gov (United States)

    Ferrari, Julia; Vavre, Fabrice

    2011-05-12

    Bacterial symbionts are widespread in insects and other animals. Most of them are predominantly vertically transmitted, along with their hosts' genes, and thus extend the heritable genetic variation present in one species. These passengers have a variety of repercussions on the host's phenotypes: besides the cost imposed on the host for maintaining the symbiont population, they can provide fitness advantages to the host or manipulate the host's reproduction. We argue that insect symbioses are ideal model systems for community genetics. First, bacterial symbionts directly or indirectly affect the interactions with other species within a community. Examples include their involvement in modifying the use of host plants by phytophagous insects, in providing resistance to natural enemies, but also in reducing the global genetic diversity or gene flow between populations within some species. Second, one emerging picture in insect symbioses is that many species are simultaneously infected with more than one symbiont, which permits studying the factors that shape bacterial communities; for example, horizontal transmission, interactions between host genotype, symbiont genotype and the environment and interactions among symbionts. One conclusion is that insects' symbiotic complements are dynamic communities that affect and are affected by the communities in which they are embedded.

  15. Bacterial and protist community changes during a phytoplankton bloom

    KAUST Repository

    Pearman, John K.

    2015-10-01

    The present study aims to characterize the change in the composition and structure of the bacterial and microzooplankton planktonic communities in relation to the phytoplankton community composition during a bloom. High-throughput amplicon sequencing of regions of the 16S and 18S rRNA gene was undertaken on samples collected during a 20 day (d) mesocosm experiment incorporating two different nutrient addition treatments [Nitrate and Phosphate (NPc) and Nitrate, Phosphate and Silicate (NPSc)] as well as a control. This approach allowed us to discriminate the changes in species composition across a broad range of phylogenetic groups using a common taxonomic level. Diatoms dominated the bloom in the NPSc treatment while dinoflagellates were the dominant phytoplankton in the control and NPc treatment. Network correlations highlighted significant interactions between OTUs within each treatment including changes in the composition of Paraphysomonas OTUs when the dominant Chaetoceros OTU switched. The microzooplankton community composition responded to changes in the phytoplankton composition while the prokaryotic community responded more to changes in ammonia concentration.

  16. Associations between bacterial communities of house dust and infant gut

    Energy Technology Data Exchange (ETDEWEB)

    Konya, T.; Koster, B. [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada); Maughan, H. [Department of Cell and Systems Biology, University of Toronto (Canada); Escobar, M. [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada); Azad, M.B. [Department of Pediatrics, University of Alberta (Canada); Guttman, D.S. [Department of Cell and Systems Biology, University of Toronto (Canada); Sears, M.R. [Department of Medicine, McMaster University (Canada); Becker, A.B. [University of Manitoba (Canada); Brook, J.R. [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada); Environment Canada (Canada); Takaro, T.K. [Faculty of Health Science, Simon Fraser University (Canada); Kozyrskyj, A.L. [Department of Pediatrics, University of Alberta (Canada); Scott, J.A., E-mail: james.scott@utoronto.ca [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada)

    2014-05-01

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust–stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership.

  17. Associations between bacterial communities of house dust and infant gut.

    Science.gov (United States)

    Konya, T; Koster, B; Maughan, H; Escobar, M; Azad, M B; Guttman, D S; Sears, M R; Becker, A B; Brook, J R; Takaro, T K; Kozyrskyj, A L; Scott, J A

    2014-05-01

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust-stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership.

  18. Assisting community management of groundwater: Irrigator attitudes in two watersheds in Rajasthan and Gujarat, India

    Science.gov (United States)

    Varua, M. E.; Ward, J.; Maheshwari, B.; Oza, S.; Purohit, R.; Hakimuddin; Chinnasamy, P.

    2016-06-01

    The absence of either state regulations or markets to coordinate the operation of individual wells has focussed attention on community level institutions as the primary loci for sustainable groundwater management in Rajasthan and Gujarat, India. The reported research relied on theoretical propositions that livelihood strategies, groundwater management and the propensity to cooperate are associated with the attitudinal orientations of well owners in the Meghraj and Dharta watersheds, located in Gujarat and Rajasthan respectively. The research tested the hypothesis that attitudes to groundwater management and farming practices, household income and trust levels of assisting agencies were not consistent across the watersheds, implying that a targeted approach, in contrast to default uniform programs, would assist communities craft rules to manage groundwater across multiple hydro-geological settings. Hierarchical cluster analysis of attitudes held by survey respondents revealed four statistically significant discrete clusters, supporting acceptance of the hypothesis. Further analyses revealed significant differences in farming practices, household wealth and willingness to adapt across the four groundwater management clusters. In conclusion, the need to account for attitudinal diversity is highlighted and a framework to guide the specific design of processes to assist communities craft coordinating instruments to sustainably manage local aquifers described.

  19. Responses of Baltic Sea ice and open-water natural bacterial communities to salinity change.

    Science.gov (United States)

    Kaartokallio, Hermanni; Laamanen, Maria; Sivonen, Kaarina

    2005-08-01

    To investigate the responses of Baltic Sea wintertime bacterial communities to changing salinity (5 to 26 practical salinity units), an experimental study was conducted. Bacterial communities of Baltic seawater and sea ice from a coastal site in southwest Finland were used in two batch culture experiments run for 17 or 18 days at 0 degrees C. Bacterial abundance, cell volume, and leucine and thymidine incorporation were measured during the experiments. The bacterial community structure was assessed using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rRNA genes with sequencing of DGGE bands from initial communities and communities of day 10 or 13 of the experiment. The sea ice-derived bacterial community was metabolically more active than the open-water community at the start of the experiment. Ice-derived bacterial communities were able to adapt to salinity change with smaller effects on physiology and community structure, whereas in the open-water bacterial communities, the bacterial cell volume evolution, bacterial abundance, and community structure responses indicated the presence of salinity stress. The closest relatives for all eight partial 16S rRNA gene sequences obtained were either organisms found in polar sea ice and other cold habitats or those found in summertime Baltic seawater. All sequences except one were associated with the alpha- and gamma-proteobacteria or the Cytophaga-Flavobacterium-Bacteroides group. The overall physiological and community structure responses were parallel in ice-derived and open-water bacterial assemblages, which points to a linkage between community structure and physiology. These results support previous assumptions of the role of salinity fluctuation as a major selective factor shaping the sea ice bacterial community structure.

  20. Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest.

    Science.gov (United States)

    Kembel, Steven W; O'Connor, Timothy K; Arnold, Holly K; Hubbell, Stephen P; Wright, S Joseph; Green, Jessica L

    2014-09-23

    The phyllosphere--the aerial surfaces of plants, including leaves--is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density-growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant-microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function.

  1. Vaginal and Uterine Bacterial Communities in Postpartum Lactating Cows

    Directory of Open Access Journals (Sweden)

    Brooke A. Clemmons

    2017-06-01

    abundance of unassigned taxa found in the uterus may play a significant biological role in the reproductive status of the animal. The study represents an initial dataset for comparing bacterial communities prior to establishment of pregnancy.

  2. Highly heterogeneous soil bacterial communities around Terra Nova Bay of Northern Victoria Land, Antarctica.

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    Mincheol Kim

    Full Text Available Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment.

  3. Impact of oil on bacterial community structure in bioturbated sediments.

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    Magalie Stauffert

    Full Text Available Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions--with tidal cycles and natural seawater--was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g⁻¹ wet sediment, the common burrowing organism Hediste (Nereis diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by

  4. Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters

    DEFF Research Database (Denmark)

    Gülay, Arda; Musovic, Sanin; Albrechtsen, Hans-Jørgen

    2016-01-01

    Here, we document microbial communities in rapid gravity filtration units, specifically serial rapid sand filters (RSFs), termed prefilters (PFs) and after- filters (AFs), fed with anoxic groundwaters low in organic carbon to prepare potable waters. A comprehensive 16S rRNA-based amplicon...

  5. The dynamics of the bacterial communities developed in maize silage.

    Science.gov (United States)

    Gharechahi, Javad; Kharazian, Zohreh Akhavan; Sarikhan, Sajjad; Jouzani, Gholamreza Salehi; Aghdasi, Mahnaz; Hosseini Salekdeh, Ghasem

    2017-07-11

    Ensilage provides an effective means of conserving summer-grown green forage to supply as winter feed to ruminants. The fermentation process involved in the ensilage process relies on lactic acid bacteria (LAB). Here, 16S ribosomal DNA amplicon pyrosequencing was used to follow the dynamic behaviour of the LAB community during the ensilage of maize biomass, with a view to identify the key species involved in the process. The biomass used for ensilage was a single-cross maize hybrid, harvested at the milk-line stage. The crop was grown at three contrasting locations. Aspects of the physico-chemical composition of the material and the LAB species present were sampled at 0, 3, 6, 14, 21 and 32 days after ensilage was initiated. In all three cases, members of the Leuconostocaceae family dominated the epiphytic bacterial community, notably Leuconostoc and Weissella, but some variation was noted in the abundance of certain Leuconostocaceae and Lactobacillaceae species, as well as that of some Acetobacteraceae, Enterobacteriaceae and Moraxellaceae species. The constellation of the microbiome which developed during the ensilage process differed markedly from that of the epiphytic one, with Lactobacillaceae, particularly Lactobacillus and Pediococcus spp. dominating. The abundance of heterofermentative Leuconostocaceae spp. in the epiphytic community and the extent of the transition from hetero- to homo-fermentation during the initial ensilage period are important factors in determining silage quality. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  6. Links between Plant and Rhizoplane Bacterial Communities in Grassland Soils, Characterized Using Molecular Techniques

    Science.gov (United States)

    Nunan, Naoise; Daniell, Timothy J.; Singh, Brajesh K.; Papert, Artemis; McNicol, James W.; Prosser, James I.

    2005-01-01

    Molecular analysis of grassland rhizosphere soil has demonstrated complex and diverse bacterial communities, with resultant difficulties in detecting links between plant and bacterial communities. These studies have, however, analyzed “bulk” rhizosphere soil, rather than rhizoplane communities, which interact most closely with plants through utilization of root exudates. The aim of this study was to test the hypothesis that plant species was a major driver for bacterial rhizoplane community composition on individual plant roots. DNA extracted from individual roots was used to determine plant identity, by analysis of the plastid tRNA leucine (trnL) UAA gene intron, and plant-related bacterial communities. Bacterial communities were characterized by analysis of PCR-amplified 16S rRNA genes using two fingerprinting methods: terminal restriction fragment length polymorphisms (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). Links between plant and bacterial rhizoplane communities could not be detected by visual examination of T-RFLP patterns or DGGE banding profiles. Statistical analysis of fingerprint patterns did not reveal a relationship between bacterial community composition and plant species but did demonstrate an influence of plant community composition. The data also indicated that topography and other, uncharacterized, environmental factors are important in driving bacterial community composition in grassland soils. T-RFLP had greater potential resolving power than DGGE, but findings from the two methods were not significantly different. PMID:16269710

  7. Initial community and environment determine the response of bacterial communities to dispersant and oil contamination.

    Science.gov (United States)

    Ortmann, Alice C; Lu, YueHan

    2015-01-15

    Bioremediation of seawater by natural bacterial communities is one potential response to coastal oil spills, but the success of the approach may vary, depending on geographical location, oil composition and the timing of spill. The short term response of coastal bacteria to dispersant, oil and dispersed oil was characterized using 16S rRNA gene tags in two mesocosm experiments conducted two months apart. Despite differences in the amount of oil-derived alkanes across the treatments and experiments, increases in the contributions of hydrocarbon degrading taxa and decreases in common estuarine bacteria were observed in response to dispersant and/or oil. Between the two experiments, the direction and rates of changes in particulate alkane concentrations differed, as did the magnitude of the bacterial response to oil and/or dispersant. Together, our data underscore large variability in bacterial responses to hydrocarbon pollutants, implying that bioremediation success varies with starting biological and environmental conditions.

  8. Groundwater abstraction management in Sana'a Basin, Yemen: a local community approach

    Science.gov (United States)

    Taher, Taha M.

    2016-09-01

    Overexploitation of groundwater resources in Sana'a Basin, Yemen, is causing severe water shortages associated water quality degradation. Groundwater abstraction is five times higher than natural recharge and the water-level decline is about 4-8 m/year. About 90 % of the groundwater resource is used for agricultural activities. The situation is further aggravated by the absence of a proper water-management approach for the Basin. Water scarcity in the Wadi As-Ssirr catchment, the study area, is the most severe and this area has the highest well density (average 6.8 wells/km2) compared with other wadi catchments. A local scheme of groundwater abstraction redistribution is proposed, involving the retirement of a substantial number of wells. The scheme encourages participation of the local community via collective actions to reduce the groundwater overexploitation, and ultimately leads to a locally acceptable, manageable groundwater abstraction pattern. The proposed method suggests using 587 wells rather than 1,359, thus reducing the well density to 2.9 wells/km2. Three scenarios are suggested, involving different reductions to the well yields and/or the number of pumping hours for both dry and wet seasons. The third scenario is selected as a first trial for the communities to action; the resulting predicted reduction, by 2,371,999 m3, is about 6 % of the estimated annual demand. Initially, the groundwater abstraction volume should not be changed significantly until there are protective measures in place, such as improved irrigation efficiency, with the aim of increasing the income of farmers and reducing water use.

  9. Metagenomic data of free cyanide and thiocyanate degrading bacterial communities

    Directory of Open Access Journals (Sweden)

    Lukhanyo Mekuto

    2017-08-01

    Full Text Available The data presented in this article contains the bacterial community structure of the free cyanide (CN- and thiocyanate (SCN- degrading organisms that were isolated from electroplating wastewater and synthetic SCN- containing wastewater. PCR amplification of the 16S rRNA V1-V3 regions was undertaken using the 27F and 518R oligonucleotide primers following the metacommunity DNA extraction procedure. The PCR amplicons were processed using the illumina® reaction kits as per manufacturer׳s instruction and sequenced using the illumina® MiSeq-2000, using the MiSeq V3 kit. The data was processed using bioinformatics tools such as QIIME and the raw sequence files are available via NCBI׳s Sequence Read Archive (SRA database.

  10. Boom clay borehole water, home of a diverse bacterial community

    Energy Technology Data Exchange (ETDEWEB)

    Wouters, Katinka; Moors, Hugo; Leys, Natalie [Belgian Nuclear Research Centre (SCK-CEN), Mol (Belgium)

    2013-07-01

    For over two decades, Boom Clay has been studied in the framework of geological disposal of nuclear waste thereby mainly addressing its geochemical properties. Today, also the microbiological properties and the possibility of microbes interacting with radionuclides or repository components including the waste form, in a host formation like Boom Clay are considered [2,3]. In the past, a reference composition for synthetic Boom Clay pore water (BCPW) was derived, based on interstitial water sampled from different layers within the Boom clay [1]. Similarly, the primary aim of this microbiological study was to determine the core BCPW bacterial community and identify representative water samples for future microbial directed lab experiments. In this respect, BCPW was sampled from different Boom Clay layers using the Morpheus piezometer and subsequently analysed by microscopy and molecular techniques, in search for overall shared and abundant micro-organisms. (authors)

  11. Dynamics of bacterial community in the gut of Cornu aspersum

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    ZDRAVKA KOLEVA

    2015-12-01

    Full Text Available The dynamics of the bacterial community in the intestinal tract of Cornu aspersum was investigated during different states of its life cycle. Two approaches were applied – culture and non-culture. The non-culture approach was performed by ARDRA of 16S rDNA using two of the six tested endonucleases. Data were analyzed by hierarchical cluster analysis. The restriction of 16S rDNA samples from the snail of different physiological states with endonucleases HinfI and Csp6I resulted in generation of different profiles depending on the snail states. By the culture approach we found that the total number of cultivable bacteria, representatives of Enterobacteriaceae, lactic acid bacteria, amylolitic and cellulolytic bacteria were the most abundant in active state of the snails. Cellulolytic bacteria were not detected in juveniles of C. aspersum. Escherichia coli, Clostridium perfringens as well as bacteria from the genus Salmonella, Shigella and Pseudomonas were not detected. Bacteria of the genus Aeromonas were found in juveniles of C. aspersum, after that their number decrease and were not found in hibernating snails. On the base of the two applied approaches this study shows that the bacterial flora in the intestinal tract of C. aspersum is affected by the seasonal and environmental variations and undergoes quantitative and qualitative changes during the different states of the life cycle. The snails harbor in their gut intestinal bacteria, which possess biochemical potentiality to degrade the plant components.

  12. Viral impacts on bacterial communities in Arctic cryoconite

    DEFF Research Database (Denmark)

    Bellas, Christopher M.; Anesio, Alexandre M.; Telling, Jon

    2013-01-01

    The surfaces of glaciers are extreme ecosystems dominated by microbial communities. Viruses are found in abundance here, with a high frequency of bacteria displaying visible virus infection. In this study, viral and bacterial production was measured in Arctic cryoconite holes to address the control...... that viruses play in these highly truncated ecosystems. Mean bacterial carbon production in the sediments of cryoconite holes was found to be 57.8 +/- 12.9 ng C g(-1) dry wt. h(-1), which predicted a mean of 1.89-5.41 x 10(6) cells g(-1) dry wt. h(-1) based on a range of conversion factors. Relative to this......, virus production was found to be high, up to 8.98 x 10(7) virus like particles g(-1) dry wt. h(-1) were produced, which is comparable to virus production in sediments around the globe. The virus burst size was assessed by transmission electron microscopy and found to be amongst the lowest recorded...

  13. Co-acclimation of bacterial communities under stresses of hydrocarbons with different structures

    Science.gov (United States)

    Wang, Hui; Wang, Bin; Dong, Wenwen; Hu, Xiaoke

    2016-10-01

    Crude oil is a complex mixture of hydrocarbons with different structures; its components vary in bioavailability and toxicity. It is important to understand how bacterial communities response to different hydrocarbons and their co-acclimation in the process of degradation. In this study, microcosms with the addition of structurally different hydrocarbons were setup to investigate the successions of bacterial communities and the interactions between different bacterial taxa. Hydrocarbons were effectively degraded in all microcosms after 40 days. High-throughput sequencing offered a great quantity of data for analyzing successions of bacterial communities. The results indicated that the bacterial communities responded dramatically different to various hydrocarbons. KEGG database and PICRUSt were applied to predict functions of individual bacterial taxa and networks were constructed to analyze co-acclimations between functional bacterial groups. Almost all functional genes catalyzing degradation of different hydrocarbons were predicted in bacterial communities. Most of bacterial taxa were believed to conduct biodegradation processes via interactions with each other. This study addressed a few investigated area of bacterial community responses to structurally different organic pollutants and their co-acclimation and interactions in the process of biodegradation. The study could provide useful information to guide the bioremediation of crude oil pollution.

  14. Influences of plant type on bacterial and archaeal communities in constructed wetland treating polluted river water.

    Science.gov (United States)

    Long, Yan; Yi, Hao; Chen, Sili; Zhang, Zhengke; Cui, Kai; Bing, Yongxin; Zhuo, Qiongfang; Li, Bingxin; Xie, Shuguang; Guo, Qingwei

    2016-10-01

    Both bacteria and archaeal communities can play important roles in biogeochemical processes in constructed wetland (CW) system. However, the influence of plant type on microbial community in surface water CW remains unclear. The present study investigated bacterial and archaeal communities in five surface water CW systems with different plant species. The abundance, richness, and diversity of both bacterial and archaeal communities considerably differed in these five CW systems. Compared with the other three CW systems, the CW systems planted with Vetiveria zizanioides or Juncus effusus L. showed much higher bacterial abundance but lower archaeal abundance. Bacteria outnumbered archaea in each CW system. Moreover, the CW systems planted with V. zizanioides or J. effusus L. had relatively lower archaeal but higher bacterial richness and diversity. In each CW system, bacterial community displayed much higher richness and diversity than archaeal community. In addition, a remarkable difference of both bacterial and archaeal community structures was observed in the five studied CW systems. Proteobacteria was the most abundant bacterial group (accounting for 33-60 %). Thaumarchaeota organisms (57 %) predominated in archaeal communities in CW systems planted with V. zizanioides or J. effusus L., while Woesearchaeota (23 or 24 %) and Euryarchaeota (23 or 15 %) were the major archaeal groups in CW systems planted with Cyperus papyrus or Canna indica L. Archaeal community in CW planted with Typha orientalis Presl was mainly composed of unclassified archaea. Therefore, plant type exerted a considerable influence on microbial community in surface water CW system.

  15. Local and regional factors influencing bacterial community assembly.

    Science.gov (United States)

    Lindström, Eva S; Langenheder, Silke

    2012-02-01

    The classical view states that microbial biogeography is not affected by dispersal barriers or historical events, but only influenced by the local contemporary habitat conditions (species sorting). This has been challenged during recent years by studies suggesting that also regional factors such as mass effect, dispersal limitation and neutral assembly are important for the composition of local bacterial communities. Here we summarize results from biogeography studies in different environments, i.e. in marine, freshwater and soil as well in human hosts. Species sorting appears to be the most important mechanism. However, this result might be biased since this is the mechanism that is easiest to measure, detect and interpret. Hence, the importance of regional factors may have been underestimated. Moreover, our survey indicates that different assembly mechanisms might be important for different parts of the total community, differing, for example, between generalists and specialists, and between taxa of different dispersal ability and motility. We conclude that there is a clear need for experimental studies, first, to clearly separate regional and local factors in order to study their relative importance, and second, to test whether there are differences in assembly mechanisms depending on different taxonomic or functional groups.

  16. Bacterial communities involved in sulfur transformations in wastewater treatment plants.

    Science.gov (United States)

    Meyer, Daniel Derrossi; de Andrade, Pedro Avelino Maia; Durrer, Ademir; Andreote, Fernando Dini; Corção, Gertrudes; Brandelli, Adriano

    2016-12-01

    The main sulfate-reducing (SRB) and sulfur-oxidizing bacteria (SOB) in six wastewater treatment plants (WWTPs) located at southern Brazil were described based on high-throughput sequencing of the 16S rDNA. Specific taxa of SRB and SOB were correlated with some abiotic factors, such as the source of the wastewater, oxygen content, sample type, and physical chemical attributes of these WWTPs. When the 22 families of SRB and SOB were clustered together, the samples presented a striking distribution, demonstrating grouping patterns according to the sample type. For SOB, the most abundant families were Spirochaetaceae, Chromatiaceae, Helicobacteriaceae, Rhodospirillaceae, and Neisseriaceae, whereas, for SRB, were Syntrophaceae, Desulfobacteraceae, Nitrospiraceae, and Desulfovibriaceae. The structure and composition of the major families related to the sulfur cycle were also influenced by six chemical attributes (sulfur, potassium, zinc, manganese, phosphorus, and nitrogen). Sulfur was the chemical attribute that most influenced the variation of bacterial communities in the WWTPs (λ = 0.14, p = 0.008). The OTUs affiliated to Syntrophus showed the highest response to the increase of total sulfur. All these findings can contribute to improve the understanding in relation to the sulfur-oxidizing and sulfate-reducing communities in WWTPs aiming to reduce H2S emissions.

  17. Metabolic Complementation in Bacterial Communities: Necessary Conditions and Optimality

    Science.gov (United States)

    Mori, Matteo; Ponce-de-León, Miguel; Peretó, Juli; Montero, Francisco

    2016-01-01

    Bacterial communities may display metabolic complementation, in which different members of the association partially contribute to the same biosynthetic pathway. In this way, the end product of the pathway is synthesized by the community as a whole. However, the emergence and the benefits of such complementation are poorly understood. Herein, we present a simple model to analyze the metabolic interactions among bacteria, including the host in the case of endosymbiotic bacteria. The model considers two cell populations, with both cell types encoding for the same linear biosynthetic pathway. We have found that, for metabolic complementation to emerge as an optimal strategy, both product inhibition and large permeabilities are needed. In the light of these results, we then consider the patterns found in the case of tryptophan biosynthesis in the endosymbiont consortium hosted by the aphid Cinara cedri. Using in-silico computed physicochemical properties of metabolites of this and other biosynthetic pathways, we verified that the splitting point of the pathway corresponds to the most permeable intermediate. PMID:27774085

  18. The Role of Transdisciplinary Approach and Community Participation in Village Scale Groundwater Management: Insights from Gujarat and Rajasthan, India

    Directory of Open Access Journals (Sweden)

    Basant Maheshwari

    2014-11-01

    Full Text Available Sustainable use of groundwater is becoming critical in India and requires effective participation from local communities along with technical, social, economic, policy and political inputs. Access to groundwater for farming communities is also an emotional and complex issue as their livelihood and survival depends on it. In this article, we report on transdisciplinary approaches to understanding the issues, challenges and options for improving sustainability of groundwater use in States of Gujarat and Rajasthan, India. In this project, called Managed Aquifer Recharge through Village level Intervention (MARVI, the research is focused on developing a suitable participatory approach and methodology with associated tools that will assist in improving supply and demand management of groundwater. The study was conducted in the Meghraj watershed in Aravalli district, Gujarat, and the Dharta watershed in Udaipur district, Rajasthan, India. The study involved the collection of hydrologic, agronomic and socio-economic data and engagement of local village and school communities through their role in groundwater monitoring, field trials, photovoice activities and education campaigns. The study revealed that availability of relevant and reliable data related to the various aspects of groundwater and developing trust and support between local communities, NGOs and government agencies are the key to moving towards a dialogue to decide on what to do to achieve sustainable use of groundwater. The analysis of long-term water table data indicated considerable fluctuation in groundwater levels from year to year or a net lowering of the water table, but the levels tend to recover during wet years. This provides hope that by improving management of recharge structures and groundwater pumping, we can assist in stabilizing the local water table. Our interventions through Bhujal Jankaars (BJs, (a Hindi word meaning “groundwater informed” volunteers, schools

  19. Characterization of the Bacterial Communities of Life Stages of Free Living Lone Star Ticks (Amblyomma americanum)

    OpenAIRE

    Amanda Jo Williams-Newkirk; Rowe, Lori A.; Mixson-Hayden, Tonya R.; Dasch, Gregory A.

    2014-01-01

    The lone star tick (Amblyomma americanum) is an abundant and aggressive biter of humans, domestic animals, and wildlife in the southeastern-central USA and an important vector of several known and suspected zoonotic bacterial pathogens. However, the biological drivers of bacterial community variation in this tick are still poorly defined. Knowing the community context in which tick-borne bacterial pathogens exist and evolve is required to fully understand the ecology and immunobiology of the ...

  20. Bacterial Community Composition and Potential Driving Factors in Different Reef Habitats of the Spermonde Archipelago, Indonesia

    Directory of Open Access Journals (Sweden)

    Hauke F. Kegler

    2017-04-01

    Full Text Available Coastal eutrophication is a key driver of shifts in bacterial communities on coral reefs. With fringing and patch reefs at varying distances from the coast the Spermonde Archipelago in southern Sulawesi, Indonesia offers ideal conditions to study the effects of coastal eutrophication along a spatially defined gradient. The present study investigated bacterial community composition of three coral reef habitats: the water column, sediments, and mucus of the hard coral genus Fungia, along that cross-shelf environmental and water quality gradient. The main research questions were: (1 How do water quality and bacterial community composition change along a coastal shelf gradient? (2 Which water quality parameters influence bacterial community composition? (3 Is there a difference in bacterial community composition among the investigated habitats? For this purpose, a range of key water parameters were measured at eight stations in distances from 2 to 55 km from urban Makassar. This was supplemented by sampling of bacterial communities of important microbial habitats using 454 pyrosequencing. Findings revealed that the population center Makassar had a strong effect on the concentrations of Chlorophyll a, suspended particulate matter (SPM, and transparent exopolymer particles (TEP, which were all significantly elevated at the inshore compared the other seven sites. Shifts in the bacterial communities were specific to each sampled habitat. Two OTUs, belonging to the genera Escherichia/Shigella (Gammaproteobacteria and Ralstonia (Betaproteobacteria, respectively, both dominated the bacterial community composition of the both size fractions of the water column and coral mucus. The sampled reef sediments were more diverse, and no single OTUs was dominant. There was no gradual shift in bacterial classes or OTUs within the sampled habitats. In addition, we observed very distinct communities between the investigated habitats. Our data show strong changes in the

  1. [Groundwater].

    Science.gov (United States)

    González De Posada, Francisco

    2012-01-01

    From the perspective of Hydrogeology, the concept and an introductory general typology of groundwater are established. From the perspective of Geotechnical Engineering works, the physical and mathematical equations of the hydraulics of permeable materials, which are implemented, by electric analogical simulation, to two unique cases of global importance, are considered: the bailing during the construction of the dry dock of the "new shipyard of the Bahia de Cádiz" and the waterproofing of the "Hatillo dam" in the Dominican Republic. From a physical fundamental perspective, the theories which are the subset of "analogical physical theories of Fourier type transport" are related, among which the one constituted by the laws of Adolf Fick in physiology occupies a historic role of some relevance. And finally, as a philosophical abstraction of so much useful mathematical process, the one which is called "the Galilean principle of the mathematical design of the Nature" is dealt with.

  2. Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time

    Directory of Open Access Journals (Sweden)

    Sheila Torres

    2017-03-01

    Full Text Available It has previously been shown that domestic dogs and their household owners share bacterial populations, and that sharing of bacteria between humans is facilitated through the presence of dogs in the household. However, less is known regarding the bacterial communities of dogs, how these communities vary by location and over time, and how cohabitation of dogs themselves influences their bacterial community. Furthermore, the effects of factors such as breed, hair coat length, sex, shedding, and age on the canine skin microbiome is unknown. This study sampled the skin bacterial communities of 40 dogs belonging to 20 households longitudinally across three seasons (spring, summer, and winter. Significant differences in bacterial community structure between samples were identified when stratified by season, but not by dog sex, age, breed, hair type, or skin site. Cohabitating dogs were more likely to share bacteria of the skin than non-cohabitating dogs. Similar to human bacterial microbiomes, dogs’ microbiomes were more similar to their own microbiomes over time than to microbiomes of other individuals. Dogs sampled during the same season were also more similar to each other than to dogs from different seasons, irrespective of household. However, there were very few core operational taxonomic units (OTUs identified across all dogs sampled. Taxonomic classification revealed Propionibacterium acnes and Haemophilus sp. as key members of the dog skin bacterial community, along with Corynebacterium sp. and Staphylococcus epidermidis. This study shows that the skin bacterial community structure of dogs is highly individualized, but can be shared among dogs through cohabitation.

  3. Detection of intracellular bacterial communities in human urinary tract infection.

    Directory of Open Access Journals (Sweden)

    David A Rosen

    2007-12-01

    Full Text Available BACKGROUND: Urinary tract infections (UTIs are one of the most common bacterial infections and are predominantly caused by uropathogenic Escherichia coli (UPEC. While UTIs are typically considered extracellular infections, it has been recently demonstrated that UPEC bind to, invade, and replicate within the murine bladder urothelium to form intracellular bacterial communities (IBCs. These IBCs dissociate and bacteria flux out of bladder facet cells, some with filamentous morphology, and ultimately establish quiescent intracellular reservoirs that can seed recurrent infection. This IBC pathogenic cycle has not yet been investigated in humans. In this study we sought to determine whether evidence of an IBC pathway could be found in urine specimens from women with acute UTI. METHODS AND FINDINGS: We collected midstream, clean-catch urine specimens from 80 young healthy women with acute uncomplicated cystitis and 20 asymptomatic women with a history of UTI. Investigators were blinded to culture results and clinical history. Samples were analyzed by light microscopy, immunofluorescence, and electron microscopy for evidence of exfoliated IBCs and filamentous bacteria. Evidence of IBCs was found in 14 of 80 (18% urines from women with UTI. Filamentous bacteria were found in 33 of 80 (41% urines from women with UTI. None of the 20 urines from the asymptomatic comparative group showed evidence of IBCs or filaments. Filamentous bacteria were present in all 14 of the urines with IBCs compared to 19 (29% of 66 samples with no evidence of IBCs (p < 0.001. Of 65 urines from patients with E. coli infections, 14 (22% had evidence of IBCs and 29 (45% had filamentous bacteria, while none of the gram-positive infections had IBCs or filamentous bacteria. CONCLUSIONS: The presence of exfoliated IBCs and filamentous bacteria in the urines of women with acute cystitis suggests that the IBC pathogenic pathway characterized in the murine model may occur in humans. The

  4. Gut bacterial communities across tadpole ecomorphs in two diverse tropical anuran faunas

    Science.gov (United States)

    Vences, Miguel; Lyra, Mariana L.; Kueneman, Jordan G.; Bletz, Molly C.; Archer, Holly M.; Canitz, Julia; Handreck, Svenja; Randrianiaina, Roger-Daniel; Struck, Ulrich; Bhuju, Sabin; Jarek, Michael; Geffers, Robert; McKenzie, Valerie J.; Tebbe, Christoph C.; Haddad, Célio F. B.; Glos, Julian

    2016-04-01

    Animal-associated microbial communities can play major roles in the physiology, development, ecology, and evolution of their hosts, but the study of their diversity has yet focused on a limited number of host species. In this study, we used high-throughput sequencing of partial sequences of the bacterial 16S rRNA gene to assess the diversity of the gut-inhabiting bacterial communities of 212 specimens of tropical anuran amphibians from Brazil and Madagascar. The core gut-associated bacterial communities among tadpoles from two different continents strongly overlapped, with eight highly represented operational taxonomic units (OTUs) in common. In contrast, the core communities of adults and tadpoles from Brazil were less similar with only one shared OTU. This suggests a community turnover at metamorphosis. Bacterial diversity was higher in tadpoles compared to adults. Distinct differences in composition and diversity occurred among gut bacterial communities of conspecific tadpoles from different water bodies and after experimental fasting for 8 days, demonstrating the influence of both environmental factors and food on the community structure. Communities from syntopic tadpoles clustered by host species both in Madagascar and Brazil, and the Malagasy tadpoles also had species-specific isotope signatures. We recommend future studies to analyze the turnover of anuran gut bacterial communities at metamorphosis, compare the tadpole core communities with those of other aquatic organisms, and assess the possible function of the gut microbiota as a reservoir for protective bacteria on the amphibian skin.

  5. Resource availability and spatial heterogeneity control bacterial community response to nutrient enrichment in lakes.

    Directory of Open Access Journals (Sweden)

    Kathijo Jankowski

    Full Text Available The diversity and composition of ecological communities often co-vary with ecosystem productivity. However, the relative importance of productivity, or resource abundance, versus the spatial distribution of resources in shaping those ecological patterns is not well understood, particularly for the bacterial communities that underlie most important ecosystem functions. Increasing ecosystem productivity in lakes has been shown to influence the composition and ecology of bacterial communities, but existing work has only evaluated the effect of increasing resource supply and not heterogeneity in how those resources are distributed. We quantified how bacterial communities varied with the trophic status of lakes and whether community responses differed in surface and deep habitats in response to heterogeneity in nutrient resources. Using ARISA fingerprinting, we found that bacterial communities were more abundant, richer, and more distinct among habitats as lake trophic state and vertical heterogeneity in nutrients increased, and that spatial resource variation produced habitat specific responses of bacteria in response to increased productivity. Furthermore, changes in communities in high nutrient lakes were not produced by turnover in community composition but from additional taxa augmenting core bacterial communities found in lower productivity lakes. These data suggests that bacterial community responses to nutrient enrichment in lakes vary spatially and are likely influenced disproportionately by rare taxa.

  6. Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice

    Energy Technology Data Exchange (ETDEWEB)

    Howe, Adina; Ringus, Daina L.; Williams, Ryan J.; Choo, Zi-Ning; Greenwald, Stephanie M.; Owens, Sarah M.; Coleman, Maureen L.; Meyer, Folker; Chang, Eugene B.

    2015-10-16

    To improve our understanding of the stability of mammalian intestinal communities, we characterized the responses of both bacterial and viral communities in murine fecal samples to dietary changes between high- and low-fat (LF) diets. Targeted DNA extraction methods for bacteria, virus-like particles and induced prophages were used to generate bacterial and viral metagenomes as well as 16S ribosomal RNA amplicons. Gut microbiome communities from two cohorts of C57BL/6 mice were characterized in a 6-week diet perturbation study in response to high fiber, LF and high-refined sugar, milkfat (MF) diets. The resulting metagenomes from induced bacterial prophages and extracellular viruses showed significant overlap, supporting a largely temperate viral lifestyle within these gut microbiomes. The resistance of baseline communities to dietary disturbances was evaluated, and we observed contrasting responses of baseline LF and MF bacterial and viral communities. In contrast to baseline LF viral communities and bacterial communities in both diet treatments, baseline MF viral communities were sensitive to dietary disturbances as reflected in their non-recovery during the washout period. The contrasting responses of bacterial and viral communities suggest that these communities can respond to perturbations independently of each other and highlight the potentially unique role of viruses in gut health.

  7. Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice

    Science.gov (United States)

    Howe, Adina; Ringus, Daina L; Williams, Ryan J; Choo, Zi-Ning; Greenwald, Stephanie M; Owens, Sarah M; Coleman, Maureen L; Meyer, Folker; Chang, Eugene B

    2016-01-01

    To improve our understanding of the stability of mammalian intestinal communities, we characterized the responses of both bacterial and viral communities in murine fecal samples to dietary changes between high- and low-fat (LF) diets. Targeted DNA extraction methods for bacteria, virus-like particles and induced prophages were used to generate bacterial and viral metagenomes as well as 16S ribosomal RNA amplicons. Gut microbiome communities from two cohorts of C57BL/6 mice were characterized in a 6-week diet perturbation study in response to high fiber, LF and high-refined sugar, milkfat (MF) diets. The resulting metagenomes from induced bacterial prophages and extracellular viruses showed significant overlap, supporting a largely temperate viral lifestyle within these gut microbiomes. The resistance of baseline communities to dietary disturbances was evaluated, and we observed contrasting responses of baseline LF and MF bacterial and viral communities. In contrast to baseline LF viral communities and bacterial communities in both diet treatments, baseline MF viral communities were sensitive to dietary disturbances as reflected in their non-recovery during the washout period. The contrasting responses of bacterial and viral communities suggest that these communities can respond to perturbations independently of each other and highlight the potentially unique role of viruses in gut health. PMID:26473721

  8. Response of fungal, bacterial and ureolytic communities to synthetic sheep urine deposition in a grassland soil.

    Science.gov (United States)

    Singh, Brajesh K; Nunan, Naoise; Millard, Peter

    2009-10-01

    In grazed pastures, soil pH is raised in urine patches, causing dissolution of organic carbon and increased ammonium and nitrate concentrations, with potential effects on the structure and functioning of soil microbial communities. Here we examined the effects of synthetic sheep urine (SU) in a field study on dominant soil bacterial and fungal communities associated with bulk soil and plant roots (rhizoplane), using culture-independent methods and a new approach to investigate the ureolytic community. A differential response of bacteria and fungal communities to SU treatment was observed. The bacterial community showed a clear shift in composition after SU treatment, which was more pronounced in bulk soil than on the rhizoplane. The fungal community did not respond to SU treatment; instead, it was more affected by the time of sampling. Redundancy analysis of data indicated that the variation in the bacterial community was related to change in soil pH, while fungal community was more responsive to dissolution of organic carbon. Like the universal bacterial community, the ureolytic community was influenced by the SU treatment. However, different taxa within the ureolytic bacterial community responded differentially to the treatment. The ureolytic community comprised of members from a range of phylogenetically different taxa and could be used to measure the effect of environmental perturbations on the functional diversity of natural ecosystems.

