WorldWideScience

Sample records for methanogenic community composition

  1. Effect of ammonium and acetate on methanogenic pathway and methanogenic community composition

    DEFF Research Database (Denmark)

    Fotidis, Ioannis; Karakashev, Dimitar Borisov; Kotsopoulos, T. A.

    2013-01-01

    exposure to different ammonia concentrations. The methanogenic pathway was determined by following the production of (14) CH(4) and (14) CO(2) from acetate labeled in the methyl group (C-2). Microbial communities' composition was determined by fluorescence in situ hybridization. Upon acclimatization......Methanogenesis from acetate (aceticlastic methanogenesis or syntrophic acetate oxidation (SAO) coupled with hydrogenotrophic methanogenesis) is the most important step for the biogas process. The major environmental factors influencing methanogenesis are volatile fatty acids, ammonia, p...

  2. Methane emission and community composition patterns of rumen bacteria and methanogens in Holstein dairy cows as affected by silage type and dietary fat

    DEFF Research Database (Denmark)

    Poulsen, Morten; Højberg, Ole; Canibe, Nuria

    ) to investigate effects of silages with different methanogenic potential (early grass, late grass, and maize) combined with a CH4-reducing feed additive (crushed rapeseed) on bacterial and methanogenic communities in the rumen. Bacterial and methanogenic community patterns were evaluated by T-RFLP analysis of 16S...... rRNA and methyl co-enzyme M reductase (mcrA) genes, respectively. Methanogen abundances were evaluated by qPCR using two mcrA-targeting primer sets. Silage type significantly affected CH4 emissions and rumen acetate:propionate ratios, being highest for late grass and lowest for maize. Dietary fat...... significantly reduced the gross energy lost as CH4 regardless of silage type. Silage type significantly affected the bacterial community composition pattern; the grass silages favored potential hemicellulose- and cellulose-degrading bacteria, while the maize silage mainly favored potentially starch...

  3. Community Structure in Methanogenic Enrichments Provides Insight into Syntrophic Interactions in Hydrocarbon-Impacted Environments

    DEFF Research Database (Denmark)

    Fowler, Jane; Toth, Courtney R. A.; Gieg, Lisa M.

    2016-01-01

    , but such information has important implications for bioremediation and microbial enhanced energy recovery technologies. Many factors such as changing environmental conditions or substrate variations can influence the composition and biodegradation capabilities of syntrophic microbial communities in hydrocarbon......The methanogenic biodegradation of crude oil involves the conversion of hydrocarbons to methanogenic substrates by syntrophic bacteria and subsequent methane production by methanogens. Assessing the metabolic roles played by various microbial species in syntrophic communities remains a challenge......-impacted environments. In this study, a methanogenic crude oil-degrading enrichment culture was successively transferred onto the single long chain fatty acids palmitate or stearate followed by their parent alkanes, hexadecane or octadecane, respectively, in order to assess the impact of different substrates...

  4. Conductive properties of methanogenic biofilms.

    Science.gov (United States)

    Li, Cheng; Lesnik, Keaton Larson; Liu, Hong

    2018-02-01

    Extracellular electron transfer between syntrophic partners needs to be efficiently maintained in methanogenic environments. Direct extracellular electron transfer via electrical current is an alternative to indirect hydrogen transfer but requires construction of conductive extracellular structures. Conductive mechanisms and relationship between conductivity and the community composition in mixed-species methanogenic biofilms are not well understood. The present study investigated conductive behaviors of methanogenic biofilms and examined the correlation between biofilm conductivity and community composition between different anaerobic biofilms enriched from the same inoculum. Highest conductivity observed in methanogenic biofilms was 71.8±4.0μS/cm. Peak-manner response of conductivity upon changes over a range of electrochemical potentials suggests that electron transfer in methanogenic biofilms occurs through redox driven super-exchange. The strong correlation observed between biofilm conductivity and Geobacter spp. in the metabolically diverse anaerobic communities suggests that the efficiency of DEET may provide pressure for microbial communities to select for species that can produce electrical conduits. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Molecular Characterization of Methanogenic Communities in Core Sediments of the Dajiuhu Peatland, Central China

    Science.gov (United States)

    Wang, R.; Wang, H.

    2017-12-01

    Methane (CH4) is an important greenhouse gas with a global warming potential 22 times greater than carbon dioxide. Large amounts of CH4 can be produced and released by methanogenesis in peatland ecosystems, which make peatland ecosystems play an important role in mediating global climate change. Here we report the abundance and distribution of methanogenic communities and their correlation with physicochemical parameters along two sediment cores in the Dajiuhu Peatland via quantitative PCR, clone library construction of functional genes and statistical analysis. Uncultured Group and Fen Cluster were found to be the dominant methanogens at the upper part of the cores, and Rice and Related Rice Cluster became dominant in the bottom of the cores. Quantitative PCR showed that abundances of methanogenic communities ranged from 104 to 106 copies/ng DNA throughout the cores. Canonical Correlation Analysis (CCA) indicated that dissolved oxygen (DO) (P=0.046, F=1.4) was the main factor significantly controlling methanogenic communities. Our results enhance the understanding of the compositions and variations of methanogenic communities vertically and greatly help us to further investigate process of microbial methanogenesis in Dajiuhu Peatland.

  6. The dominant acetate degradation pathway/methanogenic composition in full-scale anaerobic digesters operating under different ammonia levels

    DEFF Research Database (Denmark)

    Fotidis, Ioannis; Karakashev, Dimitar Borisov; Angelidaki, Irini

    2014-01-01

    Ammonia is a major environmental factor influencing biomethanation in full-scale anaerobic digesters. In this study, the effect of different ammonia levels on methanogenic pathways and methanogenic community composition of full-scale biogas plants was investigated. Eight full-scale digesters...... operating under different ammonia levels were sampled, and the residual biogas production was followed in fed-batch reactors. Acetate, labelled in the methyl group, was used to determine the methanogenic pathway by following the 14CH4 and 14CO2 production. Fluorescence in situ hybridisation was used...... to determine the methanogenic communities’ composition. Results obtained clearly demonstrated that syntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis was the dominant pathway in all digesters with high ammonia levels (2.8–4.57 g NH4 +-N L−1), while acetoclastic methanogenic pathway...

  7. Biomethane potential of industrial paper wastes and investigation of the methanogenic communities involved.

    Science.gov (United States)

    Walter, Andreas; Silberberger, Sandra; Juárez, Marina Fernández-Delgado; Insam, Heribert; Franke-Whittle, Ingrid H

    2016-01-01

    Cellulose-containing waste products from the agricultural or industrial sector are potentially one of the largest sources of renewable energy on earth. In this study, the biomethane potential (BMP) of two types of industrial paper wastes, wood and pulp residues (WR and PR, respectively), were evaluated under both mesophilic and thermophilic conditions, and various pretreatment methods were applied in the attempt to increase the methane potential during anaerobic digestion. The methanogenic community composition was investigated with denaturing gradient gel electrophoresis (DGGE) and the ANAEROCHIP microarray, and dominant methanogens were quantitated using quantitative PCR. All pretreatments investigated in this study with the exception of the alkaline pretreatment of PR were found to increase the BMP of two paper industry wastes. However, the low recalcitrance level of the PR resulted in the pretreatments being less effective in increasing BMP when compared with those for WR. These results were supported by the physico-chemical data. A combined application of ultrasound and enzymatic pretreatment was found to be the best strategy for increasing methane yields. The retention time of substrates in the reactors strongly influenced the BMP of wastes subjected to the different pretreatments. In sludges from both paper wastes subjected to the various pretreatments, mixotrophic Methanosarcina species were found to dominate the community, accompanied by a consortium of hydrogenotrophic genera. Pretreating industrial paper wastes could be a potentially viable option for increasing the overall degradation efficiency and decreasing reactor retention time for the digestion of complex organic matter such as lignocellulose or hemicellulose. This would help reduce the environmental burden generated from paper production. Although there were minor differences in the methanogenic communities depending on the temperature of anaerobic digestion, there was little effect of substrate

  8. Methanogen community composition and rates of methane consumption in Canadian High Arctic permafrost soils.

    Science.gov (United States)

    Allan, J; Ronholm, J; Mykytczuk, N C S; Greer, C W; Onstott, T C; Whyte, L G

    2014-04-01

    Increasing permafrost thaw, driven by climate change, has the potential to result in organic carbon stores being mineralized into carbon dioxide (CO2) and methane (CH4) through microbial activity. This study examines the effect of increasing temperature on community structure and metabolic activity of methanogens from the Canadian High Arctic, in an attempt to predict how warming will affect microbially controlled CH4 soil flux. In situ CO2 and CH4 flux, measured in 2010 and 2011 from ice-wedge polygons, indicate that these soil formations are a net source of CO2 emissions, but a CH4 sink. Permafrost and active layer soil samples were collected at the same sites and incubated under anaerobic conditions at warmer temperatures, with and without substrate amendment. Gas flux was measured regularly and indicated an increase in CH4 flux after extended incubation. Pyrosequencing was used to examine the effects of an extended thaw cycle on methanogen diversity and the results indicate that in situ methanogen diversity, based on the relative abundance of the 16S ribosomal ribonucleic acid (rRNA) gene associated with known methanogens, is higher in the permafrost than in the active layer. Methanogen diversity was also shown to increase in both the active layer and permafrost soil after an extended thaw. This study provides evidence that although High Arctic ice-wedge polygons are currently a sink for CH4, higher arctic temperatures and anaerobic conditions, a possible result of climate change, could result in this soil becoming a source for CH4 gas flux. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

  9. Time Course-Dependent Methanogenic Crude Oil Biodegradation: Dynamics of Fumarate Addition Metabolites, Biodegradative Genes, and Microbial Community Composition

    Directory of Open Access Journals (Sweden)

    Courtney R. A. Toth

    2018-01-01

    Full Text Available Biodegradation of crude oil in subsurface petroleum reservoirs has adversely impacted most of the world's oil, converting this resource to heavier forms that are of lower quality and more challenging to recover. Oil degradation in deep reservoir environments has been attributed to methanogenesis over geological time, yet our understanding of the processes and organisms mediating oil transformation in the absence of electron acceptors remains incomplete. Here, we sought to identify hydrocarbon activation mechanisms and reservoir-associated microorganisms that may have helped shape the formation of biodegraded oil by incubating oilfield produced water in the presence of light (°API = 32 or heavy crude oil (°API = 16. Over the course of 17 months, we conducted routine analytical (GC, GC-MS and molecular (PCR/qPCR of assA and bssA genes, 16S rRNA gene sequencing surveys to assess microbial community composition and activity changes over time. Over the incubation period, we detected the formation of transient hydrocarbon metabolites indicative of alkane and alkylbenzene addition to fumarate, corresponding with increases in methane production and fumarate addition gene abundance. Chemical and gene-based evidence of hydrocarbon biodegradation under methanogenic conditions was supported by the enrichment of hydrocarbon fermenters known to catalyze fumarate addition reactions (e.g., Desulfotomaculum, Smithella, along with syntrophic bacteria (Syntrophus, methanogenic archaea, and several candidate phyla (e.g., “Atribacteria”, “Cloacimonetes”. Our results reveal that fumarate addition is a possible mechanism for catalyzing the methanogenic biodegradation of susceptible saturates and aromatic hydrocarbons in crude oil, and we propose the roles of community members and candidate phyla in our cultures that may be involved in hydrocarbon transformation to methane in crude oil systems.

  10. Windrow composting mitigated CH4 emissions: characterization of methanogenic and methanotrophic communities in manure management.

    Science.gov (United States)

    Chen, Ruirui; Wang, Yiming; Wei, Shiping; Wang, Wei; Lin, Xiangui

    2014-12-01

    With increasing livestock breeding, methane (CH4 ) emissions from manure management will increasingly contribute more to atmospheric CH4 concentration. The dynamics of methanogens and methanotrophs have not yet been studied in the manure environment. The current study combines surface CH4 emissions with methanogenic and methanotrophic community analyses from two management practices, windrow composting (WCOM) and solid storage (SSTO). Our results showed that there was an c. 50% reduction of CH4 emissions with WCOM compared with SSTO over a 50-day period. A sharp decrease in the quantities of both methanogens and methanotrophs in WCOM suggested that CH4 mitigation was mainly due to decreased CH4 production rather than increased CH4 oxidation. Pyrosequencing analysis demonstrated that aeration caused a clear shift of dominant methanogens in the manure, with specifically a significant decrease in Methanosarcina and increase in Methanobrevibacter. The composition of methanogenic community was influenced by manure management and regulated CH4 production. A sharp increase in the quantity of methanotrophs in SSTO suggested that microbial CH4 oxidation is an important sink for the CH4 produced. The increased abundance of Methylococcaceae in SSTO suggested that Type I methanotrophs have an advantage in CH4 oxidation in occupying niches under low CH4 and high O2 conditions. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2014-10-01

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

  12. Response of Methanogenic Microbial Communities to Desiccation Stress in Flooded and Rain-Fed Paddy Soil from Thailand

    Directory of Open Access Journals (Sweden)

    Andreas Reim

    2017-05-01

    Full Text Available Rice paddies in central Thailand are flooded either by irrigation (irrigated rice or by rain (rain-fed rice. The paddy soils and their microbial communities thus experience permanent or arbitrary submergence, respectively. Since methane production depends on anaerobic conditions, we hypothesized that structure and function of the methanogenic microbial communities are different in irrigated and rain-fed paddies and react differently upon desiccation stress. We determined rates and relative proportions of hydrogenotrophic and aceticlastic methanogenesis before and after short-term drying of soil samples from replicate fields. The methanogenic pathway was determined by analyzing concentrations and δ13C of organic carbon and of CH4 and CO2 produced in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis. We also determined the abundance (qPCR of genes and transcripts of bacterial 16S rRNA, archaeal 16S rRNA and methanogenic mcrA (coding for a subunit of the methyl coenzyme M reductase and the composition of these microbial communities by T-RFLP fingerprinting and/or Illumina deep sequencing. The abundances of genes and transcripts were similar in irrigated and rain-fed paddy soil. They also did not change much upon desiccation and rewetting, except the transcripts of mcrA, which increased by more than two orders of magnitude. In parallel, rates of CH4 production also increased, in rain-fed soil more than in irrigated soil. The contribution of hydrogenotrophic methanogenesis increased in rain-fed soil and became similar to that in irrigated soil. However, the relative microbial community composition on higher taxonomic levels was similar between irrigated and rain-fed soil. On the other hand, desiccation and subsequent anaerobic reincubation resulted in systematic changes in the composition of microbial communities for both Archaea and Bacteria. It is noteworthy that differences in the community composition were

  13. Investigation into the effect of high concentrations of volatile fatty acids in anaerobic digestion on methanogenic communities

    Energy Technology Data Exchange (ETDEWEB)

    Franke-Whittle, Ingrid H., E-mail: ingrid.whittle@uibk.ac.at [Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck (Austria); Walter, Andreas [Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck (Austria); Ebner, Christian [Abwasserverband Zirl und Umgebung, Meilbrunnen 5, 6170 Zirl (Austria); Insam, Heribert [Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck (Austria)

    2014-11-15

    Highlights: • Different methanogenic communities in mesophilic and thermophilic reactors. • High VFA levels do not cause major changes in archaeal communities. • Real-time PCR indicated greater diversity than ANAEROCHIP microarray. - Abstract: A study was conducted to determine whether differences in the levels of volatile fatty acids (VFAs) in anaerobic digester plants could result in variations in the indigenous methanogenic communities. Two digesters (one operated under mesophilic conditions, the other under thermophilic conditions) were monitored, and sampled at points where VFA levels were high, as well as when VFA levels were low. Physical and chemical parameters were measured, and the methanogenic diversity was screened using the phylogenetic microarray ANAEROCHIP. In addition, real-time PCR was used to quantify the presence of the different methanogenic genera in the sludge samples. Array results indicated that the archaeal communities in the different reactors were stable, and that changes in the VFA levels of the anaerobic digesters did not greatly alter the dominating methanogenic organisms. In contrast, the two digesters were found to harbour different dominating methanogenic communities, which appeared to remain stable over time. Real-time PCR results were inline with those of microarray analysis indicating only minimal changes in methanogen numbers during periods of high VFAs, however, revealed a greater diversity in methanogens than found with the array.

  14. Snapshot of methanogen sensitivity to temperature in Zoige wetland from Tibetan plateau

    Directory of Open Access Journals (Sweden)

    Li eFu

    2015-02-01

    Full Text Available Zoige wetland in Tibetan plateau represents a cold environment at high altitude where significant methane emission has been observed. However, it remains unknown how the production and emission of CH4 from Zoige wetland will respond to a warming climate. Here we investigated the temperature sensitivity of methanogen community in a Zoige wetland soil under the laboratory incubation conditions. One soil sample was collected and the temperature sensitivity of the methanogenic activity, the structure of methanogen community and the methanogenic pathways were determined. We found that the response of methanogenesis to temperature could be separated into two phases, a high sensitivity in the low temperature range and a modest sensitivity under mesophilic conditions, respectively. The aceticlastic methanogens Methanosarcinaceae were the main methanogens at low temperatures, while hydrogenotrophic Methanobacteriales, Methanomicrobiales and Methanocellales were more abundant at higher temperatures. The total abundance of mcrA genes increased with temperature indicating that the growth of methanogens was stimulated. The growth of hydrogenotrophic methanogens, however, was faster than aceticlastic ones resulting in the shift of methanogen community. Determination of carbon isotopic signatures indicated that methanogenic pathway was also shifted from mainly aceticlastic methanogenesis to a mixture of hydrogenotrophic and aceticlastic methanogenesis with the increase of temperature. Collectively, the shift of temperature responses of methanogenesis was in accordance with the changes in methanogen composition and methanogenic pathway in this Zoige wetland sample. It appears that the aceticlastic methanogenesis dominated at low temperatures is more sensitive than the hydrogenotrophic one at higher temperatures.

  15. Mitigation of methane emission from Holstein dairy cows: Effects of dietary manipulation on bacterial and methanogen communities

    DEFF Research Database (Denmark)

    Poulsen, Morten

    2012-01-01

    ). Future demands for meat and milk are expected to increase, with concomitant increase in CH4 emissions to the atmosphere. Thus, reducing CH4 emission from ruminant production constitutes a massive challenge. Using in vitro rumen fluid fermentations and in vivo animal trials we investigated 1) effects...... of carbohydrate fermentation and pH on CH4 production and on bacterial community composition, and 2) effects of dietary manipulation (primarily through fat supplementation aiming at reducing enteric CH4 production) on community composition and activity of the rumen microbiota, with particular focus...... on methanogenic archaea. In vitro fermentations revealed that pH and carbohydrate source had only minor effects on the rumen bacterial community composition, but significantly affected volatile fatty acid production patterns. pH significantly affected CH4 emission from rumen fluid, with optimum CH4 production...

  16. Characterization of the methanogen community in a household anaerobic digester fed with swine manure in China.

    Science.gov (United States)

    Qin, Huibin; Lang, Huihua; Yang, Hongjiang

    2013-09-01

    Household anaerobic digesters have been installed across rural China for biogas production, but information on methanogen community structure in these small biogas units is sparsely available. By creating clone libraries for 16S rRNA and methyl coenzyme M reductase alpha subunit (mcrA) genes, we investigated the methanogenic consortia in a household biogas digester treating swine manure. Operational taxonomic units (OTUs) were defined by comparative sequence analysis, seven OTUs were identified in the 16S rRNA gene library, and ten OTUs were identified in the mcrA gene library. Both libraries were dominated by clones highly related to the type strain Methanocorpusculum labreanum Z, 64.0 % for 16S rRNA gene clones and 64.3 % for mcrA gene clones. Additionally, gas chromatography assays showed that formic acid was 84.54 % of the total volatile fatty acids and methane was 57.20 % of the biogas composition. Our results may help further isolation and characterization of methanogenic starter strains for industrial biogas production.

  17. Methane Production and Methanogenic Archaea in the Digestive Tracts of Millipedes (Diplopoda)

    Science.gov (United States)

    Šustr, Vladimír; Chroňáková, Alica; Semanová, Stanislava; Tajovský, Karel; Šimek, Miloslav

    2014-01-01

    Methane production by intestinal methanogenic Archaea and their community structure were compared among phylogenetic lineages of millipedes. Tropical and temperate millipedes of 35 species and 17 families were investigated. Species that emitted methane were mostly in the juliform orders Julida, Spirobolida, and Spirostreptida. The irregular phylogenetic distribution of methane production correlated with the presence of the methanogen-specific mcrA gene. The study brings the first detailed survey of methanogens’ diversity in the digestive tract of millipedes. Sequences related to Methanosarcinales, Methanobacteriales, Methanomicrobiales and some unclassified Archaea were detected using molecular profiling (DGGE). The differences in substrate preferences of the main lineages of methanogenic Archaea found in different millipede orders indicate that the composition of methanogen communities may reflect the differences in available substrates for methanogenesis or the presence of symbiotic protozoa in the digestive tract. We conclude that differences in methane production in the millipede gut reflect differences in the activity and proliferation of intestinal methanogens rather than an absolute inability of some millipede taxa to host methanogens. This inference was supported by the general presence of methanogenic activity in millipede faecal pellets and the presence of the 16S rRNA gene of methanogens in all tested taxa in the two main groups of millipedes, the Helminthophora and the Pentazonia. PMID:25028969

  18. Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments.

    Science.gov (United States)

    Chaudhary, Prem Prashant; Brablcová, Lenka; Buriánková, Iva; Rulík, Martin

    2013-09-01

    Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.

  19. Confocal Raman microspectroscopy reveals a convergence of the chemical composition in methanogenic archaea from a Siberian permafrost-affected soil.

    Science.gov (United States)

    Serrano, Paloma; Hermelink, Antje; Lasch, Peter; de Vera, Jean-Pierre; König, Nicole; Burckhardt, Oliver; Wagner, Dirk

    2015-12-01

    Methanogenic archaea are widespread anaerobic microorganisms responsible for the production of biogenic methane. Several new species of psychrotolerant methanogenic archaea were recently isolated from a permafrost-affected soil in the Lena Delta (Siberia, Russia), showing an exceptional resistance against desiccation, osmotic stress, low temperatures, starvation, UV and ionizing radiation when compared to methanogens from non-permafrost environments. To gain a deeper insight into the differences observed in their resistance, we described the chemical composition of methanogenic strains from permafrost and non-permafrost environments using confocal Raman microspectroscopy (CRM). CRM is a powerful tool for microbial identification and provides fingerprint-like information about the chemical composition of the cells. Our results show that the chemical composition of methanogens from permafrost-affected soils presents a high homology and is remarkably different from strains inhabiting non-permafrost environments. In addition, we performed a phylogenetic reconstruction of the studied strains based on the functional gene mcrA to prove the different evolutionary relationship of the permafrost strains. We conclude that the permafrost methanogenic strains show a convergent chemical composition regardless of their genotype. This fact is likely to be the consequence of a complex adaptive process to the Siberian permafrost environment and might be the reason underlying their resistant nature. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  20. [Effects of selective methanogenic inhibitors on methanogenesis and methanogenic communities in acetate degrading cultures].

    Science.gov (United States)

    Ma, Tingting; Cheng, Lei; Liu, Laiyan; Dai, Lirong; Zhou, Zheng; Zhang, Hui

    2015-05-04

    We evaluated the role of syntrophic acetate oxidation coupled with hydrogenotrophic methanogens in three different methanogenic consortia. Three methanogenic hexadecane degrading consortia named Y15, M82 and SK were taken from the same oily sludge of Shengli oil-field and enriched. They were incubated at 15, 35 and 55 °C, respectively. The consortia amended with acetate and inhibitors of NH4Cl or CH3F were further transferred and incubated at corresponding temperatures. The cultures atlate logarithmic phase were collected for terminal restriction fragment length polymorphism (T-RFLP) combined with cloning and phylogenetic analysis of 16S rRNA gene fragments. Gas chromatograph analysis showed that all of the consortia could grow and produce methane, but the lag phase was delayed and the growth rate was retarded in the cultures amended with inhibitor. Combination analysis of T-RFLP and clone library revealed the predominance of obligate aceticlastic Methanosaeta in the acetate cultures of Y15, M82 and SK. Under the mesophilic and thermophilic conditions, after add inginhibitor the relative abundance of aceticlastic methanogen decreased but hydrogenotrophic methanogen increased. Syntrophic acetate oxidation during methanogenic degradation of petroleum hydrocarbons occurs under mesophilic and thermophilic conditions, although the situation at low temperature seems uncertain.

  1. Mature fine tailings from oil sands processing harbour diverse methanogenic communities

    Energy Technology Data Exchange (ETDEWEB)

    Penner, T.J.; Foght, J.M. [Alberta Univ., Edmonton, AB (Canada). Dept. of Biological Sciences

    2010-06-15

    Syncrude's bitumen extraction process produces a fine tailings slurry consisting of water, sand, fines, residual bitumen and naphtha diluent. Following rapid settling of the sand fraction, the tailings are stored in large settling ponds to form a thick mature fine tailings (MFT). This paper discussed the potential benefits of methane production on management of the settling basins. Enhanced methanogenesis accelerates densification and improves the rheological properties of MFT. In this study molecular techniques were used to characterize the methanogenic communities in uncultivated MFT samples to determine the diversity present in the Mildred Lake Settling Basin (MLSB) and West In-Pit tailings deposit. The flux of methane is currently estimated at about 40 million L/day at the MLSB. Clone libraries of amplified archaeal and bacterial 16S rRNA genes were created in order to analyze the methanogenic consortia in MFT samples from depth profiles in the 2 tailings deposits. The archaeal sequences, whose closest matches were primarily cultivated methanogens, were comparable within and between basins and were mostly affiliated with acetoclastic Methanosaeta spp. However, bacterial clone libraries were diverse, with most sequences relating to Proteobacteria, including some presumptive nitrate-, iron-, or sulfate-reducing, hydrocarbon-degrading genera. The study showed that MFT consists of a diverse community of prokaryotes that may be responsible for producing methane from substrates indigenous to the MFT. These findings contribute to a better understanding of the biogenesis of methane and densification of MFT in oil sands tailings deposits. The results from this study will help determine strategies to control and exploit microbial activities in these large systems and improve the understanding of methanogenic environments. 43 refs., 2 tabs., 3 figs.