  9. Potential Use of Bacterial Community Succession in Decaying Human Bone for Estimating Postmortem Interval.

    Science.gov (United States)

    Damann, Franklin E; Williams, Daniel E; Layton, Alice C

    2015-07-01

    Bacteria are taphonomic agents of human decomposition, potentially useful for estimating postmortem interval (PMI) in late-stage decomposition. Bone samples from 12 individuals and three soil samples were analyzed to assess the effects of decomposition and advancing time on bacterial communities. Results indicated that partially skeletonized remains maintained a presence of bacteria associated with the human gut, whereas bacterial composition of dry skeletal remains maintained a community profile similar to soil communities. Variation in the UniFrac distances was significantly greater between groups than within groups (p < 0.001) for the unweighted metric and not the weighted metric. The members of the bacterial communities were more similar within than between decomposition stages. The oligotrophic environment of bone relative to soft tissue and the physical protection of organic substrates may preclude bacterial blooms during the first years of skeletonization. Therefore, community membership (unweighted) may be better for estimating PMI from skeletonized remains than community structure (weighted).

  10. Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land, Antarctica

    OpenAIRE

    Mincheol Kim; Ahnna Cho; Hyoun Soo Lim; Soon Gyu Hong; Ji Hee Kim; Joohan Lee; Taejin Choi; Tae Seok Ahn; Ok-Sun Kim

    2015-01-01

    Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environm...

  11. Matrix composition and community structure analysis of a novel bacterial pyrite leaching community.

    Science.gov (United States)

    Ziegler, Sibylle; Ackermann, Sonia; Majzlan, Juraj; Gescher, Johannes

    2009-09-01

    Here we describe a novel bacterial community that is embedded in a matrix of carbohydrates and bio/geochemical products of pyrite (FeS(2)) oxidation. This community grows in stalactite-like structures--snottites--on the ceiling of an abandoned pyrite mine at pH values of 2.2-2.6. The aqueous phase in the matrix contains 200 mM of sulfate and total iron concentrations of 60 mM. Micro-X-ray diffraction analysis showed that jarosite [(K,Na,H(3)O)Fe(3)(SO(4))(2)(OH)(6)] is the major mineral embedded in the snottites. X-ray absorption near-edge structure experiments revealed three different sulfur species. The major signal can be ascribed to sulfate, and the other two features may correspond to thiols and sulfoxides. Arabinose was detected as the major sugar component in the extracellular polymeric substance. Via restriction fragment length polymorphism analysis, a community was found that mainly consists of iron oxidizing Leptospirillum and Ferrovum species but also of bacteria that could be involved in dissimilatory sulfate and dissimilatory iron reduction. Each snottite can be regarded as a complex, self-contained consortium of bacterial species fuelled by the decomposition of pyrite.

  12. Bacterial Chemotaxis Toward A NAPL Source Within A Pore-Scale Model Subject to A Range of Groundwater Flow Velocities

    Science.gov (United States)

    Wang, X.; Ford, R. M.

    2010-12-01

    Organic solvents such as toluene are the most widely distributed pollutants in groundwater. Biodegradation of these industrial pollutants requires that microorganisms in the aqueous phase are brought in contact with sources of contamination, which may be dispersed as pore-size organic-phase droplets within the saturated soil matrix. Chemotaxis toward chemical pollutants provides a mechanism for bacteria to migrate to locations of high contamination, which may not normally be accessible to bacteria carried along by groundwater flow, and thus it may improve the efficiency of bioremediation. A microfluidic device was designed to mimic the dissolution of an organic-phase contaminant from a single pore into a larger macropore representing a preferred pathway for microorganisms that are carried along by groundwater flow. The glass windows of the µ-chip allowed image analysis of bacterial distributions within the vicinity of the organic contaminant. Concentrations of chemotactic bacteria P. putida F1 near the organic/aqueous interface were 25% greater than those of a nonchemotactic mutant in the vicinity of toluene for a fluid velocity of 0.5 m/d. For E. coli responding to phenol, the bacterial concentrations were 60% greater than the controls, also at a velocity of 0.5 m/d. Velocities in the macropore were varied over a range that is typical of groundwater velocities from 0.5 to 10 m/d. The accumulation of chemotactic bacteria near the NAPL (nonaqueous phase liquid) chemoattractant source decreased as the fluid velocity increased. At the higher velocities, accumulation of chemotactic bacteria was comparable to the non-chemotactic control experiments. Computer-based simulation using finite element analysis software (COMSOL) was also performed to understand the effects of various model parameters on bacterial chemotaxis to NAPL. There was good agreement between the simulations (generated using reasonable values of the model parameters) and the experimental data for P

  13. Pyrosequencing based profiling of the bacterial community in the Chilika Lake, the largest lagoon of India

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    Arnab Pramanik

    2015-06-01

    Full Text Available Brackish water lake is the most extraordinary reservoir for bacterial community with an adaptability of tolerance to saline stress. In the present study, metagenomic approach was implemented utilising 454-pyrosequencing platform to gain deeper insights into the bacterial diversity profile of the soil sediment of Chilika Lake, Odisha, India. Metagenome contained 68,150 sequences with 31,896,430 bp and 56.79% G+C content. Metagenome sequences data are now available at NCBI under the Sequence Read Archive (SRA database with accession no. SRX753382. Bacterial community metagenome sequences were analysed by MG-RAST server representing the presence of 16,212 species belonging to 45 different phyla. The dominating phyla were Proteobacteria, Chloroflexi, Firmicutes, Acidobacteria, Actinobacteria, Bacteroidetes and Planctomycetes. The analysis of bacterial community datasets obtained from two different saline soil sediments revealed significant differences in bacterial community composition and diversity value providing better understanding of the ecosystem dynamics of Chilika Lake.

  14. The Arbuscular Mycorrhizal Fungus Funneliformis mosseae Alters Bacterial Communities in Subtropical Forest Soils during Litter Decomposition

    Directory of Open Access Journals (Sweden)

    Heng Gui

    2017-06-01

    Full Text Available Bacterial communities and arbuscular mycorrhizal fungi (AMF co-occur in the soil, however, the interaction between these two groups during litter decomposition remains largely unexplored. In order to investigate the effect of AMF on soil bacterial communities, we designed dual compartment microcosms, where AMF (Funneliformis mosseae was allowed access (AM to, or excluded (NM from, a compartment containing forest soil and litterbags. Soil samples from this compartment were analyzed at 0, 90, 120, 150, and 180 days. For each sample, Illumina sequencing was used to assess any changes in the soil bacterial communities. We found that most of the obtained operational taxonomic units (OTUs from both treatments belonged to the phylum of Proteobacteria, Acidobacteria, and Actinobacteria. The community composition of bacteria at phylum and class levels was slightly influenced by both time and AMF. In addition, time and AMF significantly affected bacterial genera (e.g., Candidatus Solibacter, Dyella, Phenylobacterium involved in litter decomposition. Opposite to the bacterial community composition, we found that overall soil bacterial OTU richness and diversity are relatively stable and were not significantly influenced by either time or AMF inoculation. OTU richness at phylum and class levels also showed consistent results with overall bacterial OTU richness. Our study provides new insight into the influence of AMF on soil bacterial communities at the genus level.

  15. Effects of hydraulic frac fluids and formation waters on groundwater microbial communities

    Science.gov (United States)

    Krueger, Martin; Jimenez, Nuria

    2017-04-01

    Shale gas is being considered as a complementary energy resource to other fossil fuels. Its exploitation requires using advanced drilling techniques and hydraulic stimulation (fracking). During fracking operations, large amounts of fluids (fresh water, proppants and chemicals) are injected at high pressures into the formations, to create fractures and fissures, and thus to release gas from the source rock into the wellbore. The injected fluid partly remains in the formation, while up to 40% flows back to the surface, together with reservoir waters, sometimes containing dissolved hydrocarbons, high salt concentrations, etc. The aim of our study was to investigate the potential impacts of frac or geogenic chemicals, frac fluid, formation water or flowback on groudnwater microbial communities. Laboratory experiments under in situ conditions (i.e. at in situ temperature, high pressure) were conducted using groundwater samples from three different locations. Series of microcosms containing R2 broth medium or groundwater spiked with either single frac chemicals (including biocides), frac fluids, artificial reservoir water, NaCl, or different mixtures of reservoir water and frac fluid (to simulate flowback) were incubated in the dark. Controls included non-amended and non-inoculated microcosms. Classical microbiological methods and molecular analyses were used to assess changes in the microbial abundance, community structure and function in response to the different treatments. Microbial communities were quite halotolerant and their growth benefited from low concentrations of reservoir waters or salt, but they were negatively affected by higher concentrations of formation waters, salt, biocides or frac fluids. Changes on the microbial community structure could be detected by T-RFLP. Single frac components like guar gum or choline chloride were used as substrates, while others like triethanolamine or light oil distillate hydrogenated prevented microbial growth in

  16. Effects of hydraulic frac fluids and formation waters on groundwater microbial communities

    Science.gov (United States)

    Jiménez, Núria; Krüger, Martin

    2015-04-01

    Shale gas is being considered as a complementary energy resource to other fossil fuels. Its exploitation requires using advanced drilling techniques and hydraulic stimulation (fracking). During fracking operations, large amounts of fluids (fresh water, proppants and chemicals) are injected at high pressures into the formations, to create fractures and fissures, and thus to release gas from the source rock into the wellbore. The injected fluid partly remains in the formation, while up to 40% flows back to the surface, together with reservoir waters, sometimes containing dissolved hydrocarbons, high salt concentrations, etc. The aim of our study was to investigate the potential impacts of frac or geogenic chemicals, frac fluid, formation water or flowback on groudnwater microbial communities. Laboratory experiments under in situ conditions (i.e. at in situ temperatures, with high pressure, etc.) were conducted using groundwater samples from three different locations. Series of microcosms (3 of each kind) containing R2 broth medium or groundwater spiked with either single frac chemicals (including biocides), frac fluids, artificial reservoir water, NaCl, or different mixtures of reservoir water and frac fluid (to simulate flowback) were incubated in the dark. Controls included non-amended and non-inoculated microcosms. Classical microbiological methods and molecular analyses were used to assess changes in the microbial abundance, community structure and function in response to the different treatments. Microbial communities were quite halotolerant and their growth benefited from low concentrations of reservoir waters or salt, but they were negatively affected by higher concentrations of formation waters, salt, biocides, frac fluids or flowback. Changes on the microbial community structure could be detected by T-RFLP. Single frac components like guar gum or choline chloride could be used as substrates, while the effects of others like triethanolamine or light oil

  17. Bacterial community analysis of Tatsoi cultivated by hydroponics.

    Science.gov (United States)

    Koo, Ok K; Kim, Hun; Kim, Hyun J; Baker, Christopher A; Ricke, Steven C

    2016-07-02

    Tatsoi (Brassica narinosa) is a popular Asian salad green that is mostly consumed as a source of fresh produce. The purpose of this study was to assess the microbial diversity of Tatsoi cultivated in a hydroponic system and of its ecosystem. Tatsoi leaves, nutrient solution, and perlite/earth samples from a trickle feed system (TFS) and an ebb-and-flow system (EFS) were collected and their microbial communities were analyzed by pyrosequencing analysis. The results showed that most bacteria in the leaves from the TFS contained genus Sporosarcina (99.6%), while Rhizobium (60.4%) was dominant in the leaves from the EFS. Genus Paucibacter (18.21%) and Pelomonas (12.37%) were the most abundant microbiota in the nutrient solution samples of the TFS. In the EFS, the nutrient solution samples contained mostly genus Rhodococcus and Acinetobacter. Potential microbial transfer between the leaves and the ecosystem was observed in the EFS, while samples in the TFS were found to share only one species between the leaves, nutrient solution, and earth. Together, these results show that the bacterial populations in Tatsoi and in its ecosystem are highly diverse based on the cultivation system.

  18. Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community.

    Science.gov (United States)

    Hemme, Christopher L; Green, Stefan J; Rishishwar, Lavanya; Prakash, Om; Pettenato, Angelica; Chakraborty, Romy; Deutschbauer, Adam M; Van Nostrand, Joy D; Wu, Liyou; He, Zhili; Jordan, I King; Hazen, Terry C; Arkin, Adam P; Kostka, Joel E; Zhou, Jizhong

    2016-04-05

    Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe(2+)/Pb(2+) permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co(2+)/Zn(2+)/Cd(2+) efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome. Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main

  19. Bacterial communities associated with white shrimp (Litopenaeus vannamei larvae at early developmental stages

    Directory of Open Access Journals (Sweden)

    ANTONIUS SUWANTO

    2010-04-01

    Full Text Available Bacterial communities associated with white shrimp (Litopenaeus vannamei larvae at early developmental stages. Biodiversitas 11 (2: 65-68.Terminal Restriction Fragment Length Polymorphism (T-RFLP was used to monitor the dynamics of the bacterial communities associated with early developmental stages of white shrimp (Litopenaeus vannamei larvae. Samples for analysis were egg, hatching nauplii, 24 hours old nauplii, and 48 hours old nauplii which were collected from one cycle of production at commercial hatchery. T-RFLP results indicated that the bacterial community associated with early stages of shrimp development might be transferred vertically from broodstock via egg. There was no significant difference between bacterial communities investigated, except the bacterial community of 48 hours old nauplii. Diversity analyses showed that the bacterial community of egg had the highest diversity and evenness, meanwhile the bacterial community of 48 hours old nauplii had the lowest diversity. Nine phylotypes were found at all stages with high abundance. Those TRFs were identified as γ- proteobacteria, α-proteobacteria, and bacteroidetes group.

  20. Soil phosphorus depletion and shifts in plant communities change bacterial community structure in a long-term grassland management trial.

    Science.gov (United States)

    Adair, Karen L; Wratten, Steve; Lear, Gavin

    2013-06-01

    Agricultural systems rely on healthy soils and their sustainability requires understanding the long-term impacts of agricultural practices on soils, including microbial communities. We examined the impact of 17 years of land management on soil bacterial communities in a New Zealand randomized-block pasture trial. Significant variation in bacterial community structure related to mowing and plant biomass removal, while nitrogen fertilizer had no effect. Changes in soil chemistry and legume abundance described 52% of the observed variation in the bacterial community structure. Legumes (Trifolium species) were absent in unmanaged plots but increased in abundance with management intensity; 11% of the variation in soil bacterial community structure was attributed to this shift in the plant community. Olsen P explained 10% of the observed heterogeneity, which is likely due to persistent biomass removal resulting in P limitation; Olsen P was significantly lower in plots with biomass removed (14 mg kg(-1) ± 1.3SE) compared with plots that were not mown, or where biomass was left after mowing (32 mg kg(-1) ± 1.6SE). Our results suggest that removal of plant biomass and associated phosphorus, as well as shifts in the plant community, have greater long-term impacts on soil bacterial community structure than application of nitrogen fertilizers.

  1. 16S rRNA survey revealed complex bacterial communities and evidence of bacterial interference on human adenoids.

    Science.gov (United States)

    Ren, Tiantian; Glatt, Dominique Ulrike; Nguyen, Tam Nhu; Allen, Emma Kaitlynn; Early, Stephen V; Sale, Michele; Winther, Birgit; Wu, Martin

    2013-02-01

    Adenoid microbiota plays an important role in the development of various infectious and non-infectious diseases of the upper airways, such as otitis media, adenotonsillitis, rhinosinusitis and adenoid hypertrophy. Studies have suggested that adenoids could act as a potential reservoir of opportunistic pathogens. However, previous bacterial surveys of adenoids were mainly culture based and therefore might only provide an incomplete and potentially biased assessment of the microbial diversity. To develop an in-depth and comprehensive understanding of the adenoid microbial communities and test the 'pathogen reservoir hypothesis', we carried out a 16S rRNA based, culture-independent survey of bacterial communities on 67 human adenoids removed by surgery. Our survey revealed highly diverse adenoid bacterial communities distinct from those of other body habitats. Despite large interpersonal variations, adenoid microbiota shared a core set of taxa and can be classified into at least five major types based on its bacterial species composition. Our results support the 'pathogen reservoir hypothesis' as we found common pathogens of otitis media to be both prevalent and abundant. Co-occurrence analyses revealed evidence consistent with the bacterial interference theory in that multiple common pathogens showed 'non-coexistence' relationships with non-pathogenic members of the commensal microflora.

  2. Bacterial Community Structure is Indicative of Chemical Inputs in the Upper Mississippi River

    Directory of Open Access Journals (Sweden)

    Christopher eStaley

    2014-10-01

    Full Text Available Local and regional associations between bacterial communities and nutrient and chemical concentrations were assessed in the Upper Mississippi River in Minnesota to determine if community structure was associated with discrete types of chemical inputs associated with different land cover. Bacterial communities were characterized by Illumina sequencing of the V6 region of 16S rDNA and compared to > 40 chemical and nutrient concentrations. Local bacterial community structure was shaped primarily by associations among bacterial orders. However, order abundances were correlated regionally with nutrient and chemical concentrations, and were also related to major land coverage types. Total organic carbon and total dissolved solids were among the primary abiotic factors associated with local community composition and co-varied with land cover. Escherichia coli concentration was poorly related to community composition or nutrient concentrations. Abundances of fourteen bacterial orders were related to land coverage type, and seven showed significant differences in abundance (P ≤ 0.046 between forested or anthropogenically-impacted sites. This study identifies specific bacterial orders that were associated with chemicals and nutrients derived from specific land cover types and may be useful in assessing water quality. Results of this study reveal the need to investigate community dynamics at both the local and regional scales and to identify shifts in taxonomic community structure that may be useful in determining sources of pollution in the Upper Mississippi River.

  3. Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska.

    Science.gov (United States)

    Kim, Hye Min; Jung, Ji Young; Yergeau, Etienne; Hwang, Chung Yeon; Hinzman, Larry; Nam, Sungjin; Hong, Soon Gyu; Kim, Ok-Sun; Chun, Jongsik; Lee, Yoo Kyung

    2014-08-01

    The subarctic region is highly responsive and vulnerable to climate change. Understanding the structure of subarctic soil microbial communities is essential for predicting the response of the subarctic soil environment to climate change. To determine the composition of the bacterial community and its relationship with soil properties, we investigated the bacterial community structure and properties of surface soil from the moist acidic tussock tundra in Council, Alaska. We collected 70 soil samples with 25-m intervals between sampling points from 0-10 cm to 10-20 cm depths. The bacterial community was analyzed by pyrosequencing of 16S rRNA genes, and the following soil properties were analyzed: soil moisture content (MC), pH, total carbon (TC), total nitrogen (TN), and inorganic nitrogen (NH4+ and NO3-). The community compositions of the two different depths showed that Alphaproteobacteria decreased with soil depth. Among the soil properties measured, soil pH was the most significant factor correlating with bacterial community in both upper and lower-layer soils. Bacterial community similarity based on jackknifed unweighted unifrac distance showed greater similarity across horizontal layers than through the vertical depth. This study showed that soil depth and pH were the most important soil properties determining bacterial community structure of the subarctic tundra soil in Council, Alaska.

  4. Molecular ecological analysis of planktonic bacterial communities in constructed wetlands invaded by Culex (Diptera: Culicidae) mosquitoes.

    Science.gov (United States)

    Popko, David A; Han, Suk-Kyun; Lanoil, Brian; Walton, William E

    2006-11-01

    The succession of the planktonic bacterial community during the colonization by Culex (Diptera: Culicidae) mosquitoes of 0.1-ha treatment wetlands was studied using denaturing gradient gel electrophoresis (DGGE) methodology. Relationships between apparent bacterial diversity and ecological factors (water quality, total bacterial counts, and immature mosquito abundance) were determined during a 1-mo flooding period. Analysis of DGGE banding patterns indicated that days postflooding and temporal changes in water quality were the primary and secondary determinants, respectively, of diversity in bacterial communities. Lower levels of diversity were associated with later postflood stages and increases in ammoniacal nitrogen concentration and total bacterial counts. Diversity was therefore most similar for bacteria present on the same sampling date at wetland locations with similar flooding regimes and water quality, suggesting that wastewater input was the driving force shaping bacterial communities. Comparatively small changes in bacterial diversity were connected to natural processes as water flowed through the wetlands. Greater immature mosquito abundance coincided with less diverse communities composed of greater total numbers of bacteria. Five individual DGGE bands were directly associated with fluctuations in mosquito production, and an additional 16 bands were associated with hydrological aspects of the environment during the rise and fall of mosquito populations. A marked decline in mosquito numbers 21 d after inundation may have masked associations of bacterial communities and mosquito recruitment into the sparsely vegetated wetlands. DGGE was an effective tool for the characterization of bacteria in mosquito habitat in our study, and its potential application in mosquito ecology is discussed.

  5. Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere

    NARCIS (Netherlands)

    Yan, Y.; Kuramae, E.E.; De Hollander, M.; Klinkhamer, P.G.L.; van Veen, J.A.

    2017-01-01

    We studied the impact of community diversity on the selection of bacterial communities in the rhizosphere by comparing the composition and the functional traits of these communities in soil and rhizosphere. Differences in diversity were established by inoculating into sterilized soils diluted suspen

  6. Institutions in transitioning peri-urban communities: spatial differences in groundwater access

    Science.gov (United States)

    Gomes, Sharlene L.; Hermans, Leon M.

    2016-05-01

    Urbanization creates challenges for water management in an evolving socio-economic context. This is particularly relevant in transitioning peri-urban areas like Khulna, Bangladesh where competing demands have put pressure on local groundwater resources. Users are unable to sufficiently meet their needs through existing institutions. These institutions provide the rules for service provision and act as guidelines for actors to resolve their water related issues. However, the evolving peri-urban context can produce fragmented institutional arrangements. For example in Khulna, water supply is based on urban and rural boundaries that has created water access issues for peri-urban communities. This has motivated local actors to manage their groundwater needs in various ways. General institutional theories are well developed in literature, yet little is known about institutions in transitioning peri-urban areas. Institutions that fail to adapt to changing dynamics run the risk of becoming obsolete or counter-productive, hence the need for investigating institutional change mechanisms in this context. This paper examines peri-urban case studies from Khulna using the Institutional Analysis and Development framework to demonstrate how institutions have contributed to spatial differences in groundwater access with local actors investing in formal and informal institutional change as a means of accessing groundwater.

  7. Effects of remediation on the bacterial community of an acid mine drainage impacted stream.

    Science.gov (United States)

    Ghosh, Suchismita; Moitra, Moumita; Woolverton, Christopher J; Leff, Laura G

    2012-11-01

    Acid mine drainage (AMD) represents a global threat to water resources, and as such, remediation of AMD-impacted streams is a common practice. During this study, we examined bacterial community structure and environmental conditions in a low-order AMD-impacted stream before, during, and after remediation. Bacterial community structure was examined via polymerase chain reaction amplification of 16S rRNA genes followed by denaturing gradient gel electrophoresis. Also, bacterial abundance and physicochemical data (including metal concentrations) were collected and relationships to bacterial community structure were determined using BIO-ENV analysis. Remediation of the study stream altered environmental conditions, including pH and concentrations of some metals, and consequently, the bacterial community changed. However, remediation did not necessarily restore the stream to conditions found in the unimpacted reference stream; for example, bacterial abundances and concentrations of some elements, such as sulfur, magnesium, and manganese, were different in the remediated stream than in the reference stream. BIO-ENV analysis revealed that changes in pH and iron concentration, associated with remediation, primarily explained temporal alterations in bacterial community structure. Although the sites sampled in the remediated stream were in relatively close proximity to each other, spatial variation in community composition suggests that differences in local environmental conditions may have large impacts on the microbial assemblage.

  8. Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions.

    Science.gov (United States)

    He, Tianliang; Zhang, Xiaobo

    2016-04-01

    Deep-sea hydrothermal vents are considered to be one of the most spectacular ecosystems on Earth. Microorganisms form the basis of the food chain in vents controlling the vent communities. However, the diversity of bacterial communities in deep-sea hydrothermal vents from different oceans remains largely unknown. In this study, the pyrosequencing of 16S rRNA gene was used to characterize the bacterial communities of the venting sulfide, seawater, and tubeworm trophosome from East Pacific Rise, South Atlantic Ridge, and Southwest Indian Ridge, respectively. A total of 23,767 operational taxonomic units (OTUs) were assigned into 42 different phyla. Although Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant phyla in all vents, differences of bacterial diversity were observed among different vents from three oceanic regions. The sulfides of East Pacific Rise possessed the most diverse bacterial communities. The bacterial diversities of venting seawater were much lower than those of vent sulfides. The symbiotic bacteria of tubeworm Ridgeia piscesae were included in the bacterial community of vent sulfides, suggesting their significant ecological functions as the primary producers in the deep-sea hydrothermal vent ecosystems. Therefore, our study presented a comprehensive view of bacterial communities in deep-sea hydrothermal vents from different oceans.

  9. Effects of Host Plant Factors on the Bacterial Communities Associated with Two Whitefly Sibling Species.

    Science.gov (United States)

    Su, Ming-Ming; Guo, Lei; Tao, Yun-Li; Zhang, You-Jun; Wan, Fang-Hao; Chu, Dong

    2016-01-01

    Although discrepancy in the specific traits and ecological characteristics of Bemisia tabaci between species are partially attributed to the B. tabaci-associated bacteria, the factors that affect the diversity of B. tabaci-associated bacteria are not well-understood. We used the metagenomic approach to characterize the B. tabaci-associated bacterial community because the approach is an effective tool to identify the bacteria. To investigate the effects of the host plant and a virus, tomato yellow leaf curl virus (TYLCV), on the bacterial communities of B. tabaci sibling species B and Q, we analyzed the bacterial communities associated with whitefly B and Q collected from healthy cotton, healthy tomato, and TYLCV-infected tomato. The analysis used miseq-based sequencing of a variable region of the bacterial 16S rDNA gene. For the bacteria associated with B. tabaci, we found that the influence of the host plant species was greater than that of the whitefly cryptic species. With further analysis of host plants infected with the TYLCV, the virus had no significant effects on the B. tabaci-associated bacterial community. The effects of different plant hosts and TYLCV-infection on the diversity of B. tabaci-associated bacterial communities were successfully analyzed in this study. To explain why B. tabaci sibling species with different host ranges differ in performance, the analysis of the bacterial community may be essential to the explanation.

  10. Bacterial communities associated with four ctenophore genera from the German Bight (North Sea).

    Science.gov (United States)

    Hao, Wenjin; Gerdts, Gunnar; Peplies, Jörg; Wichels, Antje

    2015-01-01

    Intense research has been conducted on jellyfish and ctenophores in recent years. They are increasingly recognized as key elements in the marine ecosystem that serve as critical indicators and drivers of ecosystem performance and change. However, the bacterial community associated with ctenophores is still poorly investigated. Based on automated ribosomal intergenic spacer analysis (ARISA) and 16S ribosomal RNA gene amplicon pyrosequencing, we investigated bacterial communities associated with the frequently occurring ctenophore species Mnemiopsis leidyi, Beroe sp., Bolinopsis infundibulum and Pleurobrachia pileus at Helgoland Roads in the German Bight (North Sea). We observed significant differences between the associated bacterial communities of the different ctenophore species based on ARISA patterns. With respect to bacterial taxa, all ctenophore species were dominated by Proteobacteria as revealed by pyrosequencing. Mnemiopsis leidyi and P. pileus mainly harboured Gammaproteobacteria, with Marinomonas as the dominant phylotype of M. leidyi. By contrast, Pseudoalteromonas and Psychrobacter were the most abundant Gammaproteobacteria in P. pileus. Beroe sp. was mainly dominated by Alphaproteobacteria, particularly by the genus Thalassospira. For B. infundibulum, the bacterial community was composed of Alphaproteobacteria and Gammaproteobacteria in equal parts, which consisted of the genera Thalassospira and Marinomonas. In addition, the bacterial communities associated with M. leidyi display a clear variation over time that needs further investigation. Our results indicate that the bacterial communities associated with ctenophores are highly species- specific. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Dynamics of Bacterial Community Abundance and Structure in Horizontal Subsurface Flow Wetland Mesocosms Treating Municipal Wastewater

    Directory of Open Access Journals (Sweden)

    Kristjan Oopkaup

    2016-10-01

    Full Text Available Dynamics of bacterial community abundance and structure of a newly established horizontal subsurface flow (HSSF pilot-scale wetland were studied using high-throughput sequencing and quantitative polymerase chain reaction (PCR methods. Bacterial community abundance increased rapidly within one month and stabilised thereafter in three replicate HSSF constructed wetland (CW mesocosms. The most dominant phylum was Proteobacteria, followed by Bacteroidetes in wetland media biofilms and Firmicutes in influent wastewater. CW bacterial community diversity increased over time and was positively related to the wastewater treatment efficiency. Increase in the abundance of total bacteria in the community was accompanied with the abundance of denitrifying bacteria that promoted nitrate and nitrite removal from the wastewater. During the 150-day study period, similar patterns of bacterial community successions were observed in replicate HSSF CW mesocosms. The data indicate that successions in the bacterial community in HSSF CW are shaped by biotic interactions, with a significant contribution made by external abiotic factors such as influent chemical parameters. Network analysis of the bacterial community revealed that organic matter and nitrogen removal in HSSF CW could be, in large part, allocated to a small subset of tightly interconnected bacterial species. The diversity of bacterial community and abundance of denitrifiers were good predictors of the removal efficiency of ammonia, nitrate and total organic C in HSSF CW mesocosms, while the removal of the seven-day biochemical oxygen demand (BOD7 was best predicted by the abundance of a small set of bacterial phylotypes. The results suggest that nitrogen removal in HSSF CW consist of two main pathways. The first is heterotrophic nitrification, which is coupled with aerobic denitrification and mediated by mixotrophic nitrite-oxidizers. The second pathway is anaerobic denitrification, which leads to gaseous

  12. Community perspectives on the risk of indoor air pollution arising from contaminated groundwater.

    Science.gov (United States)

    Johnston, Jill E; Kramer, Amanda J; Gibson, Jacqueline MacDonald

    2015-05-01

    The migration of volatile contaminants into overlying buildings, known as vapor intrusion, is a health concern for people living above contaminated groundwater. As public health and environmental agencies develop protocols to evaluate vapor intrusion exposure, little attention has been paid to the experiences and opinions of communities likely to be affected by vapor intrusion. Using a community-driven research approach and qualitative interviews, we explored community perspectives on the vapor intrusion pathway and the perceived impact on community health and well-being among neighbors living atop a large, shallow-chlorinated solvent plume in San Antonio, TX. Most participants associated vapor intrusion with health risks, expressing concern about the unavoidable and uncontrollable nature of their exposure. Few were satisfied with the responsiveness of public officials. Above all, participants wanted more accurate, transparent information and additional independent scientific investigations. © The Author(s) 2015 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  13. Microbial Community-Level Physiological Profiles (CLPP) and herbicide mineralization potential in groundwater affected by agricultural land use

    DEFF Research Database (Denmark)

    Janniche, Gry Sander; Spliid, Henrik; Albrechtsen, Hans-Jørgen

    2012-01-01

    Diffuse groundwater pollution from agricultural land use may impact the microbial groundwater community, which was investigated as Community-Level Physiological Profiles (CLPP) using EcoPlate™. Water was sampled from seven piezometers and a spring in a small agricultural catchment with diffuse...... herbicide and nitrate pollution. Based on the Shannon–Wiener and Simpson's diversity indices the diversity in the microbial communities was high. The response from the EcoPlates™ showed which substrates support groundwater bacteria, and all 31 carbon sources were utilized by organisms from at least one......-galacturonic acid, tween 40, and 4-hydroxy benzoic acid as substrates, whereas none preferred 2-hydroxy benzoic acid, α-d-lactose, d,l-α-glycerol phosphate, α-ketobutyric acid, l-threonine and glycyl-l-glutamic acid. Principal Component Analysis of the CLPP's clustered the most agriculturally affected groundwater...

  14. Diversity and abundance of the bacterial community of the red Macroalga Porphyra umbilicalis: did bacterial farmers produce macroalgae?

    Directory of Open Access Journals (Sweden)

    Lilibeth N Miranda

    Full Text Available Macroalgae harbor microbial communities whose bacterial biodiversity remains largely uncharacterized. The goals of this study were 1 to examine the composition of the bacterial community associated with Porphyra umbilicalis Kützing from Schoodic Point, ME, 2 determine whether there are seasonal trends in species diversity but a core group of bacteria that are always present, and 3 to determine how the microbial community associated with a laboratory strain (P.um.1 established in the presence of antibiotics has changed. P. umbilicalis blades (n = 5, fall 2010; n = 5, winter 2011; n = 2, clonal P.um.1 were analyzed by pyrosequencing over two variable regions of the 16 S rDNA (V5-V6 and V8; 147,880 total reads. The bacterial taxa present were classified at an 80% confidence threshold into eight phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Chloroflexi, Actinobacteria, Deinococcus-Thermus, Firmicutes, and the candidate division TM7. The Bacteroidetes comprised the majority of bacterial sequences on both field and lab blades, but the Proteobacteria (Alphaproteobacteria, Gammaproteobacteria were also abundant. Sphingobacteria (Bacteroidetes and Flavobacteria (Bacteroidetes had inverse abundances on natural versus P.um.1 blades. Bacterial communities were richer and more diverse on blades sampled in fall compared to winter. Significant differences were observed between microbial communities among all three groups of blades examined. Only two OTUs were found on all 12 blades, and only one of these, belonging to the Saprospiraceae (Bacteroidetes, was abundant. Lewinella (as 66 OTUs was found on all field blades and was the most abundant genus. Bacteria from the Bacteroidetes, Proteobacteria and Planctomycetes that are known to digest the galactan sulfates of red algal cell walls were well-represented. Some of these taxa likely provide essential morphogenetic and beneficial nutritive factors to P. umbilicalis and may have had

  15. Diversity surveys of soil bacterial community by cultivation-based methods and molecular fingerprinting techniques

    Institute of Scientific and Technical Information of China (English)

    LUO Hai-feng; QI Hong-yan; ZHANG Hong-xun

    2004-01-01

    By combining the cultivation methods with molecular fingerprinting techniques, the diversity surveys of soil bacterial community in 13 areas of China were carried out. The cultivable heterotrophic diversity was investigated by colony morphology on solid LB medium. Genetic diversity was measured as bands on denaturing gradient gel electrophoresis(DGGE) by the extraction and purification of the total soil DNA, and amplification of bacterial 16S rDNA fragments by polymerase chain reaction ( PCR). The Shannon-Wiener indices of diversity (H), richness (S)and evenness( EH ) were employed to estimate the diversity of soil bacterial community. The results showed that there was an obvious diversification existed in soil from the different areas. However, the genetic diversity estimated by PCR-DGGE can provide more comprehensive information on bacterial community than the cultivation-based methods. Therefore, it is suggested to combine the traditional methods with genetic fingerprinting techniques to survey and estimate soil bacterial diversity.

  16. Soil bacterial community structure responses to precipitation reduction and forest management in forest ecosystems across Germany.

    Science.gov (United States)

    Felsmann, Katja; Baudis, Mathias; Gimbel, Katharina; Kayler, Zachary E; Ellerbrock, Ruth; Bruelheide, Helge; Bruehlheide, Helge; Bruckhoff, Johannes; Welk, Erik; Puhlmann, Heike; Weiler, Markus; Gessler, Arthur; Ulrich, Andreas

    2015-01-01

    Soil microbial communities play an important role in forest ecosystem functioning, but how climate change will affect the community composition and consequently bacterial functions is poorly understood. We assessed the effects of reduced precipitation with the aim of simulating realistic future drought conditions for one growing season on the bacterial community and its relation to soil properties and forest management. We manipulated precipitation in beech and conifer forest plots managed at different levels of intensity in three different regions across Germany. The precipitation reduction decreased soil water content across the growing season by between 2 to 8% depending on plot and region. T-RFLP analysis and pyrosequencing of the 16S rRNA gene were used to study the total soil bacterial community and its active members after six months of precipitation reduction. The effect of reduced precipitation on the total bacterial community structure was negligible while significant effects could be observed for the active bacteria. However, the effect was secondary to the stronger influence of specific soil characteristics across the three regions and management selection of overstorey tree species and their respective understorey vegetation. The impact of reduced precipitation differed between the studied plots; however, we could not determine the particular parameters being able to modify the response of the active bacterial community among plots. We conclude that the moderate drought induced by the precipitation manipulation treatment started to affect the active but not the total bacterial community, which points to an adequate resistance of the soil microbial system over one growing season.

  17. Bacterial community composition associated with freshwater algae: species specificity vs. dependency on environmental conditions and source community.

    Science.gov (United States)

    Eigemann, Falk; Hilt, Sabine; Salka, Ivette; Grossart, Hans-Peter

    2013-03-01

    We studied bacterial associations with the green alga Desmodesmus armatus and the diatom Stephanodiscus minutulus under changing environmental conditions and bacterial source communities, to evaluate whether bacteria-algae associations are species-specific or more generalized and determined by external factors. Axenic and xenic algae were incubated in situ with and without allelopathically active macrophytes, and in the laboratory with sterile and nonsterile lake water and an allelochemical, tannic acid (TA). Bacterial community composition (BCC) of algae-associated bacteria was analyzed by denaturing gradient gel electrophoresis (DGGE), nonmetric multidimensional scaling, cluster analyses, and sequencing of DGGE bands. BCC of xenic algal cultures of both species were not significantly affected by changes in their environment or bacterial source community, except in the case of TA additions. Species-specific interactions therefore appear to overrule the effects of environmental conditions and source communities. The BCC of xenic and axenic D. armatus cultures subjected to in situ bacterial colonization, however, had lower similarities (ca. 55%), indicating that bacterial precolonization is a strong factor for bacteria-algae associations irrespective of environmental conditions and source community. Our findings emphasize the ecological importance of species-specific bacteria-algae associations with important repercussions for other processes, such as the remineralization of nutrients, and organic matter dynamics. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  18. Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

    DEFF Research Database (Denmark)

    Klümper, Uli; Riber, Leise; Dechesne, Arnaud

    2014-01-01

    range of IncP- and IncPromA-type broad host range plasmids from three proteobacterial donors to a soil bacterial community. We identified transfer to many different recipients belonging to 11 different bacterial phyla. The prevalence of transconjugants belonging to diverse Gram-positive Firmicutes...... bacteria and can, therefore, directly connect large proportions of the soil bacterial gene pool. This finding reinforces the evolutionary and medical significances of these plasmids....

  19. Risk factors for community-acquired bacterial meningitis in adults

    NARCIS (Netherlands)

    Adriani, K.S.

    2015-01-01

    Bacterial meningitis is an inflammation of the meninges and occurs when bacteria invade the subarachnoid space. The meninges are the protective membranes that surround the brain and the spinal cord. Bacterial meningitis is a life-threatening disease because the proximity of the infection to the brai

  20. Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

    Science.gov (United States)

    Ulrich, Nikea; Rosenberger, Abigail; Brislawn, Colin; Wright, Justin; Kessler, Collin; Toole, David; Solomon, Caroline; Strutt, Steven; McClure, Erin

    2016-01-01

    ABSTRACT Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in which Betaproteobacteria and Gammaproteobacteria decreased in 16S rRNA gene relative abundance, while the relative abundance of members of the Firmicutes increased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains of Legionella, Campylobacter, Arcobacter, and Helicobacter, as well as bacteria of fecal origin (e.g., Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event. IMPORTANCE In order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study

  1. Invertebrate footprints on detritus processing, bacterial community structure, and spatiotemporal redox profiles

    NARCIS (Netherlands)

    Hunting, E.R.; Whatley, M.H.; van der Geest, H.G.; Mulder, C.; Kraak, M.H.S.; Breure, A.M.; Admiraal, W.

    2012-01-01

    Detritus processing is driven by a complex interplay between macroinvertebrate and microbial activities. Bioturbation/feeding activities of invertebrates in sediments are known to influence decomposition rates. However, direct effects of invertebrates on bacterial communities and detritus processing

  2. Profiling of root canal bacterial communities associated with chronic apical periodontitis from Brazilian and Norwegian subjects.