  2. Shifts of methanogenic communities in response to permafrost thaw results in rising methane emissions and soil property changes.

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    Wei, Shiping; Cui, Hongpeng; Zhu, Youhai; Lu, Zhenquan; Pang, Shouji; Zhang, Shuai; Dong, Hailiang; Su, Xin

    2018-05-01

    Permafrost thaw can bring negative consequences in terms of ecosystems, resulting in permafrost collapse, waterlogging, thermokarst lake development, and species composition changes. Little is known about how permafrost thaw influences microbial community shifts and their activities. Here, we show that the dominant archaeal community shifts from Methanomicrobiales to Methanosarcinales in response to the permafrost thaw, and the increase in methane emission is found to be associated with the methanogenic archaea, which rapidly bloom with nearly tenfold increase in total number. The mcrA gene clone libraries analyses indicate that Methanocellales/Rice Cluster I was predominant both in the original permafrost and in the thawed permafrost. However, only species belonging to Methanosarcinales showed higher transcriptional activities in the thawed permafrost, indicating a shift of methanogens from hydrogenotrophic to partly acetoclastic methane-generating metabolic processes. In addition, data also show the soil texture and features change as a result of microbial reproduction and activity induced by this permafrost thaw. Those data indicate that microbial ecology under warming permafrost has potential impacts on ecosystem and methane emissions.

  3. Phylogenetic comparison of the methanogenic communities from an acidic, oligotrophic fen and an anaerobic digester treating municipal wastewater sludge.

    Science.gov (United States)

    Steinberg, Lisa M; Regan, John M

    2008-11-01

    Methanogens play a critical role in the decomposition of organics under anaerobic conditions. The methanogenic consortia in saturated wetland soils are often subjected to large temperature fluctuations and acidic conditions, imposing a selective pressure for psychro- and acidotolerant community members; however, methanogenic communities in engineered digesters are frequently maintained within a narrow range of mesophilic and circumneutral conditions to retain system stability. To investigate the hypothesis that these two disparate environments have distinct methanogenic communities, the methanogens in an oligotrophic acidic fen and a mesophilic anaerobic digester treating municipal wastewater sludge were characterized by creating clone libraries for the 16S rRNA and methyl coenzyme M reductase alpha subunit (mcrA) genes. A quantitative framework was developed to assess the differences between these two communities by calculating the average sequence similarity for 16S rRNA genes and mcrA within a genus and family using sequences of isolated and characterized methanogens within the approved methanogen taxonomy. The average sequence similarities for 16S rRNA genes within a genus and family were 96.0 and 93.5%, respectively, and the average sequence similarities for mcrA within a genus and family were 88.9 and 79%, respectively. The clone libraries of the bog and digester environments showed no overlap at the species level and almost no overlap at the family level. Both libraries were dominated by clones related to uncultured methanogen groups within the Methanomicrobiales, although members of the Methanosarcinales and Methanobacteriales were also found in both libraries. Diversity indices for the 16S rRNA gene library of the bog and both mcrA libraries were similar, but these indices indicated much lower diversity in the 16S digester library than in the other three libraries.

  4. Methanogenic community development in anaerobic granular bioreactors treating trichloroethylene (TCE)-contaminated wastewater at 37 °C and 15 °C.

    Science.gov (United States)

    Siggins, Alma; Enright, Anne-Marie; O'Flaherty, Vincent

    2011-04-01

    Four expanded granular sludge bed (EGSB) bioreactors were seeded with a mesophilically-grown granular sludge and operated in duplicate for mesophilic (37 °C; R1 & R2) and low- (15°; R3 & R4) temperature treatment of a synthetic volatile fatty acid (VFA) based wastewater (3 kg COD m(-3) d(-1)) with one of each pair (R1 & R3) supplemented with increasing concentrations of trichloroethylene (TCE; 10, 20, 40, 60 mg l(-1)) and one acting as a control. Bioreactor performance was evaluated by % COD removal efficiency and % biogas methane (CH(4)) content. Quantitative Polymerase Chain Reaction (qPCR) was used to investigate the methanogenic community composition and dynamics in the bioreactors during the trial, while specific methanogenic activity (SMA) and toxicity assays were utilized to investigate the activity and TCE/dichloroethylene (DCE) toxicity thresholds of key trophic groups, respectively. At both 37 °C and 15 °C, TCE levels of 60 mg l(-1) resulted in the decline of % COD removal efficiencies to 29% (Day 235) and 37% (Day 238), respectively, and in % biogas CH(4) to 54% (Day 235) and 5% (Day 238), respectively. Despite the inhibitory effect of TCE on the anaerobic digestion process, the main drivers influencing methanogenic community development, as determined by qPCR and Non-metric multidimensional scaling analysis, were (i) wastewater composition and (ii) operating temperature. At the apical TCE concentration both SMA and qPCR of methanogenic archaea suggested that acetoclastic methanogens were somewhat inhibited by the presence of TCE and/or its degradation derivatives, while competition by dechlorinating organisms may have limited the availability of H(2) for hydrogenotrophic methanogenesis. In addition, there appeared to be an inverse correlation between SMA levels and TCE tolerance, a finding that was supported by the analysis of the inhibitory effect of TCE on two additional biomass sources. The results indicate that low-temperature anaerobic

  5. Methanobacterium Dominates Biocathodic Archaeal Communities in Methanogenic Microbial Electrolysis Cells

    KAUST Repository

    Siegert, Michael

    2015-07-06

    © 2015 American Chemical Society. Methane is the primary end product from cathodic current in microbial electrolysis cells (MECs) in the absence of methanogenic inhibitors, but little is known about the archaeal communities that develop in these systems. MECs containing cathodes made from different materials (carbon brushes, or plain graphite blocks or blocks coated with carbon black and platinum, stainless steel, nickel, ferrihydrite, magnetite, iron sulfide, or molybdenum disulfide) were inoculated with anaerobic digester sludge and acclimated at a set potential of -600 mV (versus a standard hydrogen electrode). The archaeal communities on all cathodes, except those coated with platinum, were predominated by Methanobacterium (median 97% of archaea). Cathodes with platinum contained mainly archaea most similar to Methanobrevibacter. Neither of these methanogens were abundant (<0.1% of archaea) in the inoculum, and therefore their high abundance on the cathode resulted from selective enrichment. In contrast, bacterial communities on the cathode were more diverse, containing primarily δ-Proteobacteria (41% of bacteria). The lack of a consistent bacterial genus on the cathodes indicated that there was no similarly selective enrichment of bacteria on the cathode. These results suggest that the genus Methanobacterium was primarily responsible for methane production in MECs when cathodes lack efficient catalysts for hydrogen gas evolution. (Figure Presented).

  6. Effect of Elevated CO2 Concentration, Elevated Temperature and No Nitrogen Fertilization on Methanogenic Archaeal and Methane-Oxidizing Bacterial Community Structures in Paddy Soil.

    Science.gov (United States)

    Liu, Dongyan; Tago, Kanako; Hayatsu, Masahito; Tokida, Takeshi; Sakai, Hidemitsu; Nakamura, Hirofumi; Usui, Yasuhiro; Hasegawa, Toshihiro; Asakawa, Susumu

    2016-09-29

    Elevated concentrations of atmospheric CO2 ([CO2]) enhance the production and emission of methane in paddy fields. In the present study, the effects of elevated [CO2], elevated temperature (ET), and no nitrogen fertilization (LN) on methanogenic archaeal and methane-oxidizing bacterial community structures in a free-air CO2 enrichment (FACE) experimental paddy field were investigated by PCR-DGGE and real-time quantitative PCR. Soil samples were collected from the upper and lower soil layers at the rice panicle initiation (PI) and mid-ripening (MR) stages. The composition of the methanogenic archaeal community in the upper and lower soil layers was not markedly affected by the elevated [CO2], ET, or LN condition. The abundance of the methanogenic archaeal community in the upper and lower soil layers was also not affected by elevated [CO2] or ET, but was significantly increased at the rice PI stage and significantly decreased by LN in the lower soil layer. In contrast, the composition of the methane-oxidizing bacterial community was affected by rice-growing stages in the upper soil layer. The abundance of methane-oxidizing bacteria was significantly decreased by elevated [CO2] and LN in both soil layers at the rice MR stage and by ET in the upper soil layer. The ratio of mcrA/pmoA genes correlated with methane emission from ambient and FACE paddy plots at the PI stage. These results indicate that the decrease observed in the abundance of methane-oxidizing bacteria was related to increased methane emission from the paddy field under the elevated [CO2], ET, and LN conditions.

  7. Long-term effects of operating temperature and sulphate addition on the methanogenic community structure of anaerobic hybrid reactors.

    Science.gov (United States)

    Pender, Seán; Toomey, Margaret; Carton, Micheál; Eardly, Dónal; Patching, John W; Colleran, Emer; O'Flaherty, Vincent

    2004-02-01

    The diversity, population dynamics, and activity profiles of methanogens in anaerobic granular sludges from two anaerobic hybrid reactors treating a molasses wastewater both mesophilically (37 degrees C) and thermophilically (55 degrees C) during a 1081 day trial were determined. The influent to one of the reactors was supplemented with sulphate, after an acclimation period of 112 days, to determine the effect of competition with sulphate-reducing bacteria on the methanogenic community structure. Sludge samples were removed from the reactors at intervals throughout the operational period and examined by amplified ribosomal DNA (rDNA) restriction analysis (ARDRA) and partial sequencing of 16S rRNA genes. In total, 18 operational taxonomic units (OTUs) were identified, 12 of which were sequenced. The methanogenic communities in both reactors changed during the operational period. The seed sludge and the reactor biomass sampled during mesophilic operation, both in the presence and absence of sulphate, was characterised by a predominance of Methanosaeta spp. Following temperature elevation, the dominant methanogenic sequences detected in the non-sulphate supplemented reactor were closely related to Methanocorpusculum parvum. By contrast, the dominant OTUs detected in the sulphate-supplemented reactor upon temperature increase were related to the hydrogen-utilising methanogen, Methanobacterium thermoautotrophicum. The observed methanogenic community structure in the reactors correlated with the operational performance of the reactors during the trial and with physiological measurements of the reactor biomass. Both reactors achieved chemical oxygen demand (COD) removal efficiencies of over 90% during mesophilic operation, with or without sulphate supplementation. During thermophilic operation, the presence of sulphate resulted in decreased reactor performance (effluent acetate concentrations of >3000 mg/l and biogas methane content of acetate at 55 degrees C was

  8. Nitrate decreases ruminal methane production with slight changes to ruminal methanogen composition of nitrate-adapted steers.

    Science.gov (United States)

    Zhao, Liping; Meng, Qingxiang; Li, Yan; Wu, Hao; Huo, Yunlong; Zhang, Xinzhuang; Zhou, Zhenming

    2018-03-20

    This study was conducted to examine effects of nitrate on ruminal methane production, methanogen abundance, and composition. Six rumen-fistulated Limousin×Jinnan steers were fed diets supplemented with either 0% (0NR), 1% (1NR), or 2% (2NR) nitrate (dry matter basis) regimens in succession. Rumen fluid was taken after two-week adaptation for evaluation of in vitro methane production, methanogen abundance, and composition measurements. Results showed that nitrate significantly decreased in vitro ruminal methane production at 6 h, 12 h, and 24 h (P methane reduction was significantly related to Methanobrevibacter and Methanoplanus abundance, and negatively correlated with Methanosphaera and Methanimicrococcus abundance.

  9. Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems.

    Science.gov (United States)

    Laskar, Folguni; Das Purkayastha, Sumi; Sen, Aniruddha; Bhattacharya, Mrinal K; Misra, Biswapriya B

    2018-02-01

    About half of the global methane (CH 4 ) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH 4 emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Kinetic and thermodynamic control of butyrate conversion in non-defined methanogenic communities.

    Science.gov (United States)

    Junicke, H; van Loosdrecht, M C M; Kleerebezem, R

    2016-01-01

    Many anaerobic conversions proceed close to thermodynamic equilibrium and the microbial groups involved need to share their low energy budget to survive at the thermodynamic boundary of life. This study aimed to investigate the kinetic and thermodynamic control mechanisms of the electron transfer during syntrophic butyrate conversion in non-defined methanogenic communities. Despite the rather low energy content of butyrate, results demonstrate unequal energy sharing between the butyrate-utilizing species (17 %), the hydrogenotrophic methanogens (9-10 %), and the acetoclastic methanogens (73-74 %). As a key finding, the energy disproportion resulted in different growth strategies of the syntrophic partners. Compared to the butyrate-utilizing partner, the hydrogenotrophic methanogens compensated their lower biomass yield per mole of electrons transferred with a 2-fold higher biomass-specific electron transfer rate. Apart from these thermodynamic control mechanisms, experiments revealed a ten times lower hydrogen inhibition constant on butyrate conversion than proposed by the Anaerobic Digestion Model No. 1, suggesting a much stronger inhibitory effect of hydrogen on anaerobic butyrate conversion. At hydrogen partial pressures exceeding 40 Pa and at bicarbonate limited conditions, a shift from methanogenesis to reduced product formation was observed which indicates an important role of the hydrogen partial pressure in redirecting electron fluxes towards reduced products such as butanol. The findings of this study demonstrate that a careful consideration of thermodynamics and kinetics is required to advance our current understanding of flux regulation in energy-limited syntrophic ecosystems.

  11. Cultivation of methanogenic community from 2-km deep subseafloor coalbeds using a continuous-flow bioreactor

    Science.gov (United States)

    Imachi, H.; Tasumi, E.; Morono, Y.; Ito, M.; Takai, K.; Inagaki, F.

    2013-12-01

    Deep subseafloor environments associated with hydrocarbon reservoirs have been least explored by previous scientific drilling and hence the nature of deep subseafloor life and its ecological roles in the carbon cycle remain largely unknown. In this study, we performed cultivation of subseafloor methanogenic communities using a continuous-flow bioreactor with polyurethane sponges, called down-flow hanging sponge (DHS) reactor. The sample used for the reactor cultivation was obtained from 2 km-deep coalbeds off the Shimokita Peninsula of Japan, the northwestern Pacific, during the Integrated Ocean Drilling Program (IODP) Expedition 337 using a riser drilling technology of the drilling vessel Chikyu. The coalbed samples were incubated anaerobically in the DHS reactor at the in-situ temperature of 40°C. Synthetic seawater supplemented with a tiny amount of yeast extract, acetate, propionate and butyrate was provided into the DHS reactor. After 34 days of the bioreactor operation, a small production of methane was observed. The methane concentration was gradually increased and the stable carbon isotopic composition of methane was consistency 13C-depleted during the bioreactor operation, indicating the occurrence of microbial methanogenesis. Microscopic observation showed that the enrichment culture contained a variety of microorganisms, including methanogen-like rod-shaped cells with F420 auto-fluorescence. Interestingly, many spore-like particles were observed in the bioreactor enrichment. Phylogenetic analysis of 16S rRNA genes showed the growth of phylogenetically diverse bacteria and archaea in the DHS reactor. Predominant archaeal components were closely related to hydrogenotrophic methanogens within the genus Methanobacterium. Some predominant bacteria were related to the spore-formers within the class Clostridia, which are overall in good agreement with microscopic observations. By analyzing ion images using a nano-scale secondary ion mass spectrometry (Nano

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

    Science.gov (United States)

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

    2013-01-01

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

  13. Methanotrophs, methanogens and microbial community structure in livestock slurry surface crusts

    DEFF Research Database (Denmark)

    Duan, Y.F.; Abu Al-Soud, Waleed; Brejnrod, Asker Daniel

    2014-01-01

    , and Methylosarcina of Type I, and Methylocystis of Type II, dominated the methane-oxidizing bacteria (MOB) community, whereas Methanocorpusculum was the predominant methanogen. Higher numbers of operational taxonomic units (OTUs) representing Type I than Type II MOB were found in all crusts. Potential CH4 oxidation...... rates were determined by incubating crusts with CH4, and CH4 oxidization was observed in cattle, but not in swine slurry crusts. Conclusions: Slurry surface crusts harbour a diverse microbial community. Type I MOB are more diverse and abundant than Type II MOB in this environment. The distinct CH4...

  14. Exploring Archaeal Communities And Genomes Across Five Deep-Sea Brine Lakes Of The Red Sea With A Focus On Methanogens

    KAUST Repository

    Guan, Yue

    2015-12-15

    The deep-sea hypersaline lakes in the Red Sea are among the most challenging, extreme, and unusual environments on the planet Earth. Despite their harshness to life, they are inhabited by diverse and novel members of prokaryotes. Methanogenesis was proposed as one of the main metabolic pathways that drive microbial colonization in similar habitats. However, not much is known about the identities of the methane-producing microbes in the Red Sea, let alone the way in which they could adapt to such poly extreme environments. Combining a range of microbial community assessment, cultivation and omics (genomics, transcriptomics, and single amplified genomics) approaches, this dissertation seeks to fill these gaps in our knowledge by studying archaeal composition, particularly methanogens, their genomic capacities and transcriptomic characteristics in order to elucidate their diversity, function, and adaptation to the deep-sea brines of the Red Sea. Although typical methanogens are not abundant in the samples collected from brine pool habitats of the Red Sea, the pilot cultivation experiment has revealed novel halophilic methanogenic species of the domain Archaea. Their physiological traits as well as their genomic and transcriptomic features unveil an interesting genetic and functional adaptive capacity that allows them to thrive in the unique deep-sea hypersaline environments in the Red Sea.

  15. Peptidolytic microbial community of methanogenic reactors from two modified UASBs of brewery industries

    Directory of Open Access Journals (Sweden)

    C. Díaz

    2010-10-01

    Full Text Available We studied the peptide-degrading anaerobic communities of methanogenic reactors from two mesophilic full-scale modified upflow anaerobic sludge blanket (UASB reactors treating brewery wastewater in Colombia. Most probable number (MPN counts varied between 7.1 x 10(8 and 6.6 x 10(9 bacteria/g volatile suspended solids VSS (Methanogenic Reactor 1 and 7.2 x 10(6 and 6.4 x 10(7 bacteria/g (VSS (Methanogenic Reactor 2. Metabolites detected in the highest positive MPN dilutions in both reactors were mostly acetate, propionate, isovalerate and, in some cases, negligible concentrations of butyrate. Using the highest positive dilutions of MPN counts, 50 dominant strains were isolated from both reactors, and 12 strains were selected for sequencing their 16S rRNA gene based on their phenotypic characteristics. The small-subunit rRNA gene sequences indicated that these strains were affiliated to the families Propionibacteriaceae, Clostridiaceae and Syntrophomonadaceae in the low G + C gram-positive group and Desulfovibrio spp. in the class d-Proteobacteria. The main metabolites detected in the highest positive dilutions of MPN and the presence of Syntrophomonadaceae indicate the effect of the syntrophic associations on the bioconversion of these substrates in methanogenic reactors. Additionally, the potential utilization of external electron acceptors for the complete degradation of amino acids by Clostridium strains confirms the relevance of these acceptors in the transformation of peptides and amino acids in these systems.

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

    Directory of Open Access Journals (Sweden)

    Jenna L Shelton

    2016-09-01

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

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

    Science.gov (United States)

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

    2006-03-01

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

  18. Environmental Drivers of Differences in Microbial Community Structure in Crude Oil Reservoirs across a Methanogenic Gradient

    OpenAIRE

    Shelton, Jenna L.; Akob, Denise M.; McIntosh, Jennifer C.; Fierer, Noah; Spear, John R.; Warwick, Peter D.; McCray, John E.

    2016-01-01

    Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, a...

  19. Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure.

    Science.gov (United States)

    Danielsson, Rebecca; Dicksved, Johan; Sun, Li; Gonda, Horacio; Müller, Bettina; Schnürer, Anna; Bertilsson, Jan

    2017-01-01

    Methane (CH 4 ) is produced as an end product from feed fermentation in the rumen. Yield of CH 4 varies between individuals despite identical feeding conditions. To get a better understanding of factors behind the individual variation, 73 dairy cows given the same feed but differing in CH 4 emissions were investigated with focus on fiber digestion, fermentation end products and bacterial and archaeal composition. In total 21 cows (12 Holstein, 9 Swedish Red) identified as persistent low, medium or high CH 4 emitters over a 3 month period were furthermore chosen for analysis of microbial community structure in rumen fluid. This was assessed by sequencing the V4 region of 16S rRNA gene and by quantitative qPCR of targeted Methanobrevibacter groups. The results showed a positive correlation between low CH 4 emitters and higher abundance of Methanobrevibacter ruminantium clade. Principal coordinate analysis (PCoA) on operational taxonomic unit (OTU) level of bacteria showed two distinct clusters ( P microbial population or host genetic differences that is reflected in bacterial and archaeal (or methanogens) populations.

  20. Establishment of a Methanogenic Benzene-Degrading Culture and its Implication in Bioremediation

    Science.gov (United States)

    Qiao, W.; Luo, F.; Bawa, N.; Guo, S.; Ye, S.; Edwards, E.

    2017-12-01

    Benzene is a known human carcinogen and it is a common pollutant in groundwater, mainly resulting from petrochemical industry. Anaerobic degradation of benzene has significant advantages over aerobic processes for in situ bioremediation. In this study, new methanogenic and sulfate-reducing benzene degrading cultures have been enriched. Microbial community composition was characterized with two other previously established benzene-degrading cultures, and their potential use in bioaugmentation is investigated. In this study, a lab microcosm study was conducted anaerobically with contaminated soil and groundwater from a former chemical plant. Benzene degradation was observed in the presence of co-contaminants and electron donor. Through repetitive amendment of benzene, two enrichment cultures have been developed under sulfate and methanogenic conditions. Results from DNA amplicon sequencing and qPCR analysis revealed that an organism similar to previously described benzene-degrading Deltaproteobacterium has been enriched. The microbial community of this culture was compared with other two methanogenic benzene-degrading enrichment cultures that were derived from an oil refinery and a decommissioned gasoline station, and have been maintained for decades. Deltaproteobacterium ORM2-like microbes were dominate in all enrichment cultures, which brought to light benzene-degrading microbes, ORM2 were enriched under different geological conditions distributed around the world. The relative abundance of methanogens was much lower compared to previously established cultures, although substantial amount of methane was produced. The peripheral organisms also vary. To investigate effectiveness of using ORM2-dominant enrichment cultures in bioremediation, microcosm studies were set up using contaminated materials, and a ORM2-dominating methanogenic benzene-degrading culture was used for bioaugmentation. Results revealed that benzene degradation was speeded up under methanogenic or

  1. Application of stable isotope measurements and microbiological analysis for detecting methanogenic activity in a temperate forest wetland

    Science.gov (United States)

    Itoh, M.; Katsuyama, C.; Kondo, N.; Ohte, N.; Kato, K.

    2009-12-01

    Generally, forest soils act as a sink for methane (CH4). However, wetlands in riparian zones are recently reported to be “hot spots” of CH4 emissions, especially in forests under a humid climate. To understand how environmental conditions (i.e. hydrological and/or geomorphic condition) control on CH4 production, we investigated both methanogenic pathways (CO2/H2 reduction and acetate fermentation) and metahanogenic microbial communities in a wetland in a temperate forest catchment, central Japan. We used stable carbon isotopic analysis for detecting change in methanogenic pathways, and applied microbiological analysis for understanding the structure of methanogenic community. CH4 emission rates in wetland were strongly dependent on soil temperatures, and were highest in summer and lowest in winter. δ13CO2 increased with CH4 production in every summer, suggesting preferential use of 12CO2 as substrate for CO2/H2 reduction methanogenesis during high CH4 production period. δ13CH4 also increased in summer with δ13CO2. δ13CH4 changed more wildly than δ13CO2 did in summer with normal precipitation when CH4 production was strongly activated under high temperature and high groundwater table condition. This indicates increase in acetoclastic methanogenesis under hot and wet condition, considering that acetclastic methnogens produce heavier CH4 than that from CO2/H2 reducing pathway. Methanogen community composition estimated by cloning and sequence analyses implied that both acetoclastic and CO2/H2 reducing methanogens prevailed in wetland soil sampled in summer. This was consistent with the results of isotope measuremaents. Our results contribute to understand fully how the CH4 production changes with environmental conditions, with considering the activities of both main methanogenic pathway (from CO2 and acetate).

  2. Methanogenic archaea

    International Nuclear Information System (INIS)

    Joblin, K.N.

    2005-01-01

    This chapter outlines procedures for enumerating, isolating, culturing and storing methanogens from ruminal digesta. The methanogens, a large and diverse group of Archaea, have unique features that separate them from the bacteria and the eukaryotes. They are the only recognized ruminal microbes belonging to the Archaea and are an integral part of the rumen microbial ecosystem. By scavenging hydrogen gas, methanogens play a key ecological role in keeping the partial pressure of hydrogen low so that fermentation can proceed efficiently. Although about 70 methanogenic species belonging to 2 1 genera have been identified from anaerobic environments, and a range of different methanogens co-exist in the rumen, to date only seven ruminal species have been isolated and purified. The population densities of methanogens in the rumen appear to be influenced by diet, and in particular by the fibre content of the diet. Sheep and cattle fed diets rich in concentrates contained 10 7 -10 8 and 10 8 - 10 9 ruminal methanogens/g, respectively, whereas sheep and dairy cows grazing pasture contained 10 9 -10 10 ruminal methanogens/g (G.N. Jarvis and K.N. Joblin, unpublished data). With careful application, methanogen population densities can readily be determined using culture methods. These appear to be similar to the population densities determined by culture-independent methods (P. Evans and K.N. Joblin, unpublished data)

  3. Heavy-machinery traffic impacts methane emissions as well as methanogen abundance and community structure in oxic forest soils.

    Science.gov (United States)

    Frey, Beat; Niklaus, Pascal A; Kremer, Johann; Lüscher, Peter; Zimmermann, Stephan

    2011-09-01

    Temperate forest soils are usually efficient sinks for the greenhouse gas methane, at least in the absence of significant amounts of methanogens. We demonstrate here that trafficking with heavy harvesting machines caused a large reduction in CH(4) consumption and even turned well-aerated forest soils into net methane sources. In addition to studying methane fluxes, we investigated the responses of methanogens after trafficking in two different forest sites. Trafficking generated wheel tracks with different impact (low, moderate, severe, and unaffected). We found that machine passes decreased the soils' macropore space and lowered hydraulic conductivities in wheel tracks. Severely compacted soils yielded high methanogenic abundance, as demonstrated by quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes, whereas these sequences were undetectable in unaffected soils. Even after a year after traffic compression, methanogen abundance in compacted soils did not decline, indicating a stability of methanogens here over time. Compacted wheel tracks exhibited a relatively constant community structure, since we found several persisting mcrA sequence types continuously present at all sampling times. Phylogenetic analysis revealed a rather large methanogen diversity in the compacted soil, and most mcrA gene sequences were mostly similar to known sequences from wetlands. The majority of mcrA gene sequences belonged either to the order Methanosarcinales or Methanomicrobiales, whereas both sites were dominated by members of the families Methanomicrobiaceae Fencluster, with similar sequences obtained from peatland environments. The results show that compacting wet forest soils by heavy machinery causes increases in methane production and release.

  4. Effects of mineral salt supplement on enteric methane emissions, ruminal fermentation and methanogen community of lactating cows.

    Science.gov (United States)

    Li, Xiaohua; Liu, Chong; Chen, Yongxing; Shi, Rongguang; Cheng, Zhenhua; Dong, Hongmin

    2017-08-01

    We evaluated the effects of mineral salt supplement on enteric methane emissions, ruminal fermentation and methanogen community of dairy cows over a whole lactation period. Ten Holstein cows fed a total mixed ration (TMR) diet were randomly allocated into two groups, one supplied with mineral salts as the treatment group and the other as the control group. The methane measurement showed that the ingestion of mineral salts lowered enteric methane emissions significantly (P methane emissions by mineral salt intake could be attributed to decreased density of methanogenic archaea and that fluctuations in methane emission over the lactation period might be related to Methanobrevibacter diversity. © 2016 Japanese Society of Animal Science.

  5. Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?

    Science.gov (United States)

    Ozuolmez, Derya; Na, Hyunsoo; Lever, Mark A; Kjeldsen, Kasper U; Jørgensen, Bo B; Plugge, Caroline M

    2015-01-01

    Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and the interactions between both groups. We tested interspecies hydrogen transfer and coexistence between marine methanogens and sulfate reducers using mixed pure cultures of two types of microorganisms. First, Desulfovibrio vulgaris subsp. vulgaris (DSM 1744), a hydrogenotrophic sulfate reducer, was cocultured together with the obligate aceticlastic methanogen Methanosaeta concilii using acetate as carbon and energy source. Next, Methanococcus maripaludis S2, an obligate H2- and formate-utilizing methanogen, was used as a partner organism to M. concilii in the presence of acetate. Finally, we performed a coexistence experiment between M. concilii and an acetotrophic sulfate reducer Desulfobacter latus AcSR2. Our results showed that D. vulgaris was able to reduce sulfate and grow from hydrogen leaked by M. concilii. In the other coculture, M. maripaludis was sustained by hydrogen leaked by M. concilii as revealed by qPCR. The growth of the two aceticlastic microbes indicated co-existence rather than competition. Altogether, our results indicate that H2 leaking from M. concilii could be used by efficient H2-scavengers. This metabolic trait, revealed from coculture studies, brings new insight to the metabolic flexibility of methanogens and sulfate reducers residing in marine environments in response to changing environmental conditions and community compositions. Using dedicated physiological studies we were able to unravel the occurrence of less obvious interactions between marine methanogens and sulfate-reducing bacteria.

  6. Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?

    Directory of Open Access Journals (Sweden)

    Derya eOzuolmez

    2015-05-01

    Full Text Available Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and the interactions between both groups. We tested interspecies hydrogen transfer and coexistence between marine methanogens and sulfate reducers using mixed pure cultures of two types of microorganisms. First, Desulfovibrio vulgaris subsp. vulgaris (DSM 1744, a hydrogenotrophic sulfate reducer, was cocultured together with the obligate aceticlastic methanogen Methanosaeta concilii using acetate as carbon and energy source. Next, Methanococcus maripaludis S2, an obligate H2- and formate-utilizing methanogen, was used as a partner organism to M. concilii in the presence of acetate. Finally, we performed a coexistence experiment between M. concilii and an acetotrophic sulfate reducer Desulfobacter latus AcSR2. Our results showed that D. vulgaris was able to reduce sulfate and grow from hydrogen leaked by M. concilii. In the other coculture, M. maripaludis was sustained by hydrogen leaked by M. concilii as revealed by qPCR. The growth of the two aceticlastic microbes indicated co-existence rather than competition. Altogether, our results indicate that H2 leaking from M. concilii could be used by efficient H2-scavengers. This metabolic trait, revealed from coculture studies, brings new insight to the metabolic flexibility of methanogens and sulfate reducers residing in marine environments in response to changing environmental conditions and community compositions. Using dedicated physiological studies we were able to unravel the occurrence of less obvious interactions between marine methanogens and sulfate-reducing bacteria.

  7. Quantifying electron fluxes in methanogenic microbial communities

    NARCIS (Netherlands)

    Junicke, H.

    2015-01-01

    Anaerobic digestion is a widely applied process in which close interactions between different microbial groups result in the formation of renewable energy in the form of biogas. Nevertheless, the regulatory mechanisms of the electron transfer between acetogenic bacteria and methanogenic archaea in

  8. Growth of methylaminotrophic, acetotrophic and hydrogenotrophic methanogenic bacteria on artificial supports.

    Science.gov (United States)

    Urrutia, H; Vidal, R; Baeza, M; Reyes, J E; Aspe, E

    1997-06-01

    The efficiency of organic matter degradation in attached biomass reactors depends on the suitable selection of artificial support for the retention of bacterial communities. We have studied the growth on glass and clay beads of methylaminotrophic, acetotrophic and hydrogenotrophic methanogenic bacterial communities isolated from anaerobic reactors. Bacterial counts were performed by the standard MPN technique. Experiments were performed in 50 ml vials for 12 days at 35 degrees C. Increase in the counts of methylaminotrophic and hydrogenotrophic methanogens occurred on both glass and clay beads. The latter support material also stimulated the growth rate of methylaminotrophic methanogens.

  9. Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil.

    Science.gov (United States)

    Bao, Qiongli; Huang, Yizong; Wang, Fenghua; Nie, Sanan; Nicol, Graeme W; Yao, Huaiying; Ding, Longjun

    2016-07-01

    Nitrogen fertilization and returning straw to paddy soil are important factors that regulate CH4 production. To evaluate the effect of rice straw and/or nitrate amendment on methanogens, a paddy soil was anaerobically incubated for 40 days. The results indicated that while straw addition increased CH4 production and the abundances of mcrA genes and their transcripts, nitrate amendment showed inhibitory effects on them. The terminal restriction fragment length polymorphism (T-RFLP) analysis based on mcrA gene revealed that straw addition obviously changed methanogenic community structure. Based on mcrA gene level, straw-alone addition stimulated Methanosarcinaceaes at the early stage of incubation (first 11 days), but nitrate showed inhibitory effect. The relative abundance of Methanobacteriaceae was also stimulated by straw addition during the first 11 days. Furthermore, Methanosaetaceae were enriched by nitrate-alone addition after 11 days, while Methanocellaceae were enriched by nitrate addition especially within the first 5 days. The transcriptional methanogenic community indicated more dynamic and complicated responses to straw and/or nitrate addition. Based on mcrA transcript level, nitrate addition alone resulted in the increase of Methanocellaceae and the shift from Methanosarcinaceae to Methanosaetaceae during the first 5 days of incubation. Straw treatments increased the relative abundance of Methanobacteriaceae after 11 days. These results demonstrate that nitrate addition influences methanogens which are transcriptionally and functionally active and can alleviate CH4 production associated with straw amendment in paddy soil incubations, presumably through competition for common substrates between nitrate-utilizing organisms and methanogens.

  10. Heavy-Machinery Traffic Impacts Methane Emissions as Well as Methanogen Abundance and Community Structure in Oxic Forest Soils▿†

    Science.gov (United States)

    Frey, Beat; Niklaus, Pascal A.; Kremer, Johann; Lüscher, Peter; Zimmermann, Stephan

    2011-01-01

    Temperate forest soils are usually efficient sinks for the greenhouse gas methane, at least in the absence of significant amounts of methanogens. We demonstrate here that trafficking with heavy harvesting machines caused a large reduction in CH4 consumption and even turned well-aerated forest soils into net methane sources. In addition to studying methane fluxes, we investigated the responses of methanogens after trafficking in two different forest sites. Trafficking generated wheel tracks with different impact (low, moderate, severe, and unaffected). We found that machine passes decreased the soils' macropore space and lowered hydraulic conductivities in wheel tracks. Severely compacted soils yielded high methanogenic abundance, as demonstrated by quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes, whereas these sequences were undetectable in unaffected soils. Even after a year after traffic compression, methanogen abundance in compacted soils did not decline, indicating a stability of methanogens here over time. Compacted wheel tracks exhibited a relatively constant community structure, since we found several persisting mcrA sequence types continuously present at all sampling times. Phylogenetic analysis revealed a rather large methanogen diversity in the compacted soil, and most mcrA gene sequences were mostly similar to known sequences from wetlands. The majority of mcrA gene sequences belonged either to the order Methanosarcinales or Methanomicrobiales, whereas both sites were dominated by members of the families Methanomicrobiaceae Fencluster, with similar sequences obtained from peatland environments. The results show that compacting wet forest soils by heavy machinery causes increases in methane production and release. PMID:21742929

  11. Methanogens at the top of the world: occurrence and potential activity of methanogens in newly deglaciated soils in high-altitude cold deserts in the Western Himalayas

    Directory of Open Access Journals (Sweden)

    Katrin eAschenbach

    2013-12-01

    Full Text Available Methanogens typically occur in reduced anoxic environments. However, in recent studies it has been shown that many aerated upland soils, including desert soils also host active methanogens. Here we show that soil samples from high–altitude cold deserts in the western Himalayas (Ladakh, India produce CH4 after incubation as slurry under anoxic conditions at rates comparable to those of hot desert soils. Samples of matured soil from three different vegetation belts (arid, steppe, and subnival were compared with younger soils originating from frontal and lateral moraines of receding glaciers. While methanogenic rates were higher in the samples from matured soils, CH4 was also produced in the samples from the recently deglaciated moraines. In both young and matured soils, those covered by a biological soil crust (biocrust were more active than their bare counterparts. Isotopic analysis showed that in both cases CH4 was initially produced from H2/CO2 but later mostly from acetate. Analysis of the archaeal community in the in situ soil samples revealed a clear dominance of sequences related to Thaumarchaeota, while the methanogenic community comprised only a minor fraction of the archaeal community. Similar to other aerated soils, the methanogenic community was comprised almost solely of the genera Methanosarcina and Methanocella, and possibly also Methanobacterium in some cases. Nevertheless, approximately 103 gdw-1 soil methanogens were already present in the young moraine soil together with cyanobacteria. Our results demonstrate that Methanosarcina and Methanocella not only tolerate atmospheric oxygen but are also able to survive in these harsh cold environments. Their occurrence in newly deglaciated soils shows that they are early colonisers of desert soils, similar to cyanobacteria, and may play a role in the development of desert biocrusts.

  12. A new combination of substrates: biogas production and diversity of the methanogenic microorganisms

    Directory of Open Access Journals (Sweden)

    Kushkevych Ivan

    2018-04-01

    Full Text Available Agriculture, food industry, and manufacturing are just some of the areas where anaerobic technology can be used. Currently, anaerobic technologies are mainly used for wastewater treatment, solid waste treatment, or for the production of electrical and thermal energy from energy crops processing. However, a clear trend is towards more intensive use of this technology in biomass and biodegradable waste processing and hydrogen or biomethane production. An enormous number of anaerobic digesters are operating worldwide but there is very little information about the effect of different substrate combinations on the methanogens community. This is due to the fact that each of the anaerobic digesters has its own unique microbial community. For the most effective management of anaerobic processes it would be important to know the composition of a consortium of anaerobic microorganisms present in anaerobic digesters processing different input combinations of raw material. This paper characterizes the effect of the input raw materials on the diversity of the methanogen community. Two predominant microorganisms in anaerobic digesters were found to be 99% identity by the sequences of the 16S rRNA gene to the Methanoculleus and Thermogymnomonas genera deposited in GenBank.

  13. Phylogenetic analysis of methanogens from the bovine rumen

    Directory of Open Access Journals (Sweden)

    Forster Robert J

    2001-05-01

    Full Text Available Abstract Background Interest in methanogens from ruminants has resulted from the role of methane in global warming and from the fact that cattle typically lose 6 % of ingested energy as methane. Several species of methanogens have been isolated from ruminants. However they are difficult to culture, few have been consistently found in high numbers, and it is likely that major species of rumen methanogens are yet to be identified. Results Total DNA from clarified bovine rumen fluid was amplified using primers specific for Archaeal 16S rRNA gene sequences (rDNA. Phylogenetic analysis of 41 rDNA sequences identified three clusters of methanogens. The largest cluster contained two distinct subclusters with rDNA sequences similar to Methanobrevibacter ruminantium 16S rDNA. A second cluster contained sequences related to 16S rDNA from Methanosphaera stadtmanae, an organism not previously described in the rumen. The third cluster contained rDNA sequences that may form a novel group of rumen methanogens. Conclusions The current set of 16S rRNA hybridization probes targeting methanogenic Archaea does not cover the phylogenetic diversity present in the rumen and possibly other gastro-intestinal tract environments. New probes and quantitative PCR assays are needed to determine the distribution of the newly identified methanogen clusters in rumen microbial communities.

  14. Methanogens in the Solar System

    Science.gov (United States)

    Taubner, Ruth-Sophie; Schleper, Christa; Firneis, Maria G.; Rittmann, Simon

    2015-04-01

    The last decade of space science revealed that potential habitats in the Solar System may not be limited to the classical habitable zone supporting life as we know it. These microorganisms were shown to thrive under extremophilic growth conditions. Here, we outline the main eco-physiological characteristics of methanogens like their response on temperature, pressure, or pH changes or their resistance against radiation or desiccation. They can withstand extreme environmental conditions which makes them intriguing organisms for astrobiological studies. On Earth, they are found for example in wetlands, in arctic and antarctic subglacial environments, in ruminants, and even in the environment surrounding the Mars Desert Research Station in Utah. These obligate anaerobic chemolithoautotrophs or chemolithoheterotrophs are able to use e.g. hydrogen and C1 compounds like CO2, formate, or methanol as energy source and carbon source, respectively. We point out their capability to be able to habitat potential extraterrestrial biospheres all over the planetary system. We will give an overview about these possible environments on Mars, icy moons like Europa or Enceladus, and minor planets. We present an overview about studies of methanogens with an astrobiological relevance and we show our conclusions about the role of methanogens for the search for extraterrestrial life in the Solar System. We will present first results of our study about the possibility to cultivate methanogens under Enceladus-like conditions. For that, based on the observations obtained by the Cassini spacecraft concerning the plume compounds, we produce a medium with a composition similar to the ocean composition of this icy moon which is far more Enceladus-like than in any (published) experiment before. Eventually, we give an outlook on the feasibility and the necessity of future astrobiological studies with these microbes. We point out the importance of future in-situ or even sample and return missions to

  15. Effects of the reduction of the hydraulic retention time to 1.5 days at constant organic loading in CSTR, ASBR, and fixed-bed reactors – Performance and methanogenic community composition

    International Nuclear Information System (INIS)

    Schmidt, Thomas; Ziganshin, Ayrat M.; Nikolausz, Marcell; Scholwin, Frank; Nelles, Michael; Kleinsteuber, Sabine; Pröter, Jürgen

    2014-01-01

    The hydraulic retention time (HRT) is one of the key parameters in biogas processes and often it is postulated that a minimum HRT of 10–25 days is obligatory in continuous stirred tank reactors (CSTR) to prevent a washout of slow growing methanogens. In this study the effects of the reduction of the HRT from 6 to 1.5 days on performance and methanogenic community composition in different systems with and without immobilization operated with simulated thin stillage (STS) at mesophilic conditions and constant organic loading rates (OLR) of 10 g L −1 d −1 of volatile solids were investigated. With the reduction of the HRT process instability was first observed in the anaerobic sequencing batch reactor (ASBR) (at HRT of 3 days) followed by the CSTR (at HRT of 2 days). The fixed bed reactor (FBR) was stable until the end of the experiment, but the reduction of the HRT to 1.5 days caused a decrease of the specific biogas production to about 450 L kg −1 of VS compared to about 600 L kg −1 of VS at HRTs of 4–5 days. Methanoculleus and Methanosarcina were the dominant genera under stable process conditions in the CSTR and the ASBR and members of Methanosaeta and Methanospirillum were only present at HRT of 4 days and lower. In the effluent of the FBR Methanosarcina spp. were not detected and Methanosaeta spp. were more abundant then in the other reactors. - Highlights: • A CSTR was operated at high OLR of 10 (g L −1  d −1  VS) and low HRT of 3 days. • Exceeding washout of methanogenic archaea did not take place. • pH and nutrient concentrations influenced the reproduction rate more than HRT. • Methanoculleus and Methanosarcina were the dominant genera in the CSTR

  16. Performance and methanogenic community of rotating disk reactor packed with polyurethane during thermophilic anaerobic digestion

    International Nuclear Information System (INIS)

    Yang, Yingnan; Tsukahara, Kenichiro; Sawayama, Shigeki

    2007-01-01

    A newly developed anaerobic rotating disk reactor (ARDR) packed with polyurethane was used in continuous mode for organic waste removal under thermophilic (55 o C) anaerobic conditions. This paper reports the effects of the rotational speed on the methanogenic performance and community in an ARDR supplied with acetic acid synthetic wastewater as the organic substrate. The best performance was obtained from the ARDR with the rotational speed (ω) of 30 rpm. The average removal of dissolved organic carbon was 98.5%, and the methane production rate was 393 ml/l-reactor/day at an organic loading rate of 2.69 g/l-reactor/day. Under these operational conditions, the reactor had a greater biomass retention capacity and better reactor performance than those at other rotational speeds (0, 5 and 60 rpm). The results of 16S rRNA phylogenetic analysis indicated that the major methanogens in the reactor belonged to the genus Methanosarcina spp. The results of real-time polymerase chain reaction (PCR) analysis suggested that the cell density of methanogenic archaea immobilized on the polyurethane foam disk could be concentrated more than 2000 times relative to those in the original thermophilic sludge. Scanning electron microphotographs showed that there were more immobilized microbes at ω of 30 rpm than 60 rpm. A rotational speed on the outer layer of the disk of 6.6 m/min could be appropriate for anaerobic digestion using the polyurethane ARDR

  17. Diversity of methanogens and sulfate-reducing bacteria in the interfaces of five deep-sea anoxic brines of the Red Sea

    KAUST Repository

    Guan, Yue

    2015-11-01

    Oceanic deep hypersaline anoxic basins (DHABs) are characterized by drastic changes in physico-chemical conditions in the transition from overlaying seawater to brine body. Brine-seawater interfaces (BSIs) of several DHABs across the Mediterranean Sea have been shown to possess methanogenic and sulfate-reducing activities, yet no systematic studies have been conducted to address the potential functional diversity of methanogenic and sulfate-reducing communities in the Red Sea DHABs. Here, we evaluated the relative abundance of Bacteria and Archaea using quantitative PCR and conducted phylogenetic analyses of nearly full-length 16S rRNA genes as well as functional marker genes encoding the alpha subunits of methyl-coenzyme M reductase (mcrA) and dissimilatory sulfite reductase (dsrA). Bacteria predominated over Archaea in most locations, the majority of which were affiliated with Deltaproteobacteria, while Thaumarchaeota were the most prevalent Archaea in all sampled locations. The upper convective layers of Atlantis II Deep, which bear increasingly harsh environmental conditions, were dominated by members of the class Thermoplasmata (Marine Benthic Group E and Mediterranean Sea Brine Lakes Group 1). Our study revealed unique microbial compositions, the presence of niche-specific groups, and collectively, a higher diversity of sulfate-reducing communities compared to methanogenic communities in all five studied locations. © 2015 Institut Pasteur.

  18. Diversity of methanogens and sulfate-reducing bacteria in the interfaces of five deep-sea anoxic brines of the Red Sea

    KAUST Repository

    Guan, Yue; Hikmawan, Tyas; Antunes, Andre; Ngugi, David; Stingl, Ulrich

    2015-01-01

    Oceanic deep hypersaline anoxic basins (DHABs) are characterized by drastic changes in physico-chemical conditions in the transition from overlaying seawater to brine body. Brine-seawater interfaces (BSIs) of several DHABs across the Mediterranean Sea have been shown to possess methanogenic and sulfate-reducing activities, yet no systematic studies have been conducted to address the potential functional diversity of methanogenic and sulfate-reducing communities in the Red Sea DHABs. Here, we evaluated the relative abundance of Bacteria and Archaea using quantitative PCR and conducted phylogenetic analyses of nearly full-length 16S rRNA genes as well as functional marker genes encoding the alpha subunits of methyl-coenzyme M reductase (mcrA) and dissimilatory sulfite reductase (dsrA). Bacteria predominated over Archaea in most locations, the majority of which were affiliated with Deltaproteobacteria, while Thaumarchaeota were the most prevalent Archaea in all sampled locations. The upper convective layers of Atlantis II Deep, which bear increasingly harsh environmental conditions, were dominated by members of the class Thermoplasmata (Marine Benthic Group E and Mediterranean Sea Brine Lakes Group 1). Our study revealed unique microbial compositions, the presence of niche-specific groups, and collectively, a higher diversity of sulfate-reducing communities compared to methanogenic communities in all five studied locations. © 2015 Institut Pasteur.

  19. Effects of Spartina alterniflora invasion on the communities of methanogens and sulfate-reducing bacteria in estuarine marsh sediments

    Directory of Open Access Journals (Sweden)

    Jemaneh eZeleke

    2013-08-01

    Full Text Available The effect of plant invasion on the microorganisms of soil sediments is very important for estuary ecology. The community structures of methanogens and sulfate-reducing bacteria (SRB as a function of Spartina alterniflora invasion in Phragmites australis-vegetated sediments of the Dongtan wetland in the Yangtze River estuary, China, were investigated using 454 pyrosequencing and quantitative real-time PCR (qPCR of the methyl coenzyme M reductase A (mcrA and dissimilatory sulfite-reductase (dsrB genes. Sediment samples were collected from two replicate locations, and each location included three sampling stands each covered by monocultures of P. australis, S. alterniflora and both plants (transition stands, respectively. qPCR analysis revealed higher copy numbers of mcrA genes in sediments from S. alterniflora stands than P. australis stands (5- and 7.5-fold more in the spring and summer, respectively, which is consistent with the higher methane flux rates measured in the S. alterniflora stands (up to 8.01 ± 5.61 mg m-2 h-1. Similar trends were observed for SRB, and they were up to two orders of magnitude higher than the methanogens. Diversity indices indicated a lower diversity of methanogens in the S. alterniflora stands than the P. australis stands. In contrast, insignificant variations were observed in the diversity of SRB with the invasion. Although Methanomicrobiales and Methanococcales, the hydrogenotrophic methanogens, dominated in the salt marsh, Methanomicrobiales displayed a slight increase with the invasion and growth of S. alterniflora, whereas the later responded differently. Methanosarcina, the metabolically diverse methanogens, did not vary with the invasion of, but Methanosaeta, the exclusive acetate utilizers, appeared to increase with S. alterniflora invasion. In SRB, sequences closely related to the families Desulfobacteraceae and Desulfobulbaceae dominated in the salt marsh, although they displayed minimal changes with the S

  20. Bacterial community structure in experimental methanogenic bioreactors and search for pathogenic clostridia as community members.

    Science.gov (United States)

    Dohrmann, Anja B; Baumert, Susann; Klingebiel, Lars; Weiland, Peter; Tebbe, Christoph C

    2011-03-01

    Microbial conversion of organic waste or harvested plant material into biogas has become an attractive technology for energy production. Biogas is produced in reactors under anaerobic conditions by a consortium of microorganisms which commonly include bacteria of the genus Clostridium. Since the genus Clostridium also harbors some highly pathogenic members in its phylogenetic cluster I, there has been some concern that an unintended growth of such pathogens might occur during the fermentation process. Therefore this study aimed to follow how process parameters affect the diversity of Bacteria in general, and the diversity of Clostridium cluster I members in particular. The development of both communities was followed in model biogas reactors from start-up during stable methanogenic conditions. The biogas reactors were run with either cattle or pig manures as substrates, and both were operated at mesophilic and thermophilic conditions. The structural diversity was analyzed independent of cultivation using a PCR-based detection of 16S rRNA genes and genetic profiling by single-strand conformation polymorphism (SSCP). Genetic profiles indicated that both bacterial and clostridial communities evolved in parallel, and the community structures were highly influenced by both substrate and temperature. Sequence analysis of 16S rRNA genes recovered from prominent bands from SSCP profiles representing Clostridia detected no pathogenic species. Thus, this study gave no indication that pathogenic clostridia would be enriched as dominant community members in biogas reactors fed with manure.