    Science.gov (United States)

    Siqueira, José F; Rôças, Isabela N; Debelian, Gilberto J; Carmo, Flávia L; Paiva, Simone S M; Alves, Flávio R F; Rosado, Alexandre S

    2008-12-01

    The aim of this study was to compare the bacterial community profiles of the root canal microbiota associated with chronic apical periodontitis from Brazilian and Norwegian patients using the denaturing gradient gel electrophoresis (DGGE) and the ribosomal intergenic spacer analysis (RISA) approaches. DNA extracted from root canal samples was subjected to polymerase chain reaction using primers appropriate for further DGGE or RISA analysis. The resulting banding patterns representative of the bacterial community structures in samples from the two locations were compared. DGGE and RISA fingerprints showed a great interindividual variability in the bacterial community profiles, irrespective of the geographic location of the patient. However, similarities among the bacterial community DGGE profiles revealed the existence of a geography-related pattern.

  3. Response of polar front phytoplankton and bacterial community to micronutrient amendments

    Digital Repository Service at National Institute of Oceanography (India)

    Jain, A.; Meena, R.M.; Naik, R.K.; Gomes, J.; Bandekar, M.; Bhat, M.; Mesquita, A.; Ramaiah, N.

    , to examine the responses of phytoplankton as well as bacterial community (BC) to these micronutrient amendments. Total chlorophyll a (Chl a) concentration increased significantly (P<0.01) in all micronutrient-enriched microcosms (MEM), with the incubation...

  4. Denaturing gradient gel electrophoresis profiling of bacterial communities composition in Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, S.K.; Ramaiah, N.

    Denaturing gradient gel electrophoresis (DGGE) was used to elucidate spatial and temporal variations in bacterial community composition (BCC) from four locations along the central west coast of India. DNA extracts from 36 water samples collected...

  5. Invertebrate footprints on detritus processing, bacterial community structure, and spatiotemporal redox profiles

    NARCIS (Netherlands)

    Hunting, E.R.; Whatley, M.H.; van der Geest, H.G.; Mulder, C.; Kraak, M.H.S.; Breure, A.M.; Admiraal, W.

    2012-01-01

    Detritus processing is driven by a complex interplay between macroinvertebrate and microbial activities. Bioturbation/feeding activities of invertebrates in sediments are known to influence decomposition rates. However, direct effects of invertebrates on bacterial communities and detritus processing

  6. Comparison of bacterial communities of conventional and A-stage activated sludge systems

    NARCIS (Netherlands)

    Gonzalez-Martinez, A.; Rodriguez-Sanchez, A.; Lotti, T.; Garcia-Ruiz, M.J.; Gonzalez-Lopez, J.; Van Loosdrecht, M.C.M.

    2016-01-01

    The bacterial community structure of 10 different wastewater treatment systems and their influents has been investigated through pyrosequencing, yielding a total of 283486 reads. These bioreactors had different technological configurations: conventional activated sludge (CAS) systems and very highly

  7. Impact of oil contamination and biostimulation on the diversity of indigenous bacterial communities in soil microcosms

    NARCIS (Netherlands)

    Evans, FF; Rosado, AS; Sebastian, GV; Casella, R; Machado, PLOA; Holmstrom, C; Kjelleberg, S; van Elsas, JD; Seldin, L

    2004-01-01

    The aim of this study was to analyse the effect of oil contamination and biostimulation (soil pH raise, and nitrogen, phosphate and sulphur addition) on the diversity of a bacterial community of an acidic Cambisol under Atlantic Forest. The experiment was based on the enumeration of bacterial popula

  8. Impact of oil contamination and biostimulation on the diversity of indigenous bacterial communities in soil microcosms

    NARCIS (Netherlands)

    Evans, FF; Rosado, AS; Sebastian, GV; Casella, R; Machado, PLOA; Holmstrom, C; Kjelleberg, S; van Elsas, JD; Seldin, L

    2004-01-01

    The aim of this study was to analyse the effect of oil contamination and biostimulation (soil pH raise, and nitrogen, phosphate and sulphur addition) on the diversity of a bacterial community of an acidic Cambisol under Atlantic Forest. The experiment was based on the enumeration of bacterial

  9. Application of nonlinear analysis methods for identifying relationships between microbial community structure and groundwater geochemistry.

    Science.gov (United States)

    Schryver, Jack C; Brandt, Craig C; Pfiffner, Susan M; Palumbo, Anthony V; Peacock, Aaron D; White, David C; McKinley, James P; Long, Philip E

    2006-02-01

    The relationship between groundwater geochemistry and microbial community structure can be complex and difficult to assess. We applied nonlinear and generalized linear data analysis methods to relate microbial biomarkers (phospholipids fatty acids, PLFA) to groundwater geochemical characteristics at the Shiprock uranium mill tailings disposal site that is primarily contaminated by uranium, sulfate, and nitrate. First, predictive models were constructed using feedforward artificial neural networks (NN) to predict PLFA classes from geochemistry. To reduce the danger of overfitting, parsimonious NN architectures were selected based on pruning of hidden nodes and elimination of redundant predictor (geochemical) variables. The resulting NN models greatly outperformed the generalized linear models. Sensitivity analysis indicated that tritium, which was indicative of riverine influences, and uranium were important in predicting the distributions of the PLFA classes. In contrast, nitrate concentration and inorganic carbon were least important, and total ionic strength was of intermediate importance. Second, nonlinear principal components (NPC) were extracted from the PLFA data using a variant of the feedforward NN. The NPC grouped the samples according to similar geochemistry. PLFA indicators of Gram-negative bacteria and eukaryotes were associated with the groups of wells with lower levels of contamination. The more contaminated samples contained microbial communities that were predominated by terminally branched saturates and branched monounsaturates that are indicative of metal reducers, actinomycetes, and Gram-positive bacteria. These results indicate that the microbial community at the site is coupled to the geochemistry and knowledge of the geochemistry allows prediction of the community composition.

  10. Application of Nonlinear Analysis Methods for Identifying Relationships Between Microbial Community Structure and Groundwater Geochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Schryver, Jack C.; Brandt, Craig C.; Pfiffner, Susan M.; Palumbo, A V.; Peacock, Aaron D.; White, David C.; McKinley, James P.; Long, Philip E.

    2006-02-01

    The relationship between groundwater geochemistry and microbial community structure can be complex and difficult to assess. We applied nonlinear and generalized linear data analysis methods to relate microbial biomarkers (phospholipids fatty acids, PLFA) to groundwater geochemical characteristics at the Shiprock uranium mill tailings disposal site that is primarily contaminated by uranium, sulfate, and nitrate. First, predictive models were constructed using feedforward artificial neural networks (NN) to predict PLFA classes from geochemistry. To reduce the danger of overfitting, parsimonious NN architectures were selected based on pruning of hidden nodes and elimination of redundant predictor (geochemical) variables. The resulting NN models greatly outperformed the generalized linear models. Sensitivity analysis indicated that tritium, which was indicative of riverine influences, and uranium were important in predicting the distributions of the PLFA classes. In contrast, nitrate concentration and inorganic carbon were least important, and total ionic strength was of intermediate importance. Second, nonlinear principal components (NPC) were extracted from the PLFA data using a variant of the feedforward NN. The NPC grouped the samples according to similar geochemistry. PLFA indicators of Gram-negative bacteria and eukaryotes were associated with the groups of wells with lower levels of contamination. The more contaminated samples contained microbial communities that were predominated by terminally branched saturates and branched monounsaturates that are indicative of metal reducers, actinomycetes, and Gram-positive bacteria. These results indicate that the microbial community at the site is coupled to the geochemistry and knowledge of the geochemistry allows prediction of the community composition.

  11. Comparative pyrosequencing analysis of bacterial community change in biofilm formed on seawater reverse osmosis membrane.

    Science.gov (United States)

    Kim, In S; Lee, Jinwook; Kima, Sung-Jo; Yu, Hye-Weon; Jang, Am

    2014-01-01

    The change in bacterial community structure induced by bacterial competition and succession was investigated during seawater reverse osmosis (SWRO) in order to elucidate a possible link between the bacterial consortium on SWRO membranes and biofouling. To date, there has been no definitive characterization of the microbial diversity in SWRO in terms of distinguishing time-dependent changes in the richness or abundance of bacterial species. For bacterial succession within biofilms on the membrane surface, SWRO using a cross-flow filtration membrane test unit was operated for 5 and 100h, respectively. As results of the pyrosequencing analysis, bacterial communities differed considerably among seawater and the 5 and 100 h samples. From a total of 33,876 pyrosequences (using a 95% sequence similarity), there were less than 1% of shared species, confirming the influence of the operational time factor and lack of similarity of these communities. During SWRO operation, the abundance of Pseudomonas stutzeri BBSPN3 (GU594474) belonging to gamma-Proteobacteria suggest that biofouling of SWRO membrane might be driven by the dominant influence of a specific species. In addition, among the bacterial competition of five bacterial species (Pseudomonas aeruginosa, Bacillus sp., Rhodobacter sp., Flavobacterium sp., and Mycobacterium sp.) competing for bacterial colonization on the SWRO membrane surfaces, it was exhibited that Bacillus sp. was the most dominant. The dominant influences ofPseudomonas sp. and Bacillus sp. on biofouling during actual SWRO is decisive depending on higher removal efficiency of the seawater pretreatment.

  12. Resource niche overlap promotes stability of bacterial community metabolism in experimental microcosms

    Directory of Open Access Journals (Sweden)

    Ellard Roy Hunting

    2015-02-01

    Full Text Available Decomposition of organic matter is an important ecosystem process governed in part by bacteria. The process of decomposition is expected to benefit from interspecific bacterial interactions such as resource partitioning and facilitation. However, the relative importance of resource niche breadth (metabolic diversity and resource niche overlap (functional redundancy on decomposition and the temporal stability of ecosystem processes received little scientific attention. Therefore, this study aims to evaluate the effect of an increase in bacterial community resemblance on both decomposition and the stability of bacterial metabolism in aquatic sediments. To this end, we performed laboratory microcosm experiments in which we examined the influence of bacterial consortia differing in number and composition of species on bacterial activity (Electron Transport System Activity, ETSA, dissolved organic carbon production and wavelet transformed measurements of redox potential (Eh. Single substrate affinities of the individual bacterial species in order to calculate the metabolic diversity of the microbial community. Results presented here indicate that bacterial activity and organic matter decomposition increase with widening of the resource niche breadth, and that metabolic stability increases with increasing overlap in bacterial resource niches, hinting that resource niche overlap can promote the stability of bacterial community metabolism.

  13. Exploration of methods used to describe bacterial communities in silage of maize (Zea mays) cultivars.

    Science.gov (United States)

    Brusetti, Lorenzo; Borin, Sara; Rizzi, Aurora; Mora, Diego; Sorlini, Claudia; Daffonchio, Daniele

    2008-01-01

    Different techniques to assess bacterial community structure and diversity were evaluated in silages prepared with four different maize cultivars, three conventional and one transgenic (cv. Tundra, event Bt-176). Plants were cultivated in the greenhouse and harvested after 30 days of growth. Silage samples were collected at successive times during fermentation and analyzed for bacterial counts and by various DNA-based fingerprinting techniques. Bacterial counts were similar between cultivars for the total culturable bacteria, sporeforming, and mesophilic and thermophilic lactic acid bacteria (LAB). Further analysis of the species composition of 388 LAB strains by intergenic transcribed spacer (ITS) PCR followed by sequencing of 16S rRNA gene did not reveal differences between cultivars. In contrast, molecular fingerprinting methods targeting whole bacterial communities, such as automated ribosomal intergenic spacers analysis (ARISA) and 16S rRNA gene length heterogeneity-PCR (LH-PCR), indicated that different maize silage batches or cultivars hosted different bacterial communities. Thus, ARISA and LH-PCR fingerprinting techniques offer a fast and sensitive method to compare bacterial communities, and to detect differences in silage bacterial communities.

  14. Distinct soil bacterial communities along a small-scale elevational gradient in alpine tundra

    Directory of Open Access Journals (Sweden)

    Congcong eShen

    2015-06-01

    Full Text Available The elevational diversity pattern for microorganisms has received great attention recently but is still understudied, and phylogenetic relatedness is rarely studied for microbial elevational distributions. Using a bar-coded pyrosequencing technique, we examined the biodiversity patterns for soil bacterial communities of tundra ecosystem along 2000–2500 m elevations on Changbai Mountain in China. Bacterial taxonomic richness displayed a linear decreasing trend with increasing elevation. Phylogenetic diversity and mean nearest taxon distance (MNTD exhibited a unimodal pattern with elevation. Bacterial communities were more phylogenetically clustered than expected by chance at all elevations based on the standardized effect size of MNTD metric. The bacterial communities differed dramatically among elevations, and the community composition was significantly correlated with soil total carbon, total nitrogen, C:N ratio, and dissolved organic carbon. Multiple ordinary least squares regression analysis showed that the observed biodiversity patterns strongly correlated with soil total carbon and C:N ratio. Taken together, this is the first time that a significant bacterial diversity pattern has been observed across a small-scale elevational gradient. Our results indicated that soil carbon and nitrogen contents were the critical environmental factors affecting bacterial elevational distribution in Changbai Mountain tundra. This suggested that ecological niche-based environmental filtering processes related to soil carbon and nitrogen contents could play a dominant role in structuring bacterial communities along the elevational gradient.

  15. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-01-01

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management. PMID:27650273

  16. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-09-01

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management.

  17. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests.

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-09-21

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management.

  18. Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

    Directory of Open Access Journals (Sweden)

    Christopher L. Hemme

    2016-04-01

    Full Text Available Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe2+/Pb2+ permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co2+/Zn2+/Cd2+ efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome.

  19. Comparative Analysis of the Composition of Intestinal Bacterial Communities in Dastarcus helophoroides Fed Different Diets

    OpenAIRE

    Wang, Wei-Wei; He, Cai; Cui, Jun; Wang, Hai-dong; Li, Meng-Lou

    2014-01-01

    The diversity of the intestinal bacterial communities in Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) larvae and adults was assayed by PCR-DGGE to determine whether different artificial diets could influence these bacterial communities. Two diets were used for feeding the larvae and four for the adults. Escherichia, Desemzia, Staphylococcus, Asticcacaulis, Cellvibrio, Aurantimonas, and Planomicrobium were isolated from the gut of the adults, with Escherichia and Staphylococ...

  20. Bacterial Community Structure and Biochemical Changes Associated With Composting of Lignocellulosic Oil Palm Empty Fruit Bunch

    OpenAIRE

    Mohd Huzairi Mohd Zainudin; Mohd Ali Hassan,; Umi Kalsom Md Shah; Norhani Abdullah; Mitsunori Tokura; Hisashi Yasueda; Yoshihito Shirai; Kenji Sakai; Azhari Samsu Baharuddin

    2013-01-01

    Bacterial community structure and biochemical changes during the composting of lignocellulosic oil palm empty bunch (EFB) and palm oil mill effluent (POME) anaerobic sludge were studied by examining the succession of the bacterial community and its association with changes in lignocellulosic components by denaturing gradient gel electrophoresis (DGGE) and the 16S rRNA gene clone library. During composting, a major reduction in cellulose after 10 days from 50% to 19% and the carbon content fro...

  1. Phosphorus chemistry and bacterial community composition interact in brackish sediments receiving agricultural discharges.

    Directory of Open Access Journals (Sweden)

    Hanna Sinkko

    Full Text Available BACKGROUND: External nutrient discharges have caused eutrophication in many estuaries and coastal seas such as the Baltic Sea. The sedimented nutrients can affect bacterial communities which, in turn, are widely believed to contribute to release of nutrients such as phosphorus from the sediment. METHODS: We investigated relationships between bacterial communities and chemical forms of phosphorus as well as elements involved in its cycling in brackish sediments using up-to-date multivariate statistical methods. Bacterial community composition was determined by terminal restriction fragment length polymorphism and cloning of the 16S rRNA gene. RESULTS AND CONCLUSIONS: The bacterial community composition differed along gradients of nutrients, especially of different phosphorus forms, from the estuary receiving agricultural phosphorus loading to the open sea. This suggests that the chemical composition of sediment phosphorus, which has been affected by riverine phosphorus loading, influenced on bacterial communities. Chemical and spatial parameters explained 25% and 11% of the variation in bacterial communities. Deltaproteobacteria, presumptively sulphate and sulphur/iron reducing, were strongly associated to chemical parameters, also when spatial autocorrelation was taken into account. Sulphate reducers correlated positively with labile organic phosphorus and total nitrogen in the open sea sediments. Sulphur/iron reducers and sulphate reducers linked to iron reduction correlated positively with aluminium- and iron-bound phosphorus, and total iron in the estuary. The sulphate and sulphur/iron reducing bacteria can thus have an important role both in the mineralization and mobilization of nutrients from sediment. SIGNIFICANCE: Novelty in our study is that relationships between bacterial community composition and different phosphorus forms, instead of total phosphorus, were investigated. Total phosphorus does not necessarily bring out interactions

  2. Spatial scaling effects on soil bacterial communities in Malaysian tropical forests.

    Science.gov (United States)

    Tripathi, Binu M; Lee-Cruz, Larisa; Kim, Mincheol; Singh, Dharmesh; Go, Rusea; Shukor, Noraini A A; Husni, M H A; Chun, Jongsik; Adams, Jonathan M

    2014-08-01

    Spatial scaling to some extent determines biodiversity patterns in larger organisms, but its role in microbial diversity patterns is much less understood. Some studies have shown that bacterial community similarity decreases with distance, whereas others do not support this. Here, we studied soil bacterial communities of tropical rainforest in Malaysia at two spatial scales: a local scale with samples spaced every 5 mover a 150-m transect, and a regional scale with samples 1 to 1,800 km apart. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1–V3 region was pyrosequenced using Roche/454 GS FLX Titanium platform. A ranked partial Mantel test showed a weak correlation between spatial distance and whole bacterial community dissimilarity, but only at the local scale. In contrast, environmental distance was highly correlated with community dissimilarity at both spatial scales,stressing the greater role of environmental variables rather than spatial distance in determining bacterial community variation at different spatial scales. Soil pH was the only environmental parameter that significantly explained the variance in bacterial community at the local scale, whereas total nitrogen and elevation were additional important factors at the regional scale.We obtained similar results at both scales when only the most abundant OTUs were analyzed. A variance partitioning analysis showed that environmental variables contributed more to bacterial community variation than spatial distance at both scales. In total, our results support a strong influence of the environment in determining bacterial community composition in the rainforests of Malaysia. However, it is possible that the remaining spatial distance effect is due to some of the myriad of other environmental factors which were not considered here, rather than dispersal limitation.

  3. Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland

    Science.gov (United States)

    Weedon, James T.; Kowalchuk, George A.; Aerts, Rien; Freriks, Stef; Röling, Wilfred F. M.; van Bodegom, Peter M.

    2017-01-01

    The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50–100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12–15% of variance explained) > temporal variation (7–11%) > climate treatment (4–9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates—evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts.

  4. Spatial scales of bacterial community diversity at cold seeps (Eastern Mediterranean Sea).

    Science.gov (United States)

    Pop Ristova, Petra; Wenzhöfer, Frank; Ramette, Alban; Felden, Janine; Boetius, Antje

    2015-06-01

    Cold seeps are highly productive, fragmented marine ecosystems that form at the seafloor around hydrocarbon emission pathways. The products of microbial utilization of methane and other hydrocarbons fuel rich chemosynthetic communities at these sites, with much higher respiration rates compared with the surrounding deep-sea floor. Yet little is known as to the richness, composition and spatial scaling of bacterial communities of cold seeps compared with non-seep communities. Here we assessed the bacterial diversity across nine different cold seeps in the Eastern Mediterranean deep-sea and surrounding seafloor areas. Community similarity analyses were carried out based on automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and high-throughput 454 tag sequencing and were combined with in situ and ex situ geochemical analyses across spatial scales of a few tens of meters to hundreds of kilometers. Seep communities were dominated by Deltaproteobacteria, Epsilonproteobacteria and Gammaproteobacteria and shared, on average, 36% of bacterial types (ARISA OTUs (operational taxonomic units)) with communities from nearby non-seep deep-sea sediments. Bacterial communities of seeps were significantly different from those of non-seep sediments. Within cold seep regions on spatial scales of only tens to hundreds of meters, the bacterial communities differed considerably, sharing cold seep ecosystems contribute substantially to the microbial diversity of the deep-sea.

  5. Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria

    Science.gov (United States)

    Srinivasan, Sujatha; Hoffman, Noah G.; Morgan, Martin T.; Matsen, Frederick A.; Fiedler, Tina L.; Hall, Robert W.; Ross, Frederick J.; McCoy, Connor O.; Bumgarner, Roger; Marrazzo, Jeanne M.; Fredricks, David N.

    2012-01-01

    Background Bacterial vaginosis (BV) is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV. Methodology/Principal Findings Broad-range 16S rRNA gene PCR and pyrosequencing were performed on vaginal swabs from 220 women with and without BV. BV was assessed by Amsel’s clinical criteria and confirmed by Gram stain. Taxonomic classification was performed using phylogenetic placement tools that assigned 99% of query sequence reads to the species level. Women with BV had heterogeneous vaginal bacterial communities that were usually not dominated by a single taxon. In the absence of BV, vaginal bacterial communities were dominated by either Lactobacillus crispatus or Lactobacillus iners. Leptotrichia amnionii and Eggerthella sp. were the only two BV-associated bacteria (BVABs) significantly associated with each of the four Amsel’s criteria. Co-occurrence analysis revealed the presence of several sub-groups of BVABs suggesting metabolic co-dependencies. Greater abundance of several BVABs was observed in Black women without BV. Conclusions/Significance The human vaginal bacterial biota is heterogeneous and marked by greater species richness and diversity in women with BV; no species is universally present. Different bacterial species have different associations with the four clinical criteria, which may account for discrepancies often observed between Amsel and Nugent (Gram stain) diagnostic criteria. Several BVABs exhibited race-dependent prevalence when analyzed in separate groups by BV status which may contribute to increased incidence of BV in

  6. Identifying the sources of nitrate contamination of groundwater in an agricultural area (Haean basin, Korea) using isotope and microbial community analyses

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Heejung [School of Earth and Environmental Sciences (BK21 SEES), Seoul National University, Seoul 151–747 (Korea, Republic of); Kaown, Dugin, E-mail: dugin1@snu.ac.kr [School of Earth and Environmental Sciences (BK21 SEES), Seoul National University, Seoul 151–747 (Korea, Republic of); Mayer, Bernhard [Department of Geoscience, University of Calgary, 2500 University Drive NW, Calgary T2N 1N4, Alberta (Canada); Lee, Jin-Yong [Department of Geology, Kangwon National University, Chuncheon 200–701 (Korea, Republic of); Hyun, Yunjung [Planning and Management Group, Korea Environment Institute, Sejong 339-007 (Korea, Republic of); Lee, Kang-Kun [School of Earth and Environmental Sciences (BK21 SEES), Seoul National University, Seoul 151–747 (Korea, Republic of)

    2015-11-15

    An integrated study based on hydrogeochemical, microbiological and dual isotopic approaches for nitrate and sulfate was conducted to elucidate sources and biogeochemical reactions governing groundwater contaminants in different seasons and under different land use in a basin of Korea. The land use in the study area is comprised of forests (58.0%), vegetable fields (27.6%), rice paddy fields (11.4%) and others (3.0%). The concentrations of NO{sub 3}–N and SO{sub 4}{sup 2−} in groundwater in vegetable fields were highest with 4.2–15.2 mg L{sup −1} and 1.6–19.7 mg L{sup −1} respectively, whereas under paddy fields NO{sub 3}–N concentrations ranged from 0 to 10.7 mg L{sup −1} and sulfate concentrations were ~ 15 mg L{sup −1}. Groundwater with high NO{sub 3}–N concentrations of > 10 mg L{sup −1} had δ{sup 15}N–NO{sub 3}{sup −} values ranging from 5.2 to 5.9‰ and δ{sup 18}O values of nitrate between 2.7 and 4.6‰ suggesting that the nitrate was mineralized from soil organic matter that was amended by fertilizer additions. Elevated concentrations of SO{sub 4}{sup 2−} with δ{sup 34}S–SO{sub 4}{sup 2−} values between 1 and 6‰ in aquifers in vegetable fields indicated that a mixture of sulfate from atmospheric deposition, mineralization of soil organic matter and from synthetic fertilizers is the source of groundwater sulfate. Elevated δ{sup 18}O–NO{sub 3}{sup −} and δ{sup 18}O–SO{sub 4}{sup 2−} values in samples collected from the paddy fields indicated that denitrification and bacterial sulfate reduction are actively occurring removing sulfate and nitrate from the groundwater. This was supported by high occurrences of denitrifying and sulfate reducing bacteria in groundwater of the paddy fields as evidenced by 16S rRNA pyrosequencing analysis. This study shows that dual isotope techniques combined with microbial data can be a powerful tool for identification of sources and microbial processes affecting NO{sub 3}{sup

  7. Contrasting Ecological Processes and Functional Compositions Between Intestinal Bacterial Community in Healthy and Diseased Shrimp.

    Science.gov (United States)

    Zhu, Jinyong; Dai, Wenfang; Qiu, Qiongfen; Dong, Chunming; Zhang, Jinjie; Xiong, Jinbo

    2016-11-01

    Intestinal bacterial communities play a pivotal role in promoting host health; therefore, the disruption of intestinal bacterial homeostasis could result in disease. However, the effect of the occurrences of disease on intestinal bacterial community assembly remains unclear. To address this gap, we compared the multifaceted ecological differences in maintaining intestinal bacterial community assembly between healthy and diseased shrimps. The neutral model analysis shows that the relative importance of neutral processes decreases when disease occurs. This pattern is further corroborated by the ecosphere null model, revealing that the bacterial community assembly of diseased samples is dominated by stochastic processes. In addition, the occurrence of shrimp disease reduces the complexity and cooperative activities of species-to-species interactions. The keystone taxa affiliated with Alphaproteobacteria and Actinobacteria in healthy shrimp gut shift to Gammaproteobacteria species in diseased shrimp. Changes in intestinal bacterial communities significantly alter biological functions in shrimp. Within a given metabolic pathway, the pattern of enrichment or decrease between healthy and deceased shrimp is correlated with its functional effects. We propose that stressed shrimp are more prone to invasion by alien strains (evidenced by more stochastic assembly and higher migration rate in diseased shrimp), which, in turn, disrupts the cooperative activity among resident species. These findings greatly aid our understanding of the underlying mechanisms that govern shrimp intestinal community assembly between health statuses.

  8. A Greenhouse Assay on the Effect of Applied Urea Amount on the Rhizospheric Soil Bacterial Communities.

    Science.gov (United States)

    Shang, Shuanghua; Yi, Yanli

    2015-12-01

    The rhizospheric bacteria play key role in plant nutrition and growth promotion. The effects of increased nitrogen inputs on plant rhizospheric soils also have impacted on whole soil microbial communities. In this study, we analyzed the effects of applied nitrogen (urea) on rhizospheric bacterial composition and diversity in a greenhouse assay using the high-throughput sequencing technique. To explore the environmental factors driving the abundance, diversity and composition of soil bacterial communities, the relationship between soil variables and the bacterial communities were also analyzed using the mantel test as well as the redundancy analysis. The results revealed significant bacterial diversity changes at different amounts of applied urea, especially between the control treatment and the N fertilized treatments. Mantel tests showed that the bacterial communities were significantly correlated with the soil nitrate nitrogen, available nitrogen, soil pH, ammonium nitrogen and total organic carbon. The present study deepened the understanding about the rhizospheric soil microbial communities under different amounts of applied urea in greenhouse conditions, and our work revealed the environmental factors affecting the abundance, diversity and composition of rhizospheric bacterial communities.

  9. Structure of bacterial communities along a hydrocarbon contamination gradient in a coastal sediment.

    Science.gov (United States)

    Paissé, Sandrine; Coulon, Frédéric; Goñi-Urriza, Marisol; Peperzak, Louis; McGenity, Terry J; Duran, Robert

    2008-11-01

    The bacterial diversity of a chronically oil-polluted retention basin sediment located in the Berre lagoon (Etang-de-Berre, France) was investigated. This study combines chemical and molecular approaches in order to define how the in situ petroleum hydrocarbon contamination level affects the bacterial community structure of a subsurface sediment. Hydrocarbon content analysis clearly revealed a gradient of hydrocarbon contamination in both the water and the sediment following the basin periphery from the pollution input to the lagoon water. The nC17 and pristane concentrations suggested alkane biodegradation in the sediments. These results, combined with those of terminal-restriction fragment length polymorphism analysis of the 16S rRNA genes, indicated that bacterial community structure was obviously associated with the gradient of oil contamination. The analysis of bacterial community composition revealed dominance of bacteria related to the Proteobacteria phylum (Gamma-, Delta-, Alpha-, Epsilon- and Betaproteobacteria), Bacteroidetes and Verrucomicrobium groups and Spirochaetes, Actinobacteria and Cyanobacteria phyla. The adaptation of the bacterial community to oil contamination was not characterized by dominance of known oil-degrading bacteria, because a predominance of populations associated to the sulphur cycle was observed. The input station presented particular bacterial community composition associated with a low oil concentration in the sediment, indicating the adaptation of this community to the oil contamination.

  10. A Phloem-Feeding Insect Transfers Bacterial Endophytic Communities between Grapevine Plants

    Directory of Open Access Journals (Sweden)

    Sebastiàn Lòpez-Fernàndez

    2017-05-01

    Full Text Available Bacterial endophytes colonize the inner tissues of host plants through the roots or through discontinuities on the plant surface, including wounds and stomata. Little is known regarding a possible role of insects in acquiring and transmitting non-phytopathogenic microorganisms from plant to plant, especially those endophytes that are beneficial symbionts providing plant protection properties and homeostatic stability to the host. To understand the ecological role of insects in the transmission of endophytic bacteria, we used freshly hatched nymphs of the American sap-feeding leafhopper Scaphoideus titanus (vector to transfer microorganisms across grapevine plants. After contact with the vector, sink plants were colonized by a complex endophytic community dominated by Proteobacteria, highly similar to that present in source plants. A similar bacterial community, but with a higher ratio of Firmicutes, was found on S. titanus. Insects feeding only on sink plants transferred an entirely different bacterial community dominated by Actinobacteria, where Mycobacterium sp., played a major role. Despite the fact that insects dwelled mostly on plant stems, the bacterial communities in plant roots resembled more closely those inside and on insects, when compared to those of above-ground plant organs. We prove here the potential of insect vectors to transfer entire endophytic bacterial communities between plants. We also describe the role of plants and bacterial endophytes in establishing microbial communities in plant-feeding insects.

  11. Bacterial community structure and diversity in a black soil as affected by long-term fertilization

    Institute of Scientific and Technical Information of China (English)

    WEI Dan; YANG Qian; ZHANG Jun-Zheng; WANG Shuang; CHEN Xue-Li; ZHANG Xi-Lin; LI Wei-Qun

    2008-01-01

    Black soil (Mollisol) is one of the main soil types in northeastern China.Biolog and polymerase chain reactiondenaturing gradient gel electrophoresis (PCR-DGGE) methods were used to examine the influence of various fertilizer combinations on the structure and function of the bacterial community in a black soil collected from Harbin,Heilongjiang Province.Biolog results showed that substrate richness and catabolic diversity of the soil bacterial community were the greatest in the chemical fertilizer and chemical fertilizer+manure treatments.The metabolic ability of the bacterial community in the manure treatment was similar to the control.DGGE fingerprinting indicated similarity in the distribution of most 16S rDNA bands among all treatments,suggesting that microorganisms with those bands were stable and not influenced by fertilization.However,chemical fertilizer increased the diversity of soil bacterial community.Principal component analysis of Biolog and DGGE data revealed that the structure and function of the bacterial community were similar in the control and manure treatments,suggesting that the application of manure increased the soil microbial population,but had no effect on the bacterial community structure.Catabolic function was similar in the chemical fertilizer and chemical fertilizer+manure treatments,but the composition structure of the soil microbes differed between them.The use of chemical fertilizers could result in a decline in the catabolic activity of fast-growing or eutrophic bacteria.

  12. Carbon transformations by attached bacterial populations in granitic groundwater from deep crystalline bed-rock of the Stripa research mine.

    Science.gov (United States)

    Ekendahl, S; Pedersen, K

    1994-07-01

    This paper presents and compares the assimilation rates of CO2 and lactate, and the lactate respiration rates, of attached bacterial populations growing in slowly flowing groundwater (1-3 mm s-1) from deep crystalline bed-rock of the Stripa research mine, Sweden. The bacteria studied grew in anoxic, high-pH (9-10) and low-redox artesian groundwater flowing up through tubing from two levels of a borehole designated V2, 812-820 m and 970-1240 m below ground. Bacteria were allowed to attach to and grow on sterile glass microscope slides in laminar-flow reactors connected to the flowing groundwater. Total numbers of bacteria were counted by acridine orange direct counts. The bacteria grew slowly, with doubling times of 34 d at 10 degrees C for the 812-820 m population, 23 d for the 970-1240 m population at 10 degrees C and 16 d for this population at 20 degrees C. Numbers of attached bacteria reached between 10(6) and 10(7) bacteria cm-2. The populations at the two levels of the borehole were different in physiology as well as in phylogeny and reflected the heterogeneity between the sampling levels. The earlier proposed presence of sulphate-reducing bacteria could not be confirmed. This is discussed in relation to results from 16S rRNA gene sequencing studies. The CO2 assimilation rates (as mol CO2 cm-2 h-1, using liquid scintillation techniques) increased with depth and temperature.(ABSTRACT TRUNCATED AT 250 WORDS)

  13. Establishment of Bacterial Herbicide Degraders in a Rapid Sand Filter for Bioremediation of Phenoxypropionate-Polluted Groundwater.

    Science.gov (United States)

    Feld, Louise; Nielsen, Tue Kjærgaard; Hansen, Lars Hestbjerg; Aamand, Jens; Albers, Christian Nyrop

    2015-11-20

    In this study, we investigated the establishment of natural bacterial degraders in a sand filter treating groundwater contaminated with the phenoxypropionate herbicides (RS)-2-(4-chloro-2-methylphenoxy)propanoic acid (MCPP) and (RS)-2-(2,4-dichlorophenoxy)propanoic acid (DCPP) and the associated impurity/catabolite 4-chlorophenoxypropanoic acid (4-CPP). A pilot facility was set up in a contaminated landfill site. Anaerobic groundwater was pumped up and passed through an aeration basin and subsequently through a rapid sand filter, which is characterized by a short residence time of the water in the filter. For 3 months, the degradation of DCPP, MCPP, and 4-CPP in the sand filter increased to 15 to 30% of the inlet concentration. A significant selection for natural bacterial herbicide degraders also occurred in the sand filter. Using a most-probable-number (MPN) method, we found a steady increase in the number of culturable phenoxypropionate degraders, reaching approximately 5 × 10(5) degraders per g sand by the end of the study. Using a quantitative PCR targeting the two phenoxypropionate degradation genes, rdpA and sdpA, encoding stereospecific dioxygenases, a parallel increase was observed, but with the gene copy numbers being about 2 to 3 log units higher than the MPN. In general, the sdpA gene was more abundant than the rdpA gene, and the establishment of a significant population of bacteria harboring sdpA occurred faster than the establishment of an rdpA gene-carrying population. The identities of the specific herbicide degraders in the sand filter were assessed by Illumina MiSeq sequencing of 16S rRNA genes from sand filter samples and from selected MPN plate wells. We propose a list of potential degrader bacteria involved in herbicide degradation, including representatives belonging to the Comamonadaceae and Sphingomonadales.

  14. The impact of shrimp farming effluent on bacterial communities in mangrove waters, Ceará, Brazil.

    Science.gov (United States)

    Sousa, O V; Macrae, A; Menezes, F G R; Gomes, N C M; Vieira, R H S F; Mendonça-Hagler, L C S

    2006-12-01

    The effects of shrimp farm effluents on bacterial communities in mangroves have been infrequently reported. Classic and molecular biology methods were used to survey bacterial communities from four mangroves systems. Water temperature, salinity, pH, total heterotrophic bacteria and maximum probable numbers of Vibrio spp. were investigated. Genetic profiles of bacterial communities were also characterized by polymerase chain reaction (PCR) amplification of eubacterial and Vibrio 16S rDNA using denaturing gradient gel electrophoresis (DGGE). Highest heterotrophic counts were registered in the mangrove not directly polluted by shrimp farming. The Enterobacteriaceae and Chryseomonas luteola dominated the heterotrophic isolates. Vibrio spp. pathogenic to humans and shrimps were identified. Eubacterial genetic profiles suggest a shared community structure independent of mangrove system. Vibrio genetic profiles were mangrove specific. Neither microbial counts nor genetic profiling revealed a significant decrease in species richness associated with shrimp farm effluent. The complex nature of mangrove ecosystems and their microbial communities is discussed.

  15. Nitrogen deposition alters soil chemical properties and bacterial communities in the Inner Mongolia grassland

    Institute of Scientific and Technical Information of China (English)

    Ximei Zhang; Xingguo Han

    2012-01-01

    Nitrogen deposition has dramatically altered biodiversity and ecosystem functioning on the earth; however,its effects on soil bacterial community and the underlying mechanisms of these effects have not been thoroughly examined.Changes in ecosystems caused by nitrogen deposition have traditionally been attributed to increased nitrogen content.In fact,nitrogen deposition not only leads to increased soil total N content,but also changes in the NH4+-N content,NO3--N content and pH,as well as changes in the heterogeneity of the four indexes.The soil indexes for these four factors,their heterogeneity and even the plant community might be routes through which nitrogen deposition alters the bacterial community.Here,we describe a 6-year nitrogen addition experiment conducted in a typical steppe ecosystem to investigate the ecological mechanism by which nitrogen deposition alters bacterial abundance,diversity and composition.We found that various characteristics of the bacterial community were explained by different environmental factors.Nitrogen deposition decreased bacterial abundance that is positively related to soil pH value.In addition,nitrogen addition decreased bacterial diversity,which is negatively related to soil total N content and positively related to soil NO3--N heterogeneity.Finally,nitrogen.addition altered bacterial composition that is significantly related to soil NH4+-N content.Although nitrogen deposition significantly altered plant biomass,diversity and composition,these characteristics of plant community did not have a significant impact on processes of nitrogen deposition that led to alterations in bacterial abundance,diversity and composition.Therefore,more sensitive molecular technologies should be adopted to detect the subtle shifts of microbial community structure induced by the changes of plant community upon nitrogen deposition.

  16. Inter- and Intraspecific Variations of Bacterial Communities Associated with Marine Sponges from San Juan Island, Washington

    KAUST Repository

    Lee, O. O.