  1. Effect of Nitrooxy Compounds with Different Molecular Structures on the Rumen Methanogenesis, Metabolic Profile, and Methanogenic Community.

    Science.gov (United States)

    Jin, Wei; Meng, Zhenxiang; Wang, Jing; Cheng, Yanfen; Zhu, Weiyun

    2017-08-01

    Rumen in vitro fermentation was used to evaluate the capacity of nitrooxy compounds to mitigate rumen methane production. The following three nitrooxy compounds, each with different molecular structures, were evaluated: 2,2-dimethyl-3-(nitrooxy) propanoic (DNP), N-[2-(Nitrooxy)ethyl]-3-pyridinecarboxamide (NPD), and nitroglycerin (NG). All three compounds substantially decreased the total gas production, methane production, and the acetate:propionate ratio, while increasing hydrogen production. The growth of methanogens was specifically inhibited by all three compounds, without affecting the abundance of bacteria, anaerobic fungi, or protozoa. However, inhibition of methanogenesis required a much higher dose of DNP when compared to NPD or NG. Further investigations were conducted on NG to determine its effects on the methanogenic community. NG reduced the relative abundance of Methanomassiliicoccales, while increasing the relative abundance of Methanobrevibacter and Methanosphaera. Overall, the results suggested that all three of these nitrooxy compounds could specifically inhibit rumen methanogenesis, but NPD and NG were much more efficient than DNP at rumen methane mitigation.

  2. Multiple Syntrophic Interactions in a Terephthalate-Degrading Methanogenic Consortium

    Energy Technology Data Exchange (ETDEWEB)

    Lykidis, Athanasios; Chen, Chia-Lung; Tringe, Susannah G.; McHardy, Alice C.; Copeland, Alex 5; Kyrpides, Nikos C.; Hugenholtz, Philip; Liu, Wen-Tso

    2010-08-05

    Terephthalate (TA) is one of the top 50 chemicals produced worldwide. Its production results in a TA-containing wastewater that is treated by anaerobic processes through a poorly understood methanogenic syntrophy. Using metagenomics, we characterized the methanogenic consortium tinside a hyper-mesophilic (i.e., between mesophilic and thermophilic), TA-degrading bioreactor. We identified genes belonging to dominant Pelotomaculum species presumably involved in TA degradation through decarboxylation, dearomatization, and modified ?-oxidation to H{sub 2}/CO{sub 2} and acetate. These intermediates are converted to CH{sub 4}/CO{sub 2} by three novel hyper-mesophilic methanogens. Additional secondary syntrophic interactions were predicted in Thermotogae, Syntrophus and candidate phyla OP5 and WWE1 populations. The OP5 encodes genes capable of anaerobic autotrophic butyrate production and Thermotogae, Syntrophus and WWE1 have the genetic potential to oxidize butyrate to COsub 2}/H{sub 2} and acetate. These observations suggest that the TA-degrading consortium consists of additional syntrophic interactions beyond the standard H{sub 2}-producing syntroph ? methanogen partnership that may serve to improve community stability.

  3. Methanobacterium Dominates Biocathodic Archaeal Communities in Methanogenic Microbial Electrolysis Cells

    KAUST Repository

    Siegert, Michael; Yates, Matthew D.; Spormann, Alfred M.; Logan, Bruce E.

    2015-01-01

    % of archaea). Cathodes with platinum contained mainly archaea most similar to Methanobrevibacter. Neither of these methanogens were abundant (<0.1% of archaea) in the inoculum, and therefore their high abundance on the cathode resulted from selective

  4. Assessment of microbial communities associated with fermentative-methanogenic biodegradation of aromatic hydrocarbons in groundwater contaminated with a biodiesel blend (B20).

    Science.gov (United States)

    Ramos, Débora Toledo; da Silva, Márcio Luís Busi; Nossa, Carlos Wolfgang; Alvarez, Pedro J J; Corseuil, Henry Xavier

    2014-09-01

    A controlled field experiment was conducted to assess the potential for fermentative-methanogenic biostimulation (by ammonium-acetate injection) to enhance biodegradation of benzene, toluene, ethylbenzene and xylenes (BTEX) as well as polycyclic aromatic hydrocarbons (PAHs) in groundwater contaminated with biodiesel B20 (20:80 v/v soybean biodiesel and diesel). Changes in microbial community structure were assessed by pyrosequencing 16S rRNA analyses. BTEX and PAH removal began 0.7 year following the release, concomitantly with the increase in the relative abundance of Desulfitobacterium and Geobacter spp. (from 5 to 52.7 % and 15.8 to 37.3 % of total Bacteria 16S rRNA, respectively), which are known to anaerobically degrade hydrocarbons. The accumulation of anaerobic metabolites acetate and hydrogen that could hinder the thermodynamic feasibility of BTEX and PAH biotransformations under fermentative/methanogenic conditions was apparently alleviated by the growing predominance of Methanosarcina. This suggests the importance of microbial population shifts that enrich microorganisms capable of interacting syntrophically to enhance the feasibility of fermentative-methanogenic bioremediation of biodiesel blend releases.

  5. Associative patterns among anaerobic fungi, methanogenic archaea and bacterial communities in response to changes in diet and age in the rumen of dairy cows

    Directory of Open Access Journals (Sweden)

    Sanjay eKumar

    2015-07-01

    Full Text Available The rumen microbiome represents a complex microbial genetic web where bacteria, anaerobic rumen fungi (ARF, protozoa and archaea work in harmony contributing to the health and productivity of ruminants. We hypothesized that the rumen microbiome shifts as the dairy cow advances in lactations and these microbial changes may contribute to differences in productivity between primiparous (first lactation and multiparous (≥ second lactation cows. To this end, we investigated shifts in the ruminal ARF and methanogenic communities in both primiparous (n=5 and multiparous (n=5 cows as they transitioned from a high forage to a high grain diet upon initiation of lactation. A total of 20 rumen samples were extracted for genomic DNA, amplified using archaeal and fungal specific primers, sequenced on a 454 platform and analyzed using QIIME. Community comparisons (Bray-Curtis index revealed the effect of diet (P < 0.01 on ARF composition, while archaeal communities differed between primiparous and multiparous cows (P < 0.05. Among ARF, several lineages were unclassified, however, phylum Neocallimastigomycota showed the presence of three known genera. Abundance of Cyllamyces and Caecomyces shifted with diet whereas, Orpinomyces was influenced by both diet and age. Methanobrevibacter constituted the most dominant archaeal genus across all samples. Co-occurrence analysis incorporating taxa from bacteria, ARF and archaea revealed syntrophic interactions both within and between microbial domains in response to change in diet as well as age of dairy cows. Notably, these interactions were numerous and complex in multiparous cows supporting our hypothesis that the rumen microbiome also matures with age to sustain the growing metabolic needs of the host. This study provides a broader picture of the ARF and methanogenic populations in the rumen of dairy cows and their co-occurrence implicates specific relationships between different microbial domains in response to

  6. Quantification of methanogenic biomass by enzyme-linked immunosorbent assay and by analysis of specific methanogenic cofactors

    Energy Technology Data Exchange (ETDEWEB)

    Gorris, L G.M.; Kemp, H A; Archer, D B

    1987-01-01

    The reliability and accuracy with which enzyme-linked immunosorbent assay (ELISA) and an assay of methanogenic cofactors detect and quantify methanogenic species were investigated. Both assays required standardization with laboratory cultures of methanogenic bacteria and were applied to mixtures of pure cultures and samples from anaerobic digesters. ELISA was shown to be a simple method for detecting and quantifying individual methanogenic species. The range of species which can be assayed is limited by the range of antisera available but, potentially, ELISA can be applied to all methanogens. Although the cofactor assay is not species-specific it can distinguish hydrogenotrophic and acetotrophic methanogens and is quantitative.

  7. Physico-chemical characteristics and methanogen communities in swine and dairy manure storage tanks: spatio-temporal variations and impact on methanogenic activity.

    Science.gov (United States)

    Barret, Maialen; Gagnon, Nathalie; Topp, Edward; Masse, Lucie; Massé, Daniel I; Talbot, Guylaine

    2013-02-01

    Greenhouse gas emissions represent a major environmental problem associated with the management of manure from the livestock industry. Methane is the primary GHG emitted during manure outdoor storage. In this paper, the variability of two swine and two dairy manure storage tanks was surveyed, in terms of physico-chemical and microbiological parameters. The impact of the inter-tank and spatio-temporal variations of these parameters on the methanogenic activity of manure was ascertained. A Partial Least Square regression was carried out, which demonstrated that physico-chemical as well as microbiological parameters had a major influence on the methanogenic activity. Among the 19 parameters included in the regression, the concentrations of VFAs had the strongest negative influence on the methane emission rate of manure, resulting from their well-known inhibitory effect. The relative abundance of two amplicons in archaeal fingerprints was found to positively influence the methanogenic activity, suggesting that Methanoculleus spp. and possibly Methanosarcina spp. are major contributors to methanogenesis in storage tanks. This work gave insights into the mechanisms, which drive methanogenesis in swine and dairy manure storage tanks. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

  8. Isotopic composition of methane and inferred methanogenic substrates along a salinity gradient in a hypersaline microbial mat system.

    Science.gov (United States)

    Potter, Elyn G; Bebout, Brad M; Kelley, Cheryl A

    2009-05-01

    The importance of hypersaline environments over geological time, the discovery of similar habitats on Mars, and the importance of methane as a biosignature gas combine to compel an understanding of the factors important in controlling methane released from hypersaline microbial mat environments. To further this understanding, changes in stable carbon isotopes of methane and possible methanogenic substrates in microbial mat communities were investigated as a function of salinity here on Earth. Microbial mats were sampled from four different field sites located within salterns in Baja California Sur, Mexico. Salinities ranged from 50 to 106 parts per thousand (ppt). Pore water and microbial mat samples were analyzed for the carbon isotopic composition of dissolved methane, dissolved inorganic carbon (DIC), and mat material (particulate organic carbon or POC). The POC delta(13)C values ranged from -6.7 to -13.5 per thousand, and DIC delta(13)C values ranged from -1.4 to -9.6 per thousand. These values were similar to previously reported values. The delta(13)C values of methane ranged from -49.6 to -74.1 per thousand; the methane most enriched in (13)C was obtained from the highest salinity area. The apparent fractionation factors between methane and DIC, and between methane and POC, within the mats were also determined and were found to change with salinity. The apparent fractionation factors ranged from 1.042 to 1.077 when calculated using DIC and from 1.038 to 1.068 when calculated using POC. The highest-salinity area showed the least fractionation, the moderate-salinity area showed the highest fractionation, and the lower-salinity sites showed fractionations that were intermediate. These differences in fractionation are most likely due to changes in the dominant methanogenic pathways and substrates used at the different sites because of salinity differences.

  9. Preferential methanogenic biodegradation of short-chain n-alkanes by microbial communities from two different oil sands tailings ponds.

    Science.gov (United States)

    Mohamad Shahimin, Mohd Faidz; Foght, Julia M; Siddique, Tariq

    2016-05-15

    Oil sands tailings ponds harbor diverse anaerobic microbial communities capable of methanogenic biodegradation of solvent hydrocarbons entrained in the tailings. Mature fine tailings (MFT) from two operators (Albian and CNRL) that use different extraction solvents were incubated with mixtures of either two (n-pentane and n-hexane) or four (n-pentane, n-hexane, n-octane and n-decane) n-alkanes under methanogenic conditions for ~600 d. Microbes in Albian MFT began methane production by ~80 d, achieving complete depletion of n-pentane and n-hexane in the two-alkane mixture and their preferential biodegradation in the four-alkane mixture. Microbes in CNRL MFT preferentially metabolized n-octane and n-decane in the four-alkane mixture after a ~80 d lag but exhibited a lag of ~360 d before commencing biodegradation of n-pentane and n-hexane in the two-alkane mixture. 16S rRNA gene pyrosequencing revealed Peptococcaceae members as key bacterial n-alkane degraders in all treatments except CNRL MFT amended with the four-alkane mixture, in which Anaerolineaceae, Desulfobacteraceae (Desulfobacterium) and Syntrophaceae (Smithella) dominated during n-octane and n-decane biodegradation. Anaerolineaceae sequences increased only in cultures amended with the four-alkane mixture and only during n-octane and n-decane biodegradation. The dominant methanogens were acetoclastic Methanosaetaceae. These results highlight preferential n-alkane biodegradation by microbes in oil sands tailings from different producers, with implications for tailings management and reclamation. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling

    Directory of Open Access Journals (Sweden)

    Hailan ePiao

    2014-07-01

    Full Text Available The rumen is known for its biomass-degrading and methane-producing phenotype. Fermentation of recalcitrant plant material necessitates the synergistic activity of diverse microbial taxonomic groups that inhabit this anaerobic environment. Although interspecies hydrogen (H2 transfer, a process during which bacterially generated H2 is transferred to methanogenic Archaea, has obtained significant attention over the last decades, the temporal variation of the different taxa involved in in situ biomass-degradation, H2 transfer and methanogenesis process remains to be established. We investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing. Switchgrass filled nylon bags were placed in the rumen of a cannulated cow and collected at nine time points for DNA extraction and 16S pyrotag profiling. The microbial community colonizing the air-dried and non-incubated switchgrass was dominated by members of the Bacilli. During in situ incubation of the switchgrass, two major shifts in the community composition were observed: Bacilli were replaced within 30 min by members belonging to the Bacteroidia and Clostridia. A second significant shift was observed after 16 h of rumen incubation, when members of the Spirochaetes and Fibrobacteria classes became more abundant in the fiber-adherent community. During the first 30 min of rumen incubation ~13% of the switchgrass dry matter was degraded, whereas little biomass degradation appeared to have occurred between 30 min and 4 h after the switchgrass was placed in the rumen. Interestingly, methanogenic members of the Euryarchaeota increased up to 3-fold during this period of reduced biomass-degradation, with peak abundance just before rates of dry matter degradation increased again. We hypothesize that during this period microbial-mediated fibrolysis was temporarily inhibited until H2 was metabolized into CH4 by methanogens.

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

    DEFF Research Database (Denmark)

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

    2018-01-01

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

  12. A comprehensive study into the molecular methodology and molecular biology of methanogenic Archaea

    DEFF Research Database (Denmark)

    Lange, M.; Ahring, Birgitte Kiær

    2001-01-01

    Methanogens belong to the kingdom of Euryarchaeota in the domain of Archaea. The Archaea differ from Bacteria in many aspects important to molecular work. Among these are cell wall composition, their sensitivity to antibiotics, their translation and transcription machinery, and their very strict ...... procedures. Efficient genetic manipulation systems, including shuttle and integration vector systems, have appeared for mesophilic, but not for thermophilic species within the last few years and will have a major impact on future investigations of methanogenic molecular biology....

  13. Quantitation and identification of methanogens and sulphate reducers in Olkiluoto groundwater

    International Nuclear Information System (INIS)

    Bomberg, M.; Nyyssoenen, M.; Itaevaara, M.

    2010-08-01

    involved in methanogenesis (mcrA) or sulphate reduction (dsrB) and enables the study of these microbial processes in the deep bedrock groundwater. In the GEOFUNC project, groundwater samples were studied from depths ranging from -14.5 m to -581 m comprising samples from both drillholes in Olkiluoto and groundwater stations in the ONKALO. Methanogenic archaea were present in almost all samples. The highest number of methanogens was detected in the samples ONK-PVA1 (-14.5 m), OL-KR40 (-349 to -351 m and -545 to -553 m) and OL-KR47 (-334 to -338 m) and OL-KR23 (-347 to -376 m). In the samples, where the salinity exceeded 19 g/l (Cl, Na, Ca), the number of methanogens was very low. Sulphate reducing bacteria were present in all studied samples. The highest number of sulphate reducers were detected in the samples ONK-PVA1 (-14.5 m), OL-KR23 (-347 to -376 m) and OLKR11 (-531 to -558 m) and OL-KR40 (-545 to -553 m), however, the last two samples are evident artefact mixtures of SO4 - and CH4 -rich groundwaters, thus they do not represent undisturbed in situ conditions in groundwater system. The diversity of methanogens changed in relation to depth and a clear division into phylogenetic groups containing either mcrA sequences from samples close to the land surface or mcrA sequences from deeper samples. The sulphate reducers were different in all studied samples. Despite their important ecological functions, both methanogens and sulphate reducers were present as only small fractions of the total microbial community in the Olkiluoto groundwater. The methanogens comprised at the most 0.44 % of the microbial community (-349 m) and the sulphate reducers 1.55 % (-14.5 m) and 1.3 % (-531 m). The results presented in this report give indications to the diversity and quantity of the populations of methanogenic archaea and sulphate reducing bacteria in the deep groundwater of Olkiluoto. In spite of the small number of methanogens and sulphate reducers in the environment there ecological

  14. Thermoplasmatales and Methanogens: Potential Association with the Crenarchaeol Production in Chinese Soils

    Directory of Open Access Journals (Sweden)

    Fuyan Li

    2017-06-01

    Full Text Available Crenarchaeol is a unique isoprenoid glycerol dibiphytanyl glycerol tetraether (iGDGT lipid, which is only identified in cultures of ammonia-oxidizing Thaumarchaeota. However, the taxonomic origins of crenarchaeol have been debated recently. The archaeal populations, other than Thaumarchaeota, may have associations with the production of crenarchaeol in ecosystems characterized by non-thaumarchaeotal microorganisms. To this end, we investigated 47 surface soils from upland and wetland soils and rice fields and another three surface sediments from river banks. The goal was to examine the archaeal community compositions in comparison with patterns of iGDGTs in four fractional forms (intact polar-, core-, monoglycosidic- and diglycosidic-lipid fractions along gradients of environments. The DistLM analysis identified that Group I.1b Thaumarchaeota were mainly responsible for changes in crenarchaeol in the overall soil samples; however, Thermoplasmatales may also contribute to it. This is further supported by the comparison of crenarchaeol between samples characterized by methanogens, Thermoplasmatales or Group I.1b Thaumarchaeota, which suggests that the former two may contribute to the crenarchaeol pool. Last, when samples containing enhanced abundance of Thermoplasmatales and methanogens were considered, crenarchaeol was observed to correlate positively with Thermoplasmatales and archaeol, respectively. Collectively, our data suggest that the crenarchaeol production is mainly derived from Thaumarchaeota and partly associated with uncultured representatives of Thermoplasmatales and archaeol-producing methanogens in soil environments that may be in favor of their growth. Our finding supports the notion that Thaumarchaeota may not be the sole source of crenarchaeol in the natural environment, which may have implication for the evolution of lipid synthesis among different types of archaea.

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

    Science.gov (United States)

    Thummes, Kathrin; Kämpfer, Peter; Jäckel, Udo

    2007-07-01

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

  16. Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions.

    Science.gov (United States)

    He, Shaomei; Malfatti, Stephanie A; McFarland, Jack W; Anderson, Frank E; Pati, Amrita; Huntemann, Marcel; Tremblay, Julien; Glavina del Rio, Tijana; Waldrop, Mark P; Windham-Myers, Lisamarie; Tringe, Susannah G

    2015-05-19

    Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhouse gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest. Wetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial communities

  17. Succession of methanogenic archaea in rice straw incorporated into a Japanese rice field: estimation by PCR-DGGE and sequence analyses

    Directory of Open Access Journals (Sweden)

    Atsuo Sugano

    2005-01-01

    Full Text Available The succession and phylogenetic profiles of methanogenic archaeal communities associated with rice straw decomposition in rice-field soil were studied by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE analysis followed by 16S rDNA sequencing. Nylon bags containing either leaf sheaths or blades were buried in the plowed layer of a Japanese rice field under drained conditions during the off-crop season and under flooded conditions after transplanting. In addition, rice straw samples that had been buried in the rice field under drained conditions during the off-crop season were temporarily removed during spring plowing and then re-buried in the same rice field under flooded conditions at transplanting. Populations of methanogenic archaea were examined by amplification of the 16S rRNA genes in the DNA extracted from the rice straw samples. No PCR product was produced for samples of leaf sheath or blade prior to burial or after burial under drained conditions, indicating that the methanogen population was very small during decomposition of rice straw under oxic conditions. Many common bands were observed in rice straw samples of leaf sheath and blade during decomposition of rice straw under flooded conditions. Cluster analysis based on DGGE patterns divided methanogenic archaeal communities into two groups before and after the mid-season drainage. Sequence analysis of DGGE bands that were commonly present were closely related to Methanomicrobiales and Rice cluster I. Methanomicrobiales, Rice cluster I and Methanosarcinales were major members before the mid-season drainage, whereas the DGGE bands that characterized methanogenic archaeal communities after the mid-season drainage were closely related to Methanomicrobiales. These results indicate that mid-season drainage affected the methanogenic archaeal communities irrespective of their location on rice straw (sheath and blade and the previous history of decomposition

  18. Thermo-alkaline pretreatment of waste activated sludge at low-temperatures: effects on sludge disintegration, methane production, and methanogen community structure.

    Science.gov (United States)

    Kim, Jaai; Yu, Youngseob; Lee, Changsoo

    2013-09-01

    Low-temperature thermo-alkaline pretreatment of waste activated sludge (WAS) was studied, within the region of 0-0.2 M NaOH and 60-90°C, for the effects of NaOH concentration and temperature on sludge degradability in anaerobic digestion (AD). Significant disintegration of sludge solids (up to 75.6%) and an increase in methane production (up to 70.6%) were observed in the pretreatment trials. Two quadratic models were successfully generated by response surface analysis (R(2)>0.9, pdisintegration (SD) and methane production (MP) respond to changes in the pretreatment conditions. The maximum responses of SD (77.8%) and MP (73.9% increase over the control) were shown at [0.16 M NaOH, 90°C] and [0.10 M NaOH, 73.7°C], respectively. NaOH addition showed a significant influence on the evolution of methanogen community structure during AD, whereas temperature did not. Aceticlastic Methanosaeta and Methanosarcina speceies were likely the major methanogens. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Methanogenic paraffin degradation proceeds via alkane addition to fumarate by 'Smithella' spp. mediated by a syntrophic coupling with hydrogenotrophic methanogens.

    Science.gov (United States)

    Wawrik, Boris; Marks, Christopher R; Davidova, Irene A; McInerney, Michael J; Pruitt, Shane; Duncan, Kathleen E; Suflita, Joseph M; Callaghan, Amy V

    2016-09-01

    Anaerobic microbial biodegradation of recalcitrant, water-insoluble substrates, such as paraffins, presents unique metabolic challenges. To elucidate this process, a methanogenic consortium capable of mineralizing long-chain n-paraffins (C28 -C50 ) was enriched from San Diego Bay sediment. Analysis of 16S rRNA genes indicated the dominance of Syntrophobacterales (43%) and Methanomicrobiales (26%). Metagenomic sequencing allowed draft genome assembly of dominant uncultivated community members belonging to the bacterial genus Smithella and the archaeal genera Methanoculleus and Methanosaeta. Five contigs encoding homologs of the catalytic subunit of alkylsuccinate synthase (assA) were detected. Additionally, mRNA transcripts for these genes, including a homolog binned within the 'Smithella' sp. SDB genome scaffold, were detected via RT-PCR, implying that paraffins are activated via 'fumarate addition'. Metabolic reconstruction and comparison with genome scaffolds of uncultivated n-alkane degrading 'Smithella' spp. are consistent with the hypothesis that syntrophically growing 'Smithella' spp. may achieve reverse electron transfer by coupling the reoxidation of ETFred to a membrane-bound FeS oxidoreductase functioning as an ETF:menaquinone oxidoreductase. Subsequent electron transfer could proceed via a periplasmic formate dehydrogenase and/or hydrogenase, allowing energetic coupling to hydrogenotrophic methanogens such as Methanoculleus. Ultimately, these data provide fundamental insight into the energy conservation mechanisms that dictate interspecies interactions salient to methanogenic alkane mineralization. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  20. Adaptation of Methanogenic Inocula to Anaerobic Digestion of Maize Silage

    Directory of Open Access Journals (Sweden)

    Martyna Wojcieszak

    2017-09-01

    Full Text Available A well-balanced microbial consortium is crucial for efficient biogas production. In turn, one of a major factor that influence on the structure of anaerobic digestion (AD consortium is a source of microorganisms which are used as an inoculum. This study evaluated the influence of inoculum sources (with various origin on adaptation of a biogas community and the efficiency of the biomethanization of maize silage. As initial inocula for AD of maize silage the samples from: (i an agricultural biogas plant (ABP which utilizes maize silage as a main substrate, (ii cattle slurry (CS, which contain elevated levels of lignocelluloses materials, and (iii raw sewage sludge (RSS with low content of plant origin materials were used. The adaptation of methanogenic consortia was monitored during a series of passages, and the functionality of the adapted consortia was verified through start-up operation of AD in two-stage reactors. During the first stages of the adaptation phase, methanogenic consortia occurred very slowly, and only after several passages did the microbial community adapts to allow production of biogas with high methane content. The ABP consortium revealed highest biogas production in the adaptation and in the start-up process. The biodiversity dynamics monitored during adaptation and start-up process showed that community profile changed in a similar direction in three studied consortia. Native communities were very distinct to each other, while at the end of the Phase II of the start-up process microbial diversity profile was similar in all consortia. All adopted bacterial communities were dominated by representatives of Porphyromonadaceae, Rikenellaceae, Ruminococcaceae, and Synergistaceae. A shift from low acetate-preferring acetoclastic Methanosaetaceae (ABP and RSS and/or hydrogenotrophic Archaea, e.g., Methanomicrobiaceae (CS prevailing in the inoculum samples to larger populations of high acetate-preferring acetoclastic

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

    Science.gov (United States)

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

    2017-12-01

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

  2. Early stages in biofilm development in methanogenic fluidized-bed reactors

    Energy Technology Data Exchange (ETDEWEB)

    Lauwers, A.M.; Heinen, W.; Gorris, L.G.M.; Drift, C. van der (Katholieke Univ. Nijmegen (Netherlands). Dept. of Microbiology and Evolution Biology)

    1990-06-01

    Biofilm development in methanogenic fluidized-bed reactors with sand as the carrier was studied on a laboratory scale. The microorganisms present in consecutive layers of the biofilm of mature sludge granules were prelimilarily characterized on the basis of their morphology, element composition and adhesion capacity and were compared to bacteria which take part in the initial colonization of sand. The early phase of biofilm development was monitored with reactors receiving waste-waters containing different mixtures of volatile fatty acids and inoculated with fluidized-bed reactor effluent for different lengths of time. The results obtained indicate that facultative anaerobic bacteria abundantly present in the outermost biofilm layers of mature sludge granules are probably the main primary colonizers of the sand. Methanothrix spp. or other methanogens were rarely observed among the primary colonizers. The course of biofilm formation was comparable under the various start-up conditions employed including variations in waste-water composition, inoculation and anaerobicity. However, omission of waste-water and thus of substrate resulted in rapid wash-out of the attached biomass. (orig.).