    2009-04-10

    This study attempted to assess whether conspecific or congeneric sponges around San Juan Island, Washington, harbor specific bacterial communities. We used a combination of culture-independent DNA fingerprinting techniques (terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis [DGGE]) and culture-dependent approaches. The results indicated that the bacterial communities in the water column consisted of more diverse bacterial ribotypes than and were drastically different from those associated with the sponges. High levels of similarity in sponge-associated bacterial communities were found only in Myxilla incrustans and Haliclona rufescens, while the bacterial communities in Halichondria panicea varied substantially among sites. Certain terminal restriction fragments or DGGE bands were consistently obtained for different individuals of M. incrustans and H. rufescens collected from different sites, suggesting that there are stable or even specific associations of certain bacteria in these two sponges. However, no specific bacterial associations were found for H. panicea or for any one sponge genus. Sequencing of nine DGGE bands resulted in recovery of seven sequences that best matched the sequences of uncultured Proteobacteria. Three of these sequences fell into the sponge-specific sequence clusters previously suggested. An uncultured alphaproteobacterium and a culturable Bacillus sp. were found exclusively in all M. incrustans sponges, while an uncultured gammaproteobacterium was unique to H. rufescens. In contrast, the cultivation approach indicated that sponges contained a large proportion of Firmicutes, especially Bacillus, and revealed large variations in the culturable bacterial communities associated with congeneric and conspecific sponges. This study revealed sponge species-specific but not genus- or site-specific associations between sponges and bacterial communities and emphasized the importance of using a combination

  17. Inter- and Intraspecific Variations of Bacterial Communities Associated with Marine Sponges from San Juan Island, Washington▿

    Science.gov (United States)

    Lee, On On; Wong, Yue Him; Qian, Pei-Yuan

    2009-01-01

    This study attempted to assess whether conspecific or congeneric sponges around San Juan Island, Washington, harbor specific bacterial communities. We used a combination of culture-independent DNA fingerprinting techniques (terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis [DGGE]) and culture-dependent approaches. The results indicated that the bacterial communities in the water column consisted of more diverse bacterial ribotypes than and were drastically different from those associated with the sponges. High levels of similarity in sponge-associated bacterial communities were found only in Myxilla incrustans and Haliclona rufescens, while the bacterial communities in Halichondria panicea varied substantially among sites. Certain terminal restriction fragments or DGGE bands were consistently obtained for different individuals of M. incrustans and H. rufescens collected from different sites, suggesting that there are stable or even specific associations of certain bacteria in these two sponges. However, no specific bacterial associations were found for H. panicea or for any one sponge genus. Sequencing of nine DGGE bands resulted in recovery of seven sequences that best matched the sequences of uncultured Proteobacteria. Three of these sequences fell into the sponge-specific sequence clusters previously suggested. An uncultured alphaproteobacterium and a culturable Bacillus sp. were found exclusively in all M. incrustans sponges, while an uncultured gammaproteobacterium was unique to H. rufescens. In contrast, the cultivation approach indicated that sponges contained a large proportion of Firmicutes, especially Bacillus, and revealed large variations in the culturable bacterial communities associated with congeneric and conspecific sponges. This study revealed sponge species-specific but not genus- or site-specific associations between sponges and bacterial communities and emphasized the importance of using a combination

  18. Airborne Bacterial Communities in Residences: Similarities and Differences with Fungi

    OpenAIRE

    2014-01-01

    Genetic analysis of indoor air has uncovered a rich microbial presence, but rarely have both the bacterial and fungal components been examined in the same samples. Here we present a study that examined the bacterial component of passively settled microbes from both indoor and outdoor air over a discrete time period and for which the fungal component has already been reported. Dust was allowed to passively settle in five common locations around a home - living room, bedroom, bathroom, kitchen,...

  19. Airborne bacterial communities in residences: similarities and differences with fungi.

    Science.gov (United States)

    Adams, Rachel I; Miletto, Marzia; Lindow, Steven E; Taylor, John W; Bruns, Thomas D

    2014-01-01

    Genetic analysis of indoor air has uncovered a rich microbial presence, but rarely have both the bacterial and fungal components been examined in the same samples. Here we present a study that examined the bacterial component of passively settled microbes from both indoor and outdoor air over a discrete time period and for which the fungal component has already been reported. Dust was allowed to passively settle in five common locations around a home - living room, bedroom, bathroom, kitchen, and balcony - at different dwellings within a university-housing complex for a one-month period at two time points, once in summer and again in winter. We amplified the bacterial 16S rRNA gene in these samples and analyzed them with high-throughput sequencing. Like fungal OTU-richness, bacterial OTU-richness was higher outdoors then indoors and was invariant across different indoor room types. While fungal composition was structured largely by season and residential unit, bacterial composition varied by residential unit and room type. Bacteria from putative outdoor sources, such as Sphingomonas and Deinococcus, comprised a large percentage of the balcony samples, while human-associated taxa comprised a large percentage of the indoor samples. Abundant outdoor bacterial taxa were also observed indoors, but the reverse was not true; this is unlike fungi, in which the taxa abundant indoors were also well-represented outdoors. Moreover, there was a partial association of bacterial composition and geographic distance, such that samples separated by even a few hundred meters tended have greater compositional differences than samples closer together in space, a pattern also observed for fungi. These data show that while the outdoor source for indoor bacteria and fungi varies in both space and time, humans provide a strong and homogenizing effect on indoor bacterial bioaerosols, a pattern not observed in fungi.

  20. Airborne bacterial communities in residences: similarities and differences with fungi.

    Directory of Open Access Journals (Sweden)

    Rachel I Adams

    Full Text Available Genetic analysis of indoor air has uncovered a rich microbial presence, but rarely have both the bacterial and fungal components been examined in the same samples. Here we present a study that examined the bacterial component of passively settled microbes from both indoor and outdoor air over a discrete time period and for which the fungal component has already been reported. Dust was allowed to passively settle in five common locations around a home - living room, bedroom, bathroom, kitchen, and balcony - at different dwellings within a university-housing complex for a one-month period at two time points, once in summer and again in winter. We amplified the bacterial 16S rRNA gene in these samples and analyzed them with high-throughput sequencing. Like fungal OTU-richness, bacterial OTU-richness was higher outdoors then indoors and was invariant across different indoor room types. While fungal composition was structured largely by season and residential unit, bacterial composition varied by residential unit and room type. Bacteria from putative outdoor sources, such as Sphingomonas and Deinococcus, comprised a large percentage of the balcony samples, while human-associated taxa comprised a large percentage of the indoor samples. Abundant outdoor bacterial taxa were also observed indoors, but the reverse was not true; this is unlike fungi, in which the taxa abundant indoors were also well-represented outdoors. Moreover, there was a partial association of bacterial composition and geographic distance, such that samples separated by even a few hundred meters tended have greater compositional differences than samples closer together in space, a pattern also observed for fungi. These data show that while the outdoor source for indoor bacteria and fungi varies in both space and time, humans provide a strong and homogenizing effect on indoor bacterial bioaerosols, a pattern not observed in fungi.

  1. Soil-borne bacterial structure and diversity does not reflect community activity in Pampa biome.

    Directory of Open Access Journals (Sweden)

    Manoeli Lupatini

    Full Text Available The Pampa biome is considered one of the main hotspots of the world's biodiversity and it is estimated that half of its original vegetation was removed and converted to agricultural land and tree plantations. Although an increasing amount of knowledge is being assembled regarding the response of soil bacterial communities to land use change, to the associated plant community and to soil properties, our understanding about how these interactions affect the microbial community from the Brazilian Pampa is still poor and incomplete. In this study, we hypothesized that the same soil type from the same geographic region but under distinct land use present dissimilar soil bacterial communities. To test this hypothesis, we assessed the soil bacterial communities from four land-uses within the same soil type by 454-pyrosequencing of 16S rRNA gene and by soil microbial activity analyzes. We found that the same soil type under different land uses harbor similar (but not equal bacterial communities and the differences were controlled by many microbial taxa. No differences regarding diversity and richness between natural areas and areas under anthropogenic disturbance were detected. However, the measures of microbial activity did not converge with the 16S rRNA data supporting the idea that the coupling between functioning and composition of bacterial communities is not necessarily correlated.

  2. Soil-borne bacterial structure and diversity does not reflect community activity in Pampa biome.

    Science.gov (United States)

    Lupatini, Manoeli; Suleiman, Afnan Khalil Ahmad; Jacques, Rodrigo Josemar Seminoti; Antoniolli, Zaida Inês; Kuramae, Eiko Eurya; de Oliveira Camargo, Flávio Anastácio; Roesch, Luiz Fernando Würdig

    2013-01-01

    The Pampa biome is considered one of the main hotspots of the world's biodiversity and it is estimated that half of its original vegetation was removed and converted to agricultural land and tree plantations. Although an increasing amount of knowledge is being assembled regarding the response of soil bacterial communities to land use change, to the associated plant community and to soil properties, our understanding about how these interactions affect the microbial community from the Brazilian Pampa is still poor and incomplete. In this study, we hypothesized that the same soil type from the same geographic region but under distinct land use present dissimilar soil bacterial communities. To test this hypothesis, we assessed the soil bacterial communities from four land-uses within the same soil type by 454-pyrosequencing of 16S rRNA gene and by soil microbial activity analyzes. We found that the same soil type under different land uses harbor similar (but not equal) bacterial communities and the differences were controlled by many microbial taxa. No differences regarding diversity and richness between natural areas and areas under anthropogenic disturbance were detected. However, the measures of microbial activity did not converge with the 16S rRNA data supporting the idea that the coupling between functioning and composition of bacterial communities is not necessarily correlated.

  3. Seasonal changes in bacterial communities associated with healthy and diseased Porites coral in southern Taiwan.

    Science.gov (United States)

    Lin, Chorng-Horng; Chuang, Chih-Hsiang; Twan, Wen-Hung; Chiou, Shu-Fen; Wong, Tit-Yee; Liu, Jong-Kang; Kao, Chyuan-Yao; Kuo, Jimmy

    2016-12-01

    We compared the bacterial communities associated with healthy scleractinian coral Porites sp. with those associated with coral infected with pink spot syndrome harvested during summer and winter from waters off the coast of southern Taiwan. Members of the bacterial community associated with the coral were characterized by means of denaturing gradient gel electrophoresis (DGGE) of a short region of the 16S rRNA gene and clone library analysis. Of 5 different areas of the 16S rRNA gene, we demonstrated that the V3 hypervariable region is most suited to represent the coral-associated bacterial community. The DNA sequences of 26 distinct bands extracted from DGGE gels and 269 sequences of the 16S rRNA gene from clone libraries were determined. We found that the communities present in diseased coral were more heterogeneous than the bacterial communities of uninfected coral. In addition, bacterial communities associated with coral harvested in the summer were more diverse than those associated with coral collected in winter, regardless of the health status of the coral. Our study suggested that the compositions of coral-associated bacteria communities are complex, and the population of bacteria varies greatly between seasons and in coral of differing health status.

  4. Contrasting bacterial communities in two indigenous Chionochloa (Poaceae) grassland soils in New Zealand.

    Science.gov (United States)

    Griffith, Jocelyn C; Lee, William G; Orlovich, David A; Summerfield, Tina C

    2017-01-01

    The cultivation of grasslands can modify both bacterial community structure and impact on nutrient cycling as well as the productivity and diversity of plant communities. In this study, two pristine New Zealand grassland sites dominated by indigenous tall tussocks (Chionochloa pallens or C. teretifolia) were examined to investigate the extent and predictability of variation of the bacterial community. The contribution of free-living bacteria to biological nitrogen fixation is predicted to be ecologically significant in these soils; therefore, the diazotrophic community was also examined. The C. teretifolia site had N-poor and poorly-drained peaty soils, and the C. pallens had N-rich and well-drained fertile soils. These soils also differ in the proportion of organic carbon (C), Olsen phosphorus (P) and soil pH. The nutrient-rich soils showed increased relative abundances of some copiotrophic bacterial taxa (including members of the Proteobacteria, Bacteroidetes and Firmicutes phyla). Other copiotrophs, Actinobacteria and the oliogotrophic Acidobacteria showed increased relative abundance in nutrient-poor soils. Greater diversity based on 16S rRNA gene sequences and the Tax4Fun prediction of enhanced spore formation associated with nutrient-rich soils could indicate increased resilience of the bacterial community. The two sites had distinct diazotrophic communities with higher diversity in C. teretifolia soils that had less available nitrate and ammonium, potentially indicating increased resilience of the diazotroph community at this site. The C. teretifolia soils had more 16S rRNA gene and nifH copies per g soil than the nutrient rich site. However, the proportion of the bacterial community that was diazotrophic was similar in the two soils. We suggest that edaphic and vegetation factors are contributing to major differences in the composition and diversity of total bacterial and diazotrophic communities at these sites. We predict the differences in the communities

  5. Phylogenetic analysis of bacterial community in deep-sea sediment from the western Pacific "warm pool"

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    A depth profile of bacterial community structure in one deep-sea sediment core of the western Pacific "warm pool" (WP) was investigated and compared with that in a sediment sample from the eastern Pacific (EP) by phylogenetic analysis of 16S rDNA fragments.Five bacterial 16S rDNA clone libraries were constructed, and t33 clones with different restriction fragment length polymorphism(RFLP) patterns were sequenced. A phylogenetic analysis of these sequences revealed that the bacterial diversity in a sample from the WP was more abundant than that in the EP sample. The bacterial population in the sediment core of WP was composed of eight major lineages of the domain bacteria. Among them the γ-Proteobacteria was the predominant and most diverse group in each section of WP sediment core, followed by the α-Proteobacteria. The genus Colwellia belonging to γ-Proteobacteria was predominant in this sample.The shift of bacterial communities among different sections of the WP sediment core was δ-, ε-Proteobacteria, and Cytopahga-Flexibacteria-Bacteroides (CFB) group. The ratios between them in the bacterial communities all showed inversely proportional to the depth of sediment. The sequences related to sulphate reducing bacteria (SRB) were detected in every section. The bacterial community structure in this sediment core might be related to the environmental characteristics of the surface seawater of the western Pacific WP.

  6. Non-random species loss in bacterial communities reduces antifungal volatile production.

    Science.gov (United States)

    Hol, W H Gera; Garbeva, Paolina; Hordijk, Cornelis; Hundscheid, P J; Gunnewiek, Paulien J A Klein; Van Agtmaal, Maaike; Kuramae, Eiko E; De Boer, Wietse

    2015-08-01

    The contribution of low-abundance microbial species to soil ecosystems is easily overlooked because there is considerable overlap between metabolic abilities (functional redundancy) of dominant and subordinate microbial species. Here we studied how loss of less abundant soil bacteria affected the production of antifungal volatiles, an important factor in the natural control of soil-borne pathogenic fungi. We provide novel empirical evidence that the loss of soil bacterial species leads to a decline in the production of volatiles that suppress root pathogens. By using dilution-to-extinction for seven different soils we created bacterial communities with a decreasing number of species and grew them under carbon-limited conditions. Communities with high bacterial species richness produced volatiles that strongly reduced the hyphal growth of the pathogen Fusarium oxysporum. For most soil origins loss of bacterial species resulted in loss of antifungal volatile production. Analysis of the volatiles revealed that several known antifungal compounds were only produced in the more diverse bacterial communities. Our results suggest that less abundant bacterial species play an important role in antifungal volatile production by soil bacterial communities and, consequently, in the natural suppression of soil-borne pathogens.

  7. Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

    Directory of Open Access Journals (Sweden)

    J. Comte

    2015-07-01

    Full Text Available Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a North–South permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa, and then analyzed these results relative to environmental variables to identify factors controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley, however the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial keystone species.

  8. Bacterial communities in Malagasy soils with differing levels of disturbance affecting botanical diversity.

    Directory of Open Access Journals (Sweden)

    Leah C Blasiak

    Full Text Available Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas.

  9. Bacterial communities in Malagasy soils with differing levels of disturbance affecting botanical diversity.

    Science.gov (United States)

    Blasiak, Leah C; Schmidt, Alex W; Andriamiarinoro, Honoré; Mulaw, Temesgen; Rasolomampianina, Rado; Applequist, Wendy L; Birkinshaw, Chris; Rejo-Fienena, Félicitée; Lowry, Porter P; Schmidt, Thomas M; Hill, Russell T

    2014-01-01

    Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas.

  10. Characterization of the contaminant bacterial communities in sugarcane first-generation industrial ethanol production.

    Science.gov (United States)

    Bonatelli, Maria L; Quecine, Maria C; Silva, Mariana S; Labate, Carlos A

    2017-09-15

    The industrial ethanolic fermentation process is operated in distilleries, either in fed-batch or continuous mode. A consequence of the large industrial ethanol production is bacterial contamination in the fermentation tanks, which is responsible for significant economic losses. To investigate this community, we accessed the profile of bacterial contaminant from two distilleries in Brazil, each operating a different fermentation mode, throughout sugarcane harvest of 2013-2014. Bacterial communities were accessed through Illumina culture-independent 16S rDNA gene sequencing, and qPCR was used to quantify total bacteria abundance. Both ethanol production modes showed similar bacterial abundance, around 105 gene copies/mL. 16S rDNA sequencing showed that 92%-99% of the sequences affiliated to Lactobacillus genus. Operational taxonomic units differently represented belonged mainly to Lactobacillus, but also to Weissella, Pediococcus, Acetobacter and Anaeosporobacter, although in lower abundance. Alpha-diversity only showed a correlation through the fermentation tanks in continuous mode, where it was always higher in the second and third tanks. Beta-diversity clearly separated the two distilleries and metagenome prediction reinforces clusterization within distilleries. Despite certain variations between bacterial community in the distilleries throughout harvest season, Lactobacillus were the main genera reported in both distilleries and bacterial community seemed to persist along time, suggesting bacterial reinfestation. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Bacterial community composition and potential driving factors in different reef habitats of the Spermonde Archipelago, Indonesia

    DEFF Research Database (Denmark)

    Kegler, Hauke F.; Lukman, Muhammad; Teichberg, Mirta

    2017-01-01

    Coastal eutrophication is a key driver of shifts in bacterial communities on coral reefs. With fringing and patch reefs at varying distances from the coast the Spermonde Archipelago in southern Sulawesi, Indonesia offers ideal conditions to study the effects of coastal eutrophication along...... a spatially defined gradient. The present study investigated bacterial community composition of three coral reef habitats: the water column, sediments, and mucus of the hard coral genus Fungia, along that cross shelf environmental and water quality gradient. The main research questions were: (1) How do water....../Shigella (Gammaproteobacteria) and Raistonia (Betaproteobacteria), respectively, both dominated the bacterial community composition of the both size fractions of the water column and coral mucus. The sampled reef sediments were more diverse, and no single OTUs was dominant. There was no gradual shift in bacterial classes...

  12. [Effects of rotation and intercropping on bacterial communities in rhizosphere soil of cucumber].

    Science.gov (United States)

    Wu, Feng-zhi; Wang, Shu; Yang, Yang

    2008-12-01

    By the method of PCR-DGGE, this paper studied the effects of rotation with wheat, soybean, villose vetch, clover, and alfalfa and intercropping with onion and garlic on the bacterial communities in rhizosphere soil of cucumber. The results showed that rotation and intercropping with test plants increased the diversity and evenness indices of bacterial communities in cucumber rhizosphere soil, and also, cucumber yield. The sequencing of DGGE bands indicated that most of the bands had high homology with uncultured bacterial species, and were of Sphingobacterium and Proteobacteria. High bacterium G+C was only detected when cucumber was intercropped with onion. The diversity of soil bacterial communities varied with the growth stages of cucumber, being the highest at vigorous fruiting stage. It was suggested that intercropping with onion and rotation with wheat were the best cultivation modes of cucumber.

  13. Wood Ash Induced pH Changes Strongly Affect Soil Bacterial Numbers and Community Composition

    DEFF Research Database (Denmark)

    Bang-Andreasen, Toke; Nielsen, Jeppe T.; Voriskova, Jana

    2017-01-01

    and sporeforming bacteria combined with 16S rRNA gene amplicon sequencing to valuate soil bacterial responses to wood ash application. Results showed that wood ash addition strongly increased soil pH and electrical conductivity. Soil pH increased from acidic through neutral at 22 t ha(-1) to alkaline at 167 t ha......-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse...... and the available results are ambiguous and remain at a general taxonomic level. Here we investigate the response of bacterial communities in a spruce forest soil to wood ash addition corresponding to 0, 5, 22, and 167 t wood ash ha(-1). We used culture-based enumerations of general bacteria, Pseudomonas...

  14. Tropical soil bacterial communities in Malaysia: pH dominates in the equatorial tropics too.

    Science.gov (United States)

    Tripathi, Binu M; Kim, Mincheol; Singh, Dharmesh; Lee-Cruz, Larisa; Lai-Hoe, Ang; Ainuddin, A N; Go, Rusea; Rahim, Raha Abdul; Husni, M H A; Chun, Jongsik; Adams, Jonathan M

    2012-08-01

    The dominant factors controlling soil bacterial community variation within the tropics are poorly known. We sampled soils across a range of land use types--primary (unlogged) and logged forests and crop and pasture lands in Malaysia. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1-V3 region was pyrosequenced using the 454 Roche machine. We found that land use in itself has a weak but significant effect on the bacterial community composition. However, bacterial community composition and diversity was strongly correlated with soil properties, especially soil pH, total carbon, and C/N ratio. Soil pH was the best predictor of bacterial community composition and diversity across the various land use types, with the highest diversity close to neutral pH values. In addition, variation in phylogenetic structure of dominant lineages (Alphaproteobacteria, Beta/Gammaproteobacteria, Acidobacteria, and Actinobacteria) is also significantly correlated with soil pH. Together, these results confirm the importance of soil pH in structuring soil bacterial communities in Southeast Asia. Our results also suggest that unlike the general diversity pattern found for larger organisms, primary tropical forest is no richer in operational taxonomic units of soil bacteria than logged forest, and agricultural land (crop and pasture) is actually richer than primary forest, partly due to selection of more fertile soils that have higher pH for agriculture and the effects of soil liming raising pH.

  15. Bacterial community in sclerotia of Cenococcum species and soil in sub-alpine forest, central Japan

    Science.gov (United States)

    Nonoyama, Y.; Narisawa, K.; Ohta, H.; Watanabe, M.

    2009-04-01

    Species of Cenococcum, ectomycorrhizal fungi, may be particularly abundant in cold- or nutrient-stressed habitats. The fungus is easily recognized by its jet-black hyphae, and distinct compact masses of fungal mycelium called sclerotia. They are hard, black, comparatively smooth and mostly spherical. Sclerotia are formed in rhizosphere and can provide sufficient inoculums for several years. The purpose of this study is to investigate bacterial community inside sclerotia, with an interest on contribution of sclerotia to microbial diversity in rhizosphere. To investigate bacterial community inside of the fungal sclerotia by 16S rDNA gene clone library, several hundred of sclerotia (ca. 1g) were collected from sub-alpine forest soil in central Japan. Furthermore, three sclerotium grains were applied to investigate internal bacteria community by culture method. The isolated bacterial strains were then proceeded to determine their 16S rDNA partial sequences. The predominant group determined by clone library analysis of 16S ribosomal RNA genes with DNA from the sclerotia was Acidobacteria in both sclerotia and soil. Bacterial community of sclerotia showed higher diversity compared to soil. On the contrary, bacterial flora isolated from single sclerotium differed each other. Additionally, the bacterial community was composed by limited species of related genus.

  16. Bacterial communities associated with the ctenophores Mnemiopsis leidyi and Beroe ovata.

    Science.gov (United States)

    Daniels, Camille; Breitbart, Mya

    2012-10-01

    Residing in a phylum of their own, ctenophores are gelatinous zooplankton that drift through the ocean's water column. Although ctenophores are known to be parasitized by a variety of eukaryotes, no studies have examined their bacterial associates. This study describes the bacterial communities associated with the lobate ctenophore Mnemiopsis leidyi and its natural predator Beroe ovata in Tampa Bay, Florida, USA. Investigations using terminal restriction fragment length polymorphism (T-RFLP) and cloning and sequencing of 16S rRNA genes demonstrated that ctenophore bacterial communities were distinct from the surrounding water. In addition, each ctenophore genus contained a unique microbiota. Ctenophore samples contained fewer bacterial operational taxonomic units (OTUs) by T-RFLP and lower diversity communities by 16S rRNA gene sequencing than the water column. Both ctenophore genera contained sequences related to bacteria previously described in marine invertebrates, and sequences similar to a sea anemone pathogen were abundant in B. ovata. Temporal sampling revealed that the ctenophore-associated bacterial communities varied over time, with no single OTU detected at all time points. This is the first report of distinct and dynamic bacterial communities associated with ctenophores, suggesting that these microbial consortia may play important roles in ctenophore ecology. Future work needs to elucidate the functional roles and mode of acquisition of these bacteria. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  17. Biostimulation and microbial community profiling reveal insights on RDX transformation in groundwater.

    Science.gov (United States)

    Wang, Dongping; Boukhalfa, Hakim; Marina, Oana; Ware, Doug S; Goering, Tim J; Sun, Fengjie; Daligault, Hajnalka E; Lo, Chien-Chi; Vuyisich, Momchilo; Starkenburg, Shawn R

    2017-04-01

    Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a high explosive released to the environment as a result of weapons manufacturing and testing worldwide. At Los Alamos National Laboratory, the Technical Area (TA) 16 260 Outfall discharged high-explosives-bearing water from a high-explosives-machining facility to Cañon de Valle during 1951 through 1996. These discharges served as a primary source of high-explosives and inorganic-element contamination in the area. Data indicate that springs, surface water, alluvial groundwater, and perched-intermediate groundwater contain explosive compounds, including RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine); HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine); and TNT (2,4,6-trinitrotoluene). RDX has been detected in the regional aquifer in several wells, and a corrective measures evaluation is planned to identify remedial alternatives to protect the regional aquifer. Perched-intermediate groundwater at Technical Area 16 is present at depths from 650 ft to 1200 ft bgs. In this study, we examined the microbial diversity in a monitoring well completed in perched-intermediate groundwater contaminated by RDX, and examined the response of the microbial population to biostimulation under varying geochemical conditions. Results show that the groundwater microbiome was dominated by Actinobacteria and Proteobacteria. A total of 1,605 operational taxonomic units (OTUs) in 96 bacterial genera were identified. Rhodococcus was the most abundant genus (30.6%) and a total of 46 OTUs were annotated as Rhodococcus. One OTU comprising 25.2% of total sequences was closely related to a RDX -degrading strain R. erythropolis HS4. A less abundant OTU from the Pseudomonas family closely related to RDX-degrading strain P. putida II-B was also present. Biostimulation significantly enriched Proteobacteria but decreased/eliminated the population of Actinobacteria. Consistent with RDX degradation, the OTU closely related to the RDX-degrading P

  18. Major phylum-level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface.

    Science.gov (United States)

    Momper, Lily; Kiel Reese, Brandi; Zinke, Laura; Wanger, Greg; Osburn, Magdalena R; Moser, Duane; Amend, Jan P

    2017-07-05

    Earth's deep subsurface biosphere (DSB) is home to a vast number and wide variety of microorganisms. Although difficult to access and sample, deep subsurface environments have been probed through drilling programs, exploration of mines and sampling of deeply sourced vents and springs. In an effort to understand the ecology of deep terrestrial habitats, we examined bacterial diversity in the Sanford Underground Research Facility (SURF), the former Homestake gold mine, in South Dakota, USA. Whole genomic DNA was extracted from deeply circulating groundwater and corresponding host rock (at a depth of 1.45 km below ground surface). Pyrotag DNA sequencing of the 16S rRNA gene revealed diverse communities of putative chemolithoautotrophs, aerobic and anaerobic heterotrophs, numerous candidate phyla and unique rock-associated microbial assemblage. There was a clear and near-total separation of communities between SURF deeply circulating fracture fluids and SURF host-rocks. Sequencing data from SURF compared against five similarly sequenced terrestrial subsurface sites in Europe and North America revealed classes Clostridia and Betaproteobacteria were dominant in terrestrial fluids. This study presents a unique analysis showing differences in terrestrial subsurface microbial communities between fracture fluids and host rock through which those fluids permeate. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  19. Molecular assessment of bacterial community dynamics and functional endpoints during sediment bioaccumulation test

    NARCIS (Netherlands)

    Diepens, N.J.; Dimitrov, M.R.; Koelmans, A.A.; Smidt, H.

    2015-01-01

    Whole sediment toxicity tests play an important role in environmental risk assessment of organic chemicals. It is not clear, however, to what extent changing microbial community composition and associated functions affect sediment test results. We assessed the development of bacterial communities in

  20. Contrasts between the cryoconite and ice-marginal bacterial communities of Svalbard glaciers

    Directory of Open Access Journals (Sweden)

    Arwyn Edwards

    2013-05-01

    Full Text Available Cryoconite holes are foci of unusually high microbial diversity and activity on glacier surfaces worldwide, comprising melt-holes formed by the darkening of ice by biogenic granular debris. Despite recent studies linking cryoconite microbial community structure to the functionality of cryoconite habitats, little is known of the processes shaping the cryoconite bacterial community. In particular, the assertions that the community is strongly influenced by aeolian transfer of biota from ice-marginal habitats and the potential for cryoconite microbes to inoculate proglacial habitats are poorly quantified despite their longevity in the literature. Therefore, the bacterial community structures of cryoconite holes on three High-Arctic glaciers were compared to bacterial communities in adjacent moraines and tundra using terminal-restriction fragment length polymorphism. Distinct community structures for cryoconite and ice-marginal communities were observed. Only a minority of phylotypes are present in both habitat types, implying that cryoconite habitats comprise distinctive niches for bacterial taxa when compared to ice-marginal habitats. Curiously, phylotype abundance distributions for both cryoconite and ice-marginal sites best fit models relating to succession. Our analyses demonstrate clearly that cryoconites have their own, distinct functional microbial communities despite significant inputs of cells from other habitats.

  1. Characterizing the bacterial communities in retail stores in the United States.

    Science.gov (United States)

    Hoisington, A; Maestre, J P; Kinney, K A; Siegel, J A

    2016-12-01

    The microorganisms present in retail environments have not been studied in detail despite the fact that these environments represent a potentially important location for exposure. In this study, HVAC filter dust samples in 13 US retail stores were collected and analyzed via pyrosequencing to characterize the indoor bacterial communities and to explore potential relationships between these communities and building and environmental parameters. Although retail stores contained a diverse bacterial community of 788 unique genera, over half of the nearly 118K sequences were attributed to the Proteobacteria phylum. Streptophyta, Bacillus, Corynebacterium, Pseudomonas, and Acinetobacter were the most prevalent genera detected. The recovered indoor airborne microbial community was statistically associated with both human oral and skin microbiota, indicating occupants are important contributors, despite a relatively low occupant density per unit volume in retail stores. Bacteria generally associated with outdoor environments were present in the indoor communities with no obvious association with air exchange rate, even when considering relative abundance. No significant association was observed between the indoor bacterial community recovered and store location, store type, or season. However, predictive functional gene profiling showed significant associations between the indoor community and season. The microbiome recovered from multiple samples collected months apart from the same building varied significantly indicating that caution is warranted when trying to characterize the bacterial community with a single sampling event.

  2. Active bacterial community structure along vertical redox gradients in Baltic Sea sediment

    Energy Technology Data Exchange (ETDEWEB)

    Jansson, Janet; Edlund, Anna; Hardeman, Fredrik; Jansson, Janet K.; Sjoling, Sara

    2008-05-15

    Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179 mV, -64 mV and -337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labeled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labeled DNA and DNA from reverse transcription PCR (rt-PCR) showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths.

  3. The gut bacterial community of mammals from marine and terrestrial habitats.

    Directory of Open Access Journals (Sweden)

    Tiffanie M Nelson

    Full Text Available After birth, mammals acquire a community of bacteria in their gastro-intestinal tract, which harvests energy and provides nutrients for the host. Comparative studies of numerous terrestrial mammal hosts have identified host phylogeny, diet and gut morphology as primary drivers of the gut bacterial community composition. To date, marine mammals have been excluded from these comparative studies, yet they represent distinct examples of evolutionary history, diet and lifestyle traits. To provide an updated understanding of the gut bacterial community of mammals, we compared bacterial 16S rRNA gene sequence data generated from faecal material of 151 marine and terrestrial mammal hosts. This included 42 hosts from a marine habitat. When compared to terrestrial mammals, marine mammals clustered separately and displayed a significantly greater average relative abundance of the phylum Fusobacteria. The marine carnivores (Antarctic and Arctic seals and the marine herbivore (dugong possessed significantly richer gut bacterial community than terrestrial carnivores and terrestrial herbivores, respectively. This suggests that evolutionary history and dietary items specific to the marine environment may have resulted in a gut bacterial community distinct to that identified in terrestrial mammals. Finally we hypothesize that reduced marine trophic webs, whereby marine carnivores (and herbivores feed directly on lower trophic levels, may expose this group to high levels of secondary metabolites and influence gut microbial community richness.

  4. Seasonal bacterial community dynamics in a full-scale enhanced biological phosphorus removal plant.

    Science.gov (United States)

    Flowers, Jason J; Cadkin, Tracey A; McMahon, Katherine D

    2013-12-01

    Activated sludge is one of the most abundant and effective wastewater treatment process used to treat wastewater, and has been used in developed countries for nearly a century. In all that time, several hundreds of studies have explored the bacterial communities responsible for treatment, but most studies were based on a handful of samples and did not consider temporal dynamics. In this study, we used the DNA fingerprinting technique called automated ribosomal intergenic spacer region analysis (ARISA) to study bacterial community dynamics over a two-year period in two different treatment trains. We also used quantitative PCR to measure the variation of five phylogenetically-defined clades within the Accumulibacter lineage, which is a model polyphosphate accumulating organism. The total bacterial community exhibited seasonal patterns of change reminiscent of those observed in lakes and oceans. Surprisingly, all five Accumulibacter clades were present throughout the study, and the total Accumulibacter community was relatively stable. However, the abundance of each clade did fluctuate through time. Clade IIA dynamics correlated positively with temperature (ρ = 0.65, p < 0.05) while Clade IA dynamics correlated negatively with temperature (ρ = -0.35, p < 0.05). This relationship with temperature hints at the mechanisms that may be driving the seasonal patterns in overall bacterial community dynamics and provides further evidence for ecological differentiation among clades within the Accumulibacter lineage. This work provides a valuable baseline for activated sludge bacterial community variation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Biofilm bacterial communities in urban drinking water distribution systems transporting waters with different purification strategies.

    Science.gov (United States)

    Wu, Huiting; Zhang, Jingxu; Mi, Zilong; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

    2015-02-01

    Biofilm formation in drinking water distribution systems (DWDS) has many adverse consequences. Knowledge of microbial community structure of DWDS biofilm can aid in the design of an effective control strategy. However, biofilm bacterial community in real DWDS and the impact of drinking water purification strategy remain unclear. The present study investigated the composition and diversity of biofilm bacterial community in real DWDSs transporting waters with different purification strategies (conventional treatment and integrated treatment). High-throughput Illumina MiSeq sequencing analysis illustrated a large shift in the diversity and structure of biofilm bacterial community in real DWDS. Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Nitrospirae, and Cyanobacteria were the major components of biofilm bacterial community. Proteobacteria (mainly Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) predominated in each DWDS biofilm, but the compositions of the dominant proteobacterial classes and genera and their proportions varied among biofilm samples. Drinking water purification strategy could shape DWDS biofilm bacterial community. Moreover, Pearson's correlation analysis indicated that Actinobacteria was positively correlated with the levels of total alkalinity and dissolved organic carbon in tap water, while Firmicutes had a significant positive correlation with nitrite nitrogen.

  6. Potential mechanisms and environmental controls of TiO2 nanoparticle effects on soil bacterial communities.

    Science.gov (United States)

    Ge, Yuan; Priester, John H; Van De Werfhorst, Laurie C; Schimel, Joshua P; Holden, Patricia A

    2013-12-17

    It has been reported that engineered nanoparticles (ENPs) alter soil bacterial communities, but the underlying mechanisms and environmental controls of such effects remain unknown. Besides direct toxicity, ENPs may indirectly affect soil bacteria by changing soil water availability or other properties. Alternatively, soil water or other environmental factors may mediate ENP effects on soil bacterial communities. To test, we incubated nano-TiO2-amended soils across a range of water potentials for 288 days. Following incubation, the soil water characteristics, organic matter, total carbon, total nitrogen, and respiration upon rewetting (an indicator of bioavailable organic carbon) were measured. Bacterial community shifts were characterized by terminal restriction fragment length polymorphism (T-RFLP). The endpoint soil water holding had been reported previously as not changing with this nano-TiO2 amendment; herein, we also found that some selected soil properties were unaffected by the treatments. However, we found that nano-TiO2 altered the bacterial community composition and reduced diversity. Nano-TiO2-induced community dissimilarities increased but tended to approach a plateau when soils became drier. Taken together, nano-TiO2 effects on soil bacteria appear to be a result of direct toxicity rather than indirectly through nano-TiO2 affecting soil water and organic matter pools. However, such directs effects of nano-TiO2 on soil bacterial communities are mediated by soil water.

  7. Diversity and Assembling Processes of Bacterial Communities in Cryoconite Holes of a Karakoram Glacier.

    Science.gov (United States)

    Ambrosini, Roberto; Musitelli, Federica; Navarra, Federico; Tagliaferri, Ilario; Gandolfi, Isabella; Bestetti, Giuseppina; Mayer, Christoph; Minora, Umberto; Azzoni, Roberto Sergio; Diolaiuti, Guglielmina; Smiraglia, Claudio; Franzetti, Andrea

    2017-05-01

    Cryoconite holes are small ponds that form on the surface of glaciers that contain a dark debris, the cryoconite, at the bottom and host active ecological communities. Differences in the structure of bacterial communities have been documented among Arctic and mountain glaciers, and among glaciers in different areas of the world. In this study, we investigated the structure of bacterial communities of cryoconite holes of Baltoro Glacier, a large (62 km in length and 524 km(2) of surface) glacier of the Karakoram, by high-throughput sequencing of the V5-V6 hypervariable regions of the 16S rRNA gene. We found that Betaproteobacteria dominated bacterial communities, with large abundance of genera Polaromonas, probably thanks to its highly versatile metabolism, and Limnohabitans, which may have been favoured by the presence of supraglacial lakes in the area where cryoconite holes were sampled. Variation in bacterial communities among different sampling areas of the glacier could be explained by divergent selective processes driven by variation in environmental conditions, particularly pH, which was the only environmental variable that significantly affected the structure of bacterial communities. This variability may be due to both temporal and spatial patterns of variation in environmental conditions.

  8. The gut bacterial community of mammals from marine and terrestrial habitats.

    Science.gov (United States)

    Nelson, Tiffanie M; Rogers, Tracey L; Brown, Mark V

    2013-01-01

    After birth, mammals acquire a community of bacteria in their gastro-intestinal tract, which harvests energy and provides nutrients for the host. Comparative studies of numerous terrestrial mammal hosts have identified host phylogeny, diet and gut morphology as primary drivers of the gut bacterial community composition. To date, marine mammals have been excluded from these comparative studies, yet they represent distinct examples of evolutionary history, diet and lifestyle traits. To provide an updated understanding of the gut bacterial community of mammals, we compared bacterial 16S rRNA gene sequence data generated from faecal material of 151 marine and terrestrial mammal hosts. This included 42 hosts from a marine habitat. When compared to terrestrial mammals, marine mammals clustered separately and displayed a significantly greater average relative abundance of the phylum Fusobacteria. The marine carnivores (Antarctic and Arctic seals) and the marine herbivore (dugong) possessed significantly richer gut bacterial community than terrestrial carnivores and terrestrial herbivores, respectively. This suggests that evolutionary history and dietary items specific to the marine environment may have resulted in a gut bacterial community distinct to that identified in terrestrial mammals. Finally we hypothesize that reduced marine trophic webs, whereby marine carnivores (and herbivores) feed directly on lower trophic levels, may expose this group to high levels of secondary metabolites and influence gut microbial community richness.

  9. Namib Desert dune/interdune transects exhibit habitat-specific edaphic bacterial communities.

    Science.gov (United States)

    Ronca, Sandra; Ramond, Jean-Baptiste; Jones, Brian E; Seely, Mary; Cowan, Don A

    2015-01-01

    The sand dunes and inter-dune zones of the hyper-arid central Namib Desert represent heterogeneous soil habitats. As little is known about their indigenous edaphic bacterial communities, we aimed to evaluate their diversity and factors of assembly and hypothesized that soil physicochemistry gradients would strongly shape dune/interdune communities. We sampled a total of 125 samples from 5 parallel dune/interdune transects and characterized 21 physico-chemical edaphic parameters coupled with 16S rRNA gene bacterial community fingerprinting using T-RFLP and 454 pyrosequencing. Multivariate analyses of T-RFLP data showed significantly different bacterial communities, related to physico-chemical gradients, in four distinct dune habitats: the dune top, slope, base and interdune zones. Pyrosequencing of 16S rRNA gene amplicon sets showed that each dune zone presented a unique phylogenetic profile, suggesting a high degree of environmental selection. The combined results strongly infer that habitat filtering is an important factor shaping Namib Desert dune bacterial communities, with habitat stability, soil texture and mineral and nutrient contents being the main environmental drivers of bacterial community structures.

  10. Bacterial and Fungal Community Structures in Loess Plateau Grasslands with Different Grazing Intensities

    Directory of Open Access Journals (Sweden)

    Huhe

    2017-04-01

    Full Text Available The Loess Plateau of China is one of the most fragile ecosystems worldwide; thus, human production activities need to be conducted very cautiously. In this study, MiSeq high-throughput sequencing was applied to assess the relationship between bacterial and fungal community structures and changes in vegetation and soil physical and chemical properties induced by grazing, in four grasslands with different levels of grazing intensity (0, 2.67, 5.33, and 8.67 sheep/ha in the semiarid region of the Loess Plateau. The relative abundances of the bacterial community in the grasslands with 2.67 and 5.33 sheep/ha were significantly higher than those in grasslands with 0 and 8.67 sheep/ha, and the fungal diversity was significantly lower for grasslands with 2.67 sheep/ha than for the other grasslands. Redundancy analysis (RDA showed that plant biomass, nitrate, and total nitrogen have significant effects on bacterial community structure, whereas nitrate and total nitrogen also significantly affect fungal community structure. Variation partitioning showed that soil and plant characteristics influence the bacterial and fungal community structures; these characteristics explained 51.9 and 52.9% of the variation, respectively. Thus, bacterial and fungal community structures are very sensitive to grazing activity and change to different extents with different grazing intensities. Based on our findings, a grazing intensity of about 2.67 sheep/ha is considered the most appropriate in semiarid grassland of the Loess Plateau.

  11. Changes in soil bacterial communities induced by the invasive plant Pennisetum setaceum in a semiarid environment

    Science.gov (United States)

    Rodriguez-Caballero, Gema; Caravaca, Fuensanta; del Mar Alguacil, María; Fernández-López, Manuel; José Fernández-González, Antonio; García-Orenes, Fuensanta; Roldán, Antonio

    2016-04-01

    Invasive alien species are considered as a global threat being among the main causes of biodiversity loss. Plant invasions have been extensively studied from different disciplines with the purpose of identifying predictor traits of invasiveness and finding solutions. However, less is known about the implication of the rhizosphere microbiota in these processes, even when it is well known the importance of the interaction between plant rhizosphere and microbial communities. The objective of this study was to determine whether native and invasive plants support different bacterial communities in their rhizospheres and whether there are bacterial indicator species that might be contributing to the invasion process of these ecosystems. We carried out a study in five independent locations under Mediterranean semiarid conditions, where the native Hyparrhenia hirta is being displaced by Pennisetum setaceum, an aggressive invasive Poaceae and soil bacterial communities were amplified and 454-pyrosequenced. Changes in the composition and structure of the bacterial communities, owing to the invasive status of the plant, were detected when the richness and alpha-diversity estimators were calculated as well as when we analyzed the PCoA axes scores. The Indicator Species Analysis results showed a higher number of indicators for invaded communities at all studied taxonomic levels. In conclusion, the effect of the invasiveness and its interaction with the soil location has promoted shifts in the rhizosphere bacterial communities which might be facilitating the invader success in these ecosystems.

  12. Two decades of warming increases diversity of a potentially lignolytic bacterial community.

    Science.gov (United States)

    Pold, Grace; Melillo, Jerry M; DeAngelis, Kristen M

    2015-01-01

    As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming.

  13. Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site.

    Science.gov (United States)

    Green, Stefan J; Prakash, Om; Jasrotia, Puja; Overholt, Will A; Cardenas, Erick; Hubbard, Daniela; Tiedje, James M; Watson, David B; Schadt, Christopher W; Brooks, Scott C; Kostka, Joel E

    2012-02-01

    The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.

  14. Microbial activity and bacterial community structure during degradation of microcystins

    DEFF Research Database (Denmark)

    Christoffersen, K.; Lyck, Susanne; Winding, A.

    2002-01-01

    Degradation of realistic microcystin concentrations in lake water with indigenous bacteria was studied in laboratory and field experiments following inoculation with lysed toxic algal material containing microcystin primarily from Microcystis sp. or purified commercial microcystin-LR to microcosms...... experiment to evaluate the effects of organic lysates on bacterial proliferation in the absence of microcystin. An exponential decline of the dissolved toxins was observed in all cases with toxins present, and the degradation rates ranged between 0.5 and 1.0 d(-1). No lag phases were observed but slow...... including microcystins, and this resulted in a net accumulation of bacterial cells. The heterotrophic nanoflagellates responded quickly to the bacterial growth and probably consumed a considerable amount of the bacteria. The microbial activities returned to initial values within 5 to 6 d as the toxins...

  15. Characterization of the bacterial communities of life stages of free living lone star ticks (Amblyomma americanum).

    Science.gov (United States)

    Williams-Newkirk, Amanda Jo; Rowe, Lori A; Mixson-Hayden, Tonya R; Dasch, Gregory A

    2014-01-01

    The lone star tick (Amblyomma americanum) is an abundant and aggressive biter of humans, domestic animals, and wildlife in the southeastern-central USA and an important vector of several known and suspected zoonotic bacterial pathogens. However, the biological drivers of bacterial community variation in this tick are still poorly defined. Knowing the community context in which tick-borne bacterial pathogens exist and evolve is required to fully understand the ecology and immunobiology of the ticks and to design effective public health and veterinary interventions. We performed a metagenomic survey of the bacterial communities of questing A. americanum and tested 131 individuals (66 nymphs, 24 males, and 41 females) from five sites in three states. Pyrosequencing was performed with barcoded eubacterial primers targeting variable 16S rRNA gene regions 5-3. The bacterial communities were dominated by Rickettsia (likely R. amblyommii) and an obligate Coxiella symbiont, together accounting for 6.7-100% of sequences per tick. DNAs from Midichloria, Borrelia, Wolbachia, Ehrlichia, Pseudomonas, or unidentified Bacillales, Enterobacteriaceae, or Rhizobiales groups were also detected frequently. Wolbachia and Midichloria significantly co-occurred in Georgia (p<0.00001), but not in other states. The significance of the Midichloria-Wolbachia co-occurrence is unknown. Among ticks collected in Georgia, nymphs differed from adults in both the composition (p = 0.002) and structure (p = 0.002) of their bacterial communities. Adults differed only in their community structure (p = 0.002) with males containing more Rickettsia and females containing more Coxiella. Comparisons among adult ticks collected in New York and North Carolina supported the findings from the Georgia collection despite differences in geography, collection date, and sample handling, implying that the differences detected are consistent attributes. The data also suggest that some members of the

  16. Characterization of the bacterial communities of life stages of free living lone star ticks (Amblyomma americanum.

    Directory of Open Access Journals (Sweden)

    Amanda Jo Williams-Newkirk

    Full Text Available The lone star tick (Amblyomma americanum is an abundant and aggressive biter of humans, domestic animals, and wildlife in the southeastern-central USA and an important vector of several known and suspected zoonotic bacterial pathogens. However, the biological drivers of bacterial community variation in this tick are still poorly defined. Knowing the community context in which tick-borne bacterial pathogens exist and evolve is required to fully understand the ecology and immunobiology of the ticks and to design effective public health and veterinary interventions. We performed a metagenomic survey of the bacterial communities of questing A. americanum and tested 131 individuals (66 nymphs, 24 males, and 41 females from five sites in three states. Pyrosequencing was performed with barcoded eubacterial primers targeting variable 16S rRNA gene regions 5-3. The bacterial communities were dominated by Rickettsia (likely R. amblyommii and an obligate Coxiella symbiont, together accounting for 6.7-100% of sequences per tick. DNAs from Midichloria, Borrelia, Wolbachia, Ehrlichia, Pseudomonas, or unidentified Bacillales, Enterobacteriaceae, or Rhizobiales groups were also detected frequently. Wolbachia and Midichloria significantly co-occurred in Georgia (p<0.00001, but not in other states. The significance of the Midichloria-Wolbachia co-occurrence is unknown. Among ticks collected in Georgia, nymphs differed from adults in both the composition (p = 0.002 and structure (p = 0.002 of their bacterial communities. Adults differed only in their community structure (p = 0.002 with males containing more Rickettsia and females containing more Coxiella. Comparisons among adult ticks collected in New York and North Carolina supported the findings from the Georgia collection despite differences in geography, collection date, and sample handling, implying that the differences detected are consistent attributes. The data also suggest that some members of

  17. Impact of cadmium on the bacterial communities in the gut of Metaphire posthuma

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Shih-Hsiung; Chen, Mu-Hsuan; Chen, Chien-Cheng; Chen, Colin S. [Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan (China); Chen, Jiun-Hong [Department of Life Science, National Taiwan University, Taipei, Taiwan (China); Chen, Ssu Ching, E-mail: osycchna@ksts.seed.net.tw [Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan (China)

    2009-12-30

    The effects of cadmium (Cd) contamination in soil onto the bacterial communities of the guts pooled from ten Metaphire posthuma were addressed during 14 days' incubation. We found that about 50% of Cd (5 mg/kg, dry weight soil) in the contaminated soil was bio-accumulated into the earthworms. DNA was extracted from the guts of M. posthuma and their dwelling soil irrespective of Cd treatment for the analysis of the bacterial communities of guts in M. posthuma and in soil by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis). A distinctive cluster of bacterial communities of the guts in the earthworm with and without Cd treatment using the analysis of unweighted pair-group method using arithmetic averages (UPGMA) was observed, indicating that the bacterial community of guts could be changed by Cd. However, no differences in the bacterial communities in soil irrespective of Cd treatment were observed, which could be resulted from the bioremediation of Cd by earthworms leading to insignificant effect of Cd on bacterial communities in soil. For the sequencing of some of the dominant bands in the DGGE profile, Bradyrhizobium japonicum, Stenotrophomonas sp. D2, and Labrys, sp. CC-BB4, whose sequences display an identity of more than 97% using blast program against a known sequence in the GeneBank database and Ribosomal database, were identified. Collectively, our results showed that earthworm treatment can decrease the concentrations of Cd in soil, and Cd cause a shift in the bacterial communities in the guts of M. posthuma. The application of M. posthuma for Cd bioremediation would be desired.

  18. Parental material and cultivation determine soil bacterial community structure and fertility.

    Science.gov (United States)

    Sun, Li; Gao, Jusheng; Huang, Ting; Kendall, Joshua R A; Shen, Qirong; Zhang, Ruifu

    2015-01-01

    Microbes are the key components of the soil environment, playing important roles during soil development. Soil parent material provides the foundation elements that comprise the basic nutritional environment for the development of microbial community. After 30 years artificial maturation of cultivation, the soil developments of three different parental materials were evaluated and bacterial community compositions were investigated using the high-throughput sequencing approach. Thirty years of cultivation increased the soil fertility and soil microbial biomass, richness and diversity, greatly changed the soil bacterial communities, the proportion of phylum Actinobacteria decreased significantly, while the relative abundances of the phyla Acidobacteria, Chloroflexi, Gemmatimonadetes, Armatimonadetes and Nitrospira were significantly increased. Soil bacterial communities of parental materials were separated with the cultivated ones, and comparisons of different soil types, granite soil and quaternary red clay soil were similar and different with purple sandy shale soil in both parental materials and cultivated treatments. Bacterial community variations in the three soil types were affected by different factors, and their alteration patterns in the soil development also varied with soil type. Soil properties (except total potassium) had a significant effect on the soil bacterial communities in all three soil types and a close relationship with abundant bacterial phyla. The amounts of nitrogen-fixing bacteria as well as the abundances of the nifH gene in all cultivated soils were higher than those in the parental materials; Burkholderia and Rhizobacte were enriched significantly with long-term cultivation. The results suggested that crop system would not deplete the nutrients of soil parental materials in early stage of soil maturation, instead it increased soil fertility and changed bacterial community, specially enriched the nitrogen-fixing bacteria to accumulate

  19. Integrated mapping of groundwater drought risk in the Southern African Development Community (SADC) region

    CSIR Research Space (South Africa)

    Villholth, KG

    2013-06-01

    Full Text Available Groundwater drought denotes the condition and hazard during a prolonged meteorological drought when groundwater resources decline and become unavailable or inaccessible for human use. Groundwater drought risk refers to the combined physical risk...

  20. Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing.

    Science.gov (United States)

    Luo, Gang; Angelidaki, Irini

    2014-09-01

    The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors.

  1. Endophytic and rhizospheric bacterial communities isolated from the medicinal plants Echinacea purpurea and Echinacea angustifolia.

    Science.gov (United States)

    Chiellini, Carolina; Maida, Isabel; Emiliani, Giovanni; Mengoni, Alessio; Mocali, Stefano; Fabiani, Arturo; Biffi, Sauro; Maggini, Valentina; Gori, Luigi; Vannacci, Alfredo; Gallo, Eugenia; Firenzuoli, Fabio; Fani, Renato

    2014-09-01

    In this work we analyzed the composition and structure of cultivable bacterial communities isolated from the stem/leaf and root compartments of two medicinal plants, Echinacea purpurea (L.) Moench and Echinacea angustifolia (DC.) Hell, grown in the same soil, as well as the bacterial community from their rhizospheric soils. Molecular PCR-based techniques were applied to cultivable bacteria isolated from the three compartments of the two plants. The results showed that the two plants and their respective compartments were characterized by different communities, indicating a low degree of strain sharing and a strong selective pressure within plant tissues. Pseudomonas was the most highly represented genus, together with Actinobacteria and Bacillus spp. The presence of distinct bacterial communities in different plant species and among compartments of the same plant species could account for the differences in the medicinal properties of the two plants. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

  2. Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps.

    Science.gov (United States)

    Yashiro, Erika; Pinto-Figueroa, Eric; Buri, Aline; Spangenberg, Jorge E; Adatte, Thierry; Niculita-Hirzel, Hélène; Guisan, Antoine; van der Meer, Jan Roelof

    2016-11-01

    Mountain ecosystems are characterized by a diverse range of climatic and topographic conditions over short distances and are known to shelter a high biodiversity. Despite important progress, still little is known on bacterial diversity in mountain areas. Here, we investigated soil bacterial biogeography at more than 100 sampling sites randomly stratified across a 700-km(2) area with 2,200-m elevation gradient in the western Swiss Alps. Bacterial grassland communities were highly diverse, with 12,741 total operational taxonomic units (OTUs) across 100 sites and an average of 2,918 OTUs per site. Bacterial community structure was correlated with local climatic, topographic, and soil physicochemical parameters with high statistical significance. We found pH (correlated with % CaO and % mineral carbon), hydrogen index (correlated with bulk gravimetric water content), and annual average number of frost days during the growing season to be among the groups of the most important environmental drivers of bacterial community structure. In contrast, bacterial community structure was only weakly stratified as a function of elevation. Contrasting patterns were discovered for individual bacterial taxa. Acidobacteria responded both positively and negatively to pH extremes. Various families within the Bacteroidetes responded to available phosphorus levels. Different verrucomicrobial groups responded to electrical conductivity, total organic carbon, water content, and mineral carbon contents. Alpine grassland bacterial communities are thus highly diverse, which is likely due to the large variety of different environmental conditions. These results shed new light on the biodiversity of mountain ecosystems, which were already identified as potentially fragile to anthropogenic influences and climate change. This article addresses the question of how microbial communities in alpine regions are dependent on local climatic and soil physicochemical variables. We benefit from a unique 700

  3. Temporal and Spatial Variations of Bacterial and Faunal Communities Associated with Deep-Sea Wood Falls.

    Science.gov (United States)

    Pop Ristova, Petra; Bienhold, Christina; Wenzhöfer, Frank; Rossel, Pamela E; Boetius, Antje

    2017-01-01

    Sinking of large organic food falls i.e. kelp, wood and whale carcasses to the oligotrophic deep-sea floor promotes the establishment of locally highly productive and diverse ecosystems, often with specifically adapted benthic communities. However, the fragmented spatial distribution and small area poses challenges for the dispersal of their microbial and faunal communities. Our study focused on the temporal dynamics and spatial distributions of sunken wood bacterial communities, which were deployed in the vicinity of different cold seeps in the Eastern Mediterranean and the Norwegian deep-seas. By combining fingerprinting of bacterial communities by ARISA and 454 sequencing with in situ and ex situ biogeochemical measurements, we show that sunken wood logs have a locally confined long-term impact (> 3y) on the sediment geochemistry and community structure. We confirm previous hypotheses of different successional stages in wood degradation including a sulphophilic one, attracting chemosynthetic fauna from nearby seep systems. Wood experiments deployed at similar water depths (1100-1700 m), but in hydrographically different oceanic regions harbored different wood-boring bivalves, opportunistic faunal communities, and chemosynthetic species. Similarly, bacterial communities on sunken wood logs were more similar within one geographic region than between different seas. Diverse sulphate-reducing bacteria of the Deltaproteobacteria, the sulphide-oxidizing bacteria Sulfurovum as well as members of the Acidimicrobiia and Bacteroidia dominated the wood falls in the Eastern Mediterranean, while Alphaproteobacteria and Flavobacteriia colonized the Norwegian Sea wood logs. Fauna and bacterial wood-associated communities changed between 1 to 3 years of immersion, with sulphate-reducers and sulphide-oxidizers increasing in proportion, and putative cellulose degraders decreasing with time. Only 6% of all bacterial genera, comprising the core community, were found at any time on

  4. Dynamic bacterial communities on reverse-osmosis membranes in a full-scale desalination plant.

    Science.gov (United States)

    Manes, C-L de O; West, N; Rapenne, S; Lebaron, P

    2011-01-01

    To better understand biofouling of seawater reverse osmosis (SWRO) membranes, bacterial diversity was characterized in the intake water, in subsequently pretreated water and on SWRO membranes from a full-scale desalination plant (FSDP) during a 9 month period. 16S rRNA gene fingerprinting and sequencing revealed that bacterial communities in the water samples and on the SWRO membranes were very different. For the different sampling dates, the bacterial diversity of the active and the total bacterial fractions of the water samples remained relatively stable over the sampling period whereas the bacterial community structure on the four SWRO membrane samples was significantly different. The richness and evenness of the SWRO membrane bacterial communities increased with usage time with an increase in the Shannon diversity index of 2.2 to 3.7. In the oldest SWRO membrane (330 days), no single operational taxonomic unit (OTU) dominated and the majority of the OTUs fell into the Alphaproteobacteria or the Planctomycetes. In striking contrast, a Betaproteobacteria OTU affiliated to the genus Ideonella was dominant and exclusively found in the membrane used for the shortest time (10 days). This suggests that bacteria belonging to this genus could be one of the primary colonizers of the SWRO membrane. Knowledge of the dominant bacterial species on SWRO membranes and their dynamics should help guide culture studies for physiological characterization of biofilm forming species.

  5. Soil bacterial and fungal communities across a pH gradient in an arable soil.

    Science.gov (United States)

    Rousk, Johannes; Bååth, Erland; Brookes, Philip C; Lauber, Christian L; Lozupone, Catherine; Caporaso, J Gregory; Knight, Rob; Fierer, Noah

    2010-10-01

    Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth.

  6. Bacterial community structure and predicted alginate metabolic pathway in an alginate-degrading bacterial consortium.

    Science.gov (United States)

    Kita, Akihisa; Miura, Toyokazu; Kawata, Satoshi; Yamaguchi, Takeshi; Okamura, Yoshiko; Aki, Tsunehiro; Matsumura, Yukihiko; Tajima, Takahisa; Kato, Junichi; Nishio, Naomichi; Nakashimada, Yutaka

    2016-03-01

    Methane fermentation is one of the effective approaches for utilization of brown algae; however, this process is limited by the microbial capability to degrade alginate, a main polysaccharide found in these algae. Despite its potential, little is known about anaerobic microbial degradation of alginate. Here we constructed a bacterial consortium able to anaerobically degrade alginate. Taxonomic classification of 16S rRNA gene, based on high-throughput sequencing data, revealed that this consortium included two dominant strains, designated HUA-1 and HUA-2; these strains were related to Clostridiaceae bacterium SK082 (99%) and Dysgonomonas capnocytophagoides (95%), respectively. Alginate lyase activity and metagenomic analyses, based on high-throughput sequencing data, revealed that this bacterial consortium possessed putative genes related to a predicted alginate metabolic pathway. However, HUA-1 and 2 did not grow on agar medium with alginate by using roll-tube method, suggesting the existence of bacterial interactions like symbiosis for anaerobic alginate degradation.

  7. Microbial Community-Level Physiological Profiles (CLPP) and herbicide mineralization potential in groundwater affected by agricultural land use

    Science.gov (United States)

    Janniche, Gry Sander; Spliid, Henrik; Albrechtsen, Hans-Jørgen

    2012-10-01

    Diffuse groundwater pollution from agricultural land use may impact the microbial groundwater community, which was investigated as Community-Level Physiological Profiles (CLPP) using EcoPlate™. Water was sampled from seven piezometers and a spring in a small agricultural catchment with diffuse herbicide and nitrate pollution. Based on the Shannon-Wiener and Simpson's diversity indices the diversity in the microbial communities was high. The response from the EcoPlates™ showed which substrates support groundwater bacteria, and all 31 carbon sources were utilized by organisms from at least one water sample. However, only nine carbon sources were utilized by all water samples: D-Mannitol, N-acetyl-D-glucosamine, putrescine, D-galacturonic acid, itaconic acid, 4-hydroxy benzoic acid, tween 40, tween 80, and L-asparagine. In all water samples the microorganisms preferred D-mannitol, D-galacturonic acid, tween 40, and 4-hydroxy benzoic acid as substrates, whereas none preferred 2-hydroxy benzoic acid, α-D-lactose, D,L-α-glycerol phosphate, α-ketobutyric acid, L-threonine and glycyl-L-glutamic acid. Principal Component Analysis of the CLPP's clustered the most agriculturally affected groundwater samples, indicating that the agricultural land use affects the groundwater microbial communities. Furthermore, the ability to mineralize atrazine and isoproturon, which have been used in the catchment, was also associated with this cluster.

  8. Soil bacterial community responses to warming and grazing in a Tibetan alpine meadow.

    Science.gov (United States)

    Li, Yaoming; Lin, Qiaoyan; Wang, Shiping; Li, Xiangzhen; Liu, Wentso; Luo, Caiyun; Zhang, Zhenhua; Zhu, Xiaoxue; Jiang, Lili; Li, Xine

    2016-01-01

    Warming and grazing significantly affect the structure and function of an alpine meadow ecosystem. Yet, the responses of soil microbes to these disturbances are not well understood. Controlled asymmetrical warming (+1.2/1.7°C during daytime/nighttime) with grazing experiments were conducted to study microbial response to warming, grazing and their interactions. Significant interactive effects of warming and grazing were observed on soil bacterial α-diversity and composition. Warming only caused significant increase in bacterial α-diversity under no-grazing conditions. Grazing induced no substantial differences in bacterial α-diversity and composition irrespective of warming. Warming, regardless of grazing, caused a significant increase in soil bacterial community similarity across space, but grazing only induced significant increases under no-warming conditions. The positive effects of warming on bacterial α-diversity and grazing on community similarity were weakened by grazing and warming, respectively. Soil and plant variables explained well the variations in microbial communities, indicating that changes in soil and plant properties may primarily regulate soil microbial responses to warming in this alpine meadow. The results suggest that bacterial communities may become more similar across space in a future, warmed climate and moderate grazing may potentially offset, at least partially, the effects of global warming on the soil microbial diversity. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Impact of Phanerochaete chrysosporium on the Functional Diversity of Bacterial Communities Associated with Decaying Wood.

    Directory of Open Access Journals (Sweden)

    Vincent Hervé

    Full Text Available Bacteria and fungi naturally coexist in various environments including forest ecosystems. While the role of saprotrophic basidiomycetes in wood decomposition is well established, the influence of these fungi on the functional diversity of the wood-associated bacterial communities has received much less attention. Based on a microcosm experiment, we tested the hypothesis that both the presence of the white-rot fungus Phanerochaete chrysosporium and the wood, as a growth substrate, impacted the functional diversity of these bacterial communities. Microcosms containing sterile sawdust were inoculated with a microbial inoculum extracted from a forest soil, in presence or in absence of P. chrysosporium and subsequently, three enrichment steps were performed. First, bacterial strains were isolated from different microcosms previously analyzed by 16S rRNA gene-based pyrosequencing. Strains isolated from P. chrysosporium mycosphere showed less antagonism against this fungus compared to the strains isolated from the initial forest soil inoculum, suggesting a selection by the fungus of less inhibitory bacterial communities. Moreover, the presence of the fungus in wood resulted in a selection of cellulolytic and xylanolytic bacterial strains, highlighting the role of mycospheric bacteria in wood decomposition. Additionally, the proportion of siderophore-producing bacteria increased along the enrichment steps, suggesting an important role of bacteria in iron mobilization in decaying-wood. Finally, taxonomic identification of 311 bacterial isolates revealed, at the family level, strong similarities with the high-throughput sequencing data as well as with other studies in terms of taxonomic composition of the wood-associated bacterial community, highlighting that the isolated strains are representative of the wood-associated bacterial communities.

  10. Impact of Phanerochaete chrysosporium on the Functional Diversity of Bacterial Communities Associated with Decaying Wood.

    Science.gov (United States)

    Hervé, Vincent; Ketter, Elodie; Pierrat, Jean-Claude; Gelhaye, Eric; Frey-Klett, Pascale

    2016-01-01

    Bacteria and fungi naturally coexist in various environments including forest ecosystems. While the role of saprotrophic basidiomycetes in wood decomposition is well established, the influence of these fungi on the functional diversity of the wood-associated bacterial communities has received much less attention. Based on a microcosm experiment, we tested the hypothesis that both the presence of the white-rot fungus Phanerochaete chrysosporium and the wood, as a growth substrate, impacted the functional diversity of these bacterial communities. Microcosms containing sterile sawdust were inoculated with a microbial inoculum extracted from a forest soil, in presence or in absence of P. chrysosporium and subsequently, three enrichment steps were performed. First, bacterial strains were isolated from different microcosms previously analyzed by 16S rRNA gene-based pyrosequencing. Strains isolated from P. chrysosporium mycosphere showed less antagonism against this fungus compared to the strains isolated from the initial forest soil inoculum, suggesting a selection by the fungus of less inhibitory bacterial communities. Moreover, the presence of the fungus in wood resulted in a selection of cellulolytic and xylanolytic bacterial strains, highlighting the role of mycospheric bacteria in wood decomposition. Additionally, the proportion of siderophore-producing bacteria increased along the enrichment steps, suggesting an important role of bacteria in iron mobilization in decaying-wood. Finally, taxonomic identification of 311 bacterial isolates revealed, at the family level, strong similarities with the high-throughput sequencing data as well as with other studies in terms of taxonomic composition of the wood-associated bacterial community, highlighting that the isolated strains are representative of the wood-associated bacterial communities.

  11. Dexamethasone in adults with community-acquired bacterial meningitis

    NARCIS (Netherlands)

    D. van de Beek; J. de Gans

    2006-01-01

    Bacterial meningitis in adults is a severe disease with high fatality and morbidity rates. Experimental studies have shown that the inflammatory response in the subarachnoid space is associated with an unfavourable outcome. In these experiments, corticosteroids, and in particular dexamethasone, were

  12. The Role of Abiotic Environmental Conditions and Herbivory in Shaping Bacterial Community Composition in Floral Nectar

    OpenAIRE

    Michal Samuni-Blank; Ido Izhaki; Sivan Laviad; Avi Bar-Massada; Yoram Gerchman; Malka Halpern

    2014-01-01

    Identifying the processes that drive community assembly has long been a central theme in ecology. For microorganisms, a traditional prevailing hypothesis states that "everything is everywhere, but the environment selects". Although the bacterial community in floral nectar may be affected by both atmosphere (air-borne bacteria) and animals as dispersal vectors, the environmental and geographic factors that shape microbial communities in floral nectar are unknown. We studied culturable bacteria...

  13. Comparison of soil bacterial communities in a natural hardwood forest and coniferous plantations in perhumid subtropical low mountains.

    Science.gov (United States)

    Lin, Yu-Te; Hu, Hsueh-Wen; Whitman, William B; Coleman, David C; Chiu, Chih-Yu

    2014-12-01

    The bacterial community of forest soils is influenced by environmental disturbance and/or meteorological temperature and precipitation. In this study, we investigated three bacterial communities in soils of a natural hardwood forest and two plantations of conifer, Calocedrus formosana and Cryptomeria japonica, in a perhumid, low mountain area. By comparison with our previous studies with similar temperature and/or precipitation, we aimed to elucidate how disturbance influences the bacterial community in forest soils and whether bacterial communities in similar forest types differ under different climate conditions. Analysis of 16S ribosomal RNA gene clone libraries revealed that Acidobacteria and Proteobacteria were the most abundant phyla in the three forest soil communities, with similar relative abundance of various bacterial groups. However, UniFrac analysis based on phylogenetic information revealed differences of bacterial communities between natural hardwood forest and coniferous plantation soils. The diversities of bacterial communities of the replanted Calocedrus and Cryptomeria forests were higher than that in natural hardwood forest. The bacterial diversity of these three forest soil were all higher than those in the same forest types at other locations with less precipitation or with lower temperature. In addition, the distribution of some of the most abundant operational taxonomic units in the three communities differed from other forest soils, including those related to Acidobacteria, α-, β- and γ-Proteobacteria. Reforestation could increase the bacterial diversity. Therefore, soil bacterial communities could be shaped by the forestry management practices and climate differences in warm and humid conditions.

  14. Diversity of Bacterial Communities of Fitness Center Surfaces in a U.S. Metropolitan Area

    Directory of Open Access Journals (Sweden)

    Nabanita Mukherjee

    2014-12-01

    Full Text Available Public fitness centers and exercise facilities have been implicated as possible sources for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial community residing on the surfaces in these indoor environments is still unknown. In this study, we investigated the overall bacterial ecology of selected fitness centers in a metropolitan area (Memphis, TN, USA utilizing culture-independent pyrosequencing of the 16S rRNA genes. Samples were collected from the skin-contact surfaces (e.g., exercise instruments, floor mats, handrails, etc. within fitness centers. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Proteobacter and Actinobacteria, with a total of 17 bacterial families and 25 bacterial genera. Most of these bacterial genera are of human and environmental origin (including, air, dust, soil, and water. Additionally, we found the presence of some pathogenic or potential pathogenic bacterial genera including Salmonella, Staphylococcus, Klebsiella, and Micrococcus. Staphylococcus was found to be the most prevalent genus. Presence of viable forms of these pathogens elevates risk of exposure of any susceptible individuals. Several factors (including personal hygiene, surface cleaning and disinfection schedules of the facilities may be the reasons for the rich bacterial diversity found in this study. The current finding underscores the need to increase public awareness on the importance of personal hygiene and sanitation for public gym users.

  15. Temporal changes in cutaneous bacterial communities of terrestrial- and aquatic-phase newts (Amphibia).

    Science.gov (United States)

    Sabino-Pinto, Joana; Galán, Pedro; Rodríguez, Silvia; Bletz, Molly C; Bhuju, Sabin; Geffers, Robert; Jarek, Michael; Vences, Miguel

    2017-08-01

    Animal-associated bacterial communities play essential roles for their host's ecology, physiology and health. Temporal dynamics of these communities are poorly understood, but might be of high relevance for amphibians with a well-expressed biphasic biology of adults where the structure of their skin changes drastically between the aquatic and terrestrial phases. Here, we investigated the temporal dynamics of cutaneous bacterial communities of Lissotriton boscai and Triturus marmoratus by monthly sampling populations from a pond and surrounding terrestrial habitats near A Coruña, Spain. These communities were characterized by 16S rRNA gene amplicons from DNA isolated from skin swabs. Newt bacterial communities displayed variation at three levels: between larvae and aquatic adults, between adult life phases (terrestrial versus aquatic), and temporally within life phases. The skin bacterial communities tended to differ to a lesser extent temporally and between larvae and adults, and more strongly between life phases. Larvae had a higher proportion of reads associated with antifungal taxa compared with adults, while no differences were found among adult life phases. Terrestrial specimens exhibited the highest community diversity. The regular transitions of adult newts between aquatic and terrestrial environments might contribute to the diversity of their skin microbiota and could increase disease resistance. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  16. Dynamics of bacterial community development in the reef coral Acropora muricata following experimental antibiotic treatment

    Science.gov (United States)

    Sweet, M. J.; Croquer, A.; Bythell, J. C.

    2011-12-01

    Development of the bacterial community associated with the coral Acropora muricata (= formosa) was monitored using 16S rRNA gene-based techniques and abundance counts over time following experimental modification of the existing microbial community using the antibiotic ciprofloxacin. Abundance of bacteria was reduced >99% by the treatment, resulting in significant changes in bacterial community structure. Following redeployment to their natural environment, some settlement and re-growth of bacteria took place within a few hours, including ribosomal types that were not present, or in low abundance, in the natural microbiota. However, complete recovery of the bacterial community required longer than 96 h, which indicates a relatively slow settlement and growth of bacteria from the water column and suggests that turnover of the natural community is similarly slow. The early developing community was dominated by antibiotic-resistant bacteria from the natural microbiota that survived the treatment and proliferated in the absence of natural competitors, but also included some non-resident ribotypes colonizing from the water column. Almost, all these opportunists were significantly reduced or eliminated within 96 h after treatment, demonstrating a high resilience in the natural bacterial community. Potential pathogens, including a Clostridium sp., inhabited the coral at low abundances, only becoming prevalent when the natural microbiota was disturbed by the treatment. The healthy coral-associated microbiota appears to be strongly controlled by microbial interactions.

  17. Responses of Soil Bacterial Communities to Nitrogen Deposition and Precipitation Increment Are Closely Linked with Aboveground Community Variation.

    Science.gov (United States)

    Li, Hui; Xu, Zhuwen; Yang, Shan; Li, Xiaobin; Top, Eva M; Wang, Ruzhen; Zhang, Yuge; Cai, Jiangping; Yao, Fei; Han, Xingguo; Jiang, Yong

    2016-05-01

    It has been predicted that precipitation and atmospheric nitrogen (N) deposition will increase in northern China; yet, ecosystem responses to the interactive effects of water and N remain largely unknown. In particular, responses of belowground microbial community to projected global change and their potential linkages to aboveground macro-organisms are rarely studied. In this study, we examined the responses of soil bacterial diversity and community composition to increased precipitation and multi-level N deposition in a temperate steppe in Inner Mongolia, China, and explored the diversity linkages between aboveground and belowground communities. It was observed that N addition caused the significant decrease in bacterial alpha-diversity and dramatic changes in community composition. In addition, we documented strong correlations of alpha- and beta-diversity between plant and bacterial communities in response to N addition. It was found that N enriched the so-called copiotrophic bacteria, but reduced the oligotrophic groups, primarily by increasing the soil inorganic N content and carbon availability and decreasing soil pH. We still highlighted that increased precipitation tended to alleviate the effects of N on bacterial diversity and dampen the plant-microbe connections induced by N. The counteractive effects of N addition and increased precipitation imply that even though the ecosystem diversity and function are predicted to be negatively affected by N deposition in the coming decades; the combination with increased precipitation may partially offset this detrimental effect.

  18. Attached and unattached bacterial communities in a 120-meter corehole in an acidic, crystalline rock aquifer.

    Science.gov (United States)

    Lehman, R M; Roberto, F F; Earley, D; Bruhn, D F; Brink, S E; O'Connell, S P; Delwiche, M E; Colwell, F S

    2001-05-01

    The bacteria colonizing geologic core sections (attached) were contrasted with those found suspended in the groundwater (unattached) by examining the microbiology of 16 depth-paired core and groundwater samples using a suite of culture-independent and culture-dependent analyses. One hundred twenty-two meters was continuously cored from a buried chalcopyrite ore hosted in a biotite-quartz-monzonite porphyry at the Mineral Park Mine near Kingman, Ariz. Every fourth 1.5-m core was acquired using microbiologically defensible methods, and these core sections were aseptically processed for characterization of the attached bacteria. Groundwater samples containing unattached bacteria were collected from the uncased corehole at depth intervals corresponding to the individual cores using an inflatable straddle packer sampler. The groundwater was acidic (pH 2.8 to 5.0), with low levels of dissolved oxygen and high concentrations of sulfate and metals, including ferrous iron. Total numbers of attached cells were less than 10(5) cells g of core material(-1) while unattached cells numbered about 10(5) cells ml of groundwater(-1). Attached and unattached acidophilic heterotrophs were observed throughout the depth profile. In contrast, acidophilic chemolithotrophs were not found attached to the rock but were commonly observed in the groundwater. Attached communities were composed of low numbers (numbers (ca. 10(3) CFU ml(-1)) of neutrophilic heterotrophs of limited diversity. Sulfate-reducing bacteria were restricted to the deepest samples of both core and groundwater. 16S ribosomal DNA sequence analysis of attached, acidophilic isolates indicated that organisms closely related to heterotrophic, acidophilic mesophiles such as Acidiphilium organovorum and, surprisingly, to the moderately thermophilic Alicyclobacillus acidocaldarius were present. The results indicate that viable (but possibly inactive) microorganisms were present in the buried ore and that there was substantial

  19. 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.

  20. 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.

  1. Effects of Cry1Ab Bt maize straw return on bacterial community of earthworm Eisenia fetida.

    Science.gov (United States)

    Shu, Yinghua; Zhang, Yanyan; Zeng, Huilan; Zhang, Yahui; Wang, Jianwu

    2017-04-01

    The eco-toxicological effects of Bacillus thuringiensis (Bt) maize on earthworm life-history traits were widely studied and the results were controversial, while their effects on earthworm bacterial community have been rarely studied. Here, effects of two hybrids of Bt maize [5422Bt1 (event Bt11) and 5422CBCL (MON810)] straw return on Eisenia fetida bacterial community were investigated by the terminal restriction fragment length polymorphism (T-RFLP) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) combing with DNA sequencing, compared to near-isogenic non-Bt maize (5422). Bt maize straw return had significant effects on soil nutrients, especially for available nitrogen (N). The significant differences were shown in soil bacterial community between Bt and non-Bt maize treatments on the 75(th) and 90(th) d, which was closely correlated with soil available N, P and K rather than Cry1Ab protein. There was no statistically significant difference in the bacterial community of earthworm gut contents between Bt and non-Bt maize treatments. The significant differences in the bacterial community of earthworm casts were found among three maize varieties treatments, which were closely correlated with Cry1Ab protein and N levels. The differentiated bacterial species in earthworm casts mainly belonged to Proteobacteria, including Brevundimonas, Caulobacter, Pseudomonas, Stenotrophomonas, Methylobacterium, Asticcacaulis and Achromobacter etc., which were associated with the mineralization, metabolic process and degradation of plants residues. Therefore, Bt maize straw return caused changes in the bacterial community of E. fetida casts, which was possibly caused by the direct (Cry1Ab protein) and non-expected effects (N levels) of Bt maize straw.

  2. Light structures phototroph, bacterial and fungal communities at the soil surface.

    Directory of Open Access Journals (Sweden)

    Lawrence O Davies

    Full Text Available The upper few millimeters of soil harbour photosynthetic microbial communities that are structurally distinct from those of underlying bulk soil due to the presence of light. Previous studies in arid zones have demonstrated functional importance of these communities in reducing soil erosion, and enhancing carbon and nitrogen fixation. Despite being widely distributed, comparative understanding of the biodiversity of the soil surface and underlying soil is lacking, particularly in temperate zones. We investigated the establishment of soil surface communities on pasture soil in microcosms exposed to light or dark conditions, focusing on changes in phototroph, bacterial and fungal communities at the soil surface (0-3 mm and bulk soil (3-12 mm using ribosomal marker gene analyses. Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus. The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes. However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere.