  3. Impact of high-concentrate feeding and low ruminal pH on methanogens and protozoa in the rumen of dairy cows.

    Science.gov (United States)

    Hook, Sarah E; Steele, Michael A; Northwood, Korinne S; Wright, André-Denis G; McBride, Brian W

    2011-07-01

    Non-lactating dairy cattle were transitioned to a high-concentrate diet to investigate the effect of ruminal pH suppression, commonly found in dairy cattle, on the density, diversity, and community structure of rumen methanogens, as well as the density of rumen protozoa. Four ruminally cannulated cows were fed a hay diet and transitioned to a 65% grain and 35% hay diet. The cattle were maintained on an high-concentrate diet for 3 weeks before the transition back to an hay diet, which was fed for an additional 3 weeks. Rumen fluid and solids and fecal samples were obtained prior to feeding during weeks 0 (hay), 1, and 3 (high-concentrate), and 4 and 6 (hay). Subacute ruminal acidosis was induced during week 1. During week 3 of the experiment, there was a significant increase in the number of protozoa present in the rumen fluid (P=0.049) and rumen solids (P=0.004), and a significant reduction in protozoa in the rumen fluid in week 6 (P=0.003). No significant effect of diet on density of rumen methanogens was found in any samples, as determined by real-time PCR. Clone libraries were constructed for weeks 0, 3, and 6, and the methanogen diversity of week 3 was found to differ from week 6. Week 3 was also found to have a significantly altered methanogen community structure, compared to the other weeks. Twenty-two unique 16S rRNA phylotypes were identified, three of which were found only during high-concentrate feeding, three were found during both phases of hay feeding, and seven were found in all three clone libraries. The genus Methanobrevibacter comprised 99% of the clones present. The rumen fluid at weeks 0, 3, and 6 of all the animals was found to contain a type A protozoal population. Ultimately, high-concentrate feeding did not significantly affect the density of rumen methanogens, but did alter methanogen diversity and community structure, as well as protozoal density within the rumen of nonlactating dairy cattle. Therefore, it may be necessary to monitor the

  4. Microbiology and performance of a methanogenic biofilm reactor during the start-up period.

    Science.gov (United States)

    Cresson, R; Dabert, P; Bernet, N

    2009-03-01

    To understand the interactions between anaerobic biofilm development and process performances during the start-up period of methanogenic biofilm reactor. Two methanogenic inverse turbulent bed reactors have been started and monitored for 81 days. Biofilm development (adhesion, growth, population dynamic) and characteristics (biodiversity, structure) were investigated using molecular tools (PCR-SSCP, FISH-CSLM). Identification of the dominant populations, in relation to process performances and to the present knowledge of their metabolic activities, was used to propose a global scheme of the degradation routes involved. The inoculum, which determines the microbial species present in the biofilm influences bioreactor performances during the start-up period. FISH observations revealed a homogeneous distribution of the Archaea and bacterial populations inside the biofilm. This study points out the link between biodiversity, functional stability and methanogenic process performances during start-up of anaerobic biofilm reactor. It shows that inoculum and substrate composition greatly influence biodiversity, physiology and structure of the biofilm. The combination of molecular techniques associated to a biochemical engineering approach is useful to get relevant information on the microbiology of a methanogenic growing biofilm, in relation with the start-up of the process.

  5. Metabolic interactions in methanogenic and sulfate-reducing bioreactors.

    Science.gov (United States)

    Stams, A J M; Plugge, C M; de Bok, F A M; van Houten, B H G W; Lens, P; Dijkman, H; Weijma, J

    2005-01-01

    In environments where the amount of electron acceptors is insufficient for complete breakdown of organic matter, methane is formed as the major reduced end product. In such methanogenic environments organic acids are degraded by syntrophic consortia of acetogenic bacteria and methanogenic archaea. Hydrogen consumption by methanogens is essential for acetogenic bacteria to convert organic acids to acetate and hydrogen. Several syntrophic cocultures growing on propionate and butyrate have been described. These syntrophic fatty acid-degrading consortia are affected by the presence of sulfate. When sulfate is present sulfate-reducing bacteria compete with methanogenic archaea for hydrogen and acetate, and with acetogenic bacteria for propionate and butyrate. Sulfate-reducing bacteria easily outcompete methanogens for hydrogen, but the presence of acetate as carbon source may influence the outcome of the competition. By contrast, acetoclastic methanogens can compete reasonably well with acetate-degrading sulfate reducers. Sulfate-reducing bacteria grow much faster on propionate and butyrate than syntrophic consortia.

  6. Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences.

    Science.gov (United States)

    Yadav, Shailendra; Kundu, Sharbadeb; Ghosh, Sankar K; Maitra, S S

    2015-01-01

    Methanogens, a key contributor in global carbon cycling, methane emission, and alternative energy production, generate methane gas via anaerobic digestion of organic matter. The methane emission potential depends upon methanogenic diversity and activity. Since they are anaerobes and difficult to isolate and culture, their diversity present in the landfill sites of Delhi and marshlands of Southern Assam, India, was analyzed using molecular techniques like 16S rDNA sequencing, DGGE, and qPCR. The sequencing results indicated the presence of methanogens belonging to the seventh order and also the order Methanomicrobiales in the Ghazipur and Bhalsawa landfill sites of Delhi. Sequences, related to the phyla Crenarchaeota (thermophilic) and Thaumarchaeota (mesophilic), were detected from marshland sites of Southern Assam, India. Jaccard analysis of DGGE gel using Gel2K showed three main clusters depending on the number and similarity of band patterns. The copy number analysis of hydrogenotrophic methanogens using qPCR indicates higher abundance in landfill sites of Delhi as compared to the marshlands of Southern Assam. The knowledge about "methanogenic archaea composition" and "abundance" in the contrasting ecosystems like "landfill" and "marshland" may reorient our understanding of the Archaea inhabitants. This study could shed light on the relationship between methane-dynamics and the global warming process.

  7. High frequency of Thermodesulfovibrio spp. and Anaerolineaceae in association with Methanoculleus spp. in a long-term incubation of n-alkanes-degrading methanogenic enrichment culture

    Directory of Open Access Journals (Sweden)

    Bo Liang

    2016-09-01

    Full Text Available In the present study, the microbial community and functional gene composition of a long-term active alkane-degrading methanogenic culture was established after two successive enrichment culture transfers and incubated for a total period of 1750 days. Molecular analysis was conducted after the second transfer (incubated for 750 days for both the active alkanes-degrading methanogenic enrichment cultures (T2-AE and the background control (T2-BC. A net increase of methane as the end product was detected in the headspace of the enrichment cultures amended with long-chain n-alkanes and intermediate metabolites, including octadecanoate, hexadecanoate, isocaprylate, butyrate, isobutyrate, propionate, acetate and formate were measured in the liquid cultures. The composition of microbial community shifted through the successive transfers over time of incubation. Sequences of bacterial and archaeal 16S rRNA gene (16S rDNA and mcrA functional gene indicated that bacterial sequences affiliated to Thermodesulfovibrio spp. and Anaerolineaceae and archaeal sequences falling within the genus Methanoculleus were the most frequently encountered and thus represented the dominant members performing the anaerobic degradation of long-chain n-alkanes and methanogenesis. In addition, the presence of assA functional genes encoding the alkylsuccinate synthase α subunit indicated that fumarate addition mechanism could be considered as a possible initial activation step of n-alkanes in the present study. The succession pattern of microbial communities indicates that Thermodesulfovibrio spp. could be a generalist participating in the metabolism of intermediates, while Anaerolineaceae plays a key role in the initial activation of long-chain n-alkane biodegradation.

  8. Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling.

    Science.gov (United States)

    Piao, Hailan; Lachman, Medora; Malfatti, Stephanie; Sczyrba, Alexander; Knierim, Bernhard; Auer, Manfred; Tringe, Susannah G; Mackie, Roderick I; Yeoman, Carl J; Hess, Matthias

    2014-01-01

    The rumen microbial ecosystem is known for its biomass-degrading and methane-producing phenotype. Fermentation of recalcitrant plant material, comprised of a multitude of interwoven fibers, necessitates the synergistic activity of diverse microbial taxonomic groups that inhabit the anaerobic rumen ecosystem. Although interspecies hydrogen (H2) transfer, a process during which bacterially generated H2 is transferred to methanogenic Archaea, has obtained significant attention over the last decades, the temporal variation of the different taxa involved in in situ biomass-degradation, H2 transfer and the methanogenesis process remains to be established. Here we investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing. Switchgrass filled nylon bags were placed in the rumen of a cannulated cow and collected at nine time points for DNA extraction and 16S pyrotag profiling. The microbial community colonizing the air-dried and non-incubated (0 h) switchgrass was dominated by members of the Bacilli (recruiting 63% of the pyrotag reads). During in situ incubation of the switchgrass, two major shifts in the community composition were observed: Bacilli were replaced within 30 min by members belonging to the Bacteroidia and Clostridia, which recruited 34 and 25% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 16 h of rumen incubation, when members of the Spirochaetes and Fibrobacteria classes became more abundant in the fiber-adherent community. During the first 30 min of rumen incubation ~13% of the switchgrass dry matter was degraded, whereas little biomass degradation appeared to have occurred between 30 min and 4 h after the switchgrass was placed in the rumen. Interestingly, methanogenic members of the Euryarchaeota (i.e., Methanobacteria) increased up to 3-fold during this period of reduced biomass-degradation, with peak abundance just

  9. Different cultivation methods to acclimatise ammonia-tolerant methanogenic consortia.

    Science.gov (United States)

    Tian, Hailin; Fotidis, Ioannis A; Mancini, Enrico; Angelidaki, Irini

    2017-05-01

    Bioaugmentation with ammonia tolerant-methanogenic consortia was proposed as a solution to overcome ammonia inhibition during anaerobic digestion process recently. However, appropriate technology to generate ammonia tolerant methanogenic consortia is still lacking. In this study, three basic reactors (i.e. batch, fed-batch and continuous stirred-tank reactors (CSTR)) operated at mesophilic (37°C) and thermophilic (55°C) conditions were assessed, based on methane production efficiency, incubation time, TAN/FAN (total ammonium nitrogen/free ammonia nitrogen) levels and maximum methanogenic activity. Overall, fed-batch cultivation was clearly the most efficient method compared to batch and CSTR. Specifically, by saving incubation time up to 150%, fed-batch reactors were acclimatised to nearly 2-fold higher FAN levels with a 37%-153% methanogenic activity improvement, compared to batch method. Meanwhile, CSTR reactors were inhibited at lower ammonia levels. Finally, specific methanogenic activity test showed that hydrogenotrophic methanogens were more active than aceticlastic methanogens in all FAN levels above 540mgNH 3 -NL -1 . Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Iron oxides alter methanogenic pathways of acetate in production water of high-temperature petroleum reservoir.

    Science.gov (United States)

    Pan, Pan; Hong, Bo; Mbadinga, Serge Maurice; Wang, Li-Ying; Liu, Jin-Feng; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

    2017-09-01

    Acetate is a key intermediate in anaerobic crude oil biodegradation and also a precursor for methanogenesis in petroleum reservoirs. The impact of iron oxides, viz. β-FeOOH (akaganéite) and magnetite (Fe 3 O 4 ), on the methanogenic acetate metabolism in production water of a high-temperature petroleum reservoir was investigated. Methane production was observed in all the treatments amended with acetate. In the microcosms amended with acetate solely about 30% of the acetate utilized was converted to methane, whereas methane production was stimulated in the presence of magnetite (Fe 3 O 4 ) resulting in a 48.34% conversion to methane. Methane production in acetate-amended, β-FeOOH (akaganéite)-supplemented microcosms was much faster and acetate consumption was greatly improved compared to the other conditions in which the stoichiometric expected amounts of methane were not produced. Microbial community analysis showed that Thermacetogenium spp. (known syntrophic acetate oxidizers) and hydrogenotrophic methanogens closely related to Methanothermobacter spp. were enriched in acetate and acetate/magnetite (Fe 3 O 4 ) microcosms suggesting that methanogenic acetate metabolism was through hydrogenotrophic methanogenesis fueled by syntrophic acetate oxidizers. The acetate/β-FeOOH (akaganéite) microcosms, however, differed by the dominance of archaea closely related to the acetoclastic Methanosaeta thermophila. These observations suggest that supplementation of β-FeOOH (akaganéite) accelerated the production of methane further, driven the alteration of the methanogenic community, and changed the pathway of acetate methanogenesis from hydrogenotrophic methanogenesis fueled by syntrophic acetate oxidizers to acetoclastic.

  11. Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Iain; Ulrich, Luke E.; Lupa, Boguslaw; Susanti, Dwi; Porat, Iris; Hooper, Sean D.; Lykidis, Athanasios; Sieprawska-Lupa, Magdalena; Dharmarajan, Lakshmi; Goltsman, Eugene; Lapidus, Alla; Saunders, Elizabeth; Han, Cliff; Land, Miriam; Lucas, Susan; Mukhopadhyay, Biswarup; Whitman, William B.; Woese, Carl; Bristow, James; Kyrpides, Nikos

    2009-05-01

    Methanomicrobiales is the least studied order of methanogens. While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens. In order to improve our understanding of this lineage, we have completely sequenced the genomes of two members of this order, Methanocorpusculum labreanum Z and Methanoculleus marisnigri JR1, and compared them with the genome of a third, Methanospirillum hungatei JF-1. Similar to Class I methanogens, Methanomicrobiales use a partial reductive citric acid cycle for 2-oxoglutarate biosynthesis, and they have the Eha energy-converting hydrogenase. In common with Methanosarcinales, Methanomicrobiales possess the Ech hydrogenase and at least some of them may couple formylmethanofuran formation and heterodisulfide reduction to transmembrane ion gradients. Uniquely, M. labreanum and M. hungatei contain hydrogenases similar to the Pyrococcus furiosus Mbh hydrogenase, and all three Methanomicrobiales have anti-sigma factor and anti-anti-sigma factor regulatory proteins not found in other methanogens. Phylogenetic analysis based on seven core proteins of methanogenesis and cofactor biosynthesis places the Methanomicrobiales equidistant from Class I methanogens and Methanosarcinales. Our results indicate that Methanomicrobiales, rather than being similar to Class I methanogens or Methanomicrobiales, share some features of both and have some unique properties. We find that there are three distinct classes of methanogens: the Class I methanogens, the Methanomicrobiales (Class II), and the Methanosarcinales (Class III).

  12. Activation of CO2-reducing methanogens in oil reservoir after addition of nutrient.

    Science.gov (United States)

    Yang, Guang-Chao; Zhou, Lei; Mbadinga, Serge Maurice; You, Jing; Yang, Hua-Zhen; Liu, Jin-Feng; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

    2016-12-01

    Nutrient addition as part of microbial enhanced oil recovery (MEOR) operations have important implications for more energy recovery from oil reservoirs, but very little is known about the in situ response of microorganisms after intervention. An analysis of two genes as biomarkers, mcrA encoding the key enzyme in methanogenesis and fthfs encoding the key enzyme in acetogenesis, was conducted during nutrient addition in oil reservoir. Clone library data showed that dominant mcrA sequences changed from acetoclastic (Methanosaetaceae) to CO 2 -reducing methanogens (Methanomicrobiales and Methanobacteriales), and the authentic acetogens affiliated to Firmicutes decreased after the intervention. Principal coordinates analysis (PCoA) and Jackknife environment clusters revealed evidence on the shift of the microbial community structure among the samples. Quantitative analysis of methanogens via qPCR showed that Methanobacteriales and Methanomicrobiales increased after nutrient addition, while acetoclastic methanogens (Methanosaetaceae) changed slightly. Nutrient treatment activated native CO 2 -reducing methanogens in oil reservoir. The high frequency of Methanobacteriales and Methanomicrobiales (CO 2 -reducers) after nutrient addition in this petroleum system suggested that CO 2 -reducing methanogenesis was involved in methane production. The nutrient addition could promote the methane production. The results will likely improve strategies of utilizing microorganisms in subsurface environments. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  13. Different cultivation methods to acclimatise ammonia-tolerant methanogenic consortia

    DEFF Research Database (Denmark)

    Tian, Hailin; Fotidis, Ioannis; Mancini, Enrico

    2017-01-01

    reactors (i.e. batch, fed-batch and continuous stirred-tank reactors (CSTR)) operated at mesophilic (37°C) and thermophilic (55°C) conditions were assessed, based on methane production efficiency, incubation time, TAN/FAN (total ammonium nitrogen/free ammonia nitrogen) levels and maximum methanogenic...... activity. Overall, fed-batch cultivation was clearly the most efficient method compared to batch and CSTR. Specifically, by saving incubation time up to 150%, fed-batch reactors were acclimatised to nearly 2-fold higher FAN levels with a 37%-153% methanogenic activity improvement, compared to batch method....... Meanwhile, CSTR reactors were inhibited at lower ammonia levels. Finally, specific methanogenic activity test showed that hydrogenotrophic methanogens were more active than aceticlastic methanogens in all FAN levels above 540 mg NH3-N L-1....

  14. Considerations in the use of fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy to characterize rumen methanogens and define their spatial distributions.

    Science.gov (United States)

    Valle, Edith R; Henderson, Gemma; Janssen, Peter H; Cox, Faith; Alexander, Trevor W; McAllister, Tim A

    2015-06-01

    In this study, methanogen-specific coenzyme F420 autofluorescence and confocal laser scanning microscopy were used to identify rumen methanogens and define their spatial distribution in free-living, biofilm-, and protozoa-associated microenvironments. Fluorescence in situ hybridization (FISH) with temperature-controlled hybridization was used in an attempt to describe methanogen diversity. A heat pretreatment (65 °C, 1 h) was found to be a noninvasive method to increase probe access to methanogen RNA targets. Despite efforts to optimize FISH, 16S rRNA methanogen-specific probes, including Arch915, bound to some cells that lacked F420, possibly identifying uncharacterized Methanomassiliicoccales or reflecting nonspecific binding to other members of the rumen bacterial community. A probe targeting RNA from the methanogenesis-specific methyl coenzyme M reductase (mcr) gene was shown to detect cultured Methanosarcina cells with signal intensities comparable to those of 16S rRNA probes. However, the probe failed to hybridize with the majority of F420-emitting rumen methanogens, possibly because of differences in cell wall permeability among methanogen species. Methanogens were shown to integrate into microbial biofilms and to exist as ecto- and endosymbionts with rumen protozoa. Characterizing rumen methanogens and defining their spatial distribution may provide insight into mitigation strategies for ruminal methanogenesis.

  15. Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows.

    Science.gov (United States)

    Kumar, Sanjay; Indugu, Nagaraju; Vecchiarelli, Bonnie; Pitta, Dipti W

    2015-01-01

    The rumen microbiome represents a complex microbial genetic web where bacteria, anaerobic rumen fungi (ARF), protozoa and archaea work in harmony contributing to the health and productivity of ruminants. We hypothesized that the rumen microbiome shifts as the dairy cow advances in lactations and these microbial changes may contribute to differences in productivity between primiparous (first lactation) and multiparous (≥second lactation) cows. To this end, we investigated shifts in the ruminal ARF and methanogenic communities in both primiparous (n = 5) and multiparous (n = 5) cows as they transitioned from a high forage to a high grain diet upon initiation of lactation. A total of 20 rumen samples were extracted for genomic DNA, amplified using archaeal and fungal specific primers, sequenced on a 454 platform and analyzed using QIIME. Community comparisons (Bray-Curtis index) revealed the effect of diet (P bacteria, ARF and archaea revealed syntrophic interactions both within and between microbial domains in response to change in diet as well as age of dairy cows. Notably, these interactions were numerous and complex in multiparous cows, supporting our hypothesis that the rumen microbiome also matures with age to sustain the growing metabolic needs of the host. This study provides a broader picture of the ARF and methanogenic populations in the rumen of dairy cows and their co-occurrence implicates specific relationships between different microbial domains in response to diet and age.

  16. Comparison of methanogen diversity of yak (Bos grunniens) and cattle (Bos taurus) from the Qinghai-Tibetan plateau, China

    Science.gov (United States)

    2012-01-01

    Background Methane emissions by methanogen from livestock ruminants have significantly contributed to the agricultural greenhouse gas effect. It is worthwhile to compare methanogen from “energy-saving” animal (yak) and normal animal (cattle) in order to investigate the link between methanogen structure and low methane production. Results Diversity of methanogens from the yak and cattle rumen was investigated by analysis of 16S rRNA gene sequences from rumen digesta samples from four yaks (209 clones) and four cattle (205 clones) from the Qinghai-Tibetan Plateau area (QTP). Overall, a total of 414 clones (i.e. sequences) were examined and assigned to 95 operational taxonomic units (OTUs) using MOTHUR, based upon a 98% species-level identity criterion. Forty-six OTUs were unique to the yak clone library and 34 OTUs were unique to the cattle clone library, while 15 OTUs were found in both libraries. Of the 95 OTUs, 93 putative new species were identified. Sequences belonging to the Thermoplasmatales-affiliated Linage C (TALC) were found to dominate in both libraries, accounting for 80.9% and 62.9% of the sequences from the yak and cattle clone libraries, respectively. Sequences belonging to the Methanobacteriales represented the second largest clade in both libraries. However, Methanobrevibacter wolinii (QTPC 110) was only found in the cattle library. The number of clones from the order Methanomicrobiales was greater in cattle than in the yak clone library. Although the Shannon index value indicated similar diversity between the two libraries, the Libshuff analysis indicated that the methanogen community structure of the yak was significantly different than those from cattle. Conclusion This study revealed for the first time the molecular diversity of methanogen community in yaks and cattle in Qinghai-Tibetan Plateau area in China. From the analysis, we conclude that yaks have a unique rumen microbial ecosystem that is significantly different from that of cattle

  17. Comparison of methanogen diversity of yak (Bos grunniens and cattle (Bos taurus from the Qinghai-Tibetan plateau, China

    Directory of Open Access Journals (Sweden)

    Huang Xiao

    2012-10-01

    Full Text Available Abstract Background Methane emissions by methanogen from livestock ruminants have significantly contributed to the agricultural greenhouse gas effect. It is worthwhile to compare methanogen from “energy-saving” animal (yak and normal animal (cattle in order to investigate the link between methanogen structure and low methane production. Results Diversity of methanogens from the yak and cattle rumen was investigated by analysis of 16S rRNA gene sequences from rumen digesta samples from four yaks (209 clones and four cattle (205 clones from the Qinghai-Tibetan Plateau area (QTP. Overall, a total of 414 clones (i.e. sequences were examined and assigned to 95 operational taxonomic units (OTUs using MOTHUR, based upon a 98% species-level identity criterion. Forty-six OTUs were unique to the yak clone library and 34 OTUs were unique to the cattle clone library, while 15 OTUs were found in both libraries. Of the 95 OTUs, 93 putative new species were identified. Sequences belonging to the Thermoplasmatales-affiliated Linage C (TALC were found to dominate in both libraries, accounting for 80.9% and 62.9% of the sequences from the yak and cattle clone libraries, respectively. Sequences belonging to the Methanobacteriales represented the second largest clade in both libraries. However, Methanobrevibacter wolinii (QTPC 110 was only found in the cattle library. The number of clones from the order Methanomicrobiales was greater in cattle than in the yak clone library. Although the Shannon index value indicated similar diversity between the two libraries, the Libshuff analysis indicated that the methanogen community structure of the yak was significantly different than those from cattle. Conclusion This study revealed for the first time the molecular diversity of methanogen community in yaks and cattle in Qinghai-Tibetan Plateau area in China. From the analysis, we conclude that yaks have a unique rumen microbial ecosystem that is significantly different

  18. Methane production potential and microbial community structure for different forest soils

    Science.gov (United States)

    Matsumoto, Y.; Ueyama, M.; Kominami, Y.; Endo, R.; Tokumoto, H.; Hirano, T.; Takagi, K.; Takahashi, Y.; Iwata, H.; Harazono, Y.

    2017-12-01

    Forest soils are often considered as a methane (CH4) sink, but anaerobic microsites potentially decrease the sink at the ecosystem scale. In this study, we measured biological CH4 production potential of soils at various ecosystems, including upland forests, a lowland forest, and a bog, and analyzed microbial community structure using 16S ribosomal RNA (rRNA) genes. Three different types of soil samples (upland, bank of the stream, and center of the stream) were collected from Yamashiro forest meteorology research site (YMS) at Kyoto, Japan, on 11 May 2017. The soils were incubated at dark and anaerobic conditions under three different temperatures (37°C, 25°C, and 10°C) from 9 June 2017. The upland soils emitted CH4 with largest yields among the three soils at 37°C and 25°C, although no CH4 emission was observed at 10°C. For all temperature ranges, the emission started to increase with a 14- to 20-days lag after the start of the incubation. The lag indicates a slow transition to anaerobic conditions; as dissolved oxygen in water decreased, the number and/or activity of anaerobic bacteria like methanogens increased. The soils at the bank and center of the stream emitted CH4 with smaller yields than the upland soils in the three temperature ranges. The microbial community analyses indicate that methanogenic archaea presented at the three soils including the aerobic upland soil, but compositions of methanogenic archaea were different among the soils. In upland soils, hydrogenotrophic methanogens, such as Methanobacterium and Methanothermobacter, consisted almost all of the total methanogen detected. In the bank and center of the stream, soils contained approximately 10-25% of acetoclastic methanogens, such as Methanosarcina and Methanosaeta, among the total methanogen detected. Methanotrophs, a genus of Methanobacteriaceae, was appeared in the all types of soils. We will present results from same incubation and 16S rRNA analyses for other ecosystems, including

  19. Molecular Genetic Diversity and Quantitation of Methanogen in Ruminal Fluid of Buffalo (Bubalus bubalis Fed Ration (Wheat Straw and Concentrate Mixture Diet

    Directory of Open Access Journals (Sweden)

    K. M. Singh

    2013-01-01

    Full Text Available High roughage diet causes more methane emissions; however, the total methanogen abundance is not influenced by roughage proportion. Technologies to reduce methane emissions are lacking, and development of inhibitors and vaccines that mitigate rumen-derived methane by targeting methanogens relies on present knowledge of the methanogens. In this work, we have investigated molecular diversity of rumen methanogens of Surti buffalo. DNA from rumen fluid was extracted, and 16S rRNA encoding genes were amplified using methanogen specific primer to generate 16S rDNA clone libraries. Seventy-six clones were randomly selected and analysed by RFLP resulting in 21 operational taxonomic units (OTUs. BLAST analysis with available sequences in database revealed sequences of 13 OTUs (55 clones showing similarity with Methanomicrobium sp, 3 OTUs (15 clones with Methanobrevibacter sp. The remaining 5 OTUs (6 clones belonged to uncultured archaea. The phylogenetic analysis indicated that methanogenic communities found in the library were clustered in the order of Methanomicrobiales (18 OTUs and Methanobacteriales (3 OTUs. The population of Methanomicrobiales, Methanobacteriales, and Methanococcales were also observed, accounting for 1.94%, 0.72%, and 0.47% of total archaea, respectively.

  20. Analysis of alkane-dependent methanogenic community derived from production water of a high-temperature petroleum reservoir

    Energy Technology Data Exchange (ETDEWEB)

    Mbadinga, Serge Maurice; Li, Kai-Ping; Zhou, Lei; Wang, Li-Ying; Yang, Shi-Zhong; Liu, Jin-Feng; Mu, Bo-Zhong [East China Univ. of Science and Technology, Shanghai (China). State Key Lab. of Bioreactor Engineering and Inst. of Applied Chemistry; Gu, Ji-Dong [Hong Kong Univ. (China). School of Biological Sciences

    2012-10-15

    Microbial assemblage in an n-alkanes-dependent thermophilic methanogenic enrichment cultures derived from production waters of a high-temperature petroleum reservoir was investigated in this study. Substantially higher amounts of methane were generated from the enrichment cultures incubated at 55 C for 528 days with a mixture of long-chain n-alkanes (C{sub 15}-C{sub 20}). Stoichiometric estimation showed that alkanes-dependent methanogenesis accounted for about 19.8% of the total amount of methane expected. Hydrogen was occasionally detected together with methane in the gas phase of the cultures. Chemical analysis of the liquid cultures resulted only in low concentrations of acetate and formate. Phylogenetic analysis of the enrichment revealed the presence of several bacterial taxa related to Firmicutes, Thermodesulfobiaceae, Thermotogaceae, Nitrospiraceae, Dictyoglomaceae, Candidate division OP8 and others without close cultured representatives, and Archaea predominantly related to uncultured members in the order Archaeoglobales and CO{sub 2}-reducing methanogens. Screening of genomic DNA retrieved from the alkanes-amended enrichment cultures also suggested the presence of new alkylsuccinate synthase alpha-subunit (assA) homologues. These findings suggest the presence of poorly characterized (putative) anaerobic n-alkanes degraders in the thermophilic methanogenic enrichment cultures. Our results indicate that methanogenesis of alkanes under thermophilic condition is likely to proceed via syntrophic acetate and/or formate oxidation linked with hydrogenotrophic methanogenesis. (orig.)

  1. Performance of thermophilic anaerobic digesters using inoculum mixes with enhanced methanogenic diversity

    KAUST Repository

    Ghanimeh, Sophia

    2017-05-30

    BACKGROUND Reportedly, various mixes of seeds were quasi-randomly selected to startup anaerobic digesters. In contrast, this study examines the impact of inoculating thermophilic anaerobic digesters with a designed mix of non-acclimated seeds based on their methanogen composition, using Quantitative Polymerase Chain Reaction (QPCR) of 16S rRNA gene, to achieve high abundance and diversity of methanogens. RESULTS Based on QPCR results, two seed mixes were selected to inoculate two anaerobic digesters: digester (A) was inoculated with a control seed consisting of digestate, manure, and activated sludge; and digester (B) was inoculated with a further methanogen-enriched seed consisting of the control seed with added compost and leachate. Both seed combinations yielded a balanced microflora that is able to achieve a successful startup. However, upon reaching steady state, digester B exhibited lower propionate levels, resulting in lower VFA concentration and increased buffering capacity, indicating greater stability. Acetotrophs and hydrogenotrophs were dominated by Methanosarcinaceae and Methanobacteriales, respectively, in both digesters, exhibiting an average ratio of 66-to-34% in A and 76-to-24% in B during steady state. CONCLUSION The inoculation strategy in digester B resulted in improved stability, lower propionate concentration and 10% higher relative abundance of acetotrophs.

  2. Metabolic interactions in methanogenic and sulfate-reducing bioreactors

    NARCIS (Netherlands)

    Stams, A.J.M.; Plugge, C.M.; Bok, de F.A.M.; Houten, van B.H.G.W.; Lens, P.N.L.; Dijkman, H.; Weijma, J.

    2005-01-01

    In environments where the amount of electron acceptors is insufficient for complete breakdown of organic matter, methane is formed as the major reduced end product. In such methanogenic environments organic acids are degraded by syntrophic consortia of acetogenic bacteria and methanogenic archaea.

  3. Interspecies electron transfer in methanogenic propionate degrading consortia

    NARCIS (Netherlands)

    Bok, de F.A.M.; Plugge, C.M.; Stams, A.J.M.

    2004-01-01

    Propionate is a key intermediate in the conversion of complex organic matter under methanogenic conditions. Oxidation of this compound requires obligate syntrophic consortia of acetogenic proton- and bicarbonate reducing bacteria and methanogenic archaea. Although H-2 acts as an electron-carrier in

  4. Effects of biopretreatment on pyrolysis behaviors of corn stalk by methanogen.

    Science.gov (United States)

    Wang, Tipeng; Ye, Xiaoning; Yin, Jun; Lu, Qiang; Zheng, Zongming; Dong, Changqing

    2014-07-01

    The study investigated the effects of methanogen pretreatment on pyrolysis behaviors of corn stalk (CS) by using Py-GC/MS analysis and thermogravimetric analysis. Results indicated that biopretreatment changed considerably the pyrolysis behaviors of CS from four weight loss stages to two weight loss stages. Increasing biopretreatment time from 5 days to 25 days enhanced the kinds and contents of chemicals in volatile products. In pyrolysis products, the contents of sugars, linear ketones and furans decreased from 1.43%, 12.60% and 7.38% to 1.25%, 10.22% and 3.25%, respectively, and the contents of phenols increased from 15.08% to 27.84%. The most content change from 6.83% to 13.63% indicated that methanogen pretreatment improved the pyrolysis selectivity of CS to product the 4-VP, but it was disadvantageous to 5-hydroxymethyl furfural, levoglucose and furfural. The changes of chemical compositions and structure of CS after biopretreatment were the main reason of the differences. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Phenotypic properties and microbial diversity of methanogenic granules from a full-scale UASB reactor treating brewery wastewater

    NARCIS (Netherlands)

    Diaz, E.E.; Stams, A.J.M.; Amils, R.; Sanz, J.L.

    2006-01-01

    Methanogenic granules from an anaerobic bioreactor that treated wastewater of a beer brewery consisted of different morphological types of granules. In this study, the microbial compositions of the different granules were analyzed by molecular microbiological techniques: cloning, denaturing gradient

  6. Changes in Rumen Microbial Community Composition during Adaption to an In Vitro System and the Impact of Different Forages.

    Directory of Open Access Journals (Sweden)

    Melanie B Lengowski

    Full Text Available This study examined ruminal microbial community composition alterations during initial adaption to and following incubation in a rumen simulation system (Rusitec using grass or corn silage as substrates. Samples were collected from fermenter liquids at 0, 2, 4, 12, 24, and 48 h and from feed residues at 0, 24, and 48 h after initiation of incubation (period 1 and on day 13 (period 2. Microbial DNA was extracted and real-time qPCR was used to quantify differences in the abundance of protozoa, methanogens, total bacteria, Fibrobacter succinogenes, Ruminococcus albus, Ruminobacter amylophilus, Prevotella bryantii, Selenomonas ruminantium, and Clostridium aminophilum. We found that forage source and sampling time significantly influenced the ruminal microbial community. The gene copy numbers of most microbial species (except C. aminophilum decreased in period 1; however, adaption continued through period 2 for several species. The addition of fresh substrate in period 2 led to increasing copy numbers of all microbial species during the first 2-4 h in the fermenter liquid except protozoa, which showed a postprandial decrease. Corn silage enhanced the growth of R. amylophilus and F. succinogenes, and grass silage enhanced R. albus, P. bryantii, and C. aminophilum. No effect of forage source was detected on total bacteria, protozoa, S. ruminantium, or methanogens or on total gas production, although grass silage enhanced methane production. This study showed that the Rusitec provides a stable system after an adaption phase that should last longer than 48 h, and that the forage source influenced several microbial species.

  7. Methanogenic Conversion of CO2 Into CH4

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, S.H., Ferry, J.G., Schoell, M.

    2012-05-06

    This SBIR project evaluated the potential to remediate geologic CO2 sequestration sites into useful methane gas fields by application of methanogenic bacteria. Such methanogens are present in a wide variety of natural environments, converting CO2 into CH4 under natural conditions. We conclude that the process is generally feasible to apply within many of the proposed CO2 storage reservoir settings. However, extensive further basic R&D still is needed to define the precise species, environments, nutrient growth accelerants, and economics of the methanogenic process. Consequently, the study team does not recommend Phase III commercial application of the technology at this early phase.

  8. Variation of carbon isotope fractionation in hydrogenotrophic methanogenic microbial cultures and environmental samples at different energy status

    NARCIS (Netherlands)

    Penning, H.; Plugge, C.M.; Galand, P.E.; Conrad, R.

    2005-01-01

    Methane is a major product of anaerobic degradation of organic matter and an important greenhouse gas. Its stable carbon isotope composition can be used to reveal active methanogenic pathways, if associated isotope fractionation factors are known. To clarify the causes that lead to the wide

  9. Methanogenic Transformation of Methylfurfural Compounds to Furfural

    OpenAIRE

    Boopathy, R.

    1996-01-01

    The metabolic conversion of 5-methylfurfural and 2-methylfurfural to furfural by a methanogenic bacterium, Methanococcus sp. strain B, was studied. This bacterium was found to use methylfurfural compounds as a growth substrate and to convert them stoichiometrically to furfural. For every mole of methylfurfurals metabolized, almost 1 mol of furfural and 0.7 mol of methane were produced. Several methanogenic bacteria did not carry out this conversion. The metabolic conversion of methylfurfurals...

  10. Methane production from coal by a single methanogen

    Science.gov (United States)

    Sakata, S.; Mayumi, D.; Mochimaru, H.; Tamaki, H.; Yamamoto, K.; Yoshioka, H.; Suzuki, Y.; Kamagata, Y.

    2017-12-01

    Previous geochemical studies indicate that biogenic methane greatly contributes to the formation of coalbed methane (CBM). It is unclear, however, what part of coal is used for the methane production and what types of microbes mediate the process. Here we hypothesized that methylotrophic methanogens use methoxylated aromatic compounds (MACs) derived from lignin. We incubated 11 species of methanogens belonging to order Methanosarcinales with 7 types of MACs. Two strains of methanogens, i.e., Methermicoccus shengliensis AmaM and ZC-1, produced methane from the MACs. In fact, these methanogens used over 30 types of commercially available MACs in addition to methanol and methylamines. To date, it is widely believed that methanogens use very limited number of small compounds such as hydrogen plus carbon dioxide, acetate, and methanol, and only three methanogenic pathways are recognized accordingly. Here, in contrast, two Methermicoccus strains used many types of MACs. We therefore propose this "methoxydotrophic" process as the fourth methanogenic pathway. Incubation of AmaM with 2-methoxybenzoate resulted in methanogenesis associated with the stoichiometric production of 2-hydroxybenzoate. Incubation with 2-methoxy-[7-13C] benzoate and with [13C] bicarbonate indicated that two thirds of methane carbon derived from the methoxy group and one third from CO2. Furthermore, incubation with [2-13C] acetate resulted in significant increases of 13C in both methane and CO2. These results suggest the occurrence of O-demethylation, CO2 reduction and acetyl-CoA metabolism in the methoxydotrophic methanogenesis. Furthermore, incubation of AmaM with lignite, subbituminous or bituminous coals in the bicarbonate-buffered media revealed that AmaM produced methane directly from coals via the methoxydotrophic pathway. Although 4 types of MACs were detected in the coal media in addition to methanol and methylamines, their total concentrations were too low to account for the methane

  11. The response of archaeal species to seasonal variables in a subtropical aerated soil: insight into the low abundant methanogens.

    Science.gov (United States)

    Xie, Wei; Jiao, Na; Ma, Cenling; Fang, Sa; Phelps, Tommy J; Zhu, Ruixin; Zhang, Chuanlun

    2017-08-01

    Archaea are cosmopolitan in aerated soils around the world. While the dominance of Thaumarchaeota has been reported in most soils, the methanogens are recently found to be ubiquitous but with low abundances in the aerated soil globally. However, the seasonal changes of Archaea community in the aerated soils are still in the mist. In this study, we investigated the change of Archaea in the context of environmental variables over a period of 12 months in a subtropical soil on the Chongming Island, China. The results showed that Nitrososphaera spp. were the dominant archaeal population while the methanogens were in low proportions but highly diverse (including five genera: Methanobacterium, Methanocella, Methanosaeta, Methanosarcina, and Methanomassiliicoccus) in the aerated soil samples determined by high throughput sequencing. A total of 126 LSA correlations were found in the dataset including all the 72 archaeal OTUs and 8 environmental factors. A significance index defined as the pagerank score of each OTU divided by its relative abundance was used to evaluate the significance of each OTU. The results showed that five out of 17 methanogen OTUs were significantly positively correlated with temperature, suggesting those methanogens might increase with temperature rather than being dormant in the aerated soils. Given the metabolic response of methanogens to temperature under aerated soil conditions, their contribution to the global methane cycle warrants evaluation.

  12. Studying gene regulation in methanogenic archaea.

    Science.gov (United States)

    Rother, Michael; Sattler, Christian; Stock, Tilmann

    2011-01-01

    Methanogenic archaea are a unique group of strictly anaerobic microorganisms characterized by their ability, and dependence, to convert simple C1 and C2 compounds to methane for growth. The major models for studying the biology of methanogens are members of the Methanococcus and Methanosarcina species. Recent development of sophisticated tools for molecular analysis and for genetic manipulation allows investigating not only their metabolism but also their cell cycle, and their interaction with the environment in great detail. One aspect of such analyses is assessment and dissection of methanoarchaeal gene regulation, for which, at present, only a handful of cases have been investigated thoroughly, partly due to the great methodological effort required. However, it becomes more and more evident that many new regulatory paradigms can be unraveled in this unique archaeal group. Here, we report both molecular and physiological/genetic methods to assess gene regulation in Methanococcus maripaludis and Methanosarcina acetivorans, which should, however, be applicable for other methanogens as well. Copyright © 2011 Elsevier Inc. All rights reserved.

  13. Ammonia effect on hydrogenotrophic methanogens and syntrophic acetate oxidizing bacteria

    DEFF Research Database (Denmark)

    Wang, Han; Fotidis, Ioannis; Angelidaki, Irini

    Substrates that contain high ammonia levels can cause inhibition on anaerobic digestion process and unstable biogas production. The aim of the current study was to assess the effects of different ammonia levels on pure strains of (syntrophic acetate oxidizing) SAO bacteria and hydrogenotrophic...... methanogens. Two pure strains of hydrogenotrophic methanogens (i.e: Methanoculleus bourgensis and Methanoculleus thermophiles) and two pure strains of SAO bacteria (i.e: Tepidanaerobacter acetatoxydans and Thermacetogenium phaeum) were inoculated under four different ammonia (0.26, 3, 5 and 7g NH4+-N......, the total incubation periods of hydrogenotrophic methanogens were significantly shorter compared to the SAO bacteria incubation periods. Thus, it seems that hydrogenotrophic methanogens could be equally, if not more, tolerant to high ammonia levels compared to SAO bacteria....

  14. Vaccination of Sheep with a Methanogen Protein Provides Insight into Levels of Antibody in Saliva Needed to Target Ruminal Methanogens.

    Directory of Open Access Journals (Sweden)

    Supatsak Subharat

    Full Text Available Methane is produced in the rumen of ruminant livestock by methanogens and is a major contributor to agricultural greenhouse gases. Vaccination against ruminal methanogens could reduce methane emissions by inducing antibodies in saliva which enter the rumen and impair ability of methanogens to produce methane. Presently, it is not known if vaccination can induce sufficient amounts of antibody in the saliva to target methanogen populations in the rumen and little is known about how long antibody in the rumen remains active. In the current study, sheep were vaccinated twice at a 3-week interval with a model methanogen antigen, recombinant glycosyl transferase protein (rGT2 formulated with one of four adjuvants: saponin, Montanide ISA61, a chitosan thermogel, or a lipid nanoparticle/cationic liposome adjuvant (n = 6/formulation. A control group of sheep (n = 6 was not vaccinated. The highest antigen-specific IgA and IgG responses in both saliva and serum were observed with Montanide ISA61, which promoted levels of salivary antibodies that were five-fold higher than the second most potent adjuvant, saponin. A rGT2-specific IgG standard was used to determine the level of rGT2-specific IgG in serum and saliva. Vaccination with GT2/Montanide ISA61 produced a peak antibody concentration of 7 × 1016 molecules of antigen-specific IgG per litre of saliva, and it was estimated that in the rumen there would be more than 104 molecules of antigen-specific IgG for each methanogen cell. Both IgG and IgA in saliva were shown to be relatively stable in the rumen. Salivary antibody exposed for 1-2 hours to an in vitro simulated rumen environment retained approximately 50% of antigen-binding activity. Collectively, the results from measuring antibody levels and stablility suggest a vaccination-based mitigation strategy for livestock generated methane is in theory feasible.

  15. Effects of cattle husbandry on abundance and activity of methanogenic archaea in upland soils.

    Science.gov (United States)

    Radl, Viviane; Gattinger, Andreas; Chronáková, Alica; Nemcová, Anna; Cuhel, Jiri; Simek, Miloslav; Munch, Jean Charles; Schloter, Michael; Elhottová, Dana

    2007-09-01

    In the present study, we tested the hypothesis that animal treading associated with a high input of organic matter would favour methanogenesis in soils used as overwintering pasture. Hence, methane emissions and methanogen populations were examined at sections with different degree of cattle impact in a Farm in South Bohemia, Czech Republic. In spring, methane emission positively corresponded to the gradient of animal impact. Applying phospholipid etherlipid analysis, the highest archaeal biomass was found in section severe impact (SI), followed by moderate impact (MI) and no impact. The same trend was observed for the methanogens as showed by real-time quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes. The detection of monounsaturated isoprenoid side chain hydrocarbons (i20:1) indicated the presence of acetoclastic methanogens in the cattle-impacted sites. This result was corroborated by the phylogenetic analysis of mcrA gene sequences obtained from section SI, which showed that 33% of the analysed clones belonged to the genus Methanosarcina. The majority of the sequenced clones (41%) showed close affiliations with uncultured rumen archaeons. This leads to the assumption that a substantial part of the methanogenic community in plot SI derived from the grazing cattle itself. Compared to the spring sampling, in autumn, a significant reduction in archaeal biomass and number of copies of mcrA genes was observed mainly for section MI. It can be concluded that after 5 months without cattle impact, the severely impact section maintained its methane production potential, whereas the methane production potential under moderate impact returned to background values.

  16. Prokaryotic diversity, composition structure, and phylogenetic analysis of microbial communities in leachate sediment ecosystems.

    Science.gov (United States)

    Liu, Jingjing; Wu, Weixiang; Chen, Chongjun; Sun, Faqian; Chen, Yingxu

    2011-09-01

    In order to obtain insight into the prokaryotic diversity and community in leachate sediment, a culture-independent DNA-based molecular phylogenetic approach was performed with archaeal and bacterial 16S rRNA gene clone libraries derived from leachate sediment of an aged landfill. A total of 59 archaeal and 283 bacterial rDNA phylotypes were identified in 425 archaeal and 375 bacterial analyzed clones. All archaeal clones distributed within two archaeal phyla of the Euryarchaeota and Crenarchaeota, and well-defined methanogen lineages, especially Methanosaeta spp., are the most numerically dominant species of the archaeal community. Phylogenetic analysis of the bacterial library revealed a variety of pollutant-degrading and biotransforming microorganisms, including 18 distinct phyla. A substantial fraction of bacterial clones showed low levels of similarity with any previously documented sequences and thus might be taxonomically new. Chemical characteristics and phylogenetic inferences indicated that (1) ammonium-utilizing bacteria might form consortia to alleviate or avoid the negative influence of high ammonium concentration on other microorganisms, and (2) members of the Crenarchaeota found in the sediment might be involved in ammonium oxidation. This study is the first to report the composition of the microbial assemblages and phylogenetic characteristics of prokaryotic populations extant in leachate sediment. Additional work on microbial activity and contaminant biodegradation remains to be explored.

  17. Simultaneous production of acetate and methane from glycerol by selective enrichment of hydrogenotrophic methanogens in extreme-thermophilic (70 °C) mixed culture fermentation

    International Nuclear Information System (INIS)

    Zhang, Fang; Zhang, Yan; Chen, Yun; Dai, Kun; Loosdrecht, Mark C.M. van; Zeng, Raymond J.

    2015-01-01

    Highlights: • Simultaneous production of acetate and methane from glycerol was investigated. • Acetate accounted for more than 90% of metabolites in liquid solutions. • The maximum concentration of acetate was above 13 g/L. • 93% of archaea were hydrogenotrophic methanogens. • Thermoanaerobacter was main bacterium and its percentage was 92%. - Abstract: The feasibility of simultaneous production of acetate and methane from glycerol was investigated by selective enrichment of hydrogenotrophic methanogens in an extreme-thermophilic (70 °C) fermentation. Fed-batch experiments showed acetate was produced at the concentration up to 13.0 g/L. A stable operation of the continuous stirred tank reactor (CSTR) was reached within 100 days. Acetate accounted for more than 90 w/w% of metabolites in the fermentation liquid. The yields of methane and acetate were close to the theoretical yields with 0.74–0.80 mol-methane/mol-glycerol and 0.63–0.70 mol-acetate/mol-glycerol. The obtained microbial community was characterized. Hydrogenotrophic methanogens, mainly Methanothermobacter thermautotrophicus formed 93% of the methanogenogenic community. This confirms that a high temperature (70 °C) could effectively select for hydrogenotrophic methanogenic archaea. Thermoanaerobacter spp. was the main bacterium forming 91.5% of the bacterial population. This work demonstrated the conversion of the byproduct of biodiesel production, glycerol, to acetate as a chemical and biogas for energy generation

  18. Pyridine-type alkaloid composition affects bacterial community composition of floral nectar.

    Science.gov (United States)

    Aizenberg-Gershtein, Yana; Izhaki, Ido; Santhanam, Rakesh; Kumar, Pavan; Baldwin, Ian T; Halpern, Malka

    2015-06-30

    Pyridine-type alkaloids are most common in Nicotiana species. To study the effect of alkaloid composition on bacterial community composition in floral nectar, we compared the nicotine-rich wild type (WT) N. attenuata, the nicotine biosynthesis-silenced N. attenuata that was rich in anatabine and the anabasine-rich WT N. glauca plants. We found that the composition of these secondary metabolites in the floral nectar drastically affected the bacterial community richness, diversity and composition. Significant differences were found between the bacterial community compositions in the nectar of the three plants with a much greater species richness and diversity in the nectar from the transgenic plant. The highest community composition similarity index was detected between the two wild type plants. The different microbiome composition and diversity, caused by the different pyridine-type alkaloid composition, could modify the nutritional content of the nectar and consequently, may contribute to the change in the nectar consumption and visitation. These may indirectly have an effect on plant fitness.