  3. Changes in assembly processes in soil bacterial communities following a wildfire disturbance.

    Science.gov (United States)

    Ferrenberg, Scott; O'Neill, Sean P; Knelman, Joseph E; Todd, Bryan; Duggan, Sam; Bradley, Daniel; Robinson, Taylor; Schmidt, Steven K; Townsend, Alan R; Williams, Mark W; Cleveland, Cory C; Melbourne, Brett A; Jiang, Lin; Nemergut, Diana R

    2013-06-01

    Although recent work has shown that both deterministic and stochastic processes are important in structuring microbial communities, the factors that affect the relative contributions of niche and neutral processes are poorly understood. The macrobiological literature indicates that ecological disturbances can influence assembly processes. Thus, we sampled bacterial communities at 4 and 16 weeks following a wildfire and used null deviation analysis to examine the role that time since disturbance has in community assembly. Fire dramatically altered bacterial community structure and diversity as well as soil chemistry for both time-points. Community structure shifted between 4 and 16 weeks for both burned and unburned communities. Community assembly in burned sites 4 weeks after fire was significantly more stochastic than in unburned sites. After 16 weeks, however, burned communities were significantly less stochastic than unburned communities. Thus, we propose a three-phase model featuring shifts in the relative importance of niche and neutral processes as a function of time since disturbance. Because neutral processes are characterized by a decoupling between environmental parameters and community structure, we hypothesize that a better understanding of community assembly may be important in determining where and when detailed studies of community composition are valuable for predicting ecosystem function.

  4. Pole-to-pole biogeography of surface and deep marine bacterial communities.

    Science.gov (United States)

    Ghiglione, Jean-François; Galand, Pierre E; Pommier, Thomas; Pedrós-Alió, Carlos; Maas, Elizabeth W; Bakker, Kevin; Bertilson, Stefan; Kirchmanj, David L; Lovejoy, Connie; Yager, Patricia L; Murray, Alison E

    2012-10-23

    The Antarctic and Arctic regions offer a unique opportunity to test factors shaping biogeography of marine microbial communities because these regions are geographically far apart, yet share similar selection pressures. Here, we report a comprehensive comparison of bacterioplankton diversity between polar oceans, using standardized methods for pyrosequencing the V6 region of the small subunit ribosomal (SSU) rRNA gene. Bacterial communities from lower latitude oceans were included, providing a global perspective. A clear difference between Southern and Arctic Ocean surface communities was evident, with 78% of operational taxonomic units (OTUs) unique to the Southern Ocean and 70% unique to the Arctic Ocean. Although polar ocean bacterial communities were more similar to each other than to lower latitude pelagic communities, analyses of depths, seasons, and coastal vs. open waters, the Southern and Arctic Ocean bacterioplankton communities consistently clustered separately from each other. Coastal surface Southern and Arctic Ocean communities were more dissimilar from their respective open ocean communities. In contrast, deep ocean communities differed less between poles and lower latitude deep waters and displayed different diversity patterns compared with the surface. In addition, estimated diversity (Chao1) for surface and deep communities did not correlate significantly with latitude or temperature. Our results suggest differences in environmental conditions at the poles and different selection mechanisms controlling surface and deep ocean community structure and diversity. Surface bacterioplankton may be subjected to more short-term, variable conditions, whereas deep communities appear to be structured by longer water-mass residence time and connectivity through ocean circulation.

  5. Archaeal and bacterial community structures in the anoxic sediment of Antarctic meromictic lake Nurume-Ike

    Science.gov (United States)

    Kurosawa, Norio; Sato, Shota; Kawarabayasi, Yutaka; Imura, Satoshi; Naganuma, Takeshi

    2010-08-01

    Prokaryotic community structures in the anoxic sediment of the Antarctic meromictic Lake Nurume-Ike were revealed by sequence analysis of 16S rRNA gene clones. The archaeal clones obtained (205 total) consisted of only three phylotypes, and were dominantly affiliated with uncultured euryarchaeotes. Specifically, 93% of the clones were identified as marine benthic group-D archaeal phylotype. In contrast to the limited archaeal diversity, 53 phylotypes were detected within 312 bacterial clones. Major bacterial phylotypes were affiliated with α-Proteobacteria (20% of clones), d-Proteobacteria (9%), Planctmycetales (7%), and Cyanobacteria (7%). A small numbers of clones belonging to γ-Proteobacteria, Actinobacteria, Spirochaetes, Flavobacteria, and Verrucomicrobia were also found. A total of 53% of the bacterial clones, consisting of 13 phylotypes, could not be classified into any known group. These results indicated that the bacterial community of Lake Nurume-Ike sediment consisted of numerous phylogenetic groups and had a diversity comparable to the diversity of other Antarctic lakes communities previously reported. Interestingly, however, there were very few phylotypes shared between the communities of lakes Nurume-Ike and five other lakes located in the Vestfold Hills area. This is the first comprehensive study to analyze more than 500 16S rDNA clones for microbial community analysis of an Antarctic lake sediment sample, and the results significantly expand current views of bacterial diversity in Antarctic lakes.

  6. Comparison of intestinal bacterial communities in grass carp,Ctenopharyngodon idellus,from two different habitats

    Institute of Scientific and Technical Information of China (English)

    NI Jiajia; YU Yuhe; ZHANG Tanglin; GAO Lei

    2012-01-01

    The intestinal bacteria of vertebrates form a close relationship with their host.External and internal conditions of the host,including its habitat,affect the intestinal bacterial community.Similarly,the intestinal bacterial community can,in turn,influence the host,particularly with respect to disease resistance.We compared the intestinal bacterial communities of grass carp that were collected from farm-ponds or a lake.We conducted denaturing gradient gel electrophoresis of amplified 16S rRNA genes,from which 66 different operational taxonomic units were identified.Using both the unweighted pair-group method with arithmetic means clustering and principal component analysis ordination,we found that the intestinal bacterial communities from the two groups of pond fish were clustered together and inset into the clusters of wild fish,except for DF-7,and there was no significant correlation between genetic diversity of grass carp and their intestinal bacterial communities(Mantel one-tailed test,R=0.157,P=0.175).Cetobacterium appeared more frequently in the intestine of grass carp collected from pond.A more thorough understanding of the role played by intestinal microbiota on fish health would be of considerable benefit to the aquaculture industry.

  7. Comparison of intestinal bacterial communities in grass carp, Ctenopharyngodon idellus, from two different habitats

    Science.gov (United States)

    Ni, Jiajia; Yu, Yuhe; Zhang, Tanglin; Gao, Lei

    2012-09-01

    The intestinal bacteria of vertebrates form a close relationship with their host. External and internal conditions of the host, including its habitat, affect the intestinal bacterial community. Similarly, the intestinal bacterial community can, in turn, influence the host, particularly with respect to disease resistance. We compared the intestinal bacterial communities of grass carp that were collected from farm-ponds or a lake. We conducted denaturing gradient gel electrophoresis of amplified 16S rRNA genes, from which 66 different operational taxonomic units were identified. Using both the unweighted pair-group method with arithmetic means clustering and principal component analysis ordination, we found that the intestinal bacterial communities from the two groups of pond fish were clustered together and inset into the clusters of wild fish, except for DF-7, and there was no significant correlation between genetic diversity of grass carp and their intestinal bacterial communities (Mantel one-tailed test, R=0.157, P=0.175). Cetobacterium appeared more frequently in the intestine of grass carp collected from pond. A more thorough understanding of the role played by intestinal microbiota on fish health would be of considerable benefit to the aquaculture industry.

  8. Bacterial communities associated with the decomposition of Fucus vesiculosus in transitional waters

    Science.gov (United States)

    Martins, Patrícia; Lopes, Marta Lobão; Rodrigues, Ana Maria; Gomes, Newton C. M.; Quintino, Victor

    2012-09-01

    In this work we study the temporal and spatial patterns of the bacterial communities associated with the decomposition of Fucus vesiculosus and a control substrate in a transitional ecosystem. Leaf-bags with 5 mm mesh-size and containing the experimental substrates were placed in three areas, euhaline, mesohaline and limnetic, covering the full salinity gradient. The substrates were submerged at day 0 and three replicates were randomly collected per site, at days 3, 7, 15, 30 and 60. The complexity and structural changes of the bacterial communities inhabiting F. vesiculosus and the control substrates were assessed by denaturing gradient gel electrophoresis (DGGE). Bacterial community fingerprints showed no significant differences between areas only at day 3, for both substrates. The bacterial community associated with F. vesiculosus showed significant differences over time in the euhaline and mesohaline areas but not in the limnetic area. A different trend was observed for the artificial substrate. Comparing the bacterial communities of F. vesiculosus and the artificial substrate, the results indicated that the significant differences between the two substrates were detected from day 7 in the euhaline area and only later, at day 15, in the other areas. These results are coherent with the fastest decomposition rate of the alga in the euhaline area, where it occurs naturally, and the slowest in the limnetic area, where it does not naturally exists.

  9. High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses

    Directory of Open Access Journals (Sweden)

    Seung Hak Yang

    2015-09-01

    Full Text Available The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gene sequences in the leachate was the highest at 6 weeks, in contrast to those at 2 and 14 weeks. The relative abundance of Firmicutes was reduced, while the proportion of Bacteroidetes and Proteobacteria increased from 3–6 weeks. The representation of phyla was restored after 14 weeks. However, the community structures between the samples taken at 1–2 and 14 weeks differed at the bacterial classification level. The trend in pH was similar to the changes seen in bacterial communities, indicating that the pH of the leachate could be related to the shift in the microbial community. The results indicate that the composition of bacterial communities in leachates of decomposing pig carcasses shifted continuously during the study period and might be influenced by the burial site.

  10. Host plant species determines symbiotic bacterial community mediating suppression of plant defenses

    Science.gov (United States)

    Chung, Seung Ho; Scully, Erin D.; Peiffer, Michelle; Geib, Scott M.; Rosa, Cristina; Hoover, Kelli; Felton, Gary W.

    2017-01-01

    Herbivore associated bacteria are vital mediators of plant and insect interactions. Host plants play an important role in shaping the gut bacterial community of insects. Colorado potato beetles (CPB; Leptinotarsa decemlineata) use several Solanum plants as hosts in their natural environment. We previously showed that symbiotic gut bacteria from CPB larvae suppressed jasmonate (JA)-induced defenses in tomato. However, little is known about how changes in the bacterial community may be involved in the manipulation of induced defenses in wild and cultivated Solanum plants of CPB. Here, we examined suppression of JA-mediated defense in wild and cultivated hosts of CPB by chemical elicitors and their symbiotic bacteria. Furthermore, we investigated associations between the gut bacterial community and suppression of plant defenses using 16 S rRNA amplicon sequencing. Symbiotic bacteria decreased plant defenses in all Solanum hosts and there were different gut bacterial communities in CPB fed on different host plants. When larvae were reared on different hosts, defense suppression differed among host plants. These results demonstrate that host plants influence herbivore gut bacterial communities and consequently affect the herbivore’s ability to manipulate JA-mediated plant defenses. Thus, the presence of symbiotic bacteria that suppress plant defenses might help CPB adapt to host plants. PMID:28045052

  11. Effects of CO2 leakage on soil bacterial communities from simulated CO2-EOR areas.

    Science.gov (United States)

    Chen, Fu; Yang, Yongjun; Ma, Yanjun; Hou, Huping; Zhang, Shaoliang; Ma, Jing

    2016-05-18

    CO2-EOR (enhanced oil recovery) has been proposed as a viable option for flooding oil and reducing anthropogenic CO2 contribution to the atmospheric pool. However, the potential risk of CO2 leakage from the process poses a threat to the ecological system. High-throughput sequencing was used to investigate the effects of CO2 emission on the composition and structure of soil bacterial communities. The diversity of bacterial communities notably decreased with increasing CO2 flux. The composition of bacterial communities varied along the CO2 flux, with increasing CO2 flux accompanied by increases in the relative abundance of Bacteroidetes and Firmicutes phyla, but decreases in the relative abundance of Acidobacteria and Chloroflexi phyla. Within the Firmicutes phylum, the genus Lactobacillus increased sharply when the CO2 flux was at its highest point. Alpha and beta diversity analysis revealed that differences in bacterial communities were best explained by CO2 flux. The redundancy analysis (RDA) revealed that differences in bacterial communities were best explained by soil pH values which related to CO2 flux. These results could be useful for evaluating the risk of potential CO2 leakages on the ecosystems associated with CO2-EOR processes.

  12. Tracing fecal pollution sources in karst groundwater by Bacteroidales genetic biomarkers, bacterial indicators, and environmental variables.

    Science.gov (United States)

    Zhang, Ya; Kelly, Walton R; Panno, Samuel V; Liu, Wen-Tso

    2014-08-15

    Fecal contamination in Midwestern karst regions was evaluated by simultaneously measuring traditional bacterial indicators (coliforms and Escherichia coli), Bacteroidales-based biomarkers, and environmental variables. Water samples from springs and wells were collected from karst regions in Illinois (IL), Wisconsin (WI), Kentucky (KY), and Missouri (MO). Quantitative PCR (Q-PCR) with seven primer sets targeting different members of Bacteroidales was used to determine the origin of fecal contamination (i.e., from human waste, livestock waste, or both). Most samples were contaminated by both human and animal waste, with a few samples showing pollution solely by one or the other. Spring water tended to have higher levels of contamination than well water, and higher concentrations of fecal biomarkers were detected in urban springs compared to rural spring systems. However, there were discrepancies on contamination profile determined by Bacteroidales-based biomarkers and by traditional bacterial indicators. Among all the environmental parameters examined, E. coli, sulfate, total dissolved solids (TDS), and silicon were significantly correlated (pgroundwater systems in Midwestern regions, and the inclusion of traditional bacterial indicators, environmental variables, and Bacteroidales-based MST is an effective approach for identifying fecal contamination in karst regions. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Geo-Chip analysis reveals reduced functional diversity of the bacterial community at a dumping site for dredged Elbe sediment.

    Science.gov (United States)

    Störmer, Rebecca; Wichels, Antje; Gerdts, Gunnar

    2013-12-15

    The dumping of dredged sediments represents a major stressor for coastal ecosystems. The impact on the ecosystem function is determined by its complexity not easy to assess. In the present study, we evaluated the potential of bacterial community analyses to act as ecological indicators in environmental monitoring programmes. We investigated the functional structure of bacterial communities, applying functional gene arrays (GeoChip4.2). The relationship between functional genes and environmental factors was analysed using distance-based multivariate multiple regression. Apparently, both the function and structure of the bacterial communities are impacted by dumping activities. The bacterial community at the dumping centre displayed a significant reduction of its entire functional diversity compared with that found at a reference site. DDX compounds separated bacterial communities of the dumping site from those of un-impacted sites. Thus, bacterial community analyses show great potential as ecological indicators in environmental monitoring.

  14. Soil bacterial community responses to revegetation of moving sand dune in semi-arid grassland.

    Science.gov (United States)

    Cao, Chengyou; Zhang, Ying; Cui, Zhenbo; Feng, Shuwei; Wang, Tingting; Ren, Qing

    2017-08-01

    Grasslands in semi-arid Northern China are widely desertified, thus inducing the formation of a large area of moving sand lands. Revegetation of the sandy land is commonly adopted to restore degraded grasslands. The structure of the soil microbial community might dramatically change during degradation and recovery because microorganisms are one of the major drivers of ecological process through their interactions with plants and soil. Assuming that soil properties are the key determinants of the structure of soil bacterial community within the same soil type, whether the vegetation type causes the significant difference in the structure of soil bacterial community during revegetation and restoration of the degraded grasslands remains poorly understood. Our study aimed to (1) investigate the response of soil bacterial communities to the changes during vegetation degradation and recovery and (2) evaluate whether the soil bacterial communities under plantations return to their native state. We detected the shifts in diversities and compositions of the soil bacterial communities and the relative abundance of dominant bacterial taxa by using the high-throughput Illumina MiSeq sequencing technique in an area covered by 32-year-old Caragana microphylla, Artemisia halodendron, Hedysarum fruticosum, Pinus sylvestris var. mongolica, Populus simonii, and Salix gordejevii sand-fixing plantations and in the native community (NC) dominated by elm, and moving sandy dune (MS). We found that the obtained operational taxonomic units by 16S rRNA gene sequencing and diversity index in MS were all significantly lower than those in NC, and the number and composition of dominant genera were significantly different between NC and MS. Interestingly, the compositions of bacterial communities and the dominant genera in different sand-fixation plantations (C. microphylla, A. halodendron, H. fruticosum, P. sylvestris var. mongolica, P. simonii, and S. gordejevii) were all similar to those of

  15. Effects of Soil and Substrate Cultivation on Lettuce Rhizosphere Bacterial Community

    Directory of Open Access Journals (Sweden)

    LIANG Yun

    2017-01-01

    Full Text Available Rhizosphere bacterial community can promote the nutrition absorption of plant root, which result in the upgrade of plant quality. Cultivation system has effect on rhizosphere bacterial community. Four treatments were set to investigate the effects of two different cultivation systems, soil and substrate systems, for two varieties of lettuce, Shengxuan NO.5 and cv. Lollo Rossca.(two cultivation systems × two varieties. Each treatment had three pots as samples with 10 lettuce plants for each pot. After 30 days of transplanting, five plants of each pot were randomly selected, and rhizosphere soil or substrate was sampled. Real-time PCR and PCR-DGGE were implied to analyze the characteristics of rhizosphere bacterial community in each treatment. Real-Time PCR detection showed that the number of the population of rhizosphere bacteria in substrate system was significantly higher than that of soil system(P<0.05. PCR-DGGE profiles revealed that the diversity of substrate system was significantly higher than that of soil system. As for Shenxuan NO.5, the Shannon-Wiener index(H, Simpson index(Dand Pielou evenness index(Eof substrate system were significantly higher than that of soil system(P<0.05, and for cv.Lollo Rossca, index H of substrate system were significantly higher than that of soil system(P<0.05. RDA revealed that soil and substrate systems had different bacterial communities, and pH and nitrate nitrogen were two main factors that determining the community structure. In addition, water content, C/N, and available phosphorus were positively correlated with the development of bacterial community. Overall, soil and substrate cultivation systems had different rhizosphere bacterial community, and the quantity and diversity were higher in substrate system due to the physiochemical difference.

  16. A bacterial community-based index to assess the ecological status of estuarine and coastal environments

    KAUST Repository

    Aylagas, Eva

    2016-10-23

    Biotic indices for monitoring marine ecosystems are mostly based on the analysis of benthic macroinvertebrate communities. Due to their high sensitivity to pollution and fast response to environmental changes, bacterial assemblages could complement the information provided by benthic metazoan communities as indicators of human-induced impacts, but so far, this biological component has not been well explored for this purpose. Here we performed 16S rRNA gene amplicon sequencing to analyze the bacterial assemblage composition of 51 estuarine and coastal stations characterized by different environmental conditions and human-derived pressures. Using the relative abundance of putative indicator bacterial taxa, we developed a biotic index that is significantly correlated with a sediment quality index calculated on the basis of organic and inorganic compound concentrations. This new index based on bacterial assemblage composition can be a sensitive tool for providing a fast environmental assessment and allow a more comprehensive integrative ecosystem approach for environmental management. © 2016.

  17. Risk factors for community-acquired bacterial meningitis

    DEFF Research Database (Denmark)

    Lundbo, Lene Fogt; Benfield, Thomas

    2017-01-01

    of these are pathogen-specific, while some are shared between different bacteria. METHODS: We searched the database PubMed to identify host risk factors for bacterial meningitis caused by the pathogens Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae type b, because they are three most common....... CONCLUSIONS: As conjugated vaccines are available for these infections, it is of utmost importance to identify high risk patients to be able to prevent invasive disease....... causative bacteria beyond the neonatal period. RESULTS: We describe a number of risk factors; including socioeconomic factors, age, genetic variation of the host and underlying medical conditions associated with increased susceptibility to invasive bacterial infections in both children and adults...

  18. Update on community-acquired bacterial meningitis: guidance and challenges.

    Science.gov (United States)

    van Ettekoven, C N; van de Beek, D; Brouwer, M C

    2017-09-01

    The existing heterogeneity in diagnostic work-up and treatment strategies in bacterial meningitis was the incentive to develop a European evidence-based guideline, which was published in 2016 by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group on Infections of the Brain (ESGIB). To summarize salient features of the guideline, identify recent developments and challenges currently faced. The ESCMID guideline, ongoing trial registries. Epidemiology, clinical symptoms, diagnostic work-up and therapy strategies of acute bacterial meningitis. The incidence of bacterial meningitis has decreased following pneumococcal and meningococcal conjugate vaccine introduction. In the diagnosis of bacterial meningitis the clinical characteristics and laboratory parameters are of limited diagnostic accuracy and therefore cerebrospinal fluid analysis remains the principal contributor to the final diagnosis. The ESCMID guideline advises to start empiric treatment within one hour of arrival in all suspected meningitis cases, and choice of antibiotics needs to be differentiated according to the patient's age, risk factors, and local resistance rates of pneumococci. Dexamethasone is the only proven adjunctive treatment and should be started together with the antibiotics. The follow-up of surviving patients should include evaluation for hearing loss and pneumococcal vaccination to prevent recurrences. Future perspectives include further development and implementation of vaccines, and new treatments aimed at further reducing the inflammatory response. Studies on implementation of the new guideline should determine adherence and evaluate whether improved prognosis can be achieved by following protocolled management strategies. Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  19. Specific features of bacterial communities in floodplain agrocenoses

    Science.gov (United States)

    Dobrovol'Skaya, T. G.; Leont'evskaya, E. A.; Sneg, A. A.; Balabko, P. N.

    2010-04-01

    The analysis of the taxonomic structure of the bacterial complexes in the alluvial soils of the Oka River valley allowed revealing the distinct differences in the spectrum of the bacterial dominants in the virgin and cultivated soils. Arthrobacter and pigment coryneform bacteria are shown to predominate in the virgin soil; bacilli and pseudomonades are common in the soil under vegetables. On cabbage leaves and carrot roots (both healthy and rotten), the spectrum of dominants is composed of two genera of enterobacteria: Pantoea and Erwinia. As a result of the plowing in of vegetables into the soil, enterobacteria accumulate; among them, phytopathogenic species are present. Within a year after this plowing in and the new yield, the enterobacteria practically disappeared, but myxobacteria and cytophages developed. Since these bacteria belong to the cellulose-destroying prokaryotes, the increase in their contents in the soil testified to their participation in the decomposition of the buried vegetable residues. Weeds are known to concentrate various bacterial forms in the phylloplane; they enter from different ecological niches: soil, water, meadow, and agricultural plants. Representatives of phytopathogenic bacteria as minor components were found on weeds.

  20. Autogenic succession and deterministic recovery following disturbance in soil bacterial communities

    DEFF Research Database (Denmark)

    Jurburg, Stephanie D.; Nunes, Ines Marques; Stegen, James C.

    2017-01-01

    The response of bacterial communities to environmental change may affect local to global nutrient cycles. However the dynamics of these communities following disturbance are poorly understood, given that they are often evaluated over macro-ecological time scales and end-point measurements. In order...... to understand the successional trajectory of soil bacterial communities following disturbances and the mechanisms controlling these dynamics at a scale relevant for these organisms, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days....... The disturbance imposed a strong selective pressure that persisted for up to 10 days, after which the importance of stochastic processes increased. Three successional stages were detected: a primary response in which surviving taxa increased in abundance; a secondary response phase during which community dynamics...

  1. Factors influencing the composition of bacterial communities found at abandoned copper-tailings dumps.

    Science.gov (United States)

    De la Iglesia, R; Castro, D; Ginocchio, R; van der Lelie, D; González, B

    2006-03-01

    To study the effect that copper residues exert on bacterial communities and the ability of bacteria to colonize different microhabitats in abandoned tailing dumps. We used the terminal-restriction fragment length polymorphism technique, a culture-independent molecular approach based on PCR amplification of ribosomal genes, to compare the structure of the bacterial communities from samples taken at two nearby located abandoned tailing dumps found in the Mediterranean-climate area of central Chile. Our results show that elevated available copper content in tailings has a strong effect on the bacterial community composition, but that other factors like pH and organic matter content also play an important role in the structure of these communities. We also found that the number of abundant bacteria in these samples was significantly lower than in soils not exposed to metal pollution. In addition to bioavailable copper, bacterial communities found in copper-tailings dumps are also affected by several other environmental factors. This first report on environmental factors influencing microbial communities in copper-tailings dumps will help to devise appropriate restoration procedures in this type of polluted habitat.

  2. Safe-site effects on rhizosphere bacterial communities in a high-altitude alpine environment.

    Science.gov (United States)

    Ciccazzo, Sonia; Esposito, Alfonso; Rolli, Eleonora; Zerbe, Stefan; Daffonchio, Daniele; Brusetti, Lorenzo

    2014-01-01

    The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites) which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS) site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P < 0.05) on 16S rRNA gene diversity revealed significant differences (P < 0.05) between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

  3. The role of abiotic environmental conditions and herbivory in shaping bacterial community composition in floral nectar.

    Science.gov (United States)

    Samuni-Blank, Michal; Izhaki, Ido; Laviad, Sivan; Bar-Massada, Avi; Gerchman, Yoram; Halpern, Malka

    2014-01-01

    Identifying the processes that drive community assembly has long been a central theme in ecology. For microorganisms, a traditional prevailing hypothesis states that "everything is everywhere, but the environment selects". Although the bacterial community in floral nectar may be affected by both atmosphere (air-borne bacteria) and animals as dispersal vectors, the environmental and geographic factors that shape microbial communities in floral nectar are unknown. We studied culturable bacterial communities in Asphodelus aestivus floral nectar and in its typical herbivorous bug Capsodes infuscatus, along an aridity gradient. Bacteria were sampled from floral nectar and bugs at four sites, spanning a geographical range of 200 km from Mediterranean to semi-arid conditions, under open and bagged flower treatments. In agreement with the niche assembly hypothesis, the differences in bacterial community compositions were explained by differences in abiotic environmental conditions. These results suggest that microbial model systems are useful for addressing macro-ecological questions. In addition, similar bacterial communities were found in the nectar and on the surface of the bugs that were documented visiting the flowers. These similarities imply that floral nectar bacteria dispersal is shaped not only by air borne bacteria and nectar consumers as previously reported, but also by visiting vectors like the mirid bugs.

  4. The role of abiotic environmental conditions and herbivory in shaping bacterial community composition in floral nectar.

    Directory of Open Access Journals (Sweden)

    Michal Samuni-Blank

    Full Text Available Identifying the processes that drive community assembly has long been a central theme in ecology. For microorganisms, a traditional prevailing hypothesis states that "everything is everywhere, but the environment selects". Although the bacterial community in floral nectar may be affected by both atmosphere (air-borne bacteria and animals as dispersal vectors, the environmental and geographic factors that shape microbial communities in floral nectar are unknown. We studied culturable bacterial communities in Asphodelus aestivus floral nectar and in its typical herbivorous bug Capsodes infuscatus, along an aridity gradient. Bacteria were sampled from floral nectar and bugs at four sites, spanning a geographical range of 200 km from Mediterranean to semi-arid conditions, under open and bagged flower treatments. In agreement with the niche assembly hypothesis, the differences in bacterial community compositions were explained by differences in abiotic environmental conditions. These results suggest that microbial model systems are useful for addressing macro-ecological questions. In addition, similar bacterial communities were found in the nectar and on the surface of the bugs that were documented visiting the flowers. These similarities imply that floral nectar bacteria dispersal is shaped not only by air borne bacteria and nectar consumers as previously reported, but also by visiting vectors like the mirid bugs.

  5. Spatial and seasonal variations in bacterial communities of the Yellow Sea by T-RFLP analysis

    Institute of Scientific and Technical Information of China (English)

    Hongyuan WANG; Xiaolu JIANG; Ya HE; Huashi GUAN

    2009-01-01

    Four typical coastal sites (rocky shore, sandy shore, mud flat shore, and artificial harbor) at the Yellow Sea were chosen to investigate the spatial and seasonal variations in bacterial communities. This was accomplished by using terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR amplified 16S rDNA fragments. Two kinds of tetrameric restriction enzymes, HhaI and MspI, were used in the experiment to depict the bacterial community diversity in different marine environments. It was found that the community compositions digested by the two enzymes separately were different. However, the results of bacterial community diversity derived from them were similar. The MDA analysis results of T-RFLP profiles coming from HhaI and MspI both exhibited a significant seasonal community shift for bacteria and a relatively low spatial variation among the four locations. With HhaI as the sample, the pair wise T-tests also revealed that variations were minor between each pair of marine environments, with R ranging from 0.198 to 0.349. However, the bacterial community structure in the mud flat site depicted a larger difference than each of the other three sites (R ranging from 0.282 to 0.349).

  6. Characterization of the diversity and temporal stability of bacterial communities in human milk.

    Directory of Open Access Journals (Sweden)

    Katherine M Hunt

    Full Text Available Recent investigations have demonstrated that human milk contains a variety of bacterial genera; however, as of yet very little work has been done to characterize the full diversity of these milk bacterial communities and their relative stability over time. To more thoroughly investigate the human milk microbiome, we utilized microbial identification techniques based on pyrosequencing of the 16S ribosomal RNA gene. Specifically, we characterized the bacterial communities present in milk samples collected from 16 women at three time-points over four weeks. Results indicated that milk bacterial communities were generally complex; several genera represented greater than 5% of the relative community abundance, and the community was often, yet not always, stable over time within an individual. These results support the conclusion that human milk, which is recommended as the optimal nutrition source for almost all healthy infants, contains a collection of bacteria more diverse than previously reported. This finding begs the question as to what role this community plays in colonization of the infant gastrointestinal tract and maintaining mammary health.

  7. Safe-Site Effects on Rhizosphere Bacterial Communities in a High-Altitude Alpine Environment

    Directory of Open Access Journals (Sweden)

    Sonia Ciccazzo

    2014-01-01

    Full Text Available The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P<0.05 on 16S rRNA gene diversity revealed significant differences (P<0.05 between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

  8. Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies.

    Science.gov (United States)

    Sickel, Wiebke; Grafe, T Ulmar; Meuche, Ivonne; Steffan-Dewenter, Ingolf; Keller, Alexander

    2016-05-01

    Carnivorous plants of the genus Nepenthes have been studied for over a century, but surprisingly little is known about associations with microorganisms. The two species Nepenthes rafflesiana and Nepenthes hemsleyana differ in their pitcher-mediated nutrient sources, sequestering nitrogen from arthropod prey and arthropods as well as bat faeces, respectively. We expected bacterial communities living in the pitchers to resemble this diet difference. Samples were taken from different parts of the pitchers (leaf, peristome, inside, outside, digestive fluid) of both species. Bacterial communities were determined using culture-independent high-throughput amplicon sequencing. Bacterial richness and community structure were similar in leaves, peristomes, inside and outside walls of both plant species. Regarding digestive fluids, bacterial richness was higher in N. hemsleyana than in N. rafflesiana. Additionally, digestive fluid communities were highly variable in structure, with strain-specific differences in community composition between replicates. Acidophilic taxa were mostly of low abundance, except the genus Acidocella, which strikingly reached extremely high levels in two N. rafflesiana fluids. In N. hemsleyana fluid, some taxa classified as vertebrate gut symbionts as well as saprophytes were enriched compared to N. rafflesiana, with saprophytes constituting potential competitors for nutrients. The high variation in community structure might be caused by a number of biotic and abiotic factors. Nitrogen-fixing bacteria were present in both study species, which might provide essential nutrients to the plant at times of low prey capture and/or rare encounters with bats.

  9. Can the Bacterial Community of a High Arctic Glacier Surface Escape Viral Control?

    Science.gov (United States)

    Rassner, Sara M. E.; Anesio, Alexandre M.; Girdwood, Susan E.; Hell, Katherina; Gokul, Jarishma K.; Whitworth, David E.; Edwards, Arwyn

    2016-01-01

    Glacial ice surfaces represent a seasonally evolving three-dimensional photic zone which accumulates microbial biomass and potentiates positive feedbacks in ice melt. Since viruses are abundant in glacial systems and may exert controls on supraglacial bacterial production, we examined whether changes in resource availability would promote changes in the bacterial community and the dynamics between viruses and bacteria of meltwater from the photic zone of a Svalbard glacier. Our results indicated that, under ambient nutrient conditions, low estimated viral decay rates account for a strong viral control of bacterial productivity, incurring a potent viral shunt of a third of bacterial carbon in the supraglacial microbial loop. Moreover, it appears that virus particles are very stable in supraglacial meltwater, raising the prospect that viruses liberated in melt are viable downstream. However, manipulating resource availability as dissolved organic carbon, nitrogen, and phosphorous in experimental microcosms demonstrates that the photic zone bacterial communities can escape viral control. This is evidenced by a marked decline in virus-to-bacterium ratio (VBR) concomitant with increased bacterial productivity and number. Pyrosequencing shows a few bacterial taxa, principally Janthinobacterium sp., dominate both the source meltwater and microcosm communities. Combined, our results suggest that viruses maintain high VBR to promote contact with low-density hosts, by the manufacture of robust particles, but that this necessitates a trade-off which limits viral production. Consequently, dominant bacterial taxa appear to access resources to evade viral control. We propose that a delicate interplay of bacterial and viral strategies affects biogeochemical cycling upon glaciers and, ultimately, downstream ecosystems. PMID:27446002

  10. Volcanic ash supports a diverse bacterial community in a marine mesocosm

    Science.gov (United States)

    Verena Witt,; Paul M Ayris,; Damby, David; Corrado Cimarelli,; Ulrich Kueppers,; Donald B Dingwell,; Gert Wörheide,

    2017-01-01

    Shallow-water coral reef ecosystems, particularly those already impaired by anthropogenic pressures, may be highly sensitive to disturbances from natural catastrophic events, such as volcanic eruptions. Explosive volcanic eruptions expel large quantities of silicate ash particles into the atmosphere, which can disperse across millions of square kilometres and deposit into coral reef ecosystems. Following heavy ash deposition, mass mortality of reef biota is expected, but little is known about the recovery of post-burial reef ecosystems. Reef regeneration depends partly upon the capacity of the ash deposit to be colonised by waterborne bacterial communities and may be influenced to an unknown extent by the physiochemical properties of the ash substrate itself. To determine the potential for volcanic ash to support pioneer bacterial colonisation, we exposed five well-characterised volcanic and coral reef substrates to a marine aquarium under low light conditions for 3 months: volcanic ash, synthetic volcanic glass, carbonate reef sand, calcite sand and quartz sand. Multivariate statistical analysis of Automated Ribosomal Intergenic Spacer Analysis (ARISA) fingerprinting data demonstrates clear segregation of volcanic substrates from the quartz and coral reef substrates over 3 months of bacterial colonisation. Overall bacterial diversity showed shared and substrate-specific bacterial communities; however, the volcanic ash substrate supported the most diverse bacterial community. These data suggest a significant influence of substrate properties (composition, granulometry and colour) on bacterial settlement. Our findings provide first insights into physicochemical controls on pioneer bacterial colonisation of volcanic ash and highlight the potential for volcanic ash deposits to support bacterial diversity in the aftermath of reef burial, on timescales that could permit cascading effects on larval settlement.

  11. Can the Bacterial Community of a High Arctic Glacier Surface Escape Viral Control?

    Science.gov (United States)

    Rassner, Sara M E; Anesio, Alexandre M; Girdwood, Susan E; Hell, Katherina; Gokul, Jarishma K; Whitworth, David E; Edwards, Arwyn

    2016-01-01

    Glacial ice surfaces represent a seasonally evolving three-dimensional photic zone which accumulates microbial biomass and potentiates positive feedbacks in ice melt. Since viruses are abundant in glacial systems and may exert controls on supraglacial bacterial production, we examined whether changes in resource availability would promote changes in the bacterial community and the dynamics between viruses and bacteria of meltwater from the photic zone of a Svalbard glacier. Our results indicated that, under ambient nutrient conditions, low estimated viral decay rates account for a strong viral control of bacterial productivity, incurring a potent viral shunt of a third of bacterial carbon in the supraglacial microbial loop. Moreover, it appears that virus particles are very stable in supraglacial meltwater, raising the prospect that viruses liberated in melt are viable downstream. However, manipulating resource availability as dissolved organic carbon, nitrogen, and phosphorous in experimental microcosms demonstrates that the photic zone bacterial communities can escape viral control. This is evidenced by a marked decline in virus-to-bacterium ratio (VBR) concomitant with increased bacterial productivity and number. Pyrosequencing shows a few bacterial taxa, principally Janthinobacterium sp., dominate both the source meltwater and microcosm communities. Combined, our results suggest that viruses maintain high VBR to promote contact with low-density hosts, by the manufacture of robust particles, but that this necessitates a trade-off which limits viral production. Consequently, dominant bacterial taxa appear to access resources to evade viral control. We propose that a delicate interplay of bacterial and viral strategies affects biogeochemical cycling upon glaciers and, ultimately, downstream ecosystems.

  12. Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima.

    Science.gov (United States)

    Herfort, Lydie; Crump, Byron C; Fortunato, Caroline S; McCue, Lee Ann; Campbell, Victoria; Simon, Holly M; Baptista, António M; Zuber, Peter

    2017-08-06

    Estuarine turbidity maxima (ETM) function as hotspots of microbial activity and diversity in estuaries, yet, little is known about the temporal and spatial variability in ETM bacterial community composition. To determine which environmental factors affect ETM bacterial populations in the Columbia River estuary, we analyzed ETM bacterial community composition (Sanger sequencing and amplicon pyrosequencing of 16S rRNA gene) and bulk heterotrophic production ((3) H-leucine incorporation rates). We collected water 20 times to cover five ETM events and obtained 42 samples characterized by different salinities, turbidities, seasons, coastal regimes (upwelling vs. downwelling), locations, and particle size. Spring and summer populations were distinct. All May samples had similar bacterial community composition despite having different salinities (1-24 PSU), but summer non-ETM bacteria separated into marine, freshwater, and brackish assemblages. Summer ETM bacterial communities varied depending on coastal upwelling or downwelling conditions and on the sampling site location with respect to tidal intrusion during the previous neap tide. In contrast to ETM, whole (>0.2 μm) and free-living (0.2-3 μm) assemblages of non-ETM waters were similar to each other, indicating that particle-attached (>3 μm) non-ETM bacteria do not develop a distinct community. Brackish water type (ETM or non-ETM) is thus a major factor affecting particle-attached bacterial communities. Heterotrophic production was higher in particle-attached than free-living fractions in all brackish waters collected throughout the water column during the rise to decline of turbidity through an ETM event (i.e., ETM-impacted waters). However, free-living communities showed higher productivity prior to or after an ETM event (i.e., non-ETM-impacted waters). This study has thus found that Columbia River ETM bacterial communities vary based on seasons, salinity, sampling location, and particle size, with the

  13. Epiphytic bacterial communities of the alga Fucus vesiculosus in oil-contaminated water areas of the Barents Sea.

    Science.gov (United States)

    Pugovkin, D V; Liaimer, A; Jensen, J B

    2016-11-01

    Taxonomic compositions of epiphytic bacterial communities in water areas differing in levels of oil pollution were revealed. In total, 82 bacterial genera belonging to 16 classes and 11 phyla were detected. All detected representatives of epiphytic bacterial communities belonged to the phyla Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria, Verrucomicrobia, Acidobacteria, Cyanobacteria, Firmicutes, and Fusobacteria and candidate division TM7. The ratio of the phyla in the communities varied depending on the levels of oil pollution. New data on taxonomic composition of uncultivated epiphytic bacterial communities of Fucus vesiculosus were obtained.

  14. Temperature adaptation of soil bacterial communities along an Antarctic climate gradient: predicting responses to climate warming

    DEFF Research Database (Denmark)

    Rinnan, Riikka; Rousk, Johannes; Yergeau, Etienne;

    2009-01-01

    the leucine incorporation technique, in order to predict future changes in temperature sensitivity of resident soil bacterial communities. Soil samples were collected along a climate gradient consisting of locations on the Antarctic Peninsula (Anchorage Island, 67 °34'S, 68 °08'W), Signy Island (60 °43'S, 45......Soil microorganisms, the central drivers of terrestrial Antarctic ecosystems, are being confronted with increasing temperatures as parts of the continent experience considerable warming. Here we determined short-term temperature dependencies of Antarctic soil bacterial community growth rates, using...... °38'W) and the Falkland Islands (51 °76'S 59 °03'W). At each location, experimental plots were subjected to warming by open top chambers (OTCs) and paired with control plots on vegetated and fell-field habitats. The bacterial communities were adapted to the mean annual temperature of their environment...