  19. Metabolic interactions between methanogenic consortia and anaerobic respiring bacteria

    DEFF Research Database (Denmark)

    Stams, A.J.; Oude Elferink, S.J.; Westermann, Peter

    2003-01-01

    Most types of anaerobic respiration are able to outcompete methanogenic consortia for common substrates if the respective electron acceptors are present in sufficient amounts. Furthermore, several products or intermediate compounds formed by anaerobic respiring bacteria are toxic to methanogenic...... consortia. Despite the potentially adverse effects, only few inorganic electron acceptors potentially utilizable for anaerobic respiration have been investigated with respect to negative interactions in anaerobic digesters. In this chapter we review competitive and inhibitory interactions between anaerobic...... respiring populations and methanogenic consortia in bioreactors. Due to the few studies in anaerobic digesters, many of our discussions are based upon studies of defined cultures or natural ecosystems...

  20. A new methanogen "Methanobrevibacter massiliense" isolated in a case of severe periodontitis.

    Science.gov (United States)

    Huynh, Hong T T; Pignoly, Marion; Drancourt, Michel; Aboudharam, Gérard

    2017-12-01

    A few methanogens have been previously recovered from periodontitis lesions, yet their repertoire may not be completed. We recovered a previously unreported methanogen species in this situation. A 64-year-old Caucasian woman was diagnosed with chronic, severe generalized periodontitis. In the presence of negative controls, an 18-month culture of periodontal pockets in anaerobe Hungate tube yielded "Methanobrevibacter massiliense" and Pyramidobacter piscolens. This case report provides evidence of the symbiotic strategy deployed by the methanogens and the anaerobes, and reports the first culture of a new methanogen, "M. massiliense".

  1. Identification of metabolically active methanogens in anaerobic digester by DNA Stable-Isotope Probing using 13C-acetate

    Directory of Open Access Journals (Sweden)

    V. Gowdaman

    2015-04-01

    Full Text Available Anaerobic digestion is gaining enormous attention due to the ability to covert organic wastes into biogas, an alternative sustainable energy. Methanogenic community plays a significant role in biogas production and also for proficient functioning of the anaerobic digester. Therefore, this study was carried out to investigate the methanogen diversity of a food waste anaerobic digester. After endogenous respiration, the digester samples were supplemented with isotopes of acetate to enrich methanogen population, and were analyzed using DNA-SIP (Stable-Isotope Probing. Following separation and fractionation of heavy (13C and light (12C DNA, PCR amplification was carried out using archaeal 16S rRNA gene followed by DGGE analysis. Sequencing of the prominent DGGE bands revealed the dominance of Methanocorpusculum labreanum species belonging to hydrogenotrophic Methanomicrobiales, which can produce methane in the presence of H2/CO2 and requires acetate for its growth. This is the first instance where Methanocorpusculum labreanum is being reported as a dominant species in an anaerobic digester operative on food waste.

  2. 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.

  3. 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.

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

    International Nuclear Information System (INIS)

    Bomberg, M.; Nyyssoenen, M.; Itaevaara, M.

    2012-06-01

    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

  5. ELISA techniques for the determination of methanogenic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Bryniok, D; Troesch, W [Fraunhofer-Institut fuer Grenzflaechen- und Bioverfahrenstechnik (IGB), Stuttgart (Germany, F.R.)

    1989-12-01

    Easy-to-handle enzyme-linked immunosorbent assay (ELISA) techniques have been developed suitable for quantitative species-specific determination of very low numbers of methanogens in complex bacterial populations. The amount and the distribution of different species of methanogens in anaerobic digestors is a reflection of the functional status of the degradation process; this can be recognized with these tests and hence may be used for process control. (orig.).

  6. Ammonia effect on hydrogenotrophic methanogens and syntrophic acetate oxidizing bacteria

    DEFF Research Database (Denmark)

    Wang, Han; Fotidis, Ioannis; Angelidaki, Irini

    2015-01-01

    tested in the study; which is contradicting to the general belief that thermophilic methanogens are more vulnerable to high ammonia loads compared to mesophilic. This unexpected finding underlines the fact that the complete knowledge of ammonia inhibition effect on hydrogenotrophic methanogens is still...

  7. Analysis of methanogenic activity in a thermophilic-dry anaerobic reactor: Use of fluorescent in situ hybridization

    International Nuclear Information System (INIS)

    Montero, B.; Garcia-Morales, J.L.; Sales, D.; Solera, R.

    2009-01-01

    Methanogenic activity in a thermophilic-dry anaerobic reactor was determined by comparing the amount of methane generated for each of the organic loading rates with the size of the total and specific methanogenic population, as determined by fluorescent in situ hybridization. A high correlation was evident between the total methanogenic activity and retention time [-0.6988Ln(x) + 2.667] (R 2 0.8866). The total methanogenic activity increased from 0.04 x 10 -8 mLCH 4 cell -1 day -1 to 0.38 x 10 -8 mLCH 4 cell -1 day -1 while the retention time decreased, augmenting the organic loading rates. The specific methanogenic activities of H 2 -utilizing methanogens and acetate-utilizing methanogens increased until they stabilised at 0.64 x 10 -8 mLCH 4 cell -1 day -1 and 0.33 x 10 -8 mLCH 4 cell -1 day -1 , respectively. The methanogenic activity of H 2 -utilizing methanogens was higher than acetate-utilizing methanogens, indicating that maintaining a low partial pressure of hydrogen does not inhibit the acetoclastic methanogenesis or the anaerobic process

  8. Reduction of Fe(III) oxides by phylogenetically and physiologically diverse thermophilic methanogens.

    Science.gov (United States)

    Yamada, Chihaya; Kato, Souichiro; Kimura, Satoshi; Ishii, Masaharu; Igarashi, Yasuo

    2014-09-01

    Three thermophilic methanogens (Methanothermobacter thermautotrophicus, Methanosaeta thermophila, and Methanosarcina thermophila) were investigated for their ability to reduce poorly crystalline Fe(III) oxides (ferrihydrite) and the inhibitory effects of ferrihydrite on their methanogenesis. This study demonstrated that Fe(II) generation from ferrihydrite occurs in the cultures of the three thermophilic methanogens only when H2 was supplied as the source of reducing equivalents, even in the cultures of Mst. thermophila that do not grow on and produce CH4 from H2/CO2. While supplementation of ferrihydrite resulted in complete inhibition or suppression of methanogenesis by the thermophilic methanogens, ferrihydrite reduction by the methanogens at least partially alleviates the inhibitory effects. Microscopic and crystallographic analyses on the ferrihydrite-reducing Msr. thermophila cultures exhibited generation of magnetite on its cell surfaces through partial reduction of ferrihydrite. These findings suggest that at least certain thermophilic methanogens have the ability to extracellularly transfer electrons to insoluble Fe(III) compounds, affecting their methanogenic activities, which would in turn have significant impacts on materials and energy cycles in thermophilic anoxic environments. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  9. Stable acetate production in extreme-thermophilic (70°C) mixed culture fermentation by selective enrichment of hydrogenotrophic methanogens

    Science.gov (United States)

    Zhang, Fang; Zhang, Yan; Ding, Jing; Dai, Kun; van Loosdrecht, Mark C. M.; Zeng, Raymond J.

    2014-06-01

    The control of metabolite production is difficult in mixed culture fermentation. This is particularly related to hydrogen inhibition. In this work, hydrogenotrophic methanogens were selectively enriched to reduce the hydrogen partial pressure and to realize efficient acetate production in extreme-thermophilic (70°C) mixed culture fermentation. The continuous stirred tank reactor (CSTR) was stable operated during 100 days, in which acetate accounted for more than 90% of metabolites in liquid solutions. The yields of acetate, methane and biomass in CSTR were 1.5 +/- 0.06, 1.0 +/- 0.13 and 0.4 +/- 0.05 mol/mol glucose, respectively, close to the theoretical expected values. The CSTR effluent was stable and no further conversion occurred when incubated for 14 days in a batch reactor. In fed-batch experiments, acetate could be produced up to 34.4 g/L, significantly higher than observed in common hydrogen producing fermentations. Acetate also accounted for more than 90% of soluble products formed in these fed-batch fermentations. The microbial community analysis revealed hydrogenotrophic methanogens (mainly Methanothermobacter thermautotrophicus and Methanobacterium thermoaggregans) as 98% of Archaea, confirming that high temperature will select hydrogenotrophic methanogens over aceticlastic methanogens effectively. This work demonstrated a potential application to effectively produce acetate as a value chemical and methane as an energy gas together via mixed culture fermentation.

  10. Magnetite production and transformation in the methanogenic consortia from coastal riverine sediments.

    Science.gov (United States)

    Zheng, Shiling; Wang, Bingchen; Liu, Fanghua; Wang, Oumei

    2017-11-01

    Minerals that contain ferric iron, such as amorphous Fe(III) oxides (A), can inhibit methanogenesis by competitively accepting electrons. In contrast, ferric iron reduced products, such as magnetite (M), can function as electrical conductors to stimulate methanogenesis, however, the processes and effects of magnetite production and transformation in the methanogenic consortia are not yet known. Here we compare the effects on methanogenesis of amorphous Fe (III) oxides (A) and magnetite (M) with ethanol as the electron donor. RNA-based terminal restriction fragment length polymorphism with a clone library was used to analyse both bacterial and archaeal communities. Iron (III)-reducing bacteria including Geobacteraceae and methanogens such as Methanosarcina were enriched in iron oxide-supplemented enrichment cultures for two generations with ethanol as the electron donor. The enrichment cultures with A and non-Fe (N) dominated by the active bacteria belong to Veillonellaceae, and archaea belong to Methanoregulaceae and Methanobacteriaceae, Methanosarcinaceae (Methanosarcina mazei), respectively. While the enrichment cultures with M, dominated by the archaea belong to Methanosarcinaceae (Methanosarcina barkeri). The results also showed that methanogenesis was accelerated in the transferred cultures with ethanol as the electron donor during magnetite production from A reduction. Powder X-ray diffraction analysis indicated that magnetite was generated from microbial reduction of A and M was transformed into siderite and vivianite with ethanol as the electron donor. Our data showed the processes and effects of magnetite production and transformation in the methanogenic consortia, suggesting that significantly different effects of iron minerals on microbial methanogenesis in the iron-rich coastal riverine environment were present.

  11. Taxonomic, phylogenetic, and ecological diversity of methanogenic Archaea

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, J.-L.; Ollivier, B. [Universite de Provence, Marseille (France). Laboratoire de Microbiologist; Patel, B.K.C. [Griffith University, Brisbane (Australia). Microbial Discovery Research Unit

    2000-07-01

    Methanogens are strict anaerobes which share a complex biochemistry for methane synthesis as part of their energy metabolism. The discovery of the unique biochemical and genetic properties of these organisms led to the concept of Archaebacteria at the end of the seventies and the proposal in 1990 for the domain Archaea. A number of studies have provided evidence that they are of economic value. The successive petroleum crisis since 1973 has led to great interest in alternative forms of energy, including recovery of methane via anaerobic digestion of wastes. Improvements in the design of digestors have been made possible by advances in understanding the ecology and physiology of methanogens. In the cattle industry, the knowledge of the fermentation processes in the rumen demonstrated a net loss of energy via the methanogenesis, and inhibitors such as Rumensin have been developed to enhance meat yields. Oil companies try to distinguish between natural gas produced by methanogens or by the thermocatalytic reactions associated with petroleum generation. Finally, studies on the global distribution of methane in the earth's atmosphere are increasing due to the sudden awareness of its possible role in the enhancement of the greenhouse effect from CO-2 accumulation, and on the reversal of stratospheric ozone depletion. This paper summarizes the recent knowledge of methanogenic Archaea with emphasis on their taxonomy and ecology. (author)

  12. Characterization of bacterial and archaeal communities in air-cathode microbial fuel cells, open circuit and sealed-off reactors

    KAUST Repository

    Chehab, Noura A.

    2013-06-18

    A large percentage of organic fuel consumed in a microbial fuel cell (MFC) is lost as a result of oxygen transfer through the cathode. In order to understand how this oxygen transfer affects the microbial community structure, reactors were operated in duplicate using three configurations: closed circuit (CC; with current generation), open circuit (OC; no current generation), and sealed off cathodes (SO; no current, with a solid plate placed across the cathode). Most (98 %) of the chemical oxygen demand (COD) was removed during power production in the CC reactor (maximum of 640 ± 10 mW/m 2), with a low percent of substrate converted to current (coulombic efficiency of 26.5 ± 2.1 %). Sealing the cathode reduced COD removal to 7 %, but with an open cathode, there was nearly as much COD removal by the OC reactor (94.5 %) as the CC reactor. Oxygen transfer into the reactor substantially affected the composition of the microbial communities. Based on analysis of the biofilms using 16S rRNA gene pyrosequencing, microbes most similar to Geobacter were predominant on the anodes in the CC MFC (72 % of sequences), but the most abundant bacteria were Azoarcus (42 to 47 %) in the OC reactor, and Dechloromonas (17 %) in the SO reactor. Hydrogenotrophic methanogens were most predominant, with sequences most similar to Methanobacterium in the CC and SO reactor, and Methanocorpusculum in the OC reactors. These results show that oxygen leakage through the cathode substantially alters the bacterial anode communities, and that hydrogenotrophic methanogens predominate despite high concentrations of acetate. The predominant methanogens in the CC reactor most closely resembled those in the SO reactor, demonstrating that oxygen leakage alters methanogenic as well as general bacterial communities. © 2013 Springer-Verlag Berlin Heidelberg.

  13. Characterization of bacterial and archaeal communities in air-cathode microbial fuel cells, open circuit and sealed-off reactors

    KAUST Repository

    Chehab, Noura A.; Li, Dong; Amy, Gary L.; Logan, Bruce E.; Saikaly, Pascal

    2013-01-01

    A large percentage of organic fuel consumed in a microbial fuel cell (MFC) is lost as a result of oxygen transfer through the cathode. In order to understand how this oxygen transfer affects the microbial community structure, reactors were operated in duplicate using three configurations: closed circuit (CC; with current generation), open circuit (OC; no current generation), and sealed off cathodes (SO; no current, with a solid plate placed across the cathode). Most (98 %) of the chemical oxygen demand (COD) was removed during power production in the CC reactor (maximum of 640 ± 10 mW/m 2), with a low percent of substrate converted to current (coulombic efficiency of 26.5 ± 2.1 %). Sealing the cathode reduced COD removal to 7 %, but with an open cathode, there was nearly as much COD removal by the OC reactor (94.5 %) as the CC reactor. Oxygen transfer into the reactor substantially affected the composition of the microbial communities. Based on analysis of the biofilms using 16S rRNA gene pyrosequencing, microbes most similar to Geobacter were predominant on the anodes in the CC MFC (72 % of sequences), but the most abundant bacteria were Azoarcus (42 to 47 %) in the OC reactor, and Dechloromonas (17 %) in the SO reactor. Hydrogenotrophic methanogens were most predominant, with sequences most similar to Methanobacterium in the CC and SO reactor, and Methanocorpusculum in the OC reactors. These results show that oxygen leakage through the cathode substantially alters the bacterial anode communities, and that hydrogenotrophic methanogens predominate despite high concentrations of acetate. The predominant methanogens in the CC reactor most closely resembled those in the SO reactor, demonstrating that oxygen leakage alters methanogenic as well as general bacterial communities. © 2013 Springer-Verlag Berlin Heidelberg.

  14. Composition and dynamic of benthic macroinvertebrates community ...

    African Journals Online (AJOL)

    the purpose to analyze the taxonomic composition, the structure of benthic macroinvertebrates community and the composite ... differences relative to the spatial and temporal variation in the taxonomic composition. ... changes in the structure of macroinvertebrates community ... 2007) with an annual growth rate of 2.4% rely.

  15. Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis

    Directory of Open Access Journals (Sweden)

    Scanlan Pauline D

    2008-05-01

    Full Text Available Abstract Background The incidence and diversity of human methanogens are insufficiently characterised in the gastrointestinal tract of both health and disease. A PCR and clone library methodology targeting the mcrA gene was adopted to facilitate the two-fold aim of surveying the relative incidence of methanogens in health and disease groups and also to provide an overview of methanogen diversity in the human gastrointestinal tract. Results DNA faecal extracts (207 in total from a group of healthy controls and five gastrointestinal disease groups were investigated. Colorectal cancer, polypectomised, irritable bowel syndrome and the control group had largely equivalent numbers of individuals positive for methanogens (range 45–50%. Methanogen incidence in the inflammatory bowel disease groups was reduced, 24% for ulcerative colitis and 30% for Crohn's disease. Four unique mcrA gene restriction fragment length polymorphism profiles were identified and bioinformatic analyses revealed that the majority of all sequences (94% retrieved from libraries were 100% identical to Methanobrevibacter smithii mcrA gene. In addition, mcrA gene sequences most closely related to Methanobrevibacter oralis and members of the order Methanosarcinales were also recovered. Conclusion The mcrA gene serves as a useful biomarker for methanogen detection in the human gut and the varying trends of methanogen incidence in the human gut could serve as important indicators of intestinal function. Although Methanobrevibacter smithii is the dominant methanogen in both the distal colon of individuals in health and disease, the diversity of methanogens is greater than previously reported. In conclusion, the low incidence of methanogens in Inflammatory Bowel Disease, the functionality of the methanogens and impact of methane production in addition to competitive interactions between methanogens and other microbial groups in the human gastrointestinal tract warrants further

  16. Growth and analysis of anaerobic wastewater methanogens using microfluidics

    Science.gov (United States)

    Steinhaus, Ben

    2005-11-01

    A micro-bioreactor (μBR) with a total system volume of 5 μl was developed using microfluidics and used to study the anaerobic waste-water methanogen methanosaeta concilli. The μBR was contained inside of an anaerobic chamber designed to be placed directly under an inverted light microscope while maintaining the reactor under a N2/CO2 gas mixture. Methanogens were cultured for periods of up to 3 months inside channels of varying width. The varying channel widths created varying fluid velocities and hence varying shear-rates inside the μBR. This allowed for direct study of the behavior and response of the anaerobe to varying shear-rates. After completion of the study, fluorescent in situ hybridization (FISH) was performed directly inside the microchannels to allow for further analysis and identification of the methanogens.

  17. Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and Methanogens in anorexic patients.

    Directory of Open Access Journals (Sweden)

    Fabrice Armougom

    Full Text Available BACKGROUND: Studies of the bacterial communities of the gut microbiota have revealed a shift in the ratio of Firmicutes and Bacteroidetes in obese patients. Determining the variations of microbial communities in feces may be beneficial for the identification of specific profiles in patients with abnormal weights. The roles of the archaeon Methanobrevibacter smithii and Lactobacillus species have not been described in these studies. METHODS AND FINDINGS: We developed an efficient and robust real-time PCR tool that includes a plasmid-based internal control and allows for quantification of the bacterial divisions Bacteroidetes, Firmicutes, and Lactobacillus as well as the methanogen M. smithii. We applied this technique to the feces of 20 obese subjects, 9 patients with anorexia nervosa, and 20 normal-weight healthy controls. Our results confirmed a reduction in the Bacteroidetes community in obese patients (p<0.01. We found a significantly higher Lactobacillus species concentration in obese patients than in lean controls (p=0.0197 or anorexic patients (p=0.0332. The M. smithii concentration was much higher in anorexic patients than in the lean population (p=0.0171. CONCLUSIONS: Lactobacillus species are widely used as growth promoters in the farm industry and are now linked to obesity in humans. The study of the bacterial flora in anorexic patients revealed an increase in M. smithii. This increase might represent an adaptive use of nutrients in this population.

  18. Potential for direct interspecies electron transfer in methanogenic wastewater digester aggregates

    DEFF Research Database (Denmark)

    Morita, Masahiko; Malvankar, Nikhil S; Franks, Ashley E

    2011-01-01

    Mechanisms for electron transfer within microbial aggregates derived from an upflow anaerobic sludge blanket reactor converting brewery waste to methane were investigated in order to better understand the function of methanogenic consortia. The aggregates were electrically conductive, with conduc...... for electron exchange in some methanogenic systems....

  19. Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy

    Directory of Open Access Journals (Sweden)

    William J. Brazelton

    2017-01-01

    Full Text Available The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms are abundant in marine hydrothermal systems heavily influenced by serpentinization, but evidence for methane-cycling archaea and bacteria in continental serpentinite springs has been limited. This report provides metagenomic and experimental evidence for active methanogenesis and methanotrophy by microbial communities in serpentinite springs of the Voltri Massif, Italy. Methanogens belonging to family Methanobacteriaceae and methanotrophic bacteria belonging to family Methylococcaceae were heavily enriched in three ultrabasic springs (pH 12. Metagenomic data also suggest the potential for hydrogen oxidation, hydrogen production, carbon fixation, fermentation, and organic acid metabolism in the ultrabasic springs. The predicted metabolic capabilities are consistent with an active subsurface ecosystem supported by energy and carbon liberated by geochemical reactions within the serpentinite rocks of the Voltri Massif.

  20. Isolation and characterization of methanogenic bacteria from ...

    African Journals Online (AJOL)

    Isolation and characterization of methanogenic bacteria from brewery wastewater in Kenya. Sylvia Injete Murunga, Duncan Onyango Mbuge, Ayub Njoroge Gitau, Urbanus Ndungwa Mutwiwa, Ingrid Namae Wekesa ...

  1. Microbiological aspects of granular methanogenic sludge

    NARCIS (Netherlands)

    Dolfing, J.

    1987-01-01

    The settling characteristics of anaerobic sludge are enhanced by the formation of microbial conglomerates. Various types of conglomerates having different structures, were distinguished in the present study, viz. granules, pellets and flocs (chapter 1). Granular methanogenic sludge, often

  2. Methanogens and Martian natural resources: Investigations regarding the possibility of biogenic methane on Mars

    Science.gov (United States)

    Chastain, Brendon Kelly

    Archaeal methanogens were suggested as terrestrial models of possible subsurface martian microbial life prior to the actual detection of methane in Mars' atmosphere. This idea gained even more interest after the methane on Mars was observed. However, the amount of methane detected was very small, and release of methane was localized and episodic. This led some scientists to doubt that an active or ancient biosphere could be the source of the methane. Moreover, even extremophilic methanogens have not been shown to metabolize in conditions exactly analogous to those known to be available on Mars. The following chapters present a realistic and viable mechanism that allows a large or ancient biosphere to be the original source of the observed methane, and they detail experimental work that was done in order to systematically investigate nutritional and conditional variables related to those that might be available in the martian subsurface. The results of the experimental work indicate that some components of Mars' regolith can support methanogenic metabolism without being detrimental to the organisms, and that certain known components of Mars' regolith can promote periods of methanogenic dormancy without being lethal to the methanogens. The results of the experimental studies also show that material known to exist at and near Mars' surface has the potential to supply electrons for biological methanogenesis and that methanogenic metabolism can occur even when artificial media, buffers, and reductants are omitted in order to create more Mars-relevant conditions. These findings may have implications regarding the viability of methanogenic organisms as a source of the observed methane and should assist future efforts to study methanogenic metabolism in conditions exactly analogous to those available in niches on Mars.

  3. Methanogenic community changes, and emissions of methane and other gases, during storage of acidified and untreated pig slurry

    DEFF Research Database (Denmark)

    Petersen, Søren O; Højberg, Ole; Poulsen, Morten

    2014-01-01

    H was nearly constant at values of 5.5 and 6.5. Ammonia losses were reduced by 84 and 49%, respectively, while CH4 emission with both acidification techniques was reduced by >90%. T-RFLP fingerprints showed little effect of acidification or storage time. A major T-RF of 105 bp could represent methanogens...

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

    DEFF Research Database (Denmark)

    Kinnunen, Marta

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

  5. Diversity and Distribution of Archaea Community along a Stratigraphic Permafrost Profile from Qinghai-Tibetan Plateau, China

    Directory of Open Access Journals (Sweden)

    Shiping Wei

    2014-01-01

    Full Text Available Accompanying the thawing permafrost expected to result from the climate change, microbial decomposition of the massive amounts of frozen organic carbon stored in permafrost is a potential emission source of greenhouse gases, possibly leading to positive feedbacks to the greenhouse effect. In this study, the community composition of archaea in stratigraphic soils from an alpine permafrost of Qinghai-Tibetan Plateau was investigated. Phylogenic analysis of 16S rRNA sequences revealed that the community was predominantly constituted by Crenarchaeota and Euryarchaeota. The active layer contained a proportion of Crenarchaeota at 51.2%, with the proportion of Euryarchaeota at 48.8%, whereas the permafrost contained 41.2% Crenarchaeota and 58.8% Euryarchaeota, based on 16S rRNA gene sequence analysis. OTU1 and OTU11, affiliated to Group 1.3b/MCG-A within Crenarchaeota and the unclassified group within Euryarchaeota, respectively, were widely distributed in all sediment layers. However, OTU5 affiliated to Group 1.3b/MCG-A was primarily distributed in the active layers. Sequence analysis of the DGGE bands from the 16S rRNAs of methanogenic archaea showed that the majority of methanogens belonged to Methanosarcinales and Methanomicrobiales affiliated to Euryarchaeota and the uncultured ZC-I cluster affiliated to Methanosarcinales distributed in all the depths along the permafrost profile, which indicated a dominant group of methanogens occurring in the cold ecosystems.