  15. Bacterial community composition and chitinase gene diversity of vermicompost with antifungal activity.

    Science.gov (United States)

    Yasir, Muhammad; Aslam, Zubair; Kim, Seon Won; Lee, Seon-Woo; Jeon, Che Ok; Chung, Young Ryun

    2009-10-01

    Bacterial communities and chitinase gene diversity of vermicompost (VC) were investigated to clarify the influence of earthworms on the inhibition of plant pathogenic fungi in VC. The spore germination of Fusarium moniliforme was reduced in VC aqueous extracts prepared from paper sludge and dairy sludge (fresh sludge, FS). The bacterial communities were examined by culture-dependent and -independent analyses. Unique clones selected from 16S rRNA libraries of FS and VC on the basis of restriction fragment length polymorphism (RFLP) fell into the major lineages of the domain bacteria Proteobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria and Firmicutes. Among culture isolates, Actinobacteria dominated in VC, while almost equal numbers of Actinobacteria and Proteobacteria were present in FS. Analysis of chitinolytic isolates and chitinase gene diversity revealed that chitinolytic bacterial communities were enriched in VC. Populations of bacteria that inhibited plant fungal pathogens were higher in VC than in FS and particularly chitinolytic isolates were most active against the target fungi.

  16. High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

    DEFF Research Database (Denmark)

    Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Bælum, Jacob

    2014-01-01

    and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon......In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High......-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized...

  17. Bacterial Community in Different Populations of Rice Brown Planthopper Nilaparvata lugens (Stål)

    Institute of Scientific and Technical Information of China (English)

    XU Hong-xing; ZHENG Xu-song; YANG Ya-jun; WANG Xin; YE Gong-yin; LU Zhong-xian

    2014-01-01

    The structures of bacterial communities in the brown planthopper (BPH) Nilaparvata lugens (Stål) from different geographic and resistant virulent populations were analyzed by using denatured gradient gel electrophoresis (DGGE). Results showed that the bacterial communities in BPH nymph from the first to the fifth instars varied with nymphal growth and development. The bacterial communities in the first-instar BPH nymph were similar to those in adults. Nine geographic BPH populations were divided into three groups based on the cluster analysis of DGGE fingerprint. The first group was from the Philippines;the second group was from Thailand and Hainan, Yunnan and Zhejiang provinces of China; and the third group was from Vietnam and Guangxi, Hunan and Jiangxi provinces of China. BPH populations adapted to different resistant rice varieties. The BPH populations from Mudgo (with resistant gene Bph1) and ASD7 (with resistant gene bph2) differed with those of the susceptible rice variety TN1.

  18. Variations of Bacterial Community Structure and Composition in Mangrove Sediment at Different Depths in Southeastern Brazil

    Directory of Open Access Journals (Sweden)

    Lucas William Mendes

    2014-12-01

    Full Text Available Tropical mangroves are considered one of the most productive ecosystems of the world, being characterized as nurseries and food sources for fish and other animals. Microorganisms play important roles in these environments, and the study of bacterial communities is of paramount importance for a better comprehension of mangrove dynamics. This study focused on the structure and composition of bacterial communities in mangrove sediments at different depths and points, located in Southeastern Brazil. Terminal Restriction Fragment Length Polymorphism (T-RFLP was used to determine the community structure, and 16S rRNA gene pyrosequencing was used to characterize the community composition. Redundancy analysis of T-RFLP patterns revealed differences in bacterial community structure according to soil attributes and depth. The parameters K and depth presented significant correlation with general community structure. Most sequences were classified into the phylum Proteobacteria (88%, which presented differences according to the depth, where the classes Betaproteobacteria (21% and Deltaproteobacteria (16% were abundant at 10 cm and Epsilonproteobacteria (35% was abundant at 40 cm depth. Clear differences were observed in community composition as shown by the differential distribution of the phyla Firmicutes (1.13% and 3.8%, for 10 cm and 40 cm respectively, Chloroflexi (2.8% and 0.75%, and Acidobacteria (2.75% and 0.57% according to the depth. Bacterial diversity measurements indicated higher diversity in shallow samples. Taken together, our findings indicate that mangrove holds a diverse bacterial community, which is shaped by the variations found in the ecosystem, such as sediment properties and depth.

  19. Dynamic Effects of Biochar on the Bacterial Community Structure in Soil Contaminated with Polycyclic Aromatic Hydrocarbons.

    Science.gov (United States)

    Song, Yang; Bian, Yongrong; Wang, Fang; Xu, Min; Ni, Ni; Yang, Xinglun; Gu, Chenggang; Jiang, Xin

    2017-08-16

    Amending soil with biochar is an effective soil remediation strategy for organic contaminants. This study investigated the dynamic effects of wheat straw biochar on the bacterial community structure during remediation by high-throughput sequencing. The wheat straw biochar amended into the soil significantly reduced the bioavailability and toxicity of polycyclic aromatic hydrocarbons (PAHs). Biochar amendment helped to maintain the bacterial diversity in the PAH-contaminated soil. The relationship between the immobilization of PAHs and the soil bacterial diversity fit a quadratic model. Before week 12 of the incubation, the incubation time was the main factor contributing to the changes in the soil bacterial community structure. However, biochar greatly affected the bacterial community structure after 12 weeks of amendment, and the effects were dependent upon the biochar type. Amendment with biochar mainly facilitated the growth of rare bacterial genera (relative abundance of 0.01-1%) in the studied soil. Therefore, the application of wheat straw biochar into PAH-contaminated soil can reduce the environmental risks of PAHs and benefit the soil microbial ecology.

  20. Impacts of poultry house environment on poultry litter bacterial community composition.

    Science.gov (United States)

    Dumas, Michael D; Polson, Shawn W; Ritter, Don; Ravel, Jacques; Gelb, Jack; Morgan, Robin; Wommack, K Eric

    2011-01-01

    Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD). Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens.

  1. Bacterial community in sediment from the Western Pacific "Warm Pool" and its relationship to environment

    Institute of Scientific and Technical Information of China (English)

    ZENG Runying; ZHAO Jing; ZHANG Rui; LIN Nianwei

    2005-01-01

    Total DNAs were extracted from different sections of deep sea sediment core sample collected from the Western Pacific "Warm Pool". The bacterial 16S ribosomal DNA (rDNA) clone libraries were constructed and analyzed by PCR-restriction fragment length polymorphism (RFLP) and DNA sequencing. The bacterial communities in these samples and their relationship to environment were analyzed consequently. The results indicated that among eight main bacterial groups found in these sediments, members of the γ-Proteobacteria were most abundant in each section of sediment core sample and the genus Colwellia belonging to γ-Proteobacteria was dominant in this area. Members of the α-Proteobacteria were found commonly existing in these samples, while members belonging to β-Proteobacteria were seldom detected. The diversity of bacterial communities from different sections of sediment core sample was δ- and ε-Proteo- bacteria and the bacterial group including genera Cytopahga, Flexibacteria and Bacteroides (CFB group). These bacteria all were inversely proportional to the depth of sediment. Phylogenetic analysis showed that there were 18%-30% and 15%-25% of total bacterial communities related to methane and sulfur metabolism respectively in each section of core sample, implicating that the metabolism of sulfur and methane played an important role in the substance and energy cycles of the Western Pacific "Warm Pool".

  2. Bacterial communities involved in soil formation and plant establishment triggered by pyrite bioweathering on arctic moraines.

    Science.gov (United States)

    Mapelli, Francesca; Marasco, Ramona; Rizzi, Agostino; Baldi, Franco; Ventura, Stefano; Daffonchio, Daniele; Borin, Sara

    2011-02-01

    In arctic glacier moraines, bioweathering primed by microbial iron oxidizers creates fertility gradients that accelerate soil development and plant establishment. With the aim of investigating the change of bacterial diversity in a pyrite-weathered gradient, we analyzed the composition of the bacterial communities involved in the process by sequencing 16S rRNA gene libraries from different biological soil crusts (BSC). Bacterial communities in three BSC of different morphology, located within 1 m distance downstream a pyritic conglomerate rock, were significantly diverse. The glacier moraine surrounding the weathered site showed wide phylogenetic diversity and high evenness with 15 represented bacterial classes, dominated by Alphaproteobacteria and pioneer Cyanobacteria colonizers. The bioweathered area showed the lowest diversity indexes and only nine bacterial families, largely dominated by Acidobacteriaceae and Acetobacteraceae typical of acidic environments, in accordance with the low pH of the BSC. In the weathered BSC, iron-oxidizing bacteria were cultivated, with counts decreasing along with the increase of distance from the rock, and nutrient release from the rock was revealed by environmental scanning electron microscopy-energy dispersive X-ray analyses. The vegetated area showed the presence of Actinomycetales, Verrucomicrobiales, Gemmatimonadales, Burkholderiales, and Rhizobiales, denoting a bacterial community typical of developed soils and indicating that the lithoid substrate of the bare moraine was here subjected to an accelerated colonization, driven by iron-oxidizing activity.

  3. Impacts of poultry house environment on poultry litter bacterial community composition.

    Directory of Open Access Journals (Sweden)

    Michael D Dumas

    Full Text Available Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD. Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens.

  4. Bacterial community characterization and biogeochemistry of sediments from a tropical upwelling system (Cabo Frio, Southeastern Brazil)

    Science.gov (United States)

    Castelo-Branco, R.; Barreiro, A.; Silva, F. S.; Carvalhal-Gomes, S. B. V.; Fontana, L. F.; Mendonça-Filho, J. G.; Vasconcelos, V.

    2016-11-01

    The Cabo Frio Upwelling System is one of the largest and most productive areas in southeastern Brazil. Although it is well-known that bacterial communities play a crucial role in the biogeochemical cycles and food chain of marine ecosystems, little is known regarding the microbial communities in the sediments of this upwelling region. In this research, we address the effect of different hydrological conditions on the biogeochemistry of sediments and the diversity of bacterial communities. Biogeochemistry profiles of sediments from four sampling stations along an inner-outer transect on the continental shelf were evaluated and denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments was used to study the bacterial community composition in these sediments. Our sequencing analysis of excised bands identified Alpha- and Gammaproteobacteria, Bacteroidetes and bacteria belonging to the Firmicutes phyla as the phylogenetic groups, indicating the existence of great diversity in these marine sediments. In this multidisciplinary study, the use of multivariate analysis was crucial for understanding how biogeochemical profiles influence bacterial community distribution. A Principal Component Analysis (PCA) indicated that the biogeochemical variables exhibited a clear spatial pattern that is mainly related to hydrological conditions. A Correspondence Analysis (CA) revealed an important association between certain taxonomic groups and specific sampling locations. Canonical Correspondence Analysis (CCA) demonstrated that the biogeochemistry influences the structure of the bacterial community in sediments. Among the bacterial groups identified, the most taxonomically diverse classes (Alphaproteobacteria and Gammaproteobacteria) were found to be distributed regardless of any studied biogeochemical variables influences, whereas other groups responded to biogeochemical conditions which, in turn, were influenced by hydrological conditions. This finding

  5. Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals?

    Science.gov (United States)

    Apprill, Amy; Robbins, Jooke; Eren, A Murat; Pack, Adam A; Reveillaud, Julie; Mattila, David; Moore, Michael; Niemeyer, Misty; Moore, Kathleen M T; Mincer, Tracy J

    2014-01-01

    Microbes are now well regarded for their important role in mammalian health. The microbiology of skin--a unique interface between the host and environment--is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae), and examine the potential for a core bacterial community and its variability with host (endogenous) or geographic/environmental (exogenous) specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding), suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp.), as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could possibly serve

  6. Humpback Whale Populations Share a Core Skin Bacterial Community: Towards a Health Index for Marine Mammals?

    Science.gov (United States)

    Apprill, Amy; Robbins, Jooke; Eren, A. Murat; Pack, Adam A.; Reveillaud, Julie; Mattila, David; Moore, Michael; Niemeyer, Misty; Moore, Kathleen M. T.; Mincer, Tracy J.

    2014-01-01

    Microbes are now well regarded for their important role in mammalian health. The microbiology of skin – a unique interface between the host and environment - is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae), and examine the potential for a core bacterial community and its variability with host (endogenous) or geographic/environmental (exogenous) specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding), suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp.), as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could possibly

  7. Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals?

    Directory of Open Access Journals (Sweden)

    Amy Apprill

    Full Text Available Microbes are now well regarded for their important role in mammalian health. The microbiology of skin--a unique interface between the host and environment--is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae, and examine the potential for a core bacterial community and its variability with host (endogenous or geographic/environmental (exogenous specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding, suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp., as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could

  8. Analysis of unculturable bacterial communities in tea orchard soils based on nested PCR-DGGE.

    Science.gov (United States)

    Zhao, Juan; Wu, Xiaobing; Nie, Chuanpeng; Wu, Ting; Dai, Wanhong; Liu, Hui; Yang, Ruyi

    2012-05-01

    The bacterial communities in the soils from tea orchards and their adjacent wasteland in Anhui Province, China were analysed by nested PCR-DGGE technique combined with sequencing. DGGE profiles revealed that the DGGE patterns of different soils were similar to each other and the most intensely bands appeared in all lanes. The bacterial genetic diversity index of tea orchard soils was lower than that of wasteland. For the tea orchard soils, Shannon's diversity index decreased in the order: 45-year-old tea orchard >25-year-old tea orchard >7-year-old tea orchard >70-year-old tea orchard. The analysis of 16S rRNA gene sequences indicated that the fragments belong to Proteobacteria, Acidobacteria, TM7, Cyanobacteria and Firmicutes. A comprehensive analysis of the bacterial community structure in the tea orchard soils indicated the bacterial community was dominantly composed of Acidobacteria, followed by Proteobacteria (Gamma and Alpha), Firmicutes, Cyanobacteria and candidate division TM7. The RDA combined with UPGMA clustering analysis showed that the more similar the environmental variables were, the more similar the bacterial community structures in tea orchard soils were.

  9. Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes

    Science.gov (United States)

    Wemheuer, Franziska; Kaiser, Kristin; Karlovsky, Petr; Daniel, Rolf; Vidal, Stefan; Wemheuer, Bernd

    2017-01-01

    Endophytic bacteria are critical for plant growth and health. However, compositional and functional responses of bacterial endophyte communities towards agricultural practices are still poorly understood. Hence, we analyzed the influence of fertilizer application and mowing frequency on bacterial endophytes in three agriculturally important grass species. For this purpose, we examined bacterial endophytic communities in aerial plant parts of Dactylis glomerata L., Festuca rubra L., and Lolium perenne L. by pyrotag sequencing of bacterial 16S rRNA genes over two consecutive years. Although management regimes influenced endophyte communities, observed responses were grass species-specific. This might be attributed to several bacteria specifically associated with a single grass species. We further predicted functional profiles from obtained 16S rRNA data. These profiles revealed that predicted abundances of genes involved in plant growth promotion or nitrogen metabolism differed between grass species and between management regimes. Moreover, structural and functional community patterns showed no correlation to each other indicating that plant species-specific selection of endophytes is driven by functional rather than phylogenetic traits. The unique combination of 16S rRNA data and functional profiles provided a holistic picture of compositional and functional responses of bacterial endophytes in agricultural relevant grass species towards management practices. PMID:28102323

  10. Functional Characterization of Bacterial Communities Responsible for Fermentation of Doenjang: A Traditional Korean Fermented Soybean Paste.

    Science.gov (United States)

    Jung, Woo Yong; Jung, Ji Young; Lee, Hyo Jung; Jeon, Che Ok

    2016-01-01

    Doenjang samples were prepared in triplicate and their microbial abundance, bacterial communities, and metabolites throughout fermentation were analyzed to investigate the functional properties of microorganisms in doenjang. Viable bacterial cells were approximately three orders of magnitude higher than fungal cells, suggesting that bacteria are more responsible for doenjang fermentation. Pyrosequencing and proton nuclear magnetic resonance spectroscopy were applied for the analysis of bacterial communities and metabolites, respectively. Bacterial community analysis based on 16S rRNA gene sequences revealed that doenjang samples included Bacillus, Enterococcus, Lactobacillus, Clostridium, Staphylococcus, Corynebacterium, Oceanobacillus, and Tetragenococcus. These genera were found either in doenjang-meju or solar salts, but not in both, suggesting two separate sources of bacteria. Bacillus and Enterococcus were dominant genera during the fermentation, but their abundances were not associated with metabolite changes, suggesting that they may not be major players in doenjang fermentation. Tetragenococcus was dominant in 108 day-doenjang samples, when lactate, acetate, putrescine, and tyramine increased quickly as glucose and fructose decreased, indicating that Tetragenococcus might be primarily responsible for organic acid and biogenic amine production. Lactobacillus was identified as a dominant group from the 179-day samples, associated with the increase of γ-aminobutyric acid (GABA) and the decrease of galactose, indicating a potential role for this genus as a major GABA producer during fermentation. The results of this study clarified the functional properties of major bacterial communities in the doenjang fermentation process, contributing to the production of safe and high-quality doenjang.

  11. Functional characterization of bacterial communities responsible for fermentation of doenjang, a traditional Korean fermented soybean paste

    Directory of Open Access Journals (Sweden)

    Woo Yong eJung

    2016-05-01

    Full Text Available Doenjang samples were prepared in triplicate and their microbial abundance, bacterial communities, and metabolites throughout fermentation were analyzed to investigate the functional properties of microorganisms in doenjang. Viable bacterial cells were approximately three orders of magnitude higher than fungal cells, suggesting that bacteria are more responsible for doenjang fermentation. Pyrosequencing and proton nuclear magnetic resonance spectroscopy were applied for the analysis of bacterial communities and metabolites, respectively. Bacterial community analysis based on 16S rRNA gene sequences revealed that doenjang samples included Bacillus, Enterococcus, Lactobacillus, Clostridium, Staphylococcus, Corynebacterium, Oceanobacillus, and Tetragenococcus. These genera were found either in doenjang-meju or solar salts, but not in both, suggesting two separate sources of bacteria. Bacillus and Enterococcus were dominant genera during the fermentation, but their abundances were not associated with metabolite changes, suggesting that they may not be major players in doenjang fermentation. Tetragenococcus was dominant in 108 day-doenjang samples, when lactate, acetate, putrescine, and tyramine increased quickly as glucose and fructose decreased, indicating that Tetragenococcus might be primarily responsible for organic acid and biogenic amine production. Lactobacillus was identified as a dominant group from the 179-day samples, associated with the increase of γ-aminobutyric acid (GABA and the decrease of galactose, indicating a potential role for this genus as a major GABA producer during fermentation. The results of this study clarified the functional properties of major bacterial communities in the doenjang fermentation process, contributing to the production of safe and high-quality doenjang.

  12. Comparative analysis of the composition of intestinal bacterial communities in Dastarcus helophoroides fed different diets.

    Science.gov (United States)

    Wang, Wei-Wei; He, Cai; Cui, Jun; Wang, Hai-Dong; Li, Meng-Lou

    2014-01-01

    The diversity of the intestinal bacterial communities in Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) larvae and adults was assayed by PCR-DGGE to determine whether different artificial diets could influence these bacterial communities. Two diets were used for feeding the larvae and four for the adults. Escherichia, Desemzia, Staphylococcus, Asticcacaulis, Cellvibrio, Aurantimonas, and Planomicrobium were isolated from the gut of the adults, with Escherichia and Staphylococcus being the main bacterial communities, and the quantities of intestinal bacterial were different in the adults fed different diets. Specifically, the amount of intestinal bacteria from the adults fed different diets had the following ranking according to the major component of the diet: ant powder > darkling beetle pupa powder > cricket powder > silkworm pupa powder. Escherichia, Bacillus, Staphylococcus, Kurthia, Planococcaceae, Ralstonia, Leptothrix, Acinetobacter, and Pseudomonas were isolated from the gut of the larvae. The quantity of intestinal bacteria from the larvae fed the darkling beetle pupae was greater than that from the larvae fed other artificial diets. This study, for the first time, investigated the effect of artificial diets on the bacterial community and the intestinal microbial diversity of D. helophoroides.

  13. Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes

    Science.gov (United States)

    Wemheuer, Franziska; Kaiser, Kristin; Karlovsky, Petr; Daniel, Rolf; Vidal, Stefan; Wemheuer, Bernd

    2017-01-01

    Endophytic bacteria are critical for plant growth and health. However, compositional and functional responses of bacterial endophyte communities towards agricultural practices are still poorly understood. Hence, we analyzed the influence of fertilizer application and mowing frequency on bacterial endophytes in three agriculturally important grass species. For this purpose, we examined bacterial endophytic communities in aerial plant parts of Dactylis glomerata L., Festuca rubra L., and Lolium perenne L. by pyrotag sequencing of bacterial 16S rRNA genes over two consecutive years. Although management regimes influenced endophyte communities, observed responses were grass species-specific. This might be attributed to several bacteria specifically associated with a single grass species. We further predicted functional profiles from obtained 16S rRNA data. These profiles revealed that predicted abundances of genes involved in plant growth promotion or nitrogen metabolism differed between grass species and between management regimes. Moreover, structural and functional community patterns showed no correlation to each other indicating that plant species-specific selection of endophytes is driven by functional rather than phylogenetic traits. The unique combination of 16S rRNA data and functional profiles provided a holistic picture of compositional and functional responses of bacterial endophytes in agricultural relevant grass species towards management practices.

  14. Diversity and composition of bacterial community in soils and lake sediments from an Arctic lake area

    Directory of Open Access Journals (Sweden)

    Nengfei Wang

    2016-07-01

    Full Text Available This study assessed the diversity and composition of bacterial communities within soils and lake sediments from an Arctic lake area (London Island, Svalbard. A total of 2,987 operational taxonomic units (OTUs were identified by high throughput sequencing, targeting bacterial 16S rRNA. The samples from four sites (three samples in each site were significantly different in geochemical properties and bacterial community composition. Proteobacteria and Acidobacteria were abundant phyla in the nine soil samples, whereas Proteobacteria and Bacteroidetes were abundant phyla in the three sediment samples. Furthermore, Actinobacteria, Chlorobi, Chlorofiexi, Elusimicrobia, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria significantly varied in their abundance among the four sampling sites. Additionally, members of the dominant genera, such as Clostridium, Luteolibacter, Methylibium, Rhodococus, and Rhodoplanes, were significantly different in their abundance among the four sampling sites. Besides, distance-based redundancy analysis revealed that pH (p < 0.001, water content (p < 0.01, ammonium nitrogen (NH4--N, p < 0.01, silicate silicon (SiO42--Si, p < 0.01, nitrite nitrogen (NO2--N, p < 0.05, organic carbon (p < 0.05, and organic nitrogen (p < 0.05 were the most significant factors that correlated with the bacterial community composition. The results suggest soils and sediments from a lake area in the Arctic harbor a high diversity of bacterial communities, which are influenced by many geochemical factors of Arctic environments.

  15. Molecular profiling of rhizosphere bacterial communities associated with Prosopis juliflora and Parthenium hysterophorus.

    Science.gov (United States)

    Jothibasu, K; Chinnadurai, C; Sundaram, Sp; Kumar, K; Balachandar, Dananjeyan

    2012-03-01

    Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

  16. Geochemistry and Microbial Communities in Iron- and Manganese-Enriched Cold Groundwater Biofiltration Units

    Science.gov (United States)

    Chang, W.; Dangeti, S.; Roshani, B.; McBeth, J. M.

    2015-12-01

    Exploring how to enhance the microbially mediated oxidization of iron (Fe) and manganese (Mn) in natural and engineered environments in cold climates requires an understanding of the interactive relationships between the geochemistry of cold groundwater and Fe- and Mn-oxidizing bacteria. This study precisely measured geochemical and microbial communities in a scaled-up biofiltration system using synchrotron-based X-ray Absorption Near-Edge Spectroscopy (XANES) analyses coupled with next-generation sequencing (Illumina Miseq). Two pilot-scale biofiltration columns for Fe (Filter 1) and Mn (Filter 2) were connected in series and installed at the Langham Water Treatment Plant in Saskatoon, Canada. The groundwater temperature ranged from 4 to 8 °C. The pilot-scale study showed that successful treatment (99% removal) of both Fe and Mn was achieved in the biofilters. However, the Mn removal was significantly retarded for four months, likely due to the slow growth of Mn-oxidizing bacteria (MnOB) in Filter 2. The removal of Mn was accelerated once the redox potential in Filter 2 exceeded +300 mV. At that point, the XANES analyses showed that the oxidization states of Mn in Filter 2 were mainly +3 and +4, confirming that Mn oxidization had occurred. Geochemical analyses (PHREEQCi) also indicated changed geochemical conditions that favoured the formation of Mn-oxides during biofiltration. Next-generation sequencing analyses indicated the enrichment of iron-oxidizing bacteria (FeOB), including Gallionella sp. and Sideroxydans sp., in Filter 1. There were high read numbers for MnOB relatives, including Pseudomonas sp., Hydrogenophaga sp., Bdellovibrio sp., and Leptothrix sp., in Filter 2. Furthermore, the addition of anthracite (coal-based filter media) positively affected the growth MnOB and enhanced Mn oxidization. The evidence obtained in this study provides insight into how Mn oxidization can be accelerated in cold groundwater treatment systems.

  17. Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils.

    Science.gov (United States)

    Delgado-Balbuena, Laura; Bello-López, Juan M; Navarro-Noya, Yendi E; Rodríguez-Valentín, Analine; Luna-Guido, Marco L; Dendooven, Luc

    2016-01-01

    Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the

  18. Bacterial communities associated with an occurrence of colored water in an urban drinking water distribution system.

    Science.gov (United States)

    Wu, Hui Ting; Mi, Zi Long; Zhang, Jing Xu; Chen, Chao; Xie, Shu Guang

    2014-08-01

    This study aimed to investigate bacterial community in an urban drinking water distribution system (DWDS) during an occurrence of colored water. Variation in the bacterial community diversity and structure was observed among the different waters, with the predominance of Proteobacteria. While Verrucomicrobia was also a major phylum group in colored water. Limnobacter was the major genus group in colored water, but Undibacterium predominated in normal tap water. The coexistence of Limnobacter as well as Sediminibacterium and Aquabacterium might contribute to the formation of colored water. Copyright © 2014 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  19. Context-dependent competition in a model gut bacterial community.

    Directory of Open Access Journals (Sweden)

    Eric J de Muinck

    Full Text Available Understanding the ecological processes that generate complex community structures may provide insight into the establishment and maintenance of a normal microbial community in the human gastrointestinal tract, yet very little is known about how biotic interactions influence community dynamics in this system. Here, we use natural strains of Escherichia coli and a simplified model microbiota to demonstrate that the colonization process on the strain level can be context dependent, in the sense that the outcome of intra-specific competition may be determined by the composition of the background community. These results are consistent with previous models for competition between organisms where one competitor has adapted to low resource environments whereas the other is optimized for rapid reproduction when resources are abundant. The genomic profiles of E. coli strains representing these differing ecological strategies provide clues for deciphering the genetic underpinnings of niche adaptation within a single species. Our findings extend the role of ecological theory in understanding microbial systems and the conceptual toolbox for describing microbial community dynamics. There are few, if any, concrete examples of context-dependent competition on a single trophic level. However, this phenomenon can have potentially dramatic effects on which bacteria will successfully establish and persist in the gastrointestinal system, and the principle should be equally applicable to other microbial ecosystems.

  20. Changes in the soil bacterial communities in a cedar plantation invaded by moso bamboo.

    Science.gov (United States)

    Lin, Yu-Te; Tang, Sen-Lin; Pai, Chuang-Wen; Whitman, William B; Coleman, David C; Chiu, Chih-Yu

    2014-02-01

    Moso bamboo is fast-growing and negatively allelopathic to neighboring plants. However, there is little information on the effects of its establishment and expansion to adjacent forest soil communities. To better understand the impacts of bamboo invasion on soil communities, the phylogenetic structure and diversity of the soil bacterial communities in moso bamboo forest, adjacent Japanese cedar plantation, and bamboo-invaded transition zone were examined using a combination of 16S rRNA gene clone libraries and bar-coded pyrosequencing techniques. Based on the number of operational taxonomic units (OTUs), Shannon diversity index, Chao1 estimator, and rarefaction analysis of both techniques, the bamboo soil bacterial community was the most diverse, followed by the transition zone, with the cedar plantation possessing the lowest diversity. The results from both techniques revealed that the Acidobacteria and Proteobacteria predominated in the three communities, though the relative abundance was different. The 250 most abundant OTUs represented about 70% of the total sequences found by pyrosequencing. Most of these OTUs were found in all three soil communities, demonstrating the overall similarity among the bacterial communities. Nonmetric multidimensional scaling analysis showed further that the bamboo and transition soil communities were more similar with each other than the cedar soils. These results suggest that bamboo invasion to the adjacent cedar plantation gradually increased the bacterial diversity and changed the soil community. In addition, while the 10 most abundant OTUs were distributed worldwide, related sequences were not abundant in soils from outside the forest studied here. This result may be an indication of the uniqueness of this region.

  1. Bacterial community structure in treated sewage sludge with mesophilic and thermophilic anaerobic digestion.

    Science.gov (United States)

    Stiborova, Hana; Wolfram, Jan; Demnerova, Katerina; Macek, Tomas; Uhlik, Ondrej

    2015-11-01

    Stabilized sewage sludge is applied to agricultural fields and farmland due to its high organic matter content. The aim of this study was to investigate the effects of two types of sludge stabilization, mesophilic anaerobic digestion (MAD) and thermophilic anaerobic digestion (TAD), on bacterial communities in sludge, including the presence of pathogenic microorganisms. Bacterial community structure and phylogenetic diversity were analyzed in four sewage sludge samples from the Czech Republic. Analysis of 16S ribosomal RNA (rRNA) genes showed that investigated sludge samples harbor diverse bacterial populations with only a few taxa present across all samples. Bacterial diversity was higher in sludge samples after MAD versus TAD treatment, and communities in MAD-treated sludge shared the highest genetic similarities. In all samples, the bacterial community was dominated by reads affiliated with Proteobacteria. The sludge after TAD treatment had considerably higher number of reads of thermotolerant/thermophilic taxa, such as the phyla Deinococcus-Thermus and Thermotogae or the genus Coprothermobacter. Only one operational taxonomic unit (OTU), which clustered with Rhodanobacter, was detected in all communities at a relative abundance >1 %. All of the communities were screened for the presence of 16S rRNA gene sequences of pathogenic bacteria using a database of 122 pathogenic species and ≥98 % identity threshold. The abundance of such sequences ranged between 0.23 and 1.57 % of the total community, with lower numbers present after the TAD treatment, indicating its higher hygienization efficiency. Sequences clustering with nontuberculous mycobacteria were present in all samples. Other detected sequences of pathogenic bacteria included Streptomyces somaliensis, Acinetobacter calcoaceticus, Alcaligenes faecalis, Gordonia spp., Legionella anisa, Bordetella bronchiseptica, Enterobacter aerogenes, Brucella melitensis, and Staphylococcus aureus.

  2. Variable effects of dispersal on productivity of bacterial communities due to changes in functional trait composition.

    Directory of Open Access Journals (Sweden)

    Ina Severin

    Full Text Available Previous studies have shown variable relationships between dispersal rate and ecosystem functioning, but the reasons for and mechanisms behind variable dispersal rate-functioning patterns are currently unknown. In this study we used six bacterial lake water communities in a laboratory experiment in order to investigate how dispersal among communities influences community productivity by evaluating three different mechanisms: 1 changes in taxonomic diversity, 2 changes in phylogenetic diversity or 3 changes in the composition of functional traits. The experiment was conducted in two phases; (A a dialysis bag experiment where the dispersal rate among six communities was manipulated and the subsequent change in bacterial diversity and growth rate was recorded, and (B a regrowth experiment where we manipulated available resources to study how well a taxon grows on certain organic carbon resources, i.e. their functional traits. From experiment (B we could thus estimate changes in functional traits in communities in experiment (A. Bacterial production was affected by dispersal, but not consistently among lakes. Neither change in taxonomic or phylogenetic diversity with dispersal could explain the observed dispersal-productivity relationships. Instead, changes in trait composition with dispersal, especially the communities' ability to use p-coumaric acid, an aromatic compound, could explain the observed dispersal-productivity relationships. Changes in this trait caused by dispersal seemed especially important for bacterial productivity in waters with a high aromaticity of the organic matter pool. We conclude that the effect of dispersal on bacterial communities can affect ecosystem functioning in different ways, through changes in functional key-traits which are important for the local environment.

  3. Characterizing changes in soil bacterial community structure in response to short-term warming

    Energy Technology Data Exchange (ETDEWEB)

    Gibbons, Sean M.; sun, Huaibo; Xiong, Jinbo; Gilbert, Jack A.; Peng, Fei; Chu, Haiyan; Chu, Haiyan

    2014-08-01

    High altitude alpine meadows are experiencing considerably greater than average increases in soil surface temperature, potentially as a result of ongoing climate change. The effects of warming on plant productivity and soil edaphic variables have been established previously, but the influence of warming on soil microbial community structure has not been well characterized. Here, the impact of 15 months of soil warming (both + 1 and + 2 degrees C) on bacterial community structure was examined in a field experiment on a Tibetan plateau alpine meadow using bar-coded pyrosequencing. Warming significantly changed (P < 0.05) the structure of the soil bacterial community, but the alpha diversity was not dramatically affected. Changes in the abundance of the Actinobacteria and Alphaproteobacteria were found to contribute the most to differences between ambient (AT) and artificially warmed conditions. A variance partitioning analysis (VPA) showed that warming directly explained 7.15% variation in bacterial community structure, while warming-induced changes in soil edaphic and plant phenotypic properties indirectly accounted for 28.3% and 20.6% of the community variance, respectively. Interestingly, certain taxa showed an inconsistent response to the two warming treatments, for example Deltaproteobacteria showed a decreased relative abundance at + 1 degrees C, but a return to AT control relative abundance at + 2 degrees C. This suggests complex microbial dynamics that could result from conditional dependencies between bacterial taxa.

  4. DNA extraction procedure affects organic-aggregate-attached bacterial community profiles from a shallow eutrophic lake.

    Science.gov (United States)

    Tang, Xiangming; Gao, Guang; Zhu, Liping; Chao, Jianying; Qin, Boqiang

    2009-06-01

    Organic aggregates (OA) in aquatic ecosystems harbour diverse microbial communities. The colonization and growth of OA-attached bacteria are important processes in the degradation and transformation of the particles. The development of efficient and comparative DNA extraction methods is one of the most critical steps in the study of the composition and diversity of OA-attached bacterial communities. To evaluate whether different DNA extraction procedures affect the measurement of bacterial community composition, we compared four in situ lysis procedures using OA from three locations in a shallow eutrophic lake (Lake Taihu, China). The extracted DNA was analyzed using denaturing gradient gel electrophoresis profiles. We found that the choice of DNA extraction protocol had a significant influence on the fingerprints of the OA-attached bacterial community. This was shown not only in the number of bands but also in their relative representation of certain DNA bands. Using the bead-beating DNA extraction method in the presence of hexadecyltrimethylammonium bromide, we found that crude microbial DNA could be extracted efficiently from different OA types. This protocol is reproducible and gives very pure DNA of relatively high molecular mass. More importantly, the protocol provided more representative and informative data on the diversity of OA-attached bacterial communities.

  5. A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole.

    Science.gov (United States)

    Pascault, Noémie; Roux, Simon; Artigas, Joan; Pesce, Stéphane; Leloup, Julie; Tadonleke, Rémy D; Debroas, Didier; Bouchez, Agnès; Humbert, Jean-François

    2014-12-01

    The pollution of lakes and rivers by pesticides is a growing problem worldwide. However, the impacts of these substances on microbial communities are still poorly understood, partly because next-generation sequencing (NGS) has rarely been used in an ecotoxicology context to study bacterial communities despite its interest for accessing rare taxa. Microcosm experiments were carried out to evaluate the effects of tebuconazole (TBZ) on the structure and composition of bacterial communities from two types of freshwater ecosystem (lakes and rivers) with differing histories of pollutant contamination (pristine vs. previously exposed sites). Pyrosequencing revealed that bacterial diversity was higher in the river than in the lakes and in previously exposed sites than in pristine sites. Lakes and river stations shared very few OTUs, and differences at the phylum level were identified between these ecosystems (i.e. the relative importance of Actinobacteria and Gammaproteobacteria). Despite differences between these ecosystems and their contamination history, no significant effect of TBZ on bacterial community structure or composition was observed. Compared to functional parameters that displayed variable responses, we demonstrated that a combination of classical methods and NGS is necessary to investigate the ecotoxicological responses of microbial communities to pollutants.

  6. Bacterial communities associated with culex mosquito larvae and two emergent aquatic plants of bioremediation importance.

    Science.gov (United States)

    Duguma, Dagne; Rugman-Jones, Paul; Kaufman, Michael G; Hall, Michael W; Neufeld, Josh D; Stouthamer, Richard; Walton, William E

    2013-01-01

    Microbes are important for mosquito nutrition, growth, reproduction and control. In this study, we examined bacterial communities associated with larval mosquitoes and their habitats. Specifically, we characterized bacterial communities associated with late larval instars of the western encephalitis mosquito (Culextarsalis), the submerged portions of two emergent macrophytes (California bulrush, Schoenoplectuscalifornicus and alkali bulrush, Schoenoplectusmaritimus), and the associated water columns to investigate potential differential use of resources by mosquitoes in different wetland habitats. Using next-generation sequence data from 16S rRNA gene hypervariable regions, the alpha diversity of mosquito gut microbial communities did not differ between pond mesocosms containing distinct monotypic plants. Proteobacteria, dominated by the genus Thorsellia (Enterobacteriaceae), was the most abundant phylum recovered from C. tarsalis larvae. Approximately 49% of bacterial OTUs found in larval mosquitoes were identical to OTUs recovered from the water column and submerged portions of the two bulrushes. Plant and water samples were similar to one another, both being dominated by Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria and Verrucomicrobia phyla. Overall, the bacterial communities within C. tarsalis larvae were conserved and did not change across sampling dates and between two distinct plant habitats. Although Thorsellia spp. dominated mosquito gut communities, overlap of mosquito gut, plant and water-column OTUs likely reveal the effects of larval feeding. Future research will investigate the role of the key indicator groups of bacteria across the different developmental stages of this mosquito species.

  7. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

    Science.gov (United States)

    Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

    2014-12-01

    Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta.

  8. Pyrosequencing-based assessment of bacterial community structure in mine soils affected by mining subsidence

    Institute of Scientific and Technical Information of China (English)

    Li Yuanyuan a; Chen Longqian a; ⇑; Wen Hongyu b; Zhou Tianjian a; Zhang Ting a

    2014-01-01

    Based on the 454 pyrosequencing approach, this research evaluated the influence of coal mining subsi-dence on soil bacterial diversity and community structure in Chinese mining area. In order to characterize the bacterial community comparatively, this study selected a field experiment site with coal-excavated subsidence soils and an adjacent site with non-disturbed agricultural soils, respectively. The dataset com-prises 24512 sequences that are affiliated to the 7 phylogenetic groups: proteobacteria, actinobacteria, bacteroidetes, gemmatimonadetes, chloroflexi, nitrospirae and unclassified phylum. Proteobacteria is the largest bacterial phylum in all samples, with a marked shift of the proportions of alpha-, beta-, and gammaproteobacteria. The results show that undisturbed soils are relatively more diverse and rich than subsided soils, and differences in abundances of dominant taxonomic groups between the two soil groups are visible. Compared with the control, soil nutrient contents decline achieves significant level in subsided soils. Correlational analysis showed bacterial diversity indices have significantly positive corre-lation with soil organic matter, total N, total P, and available K, but in negative relation with soil salinity. Ground subsidence noticeably affects the diversity and composition of soil microbial community. Degen-eration of soil fertility and soil salinization inhibits the sole-carbon-source metabolic ability of microbial community, leading to the simplification of advantage species and uneven distribution of microbial spe-cies. This work demonstrates the great potential of pyrosequencing technique in revealing microbial diversity and presents background information of microbial communities of mine subsidence land.

  9. Aquatic community response in a groundwater-fed desert lake to Holocene desiccation of the Sahara

    Science.gov (United States)

    Eggermont, Hilde; Verschuren, Dirk; Fagot, Maureen; Rumes, Bob; Van Bocxlaer, Bert; Kröpelin, Stefan

    2008-12-01

    The finely laminated sediment record of a permanent, hypersaline, desert oasis lake in the Ounianga region of northeastern Chad presents a unique opportunity to document the hydrological evolution of this groundwater-fed aquatic ecosystem during mid- and late-Holocene desiccation of the Sahara. In this study we reconstruct long-term changes in zoobenthos and zooplankton communities of Lake Yoa as their early-Holocene freshwater habitat changed into the hypersaline conditions prevailing today. Chironomid production peaked during the fresh-to-saline transition period, then stabilized at about half that of the earlier freshwater ecosystem. Quantitative salinity inferences based on fossil chironomid assemblages indicate that the fresh-to-saline transition occurred fairly abruptly between ˜4100 and 3400 cal yr BP, but that the ecosystem was buffered against shorter-term climate fluctuations due to continuous inflow of fossil groundwater. The mixture of tropical-African and southern Palaearctic chironomid faunas in the Lake Yoa fossil record required us to address several methodological issues concerning chironomid-based salinity reconstruction, and the applicability of a calibration dataset based on tropical East and West African lakes to this Sahara desert locality. The most coherent reconstruction was obtained with an inference model that applies a weighted best-modern-analogue (WMAT) transfer function to the African calibration dataset expanded with six Sahara lakes.

  10. Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

    Science.gov (United States)

    Comte, J.; Lovejoy, C.; Crevecoeur, S.; Vincent, W. F.

    2016-01-01

    Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a north-south permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa (operational taxonomic units, OTUs), and then analyzed these results relative to environmental variables to identify variables controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley; however, the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial "keystone species". These highly connected nodes (OTUs) in the network were not merely the numerically dominant taxa, and their loss would alter the organization of microbial consortia and ultimately the food web structure and functioning of these aquatic ecosystems.

  11. Structure and function of the bacterial communities during rhizoremediation of hexachlorobenzene in constructed wetlands.

    Science.gov (United States)

    Zhang, Cuiping; Wang, Bei; Dai, Xiaoyan; Li, Shuying; Lu, Guangqiu; Zhou, Yuanqing

    2017-04-01

    Vertical flow constructed wetlands (VF CWs) are considered to be effective for treating organic pollutants. The rhizosphere of macrophytes such as Phragmites sp., Typha sp. serves as an active and dynamic zone for the microbial degradation of organic pollutants. However, it is still not clear how soil bacterial communities respond to macrophytes and pollutants during the process. For this purpose, the seedlings of Phragmites australis and Typha angustifolia were planted respectively in the VF CWs added with HCB at a dose of 2 mg/kg. During 96 days of cultivation, we monitored hexachlorobenzene (HCB) removal efficiency by GC/MS and the structure of the rhizosphere bacterial communities in the different VF CWs by denaturing gradient gel electrophoresis (DGGE), and constructed bacterial clone library based on PCR-amplified 16S rRNA gene. As expected, the rhizosphere bacterial communities also remained insensitive to HCB exposure in the wetland soil. The diversity of these microbes presented two stages, from the varied up and down to equilibrium in the entire experimental period. Molecular analysis revealed that the phylum Firmicutes dominated over the bacterial communities. The genera that increased under HCB stress included the well-known HCB-degrading bacteria (Pseudomonas sp. and Alcaligenes sp.) and other common bacteria found in contaminated soil but with lesser known practical functions (Burkholderia sp., Lysinibacillus fusiformis, and Bacillus cereus). Furthermore, there was a certain variance in the relative abundances of the bacterial phyla and HCB removal efficiency among different VF CW treatments. The degradation of HCB in T. angustifolia microcosms was faster than that in P. australis and unvegetated wetlands, and the highest bacterial diversity and richness was found in the VF CWs comprising T. angustifolia.

  12. Groundwater contaminated with hexavalent chromium [Cr (VI]: a health survey and clinical examination of community inhabitants (Kanpur, India.

    Directory of Open Access Journals (Sweden)

    Priti Sharma

    Full Text Available BACKGROUND: We assessed the health effects of hexavalent chromium groundwater contamination (from tanneries and chrome sulfate manufacturing in Kanpur, India. METHODS: The health status of residents living in areas with high Cr (VI groundwater contamination (N = 186 were compared to residents with similar social and demographic features living in communities having no elevated Cr (VI levels (N = 230. Subjects were recruited at health camps in both the areas. Health status was evaluated with health questionnaires, spirometry and blood hematology measures. Cr (VI was measured in groundwater samples by diphenylcarbazide reagent method. RESULTS: Residents from communities with known Cr (VI contamination had more self-reports of digestive and dermatological disorders and hematological abnormalities. GI distress was reported in 39.2% vs. 17.2% males (AOR = 3.1 and 39.3% vs. 21% females (AOR = 2.44; skin abnormalities in 24.5% vs. 9.2% males (AOR = 3.48 and 25% vs. 4.9% females (AOR = 6.57. Residents from affected communities had greater RBCs (among 30.7% males and 46.1% females, lower MCVs (among 62.8% males and less platelets (among 68% males and 72% females than matched controls. There were no differences in leucocytes count and spirometry parameters. CONCLUSIONS: Living in communities with Cr (VI groundwater is associated with gastrointestinal and dermatological complaints and abnormal hematological function. Limitations of this study include small sample size and the lack of long term follow-up.

  13. Comparison of DNA preservation methods for environmental bacterial community samples

    Science.gov (United States)

    Gray, Michael A.; Pratte, Zoe A.; Kellogg, Christina A.

    2013-01-01

    Field collections of environmental samples, for example corals, for molecular microbial analyses present distinct challenges. The lack of laboratory facilities in remote locations is common, and preservation of microbial community DNA for later study is critical. A particular challenge is keeping samples frozen in transit. Five nucleic acid preservation methods that do not require cold storage were compared for effectiveness over time and ease of use. Mixed microbial communities of known composition were created and preserved by DNAgard™, RNAlater®, DMSO–EDTA–salt (DESS), FTA® cards, and FTA Elute® cards. Automated ribosomal intergenic spacer analysis and clone libraries were used to detect specific changes in the faux communities over weeks and months of storage. A previously known bias in FTA® cards that results in lower recovery of pure cultures of Gram-positive bacteria was also detected in mixed community samples. There appears to be a uniform bias across all five preservation methods against microorganisms with high G + C DNA. Overall, the liquid-based preservatives (DNAgard™, RNAlater®, and DESS) outperformed the card-based methods. No single liquid method clearly outperformed the others, leaving method choice to be based on experimental design, field facilities, shipping constraints, and allowable cost.

  14. Bacterial Invasion Dynamics in Zebrafish Gut Microbial Communities

    Science.gov (United States)

    Logan, Savannah; Jemielita, Matthew; Wiles, Travis; Schlomann, Brandon; Hammer, Brian; Guillemin, Karen; Parthasarathy, Raghuveer

    Microbial communities residing in the vertebrate intestine play an important role in host development and health. These communities must be in part shaped by interactions between microbial species as they compete for resources in a physically constrained system. To better understand these interactions, we use light sheet microscopy and zebrafish as a model organism to image established gut microbial communities as they are invaded by robustly-colonizing challengers. We demonstrate that features of the challenger, including motility and spatial distribution, impact success in invasion and in outcompeting the original community. We also show that physical characteristics of the host, such as the motility of the gut, play important roles in mediating inter-species competition. Finally, we examine the influence of the contact-dependent type VI secretion system (T6SS), which is used by specific bacteria to cause cell lysis by injecting toxic effector proteins into competitors. Our findings provide insights into the determinants of microbial success in the complex ecosystems found in the gut.

  15. Molecular characterization of bacterial communities in the human gastrointestinal tract

    NARCIS (Netherlands)

    Zoetendal, E.G.

    2001-01-01

    The human gastrointestinal (GI) tract is a complex ecosystem in which host and microbial cells live in close contact with each other. The microbial community in the human GI tract has an important nutritional and protective function and mainly consists of anaerobic bacteria. After birth, the germ-fr

  16. Bacterial community of cushion plant Thylacospermum ceaspitosum on elevational gradient in the Himalayan cold desert.

    Directory of Open Access Journals (Sweden)

    Klára eŘeháková

    2015-04-01

    Full Text Available Although bacterial assemblages are important components of soils in arid ecosystems, the knowledge about composition, life-strategies and environmental drivers is still fragmentary, especially in remote high-elevation mountains. We compared the quality and quantity of heterotrophic bacterial assemblages between the rhizosphere of the dominant cushion-forming plant Thylacospermum ceaspitosum and its surrounding bulk soil in two mountain ranges (East Karakoram: 4850–5250 m and Little Tibet: 5350–5850 m, in communities from cold steppes to the subnival zone in Ladakh, arid Trans-Himalaya, northwest India. Bacterial communities were characterized by molecular fingerprinting in combination with culture-dependent methods. The effects of environmental factors (elevation, mountain range, and soil physico-chemical parameters on the bacterial community composition and structure were tested by multivariate redundancy analysis and conditional inference trees. Actinobacteria dominate the cultivable part of community and represent a major bacterial lineage of cold desert soils. The most abundant genera were Streptomyces, Arthrobacter and Paenibacillus, representing both r- and K- strategists. The soil texture is the most important factor for the community structure and the total bacteria counts. Less abundant and diverse assemblages are found in East Karakoram with coarser soils derived from leucogranite bedrock, while more diverse assemblages in Little Tibet are associated with finer soils derived from easily weathering gneisses. Cushion rhizosphere is in general less diverse than bulk soil, and contains more r-strategists. K-strategists are more associated with the extremes of the gradient, with drought at lowest elevations (4850 - 5000 m and frost at the highest elevations (5750 - 5850 m. The present study illuminates the composition of soil bacterial assemblages in relation to the cushion plant Thylacospermum ceaspitosum in a xeric environment and

  17. Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards.

    Science.gov (United States)

    Wang, Hua; Yang, Shao-hui; Yang, Jing-ping; Lv, Ya-min; Zhao, Xing; Pang, Ji-liang

    2014-11-01

    It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer (OF), chemical fertilizer (CF), and unfertilized control (CK) treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA (rRNA) gene using terminal restriction fragment length polymorphism (T-RFLP) profiling. The abundances of total bacteria, total archaea, and selected functional genes (bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ) were determined by quantitative polymerase chain reaction (qPCR). The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was significantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of microbial communities and the abundance of genes involved in the nitrogen cycle.

  18. Optimization of ground-water withdrawal in the lower Fox River communities, Wisconsin

    Science.gov (United States)

    Walker, J.F.; Saad, D.A.; Krohelski, J.T.

    1998-01-01

    Pumping from closely spaced wells in the Central Brown County area and the Fox Cities area near the north shore of Lake Winnebago has resulted in the formation of deep cones of depression in the vicinity of the two pumping centers. Water-level measurements indicate there has been a steady decline in water levels in the vicinity of these two pumping centers for the past 50 years. This report describes the use of ground-water optimization modeling to efficiently allocate the ground-water resources in the Lower Fox River Valley. A 3-dimensional ground-water flow model was used along with optimization techniques to determine the optimal withdrawal rates for a variety of management alternatives. The simulations were conducted separately for the Central Brown County area and the Fox Cities area. For all simulations, the objective of the optimization was to maximize total ground-water withdrawals. The results indicate that ground water can supply nearly all of the projected 2030 demand for Central Brown County municipalities if all of the wells are managed (including the city of Green Bay), 8 new wells are installed, and the water-levels are allowed to decline to 100 ft below the bottom of the confining unit. Ground water can supply nearly all of the projected 2030 demand for the Fox Cities if the municipalities in Central Brown County convert to surface water; if Central Brown County municipalities follow the optimized strategy described above, there will be a considerable shortfall of available ground water for the Fox Cities communities. Relaxing the water-level constraint in a few wells, however, would likely result in increased availability of water. In all cases examined, optimization alternatives result in a rebound of the steady-state water levels due to projected 2030 withdrawal rates to levels at or near the bottom of the confining unit, resulting in increased well capacity. Because the simulations are steady-state, if all of the conditions of the model remain

  19. Effects of transient temperature conditions on the divergence of activated sludge bacterial community structure and function.

    Science.gov (United States)

    Nadarajah, Nalina; Allen, D Grant; Fulthorpe, Roberta R

    2007-06-01

    The effect of temperature fluctuations on bacterial community structure and function in lab-scale sequencing batch reactors treating bleached kraft mill effluent was investigated. An increase in temperature from 30 to 45 degrees C caused shifts in both bacterial community structure and function. Triplicate reactors were highly similar for 40 days following startup. After the temperature shift, their community structure and function started to diverge from each other and from the control. A multi-response permutation procedure confirmed that the variability in community structure between transient and control reactors were greater than that among the triplicate transient reactors. The fact that these disturbances manifest themselves in different ways in apparently identical reactors suggests a high degree of variability between replicate systems.

  20. Long- term manure exposure increases soil bacterial community potential for plasmid uptake

    DEFF Research Database (Denmark)

    Musovic, Sanin; Klümper, Uli; Dechesne, Arnaud;

    2014-01-01

    Microbial communities derived from soils subject to different agronomic treatments were challenged with three broad host range plasmids, RP4, pIPO2tet and pRO101, via solid surface filter matings to assess their permissiveness. Approximately 1 in 10 000 soil bacterial cells could receive and main......Microbial communities derived from soils subject to different agronomic treatments were challenged with three broad host range plasmids, RP4, pIPO2tet and pRO101, via solid surface filter matings to assess their permissiveness. Approximately 1 in 10 000 soil bacterial cells could receive...... and maintain the plasmids. The community permissiveness increased up to 100% in communities derived from manured soil. While the plasmid transfer frequency was significantly influenced by both the type of plasmid and the agronomic treatment, the diversity of the transconjugal pools was purely plasmid dependent...

  1. Analysis of bacterial and fungal communities in Marcha and Thiat, traditionally prepared amylolytic starters of India.

    Science.gov (United States)

    Sha, Shankar Prasad; Jani, Kunal; Sharma, Avinash; Anupma, Anu; Pradhan, Pooja; Shouche, Yogesh; Tamang, Jyoti Prakash

    2017-09-08

    Marcha and thiat are traditionally prepared amylolytic starters use for production of various ethnic alcoholic beverages in Sikkim and Meghalaya states in India. In the present study we have tried to investigate the bacterial and fungal community composition of marcha and thiat by using high throughput sequencing. Characterization of bacterial community depicts phylum Proteobacteria is the most dominant in both marcha (91.4%) and thiat (53.8%), followed by Firmicutes, and Actinobacteria. Estimates of fungal community composition showed Ascomycota as the dominant phylum. Presence of Zygomycota in marcha distinguishes it from the thiat. The results of NGS analysis revealed dominance of yeasts in marcha whereas molds out numbers in case of thiat. This is the first report on microbial communities of traditionally prepared amylolytic starters of India using high throughput sequencing.

  2. Variable effects of dispersal on productivity of bacterial communities due to changes in functional trait composition

    DEFF Research Database (Denmark)

    Severin, Ina; Östman, Örjan; Lindström, Eva S.

    2013-01-01

    ) a dialysis bag experiment where the dispersal rate among six communities was manipulated and the subsequent change in bacterial diversity and growth rate was recorded, and (B) a regrowth experiment where we manipulated available resources to study how well a taxon grows on certain organic carbon resources, i......Previous studies have shown variable relationships between dispersal rate and ecosystem functioning, but the reasons for and mechanisms behind variable dispersal rate - functioning patterns are currently unknown. In this study we used six bacterial lake water communities in a laboratory experiment...... in order to investigate how dispersal among communities influences community productivity by evaluating three different mechanisms: 1) changes in taxonomic diversity, 2) changes in phylogenetic diversity or 3) changes in the composition of functional traits. The experiment was conducted in two phases; (A...

  3. Seasonal fluctuations of bacterial community diversity in agricultural soil and experimental validation by laboratory disturbance experiments.

    Science.gov (United States)

    Meier, Christoph; Wehrli, Bernhard; van der Meer, Jan Roelof

    2008-08-01

    Natural fluctuations in soil microbial communities are poorly documented because of the inherent difficulty to perform a simultaneous analysis of the relative abundances of multiple populations over a long time period. Yet, it is important to understand the magnitudes of community composition variability as a function of natural influences (e.g., temperature, plant growth, or rainfall) because this forms the reference or baseline against which external disturbances (e.g., anthropogenic emissions) can be judged. Second, definition of baseline fluctuations in complex microbial communities may help to understand at which point the systems become unbalanced and cannot return to their original composition. In this paper, we examined the seasonal fluctuations in the bacterial community of an agricultural soil used for regular plant crop production by using terminal restriction fragment length polymorphism profiling (T-RFLP) of the amplified 16S ribosomal ribonucleic acid (rRNA) gene diversity. Cluster and statistical analysis of T-RFLP data showed that soil bacterial communities fluctuated very little during the seasons (similarity indices between 0.835 and 0.997) with insignificant variations in 16S rRNA gene richness and diversity indices. Despite overall insignificant fluctuations, between 8 and 30% of all terminal restriction fragments changed their relative intensity in a significant manner among consecutive time samples. To determine the magnitude of community variations induced by external factors, soil samples were subjected to either inoculation with a pure bacterial culture, addition of the herbicide mecoprop, or addition of nutrients. All treatments resulted in statistically measurable changes of T-RFLP profiles of the communities. Addition of nutrients or bacteria plus mecoprop resulted in bacteria composition, which did not return to the original profile within 14 days. We propose that at less than 70% similarity in T-RFLP, the bacterial communities risk to

  4. Bacterial Community Dynamics and Polycyclic Aromatic Hydrocarbon Degradation during Bioremediation of Heavily Creosote-Contaminated Soil

    OpenAIRE

    Viñas, Marc; Sabaté, Jordi; Espuny, María José; Solanas, Anna M.

    2005-01-01

    Bacterial community dynamics and biodegradation processes were examined in a highly creosote-contaminated soil undergoing a range of laboratory-based bioremediation treatments. The dynamics of the eubacterial community, the number of heterotrophs and polycyclic aromatic hydrocarbon (PAH) degraders, and the total petroleum hydrocarbon (TPH) and PAH concentrations were monitored during the bioremediation process. TPH and PAHs were significantly degraded in all treatments (72 to 79% and 83 to 87...

  5. Dynamics of bacterial communities in soils of rainforest fragments under restoration processes

    Science.gov (United States)

    Vasconcellos, Rafael; Zucchi, Tiago; Taketani, Rodrigo; Andreote, Fernando; Cardoso, Elke

    2014-05-01

    The Brazilian Atlantic Forest ("Mata Atlântica") has been largely studied due to its valuable and unique biodiversity. Unfortunately, this priceless ecosystem has been widely deforested and only 10% of its original area still remains. Many projects have been successfully implemented to restore its fauna and flora but there is a lack of information on how the soil bacterial communities respond to this process. Thus, our aim was to evaluate the influence of soil attributes and seasonality on soil bacterial communities of rainforest fragments under restoration processes. Soil samples from a native site and two ongoing restoration fragments with different ages of implementation (10 and 20 years) were collected and assayed by using culture-independent approaches. Our findings demonstrate that seasonality barely altered the bacterial distribution whereas soil chemical attributes and plant diversity highly influenced the bacterial community structure during the restoration process. Moreover, the strict relationship observed for two bacterial groups, Solibacteriaceae and Verrucomicrobia, one with the youngest (10 years) and the other with the oldest (native) site suggests their use as bioindicators of soil quality and soil recovery of forest fragments under restoration.

  6. Allochthonous carbon is a major regulator to bacterial growth and community composition in subarctic freshwaters

    Science.gov (United States)

    Roiha, Toni; Peura, Sari; Cusson, Mathieu; Rautio, Milla

    2016-09-01

    In the subarctic region, climate warming and permafrost thaw are leading to emergence of ponds and to an increase in mobility of catchment carbon. As carbon of terrestrial origin is increasing in subarctic freshwaters the resource pool supporting their microbial communities and metabolism is changing, with consequences to overall aquatic productivity. By sampling different subarctic water bodies for a one complete year we show how terrestrial and algal carbon compounds vary in a range of freshwaters and how differential organic carbon quality is linked to bacterial metabolism and community composition. We show that terrestrial drainage and associated nutrients supported higher bacterial growth in ponds and river mouths that were influenced by fresh terrestrial carbon than in large lakes with carbon from algal production. Bacterial diversity, however, was lower at sites influenced by terrestrial carbon inputs. Bacterial community composition was highly variable among different water bodies and especially influenced by concentrations of dissolved organic carbon (DOC), fulvic acids, proteins and nutrients. Furthermore, a distinct preference was found for terrestrial vs. algal carbon among certain bacterial tribes. The results highlight the contribution of the numerous ponds to cycling of terrestrial carbon in the changing subarctic and arctic regions.

  7. Changes of Bacterial Community Structure in Copper Mine Tailings After Colonization of Reed (Phragmites communis)

    Institute of Scientific and Technical Information of China (English)

    CHEN Yu-Qing; REN Guan-Ju; AN Shu-Qing; SUN Qing-Ye; LIU Chang-Hong; SHUANG Jing-Lei

    2008-01-01

    Soil samples were collected from both bare and vegetated mine tailings to study the changes in bacterial communities and soil chemical properties of copper mine tailings due to reed (Phragmites communis) colonization. The structures of bacterial communities were investigated using culture-independent 16S rRNA gene sequencing method. The bacterial diversity in the bare mine tailing was lower than that of the vegetated mine tailing. The former was dominated by sulfur metabolizing bacteria, whereas the latter was by nitrogen fixing bacteria. The bare mine tailing was acidic (pH = 3.78), whereas the vegetated mine tailing was near neutral (pH = 7.28). The contents of organic matter, total nitrogen, and ammonium acetate-extractable otassium in vegetated mine tailings were significantly higher than those in the bare mine tailings (P < 0.01), whereas available phosphorus and electrical conductivity were significantly lower than those in the bare mine tailings (P < 0.01). The results demonstrated that 16S rRNA gene sequencing could be successfully used to study the bacterial diversity in mine tailings. The colonization of the mine tailings by reed significantly changed the bacterial community and the chemical properties of tailings. The complex interactions between bacteria and plants deserve further investigation.

  8. Pyrosequencing reveals the influence of organic and conventional farming systems on bacterial communities.

    Directory of Open Access Journals (Sweden)

    Ru Li

    Full Text Available It has been debated how different farming systems influence the composition of soil bacterial communities, which are crucial for maintaining soil health. In this research, we applied high-throughput pyrosequencing of V1 to V3 regions of bacterial 16S rRNA genes to gain further insight into how organic and conventional farming systems and crop rotation influence bulk soil bacterial communities. A 2×2 factorial experiment consisted of two agriculture management systems (organic versus conventional and two crop rotations (flax-oat-fababean-wheat versus flax-alfalfa-alfalfa-wheat was conducted at the Glenlea Long-Term Crop Rotation and Management Station, which is Canada's oldest organic-conventional management study field. Results revealed that there is a significant difference in the composition of bacterial genera between organic and conventional management systems but crop rotation was not a discriminator factor. Organic farming was associated with higher relative abundance of Proteobacteria, while Actinobacteria and Chloroflexi were more abundant in conventional farming. The dominant genera including Blastococcus, Microlunatus, Pseudonocardia, Solirubrobacter, Brevundimonas, Pseudomonas, and Stenotrophomonas exhibited significant variation between the organic and conventional farming systems. The relative abundance of bacterial communities at the phylum and class level was correlated to soil pH rather than other edaphic properties. In addition, it was found that Proteobacteria and Actinobacteria were more sensitive to pH variation.

  9. Pyrosequencing reveals the influence of organic and conventional farming systems on bacterial communities.

    Science.gov (United States)

    Li, Ru; Khafipour, Ehsan; Krause, Denis O; Entz, Martin H; de Kievit, Teresa R; Fernando, W G Dilantha

    2012-01-01

    It has been debated how different farming systems influence the composition of soil bacterial communities, which are crucial for maintaining soil health. In this research, we applied high-throughput pyrosequencing of V1 to V3 regions of bacterial 16S rRNA genes to gain further insight into how organic and conventional farming systems and crop rotation influence bulk soil bacterial communities. A 2×2 factorial experiment consisted of two agriculture management systems (organic versus conventional) and two crop rotations (flax-oat-fababean-wheat versus flax-alfalfa-alfalfa-wheat) was conducted at the Glenlea Long-Term Crop Rotation and Management Station, which is Canada's oldest organic-conventional management study field. Results revealed that there is a significant difference in the composition of bacterial genera between organic and conventional management systems but crop rotation was not a discriminator factor. Organic farming was associated with higher relative abundance of Proteobacteria, while Actinobacteria and Chloroflexi were more abundant in conventional farming. The dominant genera including Blastococcus, Microlunatus, Pseudonocardia, Solirubrobacter, Brevundimonas, Pseudomonas, and Stenotrophomonas exhibited significant variation between the organic and conventional farming systems. The relative abundance of bacterial communities at the phylum and class level was correlated to soil pH rather than other edaphic properties. In addition, it was found that Proteobacteria and Actinobacteria were more sensitive to pH variation.

  10. The Hoopoe's Uropygial Gland Hosts a Bacterial Community Influenced by the Living Conditions of the Bird.

    Directory of Open Access Journals (Sweden)

    Sonia M Rodríguez-Ruano

    Full Text Available Molecular methods have revealed that symbiotic systems involving bacteria are mostly based on whole bacterial communities. Bacterial diversity in hoopoe uropygial gland secretion is known to be mainly composed of certain strains of enterococci, but this conclusion is based solely on culture-dependent techniques. This study, by using culture-independent techniques (based on the 16S rDNA and the ribosomal intergenic spacer region shows that the bacterial community in the uropygial gland secretion is more complex than previously thought and its composition is affected by the living conditions of the bird. Besides the known enterococci, the uropygial gland hosts other facultative anaerobic species and several obligated anaerobic species (mostly clostridia. The bacterial assemblage of this community was largely invariable among study individuals, although differences were detected between captive and wild female hoopoes, with some strains showing significantly higher prevalence in wild birds. These results alter previous views on the hoopoe-bacteria symbiosis and open a new window to further explore this system, delving into the possible sources of symbiotic bacteria (e.g. nest environments, digestive tract, winter quarters or the possible functions of different bacterial groups in different contexts of parasitism or predation of their hoopoe host.

  11. The Hoopoe's Uropygial Gland Hosts a Bacterial Community Influenced by the Living Conditions of the Bird.

    Science.gov (United States)

    Rodríguez-Ruano, Sonia M; Martín-Vivaldi, Manuel; Martín-Platero, Antonio M; López-López, J Pablo; Peralta-Sánchez, Juan M; Ruiz-Rodríguez, Magdalena; Soler, Juan J; Valdivia, Eva; Martínez-Bueno, Manuel

    2015-01-01

    Molecular methods have revealed that symbiotic systems involving bacteria are mostly based on whole bacterial communities. Bacterial diversity in hoopoe uropygial gland secretion is known to be mainly composed of certain strains of enterococci, but this conclusion is based solely on culture-dependent techniques. This study, by using culture-independent techniques (based on the 16S rDNA and the ribosomal intergenic spacer region) shows that the bacterial community in the uropygial gland secretion is more complex than previously thought and its composition is affected by the living conditions of the bird. Besides the known enterococci, the uropygial gland hosts other facultative anaerobic species and several obligated anaerobic species (mostly clostridia). The bacterial assemblage of this community was largely invariable among study individuals, although differences were detected between captive and wild female hoopoes, with some strains showing significantly higher prevalence in wild birds. These results alter previous views on the hoopoe-bacteria symbiosis and open a new window to further explore this system, delving into the possible sources of symbiotic bacteria (e.g. nest environments, digestive tract, winter quarters) or the possible functions of different bacterial groups in different contexts of parasitism or predation of their hoopoe host.

  12. The bacterial community in 'taberna' a traditional beverage of Southern Mexico.

    Science.gov (United States)

    Alcántara-Hernández, R J; Rodríguez-Álvarez, J A; Valenzuela-Encinas, C; Gutiérrez-Miceli, F A; Castañón-González, H; Marsch, R; Ayora-Talavera, T; Dendooven, L

    2010-11-01

    To characterize the bacterial community of taberna, an alcoholic traditional beverage from the Southern part of Mexico produced by the fermentation of the coyol palm sap (Acrocomia aculeate). Bacterial 16S rDNA libraries were constructed from metagenomic DNA extracted during the fermentation process at 0, 60 and 108 h. A total of 154 clones were sequenced, and 13, 10 and nine unique sequences were found at each sampling time. At the onset of the fermentation, Zymomonas mobilis, Fructobacillus spp., Pantoea agglomerans and other Gammaproteobacteria were detected. After 60 h, lactic acid bacteria were found and 30% of clones in the library were related to Lactobacillus nagelii, L. sucicola and L. sp. By the end of the experiment, i.e. after 108 h, the bacterial community included Z. mobilis, Lact. nagelii and Acetobacter pasteurianus. Our results suggest that Z. mobilis population represented an important proportion of the bacterial community (60-80%), as well as the lactobacilli during the fermentation process. The bacterial diversity was low and decreased as the fermentation progressed. This culture-independent study suggests that Z. mobilis and lactobacilli play an important role in the alcoholic fermentation of the taberna beverage. © 2010 The Authors. © 2010 The Society for Applied Microbiology.

  13. The Hoopoe's Uropygial Gland Hosts a Bacterial Community Influenced by the Living Conditions of the Bird

    Science.gov (United States)

    Rodríguez-Ruano, Sonia M.; Martín-Vivaldi, Manuel; Martín-Platero, Antonio M.; López-López, J. Pablo; Peralta-Sánchez, Juan M.; Ruiz-Rodríguez, Magdalena; Soler, Juan J.; Valdivia, Eva; Martínez-Bueno, Manuel

    2015-01-01

    Molecular methods have revealed that symbiotic systems involving bacteria are mostly based on whole bacterial communities. Bacterial diversity in hoopoe uropygial gland secretion is known to be mainly composed of certain strains of enterococci, but this conclusion is based solely on culture-dependent techniques. This study, by using culture-independent techniques (based on the 16S rDNA and the ribosomal intergenic spacer region) shows that the bacterial community in the uropygial gland secretion is more complex than previously thought and its composition is affected by the living conditions of the bird. Besides the known enterococci, the uropygial gland hosts other facultative anaerobic species and several obligated anaerobic species (mostly clostridia). The bacterial assemblage of this community was largely invariable among study individuals, although differences were detected between captive and wild female hoopoes, with some strains showing significantly higher prevalence in wild birds. These results alter previous views on the hoopoe-bacteria symbiosis and open a new window to further explore this system, delving into the possible sources of symbiotic bacteria (e.g. nest environments, digestive tract, winter quarters) or the possible functions of different bacterial groups in different contexts of parasitism or predation of their hoopoe host. PMID:26445111

  14. Exploring bacterial community structure and function associated with atrazine biodegradation in repeatedly treated soils.

    Science.gov (United States)

    Fang, Hua; Lian, Jianjun; Wang, Huifang; Cai, Lin; Yu, Yunlong

    2015-04-09

    Substantial application of the herbicide atrazine in agriculture leads to persistent contamination, which may damage the succeeding crops and pose potential threats to soil ecology and environmental health. Here, the degradation characteristics of atrazine and dynamic change of soil bacterial community structure and function as well as their relations were studied during three repeated treatments at the recommended, double, and five-fold doses. The results showed that the degradation half-life of atrazine obviously decreased with increased treatment frequency. Soil microbial functional diversity displayed a variation trend of suppression-recovery-stimulation, which was associated with increased degradation rate of atrazine. 16S amplicon sequencing was conducted to explore bacterial community structure and correlate the genus to potential atrazine degradation. A total of seven potentially atrazine-degrading bacterial genera were found including Nocardioides, Arthrobacter, Bradyrhizobium, Burkholderia, Methylobacterium, Mycobacterium, and Clostridium. These bacterial genera showed almost complete atrazine degradation pathways including dechlorination, dealkylation, hydroxylation, and ring cleavage. Furthermore, the relative abundance of four of them (i.e., Nocardioides, Arthrobacter, Methylobacterium, and Bradyrhizobium) increased with treatment frequency and atrazine concentration, suggesting that they may participate in atrazine degradation during repeated treatments. Our findings reveal the potential relationship between atrazine degradation and soil bacterial community structure in repeatedly treated soils. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Assessment of bacterial community structure in nitrifying biofilm under inorganic carbon-sufficient and -limited conditions.

    Science.gov (United States)

    Bae, Hyokwan; Chung, Yun-Chul; Yang, Heejeong; Lee, Changsoo; Aryapratama, Rio; Yoo, Young J; Lee, Seockheon

    2015-01-01

    In this work, nitrification and changes in the composition of the total bacterial community under inorganic carbon (IC)-limited conditions, in a nitrifying moving bed biofilm reactor, was investigated. A culture-independent analysis of cloning and sequencing based on the 16S rRNA gene was applied to quantify the bacterial diversity and to determine bacterial taxonomic assignment. IC concentrations had significant effects on the stability of ammonia-oxidation as indicated by the reduction of the nitrogen conversion rate with high NH4(+)-N loadings. The predominance of Nitrosomonas europaea was maintained in spite of changes in the IC concentration. In contrast, heterotrophic bacterial species contributed to a high bacterial diversity, and to a dynamic shift in the bacterial community structure, under IC-limited conditions. In this study, individual functions of heterotrophic bacteria were estimated based on taxonomic information. Possible key roles of coexisting heterotrophic bacteria are the assimilation of organic compounds of extracellular polymeric substances produced by nitrifiers, and biofilm formation by providing a filamentous structure and aggregation properties.

  16. Cytokines and Chemokines as Biomarkers of Community-Acquired Bacterial Infection

    Directory of Open Access Journals (Sweden)

    Michal Holub

    2013-01-01

    Full Text Available Routinely used biomarkers of bacterial etiology of infection, such as C-reactive protein and procalcitonin, have limited usefulness for evaluation of infections since their expression is enhanced by a number of different conditions. Therefore, several inflammatory cytokines and chemokines were analyzed with sera from patients hospitalized for moderate bacterial and viral infectious diseases. In total, 57 subjects were enrolled: 21 patients with community-acquired bacterial infections, 26 patients with viral infections, and 10 healthy subjects (control cohorts. The laboratory analyses were performed using Luminex technology, and the following molecules were examined: IL-1Ra, IL-2, IL-4, IL-6, IL-8, TNF-α, INF-γ, MIP-1β, and MCP-1. Bacterial etiology of infection was associated with significantly (P<0.001 elevated serum concentrations of IL-1Ra, IL-2, IL-6, and TNF-α in comparison to levels observed in the sera of patients with viral infections. In the patients with bacterial infections, IL-1Ra and IL-8 demonstrated positive correlation with C-reactive protein, whereas, IL-1Ra, TNF-α, and MCP-1 correlated with procalcitonin. Furthermore, elevated levels of IL-1Ra, IL-6, and TNF-α decreased within 3 days of antibiotic therapy to levels observed in control subjects. The results show IL-1Ra as a potential useful biomarker of community-acquired bacterial infection.

  17. Bacterial community composition and extracellular enzyme activity in temperate streambed sediment during drying and rewetting.

    Directory of Open Access Journals (Sweden)

    Elisabeth Pohlon

    Full Text Available Droughts are among the most important disturbance events for stream ecosystems; they not only affect stream hydrology but also the stream biota. Although desiccation of streams is common in Mediterranean regions, phases of dryness in headwaters have been observed more often and for longer periods in extended temperate regions, including Central Europe, reflecting global climate change and enhanced water withdrawal. The effects of desiccation and rewetting on the bacterial community composition and extracellular enzyme activity, a key process in the carbon flow of streams and rivers, were investigated in a typical Central European stream, the Breitenbach (Hesse, Germany. Wet streambed sediment is an important habitat in streams. It was sampled and exposed in the laboratory to different drying scenarios (fast, intermediate, slow for 13 weeks, followed by rewetting of the sediment from the fast drying scenario via a sediment core perfusion technique for 2 weeks. Bacterial community structure was analyzed using CARD-FISH and TGGE, and extracellular enzyme activity was assessed using fluorogenic model substrates. During desiccation the bacterial community composition shifted toward composition in soil, exhibiting increasing proportions of Actinobacteria and Alphaproteobacteria and decreasing proportions of Bacteroidetes and Betaproteobacteria. Simultaneously the activities of extracellular enzymes decreased, most pronounced with aminopeptidases and less pronounced with enzymes involved in the degradation of polymeric carbohydrates. After rewetting, the general ecosystem functioning, with respect to extracellular enzyme activity, recovered after 10 to 14 days. However, the bacterial community composition had not yet achieved its original composition as in unaffected sediments within this time. Thus, whether the bacterial community eventually recovers completely after these events remains unknown. Perhaps this community undergoes permanent changes

  18. The rate of change of a soil bacterial community after liming as a function of temperature.

    Science.gov (United States)

    Pettersson, M; Bååth, E

    2003-08-01

    The response of a bacterial community to liming of a forest humus soil (pH 4.9 increased to pH 7.5) was studied in the laboratory at three temperatures (5, 20, and 30 degrees C). As a comparison an unlimed soil (pH 4.9) and a soil limed in the field 15 years ago (pH around 6) were also included. The bacterial community tolerance of pH was measured using TdR incorporation. The pH of the bacterial suspensions (bacteria directly extracted from soil) was altered to 3.6 and 8.3 using different buffers before measuring TdR incorporation. The logarithmic ratio between TdR incorporation at 8.3 and 3.6 was then used as an indicator of the community pH tolerance. The rate of changes in the community tolerance to pH after liming was fastest for the soil incubated at 30 degrees C, but only minor differences in rate of change could be seen between samples incubated at 5 and 20 degrees C. Changes in phospholipid fatty acid (PLFA) pattern after increasing the pH were most rapid for the bacterial community in the soil incubated at 30 degrees C followed by the soil incubated at 20 degrees C, whereas no changes could be seen in the PLFA pattern of the soil incubated at 5 degrees C, even after 82 days' incubation. Thus, the changes in the PLFA pattern were considerably slower than the changes in bacterial community tolerance to pH measured using TdR incorporation.

  19. Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis.

    Science.gov (United States)

    Zozaya, Marcela; Ferris, Michael J; Siren, Julia D; Lillis, Rebecca; Myers, Leann; Nsuami, M Jacques; Eren, A Murat; Brown, Jonathan; Taylor, Christopher M; Martin, David H

    2016-04-19

    The epidemiology of bacterial vaginosis (BV) suggests it is sexually transmissible, yet no transmissible agent has been identified. It is probable that BV-associated bacterial communities are transferred from male to female partners during intercourse; however, the microbiota of sexual partners has not been well-studied. Pyrosequencing analysis of PCR-amplified 16S rDNA was used to examine BV-associated bacteria in monogamous couples with and without BV using vaginal, male urethral, and penile skin specimens. The penile skin and urethral microbiota of male partners of women with BV was significantly more similar to the vaginal microbiota of their female partner compared to the vaginal microbiota of non-partner women with BV. This was not the case for male partners of women with normal vaginal microbiota. Specific BV-associated species were concordant in women with BV and their male partners. In monogamous heterosexual couples in which the woman has BV, the significantly higher similarity between the vaginal microbiota and the penile skin and urethral microbiota of the male partner, supports the hypothesis that sexual exchange of BV-associated bacterial taxa is common.