  6. Seryl-tRNA Synthetases from Methanogenic Archaea: Suppression of Bacterial Amber Mutation and Heterologous Toxicity

    Directory of Open Access Journals (Sweden)

    Drasko Boko

    2010-01-01

    Full Text Available Methanogenic archaea possess unusual seryl-tRNA synthetases (SerRS, evolutionarily distinct from the SerRSs found in other archaea, eucaryotes and bacteria. Our recent X-ray structural analysis of Methanosarcina barkeri SerRS revealed an idiosyncratic N-terminal domain and catalytic zinc ion in the active site. To shed further light on substrate discrimination by methanogenic-type SerRS, we set up to explore in vivo the interaction of methanogenic-type SerRSs with their cognate tRNAs in Escherichia coli or Saccharomyces cerevisiae. The expression of various methanogenic-type SerRSs was toxic for E. coli, resulting in the synthesis of erroneous proteins, as revealed by β-galactosidase stability assay. Although SerRSs from methanogenic archaea recognize tRNAsSer from all three domains of life in vitro, the toxicity presumably precluded the complementation of endogenous SerRS function in both, E. coli and S. cerevisiae. However, despite the observed toxicity, coexpression of methanogenic-type SerRS with its cognate tRNA suppressed bacterial amber mutation.

  7. An ancient divergence among the bacteria. [methanogenic phylogeny

    Science.gov (United States)

    Balch, W. E.; Magrum, L. J.; Fox, G. E.; Wolfe, R. S.; Woese, C. R.

    1977-01-01

    The 16S ribosomal RNZs from two species of met methanogenic bacteria, the mesophile Methanobacterium ruminantium and the thermophile Methanobacterium thermoautotrophicum, have been characterized in terms of the oligonucleotides produced by digestion with T1 ribonuclease. These two organisms are found to be sufficiently related that they can be considered members of the same genus or family. However, they bear only slight resemblance to 'typical' Procaryotic genera; such as Escherichia, Bacillus and Anacystis. The divergence of the methanogenic bacteria from other bacteria may be the most ancient phylogenetic event yet detected - antedating considerably the divergence of the blue green algal line for example, from the main bacterial line.

  8. Archaea and Bacteria Acclimate to High Total Ammonia in a Methanogenic Reactor Treating Swine Waste

    Directory of Open Access Journals (Sweden)

    Sofia Esquivel-Elizondo

    2016-01-01

    Full Text Available Inhibition by ammonium at concentrations above 1000 mgN/L is known to harm the methanogenesis phase of anaerobic digestion. We anaerobically digested swine waste and achieved steady state COD-removal efficiency of around 52% with no fatty-acid or H2 accumulation. As the anaerobic microbial community adapted to the gradual increase of total ammonia-N (NH3-N from 890±295 to 2040±30 mg/L, the Bacterial and Archaeal communities became less diverse. Phylotypes most closely related to hydrogenotrophic Methanoculleus (36.4% and Methanobrevibacter (11.6%, along with acetoclastic Methanosaeta (29.3%, became the most abundant Archaeal sequences during acclimation. This was accompanied by a sharp increase in the relative abundances of phylotypes most closely related to acetogens and fatty-acid producers (Clostridium, Coprococcus, and Sphaerochaeta and syntrophic fatty-acid Bacteria (Syntrophomonas, Clostridium, Clostridiaceae species, and Cloacamonaceae species that have metabolic capabilities for butyrate and propionate fermentation, as well as for reverse acetogenesis. Our results provide evidence countering a prevailing theory that acetoclastic methanogens are selectively inhibited when the total ammonia-N concentration is greater than ~1000 mgN/L. Instead, acetoclastic and hydrogenotrophic methanogens coexisted in the presence of total ammonia-N of ~2000 mgN/L by establishing syntrophic relationships with fatty-acid fermenters, as well as homoacetogens able to carry out forward and reverse acetogenesis.

  9. Methanogenesis limitations in degraded peatlands after their hydrological restoration

    Science.gov (United States)

    Urbanová, Zuzana

    2017-04-01

    Peatlands are ecosystems that can have a high degree of carbon sequestration due to CO2 fixation and low decomposition rates, but on the other hand, they are a source of CH4. Past drainage or mining can disturb these natural functions with rewetting being the main method used to bring back their original ecosystem properties. Methanogenic community composition and its activity seems to be very sensitive to environmental changes and therefore its limited activity after restoration can reflect the not fully restored functioning of the microbial community and its processes in the rewetted peatlands. To find the cause for this methanogenesis limitation we determined the abundance and composition of the methanogenic community and methane potential production in pristine, long-term drained and rewetted bogs and spruce swamp forests (SSF) in the Šumava Mountains (Czech Republic), using high-throughput barcoded sequencing, qPCR and anaerobic incubation of peat samples in relation to peat biochemical properties. Long-term drainage led to a strongly reduced diversity, abundance and activity of the methanogenic community in both peatland types. In restored sites, methanogenic abundance and community composition reached a pristine like state, however their activity measured as CH4 production remained as low as in drained sites. Substrate limitation was expected; therefore we further added different substrates during anaerobic incubation of the peat samples. In addition to glucose and ethanol, we added natural complex substrates from peatland plants (sedges, Sphagnum) to simulate the effect of the spreading of peatland species and their litter on methanogenic activity. The results unambiguously confirmed the limitation of methanogens by substrate availability due to the previous long-term drainage and strongly decomposed peat. The addition of natural substrates led to an increase in CH4 production, which was close to values in pristine sites. The limited CH4 production

  10. Enrichment of high ammonia tolerant methanogenic culture

    DEFF Research Database (Denmark)

    Fotidis, Ioannis; Karakashev, Dimitar Borisov; Proietti, Nicolas

    Ammonia is the major toxicant in full scale anaerobic digesters of animal wastes which are rich in proteins and/or urea, such as pig or poultry wastes. Ammonia inhibition decreases methane production rates, increases volatile fatty acids concentration and leads to economic losses for the biogas...... was derived from a full scale biogas reactor (Hashøj, Denmark), fed with 75% animal manure and 25% food industries organic waste. Basal anaerobic medium was used for the enrichment along with sodium acetate (1 g HAc L-1) as a carbon source. Fluorescence insitu hybridization (FISH) was used to determine...... exclusively to strict aceticlastic methanogens. Results obtained in this study, demonstrated for the first time that strictly aceticlastic methanogens, derived from an enriched culture, can efficiently produce methane under high ammonia levels....

  11. Process Recovery after CaO Addition Due to Granule Formation in a CSTR Co-Digester—A Tool to Influence the Composition of the Microbial Community and Stabilize the Process?

    Science.gov (United States)

    Liebrich, Marietta; Kleyböcker, Anne; Kasina, Monika; Miethling-Graff, Rona; Kassahun, Andrea; Würdemann, Hilke

    2016-01-01

    The composition, structure and function of granules formed during process recovery with calcium oxide in a laboratory-scale fermenter fed with sewage sludge and rapeseed oil were studied. In the course of over-acidification and successful process recovery, only minor changes were observed in the bacterial community of the digestate, while granules appeared during recovery. Fluorescence microscopic analysis of the granules showed a close spatial relationship between calcium and oil and/or long chain fatty acids. This finding further substantiated the hypothesis that calcium precipitated with carbon of organic origin and reduced the negative effects of overloading with oil. Furthermore, the enrichment of phosphate minerals in the granules was shown, and molecular biological analyses detected polyphosphate-accumulating organisms as well as methanogenic archaea in the core. Organisms related to Methanoculleus receptaculi were detected in the inner zones of a granule, whereas they were present in the digestate only after process recovery. This finding indicated more favorable microhabitats inside the granules that supported process recovery. Thus, the granule formation triggered by calcium oxide addition served as a tool to influence the composition of the microbial community and to stabilize the process after overloading with oil. PMID:27681911

  12. Process Recovery after CaO Addition Due to Granule Formation in a CSTR Co-Digester-A Tool to Influence the Composition of the Microbial Community and Stabilize the Process?

    Science.gov (United States)

    Liebrich, Marietta; Kleyböcker, Anne; Kasina, Monika; Miethling-Graff, Rona; Kassahun, Andrea; Würdemann, Hilke

    2016-03-17

    The composition, structure and function of granules formed during process recovery with calcium oxide in a laboratory-scale fermenter fed with sewage sludge and rapeseed oil were studied. In the course of over-acidification and successful process recovery, only minor changes were observed in the bacterial community of the digestate, while granules appeared during recovery. Fluorescence microscopic analysis of the granules showed a close spatial relationship between calcium and oil and/or long chain fatty acids. This finding further substantiated the hypothesis that calcium precipitated with carbon of organic origin and reduced the negative effects of overloading with oil. Furthermore, the enrichment of phosphate minerals in the granules was shown, and molecular biological analyses detected polyphosphate-accumulating organisms as well as methanogenic archaea in the core. Organisms related to Methanoculleus receptaculi were detected in the inner zones of a granule, whereas they were present in the digestate only after process recovery. This finding indicated more favorable microhabitats inside the granules that supported process recovery. Thus, the granule formation triggered by calcium oxide addition served as a tool to influence the composition of the microbial community and to stabilize the process after overloading with oil.

  13. Process Recovery after CaO Addition Due to Granule Formation in a CSTR Co-Digester—A Tool to Influence the Composition of the Microbial Community and Stabilize the Process?

    Directory of Open Access Journals (Sweden)

    Marietta Liebrich

    2016-03-01

    Full Text Available The composition, structure and function of granules formed during process recovery with calcium oxide in a laboratory-scale fermenter fed with sewage sludge and rapeseed oil were studied. In the course of over-acidification and successful process recovery, only minor changes were observed in the bacterial community of the digestate, while granules appeared during recovery. Fluorescence microscopic analysis of the granules showed a close spatial relationship between calcium and oil and/or long chain fatty acids. This finding further substantiated the hypothesis that calcium precipitated with carbon of organic origin and reduced the negative effects of overloading with oil. Furthermore, the enrichment of phosphate minerals in the granules was shown, and molecular biological analyses detected polyphosphate-accumulating organisms as well as methanogenic archaea in the core. Organisms related to Methanoculleus receptaculi were detected in the inner zones of a granule, whereas they were present in the digestate only after process recovery. This finding indicated more favorable microhabitats inside the granules that supported process recovery. Thus, the granule formation triggered by calcium oxide addition served as a tool to influence the composition of the microbial community and to stabilize the process after overloading with oil.

  14. Unexpected competitiveness of Methanosaeta populations at elevated acetate concentrations in methanogenic treatment of animal wastewater.

    Science.gov (United States)

    Chen, Si; Cheng, Huicai; Liu, Jiang; Hazen, Terry C; Huang, Vicki; He, Qiang

    2017-02-01

    Acetoclastic methanogenesis is a key metabolic process in anaerobic digestion, a technology with broad applications in biogas production and waste treatment. Acetoclastic methanogenesis is known to be performed by two archaeal genera, Methanosaeta and Methanosarcina. The conventional model posits that Methanosaeta populations are more competitive at low acetate levels (competitiveness of Methanosaeta at elevated acetate was further supported by the enrichment of Methanosaeta with high concentrations of acetate (20 mM). The dominance of Methanosaeta in the methanogen community could be reproduced in anaerobic digesters with the direct addition of acetate to above 20 mM, again supporting the competitiveness of Methanosaeta over Methanosarcina at elevated acetate levels. This study for the first time systematically demonstrated that the dominance of Methanosaeta populations in anaerobic digestion could be linked to the competitiveness of Methanosaeta at elevated acetate concentrations. Given the importance of acetoclastic methanogenesis in biological methane production, findings from this study could have major implications for developing strategies for more effective control of methanogenic treatment processes.

  15. Assessing the Ecophysiology of Methanogens in the Context of Recent Astrobiological and Planetological Studies

    Directory of Open Access Journals (Sweden)

    Ruth-Sophie Taubner

    2015-12-01

    Full Text Available Among all known microbes capable of thriving under extreme and, therefore, potentially extraterrestrial environmental conditions, methanogens from the domain Archaea are intriguing organisms. This is due to their broad metabolic versatility, enormous diversity, and ability to grow under extreme environmental conditions. Several studies revealed that growth conditions of methanogens are compatible with environmental conditions on extraterrestrial bodies throughout the Solar System. Hence, life in the Solar System might not be limited to the classical habitable zone. In this contribution we assess the main ecophysiological characteristics of methanogens and compare these to the environmental conditions of putative habitats in the Solar System, in particular Mars and icy moons. Eventually, we give an outlook on the feasibility and the necessity of future astrobiological studies concerning methanogens.

  16. Survival of methanogens during desiccation: implications for life on Mars.

    Science.gov (United States)

    Kendrick, Michael G; Kral, Timothy A

    2006-08-01

    The relatively recent discoveries that liquid water likely existed on the surface of past Mars and that methane currently exists in the martian atmosphere have fueled the possibility of extant or extinct life on Mars. One possible explanation for the existence of the methane would be the presence of methanogens in the subsurface. Methanogens are microorganisms in the domain Archaea that can metabolize molecular hydrogen as an energy source and carbon dioxide as a carbon source and produce methane. One factor of importance is the arid nature of Mars, at least at the surface. If one is to assume that life exists below the surface, then based on the only example of life that we know, liquid water must be present. Realistically, however, that liquid water may be seasonal just as it is at some locations on our home planet. Here we report on research designed to determine how long certain species of methanogens can survive desiccation on a Mars soil simulant, JSC Mars-1. Methanogenic cells were grown on JSC Mars-1, transferred to a desiccator within a Coy anaerobic environmental chamber, and maintained there for varying time periods. Following removal from the desiccator and rehydration, gas chromatographic measurements of methane indicated survival for varying time periods. Methanosarcina barkeri survived desiccation for 10 days, while Methanobacterium formicicum and Methanothermobacter wolfeii were able to survive for 25 days.

  17. The Effects of Perchlorates on the Permafrost Methanogens: Implication for Autotrophic Life on Mars.

    Science.gov (United States)

    Shcherbakova, Viktoria; Oshurkova, Viktoria; Yoshimura, Yoshitaka

    2015-09-09

    The terrestrial permafrost represents a range of possible cryogenic extraterrestrial ecosystems on Earth-like planets without obvious surface ice, such as Mars. The autotrophic and chemolithotrophic psychrotolerant methanogens are more likely than aerobes to function as a model for life forms that may exist in frozen subsurface environments on Mars, which has no free oxygen, inaccessible organic matter, and extremely low amounts of unfrozen water. Our research on the genesis of methane, its content and distribution in permafrost horizons of different ages and origin demonstrated the presence of methane in permanently frozen fine-grained sediments. Earlier, we isolated and described four strains of methanogenic archaea of Methanobacterium and Methanosarcina genera from samples of Pliocene and Holocene permafrost from Eastern Siberia. In this paper we study the effect of sodium and magnesium perchlorates on growth of permafrost and nonpermafrost methanogens, and present evidence that permafrost hydogenotrophic methanogens are more resistant to the chaotropic agent found in Martian soil. In this paper we study the effect of sodium and magnesium perchlorates on the growth of permafrost and nonpermafrost methanogens, and present evidence that permafrost hydogenotrophic methanogens are more resistant to the chaotropic agent found in Martian soil. Furthermore, as shown in the studies strain M2(T) M. arcticum, probably can use perchlorate anion as an electron acceptor in anaerobic methane oxidation. Earth's subzero subsurface environments are the best approximation of environments on Mars, which is most likely to harbor methanogens; thus, a biochemical understanding of these pathways is expected to provide a basis for designing experiments to detect autotrophic methane-producing life forms on Mars.

  18. The Effects of Perchlorates on the Permafrost Methanogens: Implication for Autotrophic Life on Mars

    Directory of Open Access Journals (Sweden)

    Viktoria Shcherbakova

    2015-09-01

    Full Text Available The terrestrial permafrost represents a range of possible cryogenic extraterrestrial ecosystems on Earth-like planets without obvious surface ice, such as Mars. The autotrophic and chemolithotrophic psychrotolerant methanogens are more likely than aerobes to function as a model for life forms that may exist in frozen subsurface environments on Mars, which has no free oxygen, inaccessible organic matter, and extremely low amounts of unfrozen water. Our research on the genesis of methane, its content and distribution in permafrost horizons of different ages and origin demonstrated the presence of methane in permanently frozen fine-grained sediments. Earlier, we isolated and described four strains of methanogenic archaea of Methanobacterium and Methanosarcina genera from samples of Pliocene and Holocene permafrost from Eastern Siberia. In this paper we study the effect of sodium and magnesium perchlorates on growth of permafrost and nonpermafrost methanogens, and present evidence that permafrost hydogenotrophic methanogens are more resistant to the chaotropic agent found in Martian soil. In this paper we study the effect of sodium and magnesium perchlorates on the growth of permafrost and nonpermafrost methanogens, and present evidence that permafrost hydogenotrophic methanogens are more resistant to the chaotropic agent found in Martian soil. Furthermore, as shown in the studies strain M2T M. arcticum, probably can use perchlorate anion as an electron acceptor in anaerobic methane oxidation. Earth’s subzero subsurface environments are the best approximation of environments on Mars, which is most likely to harbor methanogens; thus, a biochemical understanding of these pathways is expected to provide a basis for designing experiments to detect autotrophic methane-producing life forms on Mars.

  19. Predicting community composition from pairwise interactions

    Science.gov (United States)

    Friedman, Jonathan; Higgins, Logan; Gore, Jeff

    The ability to predict the structure of complex, multispecies communities is crucial for understanding the impact of species extinction and invasion on natural communities, as well as for engineering novel, synthetic communities. Communities are often modeled using phenomenological models, such as the classical generalized Lotka-Volterra (gLV) model. While a lot of our intuition comes from such models, their predictive power has rarely been tested experimentally. To directly assess the predictive power of this approach, we constructed synthetic communities comprised of up to 8 soil bacteria. We measured the outcome of competition between all species pairs, and used these measurements to predict the composition of communities composed of more than 2 species. The pairwise competitions resulted in a diverse set of outcomes, including coexistence, exclusion, and bistability, and displayed evidence for both interference and facilitation. Most pair outcomes could be captured by the gLV framework, and the composition of multispecies communities could be predicted for communities composed solely of such pairs. Our results demonstrate the predictive ability and utility of simple phenomenology, which enables accurate predictions in the absence of mechanistic details.

  20. Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?

    NARCIS (Netherlands)

    Ozuolmez, D.; Na, H.; Lever, M.A.; Kjeldsen, K.U.; Jørgensen, B.B.; Plugge, C.M.

    2015-01-01

    Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and

  1. Fast pyrolysis product distribution of biopretreated corn stalk by methanogen.

    Science.gov (United States)

    Wang, Tipeng; Ye, Xiaoning; Yin, Jun; Jin, Zaixing; Lu, Qiang; Zheng, Zongming; Dong, Changqing

    2014-10-01

    After pretreated by methanogen for 5, 15 and 25 days, corn stalk (CS) were pyrolyzed at 250, 300, 350, 400, 450 and 500 °C by Py-GC/MS and product distribution in bio-oil was analyzed. Results indicated that methanogen pretreatment changed considerably the product distribution: the contents of sugar and phenols increased; the contents of linear carbonyls and furans decreased; the contents of linear ketones and linear acids changed slightly. Methanogen pretreatment improved significantly the pyrolysis selectivity of CS to phenols especially 4-VP. At 250 °C, the phenols content increased from 42.25% for untreated CS to 79.32% for biopretreated CS for 5 days; the 4-VP content increased from 28.6% to 60.9%. Increasing temperature was contributed to convert more lignin into 4-VP, but decreased its content in bio-oil due to more other chemicals formed. The effects of biopretreatment time on the chemicals contents were insignificant. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Microbial diversity of western Canadian subsurface coal beds and methanogenic coal enrichment cultures

    Energy Technology Data Exchange (ETDEWEB)

    Penner, Tara J.; Foght, Julia M. [Department of Biological Sciences, University of Alberta, Edmonton, Alberta (Canada); Budwill, Karen [Carbon and Energy Management, Alberta Innovates-Technology Futures, 250 Karl Clark Road, Edmonton, Alberta (Canada)

    2010-05-01

    Coalbed methane is an unconventional fuel source associated with certain coal seams. Biogenic methane can comprise a significant portion of the gas found in coal seams, yet the role of microbes in methanogenesis in situ is uncertain. The purpose of this study was to detect and identify major bacterial and archaeal species associated with coal sampled from sub-bituminous methane-producing coal beds in western Canada, and to examine the potential for methane biogenesis from coal. Enrichment cultures of coal samples were established to determine how nutrient amendment influenced the microbial community and methane production in the laboratory. 16S rRNA gene clone libraries were constructed using DNA extracted and amplified from uncultured coal samples and from methanogenic coal enrichment cultures. Libraries were screened using restriction fragment length polymorphism, and representative clones were sequenced. Most (> 50%) of the bacterial sequences amplified from uncultured coal samples were affiliated with Proteobacteria that exhibit nitrate reduction, nitrogen fixation and/or hydrogen utilization activities, including Pseudomonas, Thauera and Acidovorax spp., whereas enrichment cultures were dominated by Bacteroidetes, Clostridia and/or Lactobacillales. Archaeal 16S rRNA genes could not be amplified from uncultured coal, suggesting that methanogens are present in coal below the detection levels of our methods. However, enrichment cultures established with coal inocula produced significant volumes of methane and the archaeal clone libraries were dominated by sequences closely affiliated with Methanosarcina spp. Enrichment cultures incubated with coal plus organic nutrients produced more methane than either nutrient or coal supplements alone, implying that competent methanogenic consortia exist in coal beds but that nutrient limitations restrict their activity in situ. This report adds to the scant literature on coal bed microbiology and suggests how microbes may be

  3. Comparative community structure of archaea in rumen of buffaloes and cattle.

    Science.gov (United States)

    Paul, Shyam S; Dey, Avijit; Baro, Daoharu; Punia, Balbir S

    2017-08-01

    Detailed knowledge of the community structure of methanogens is essential for amelioration of methane emission from livestock species. Several studies have indicated that predominant methanogens of buffalo rumen are different from those in cattle. However, predominant genera of methanogens reported by individual studies varied primarily because of limited scope of sampling, sequencing of limited number of sequences and potential PCR bias in individual studies. In this study, the collective comparative diversity of methanogenic archaea in the rumen of cattle and buffaloes was examined by performing a meta-analysis of all the 16S rRNA (rrn) sequences deposited in GenBank. Ruminal methanogen sequences of buffalo were clustered into 900 species-level operational taxonomic units (OTUs), and ruminal methanogen sequences of cattle were clustered into 1522 species level OTUs. The number of species-level OTUs shared between cattle and buffaloes was 229 (10.4% of all OTUs), comprising 1746 sequences (27% of the total 6447 sequences). According to taxonomic classification by three different classifiers, Methanobrevibacter was found to be the most predominant genus both in cattle (69-71% of sequences) as well as buffaloes (65.1-68.9% of sequences). Percentage of Methanomicrobium was much higher (P cattle (4.5%). On the other hand, percentages of Methanosphaera- and Methanomassiliicoccus-like methanogens were much higher (P cattle than in buffaloes. This study indicated that there is a substantial difference in community structure of ruminal methanogens of cattle and buffaloes. The study has also indicated that the percent of species-level operational taxonomic units shared between cattle and buffalo is very low, and thus host species-specific methane mitigation strategies need to be developed for cattle and buffaloes. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  4. Methanogenic Paraffin Biodegradation: Alkylsuccinate Synthase Gene Quantification and Dicarboxylic Acid Production.

    Science.gov (United States)

    Oberding, Lisa K; Gieg, Lisa M

    2018-01-01

    applications for effective fuel-contaminated site remediation and for improved recovery from oil reservoirs. Previous studies have clearly demonstrated that short-chain alkanes (C 17 ) that comprise many fuel mixtures. Using an enrichment culture derived from a freshwater fuel-contaminated site, we demonstrate that the model waxy alkane n -octacosane can be biodegraded under methanogenic conditions by a presumed Smithella phylotype. Compared with that of controls, we show an increased abundance and expression of the assA gene, which is known to be important for anaerobic n -alkane metabolism. Metabolite analyses revealed the presence of a range of α,ω-dicarboxylic acids found only in n -octacosane-degrading cultures, a novel finding that lends insight as to how anaerobic communities may access waxes as growth substrates in anoxic environments. Copyright © 2017 American Society for Microbiology.

  5. Stereochemical studies of acyclic isoprenoids-XII. Lipids of methanogenic bacteria and possible contributions to sediments

    Science.gov (United States)

    Risatti, J.B.; Rowland, S.J.; Yon, D.A.; Maxwell, J.R.

    1984-01-01

    Abundant volatile lipids of Methanobacterium thermoautotrophicum and Methanosarcina barkeri include isoprenoid hydrocarbons (??? C30), and C15, C20 and C25 isoprenoid alcohols. M. barkeri contains 2,6,10,15,19-pentamethyleicosane, whose relative stereochemistry is the same as found in marine sediments, indicating that it is a marker of methanogenic activity. The C20, C30 and C25 alkenes in M. thermoautotrophicum also have a preferred sterochemistry; the latter have the 2,6,10,14,18-pentamethyleicosanyl skeleton, suggesting that the alkane in marine sediments may derive from methanogens. The stereochemistry of squalane in a marine sediment is also compatible with an origin in methanogens; in contrast, the stereochemistry of pristane in M. thermoautotrophicum indicates a fossil fuel contaminant origin, suggesting that this and certain other alkanes reported in archaebacteria might also be of contaminant origin. There is, therefore, little evidence at present that the pristane in immature marine sediments originates in methanogens. The C15 and C20 saturated alcohols in M. thermoautotrophicum have mainly the all-R configuration. If this is generally true for methanogens, the C20 alcohol in the Messel shale may originate mainly from methanogens, whereas that in the Green River shale may originate mainly from photosynthetic organisms. ?? 1984.

  6. Method for indirect quantification of CH4 production via H2O production using hydrogenotrophic methanogens

    Directory of Open Access Journals (Sweden)

    Ruth-Sophie eTaubner

    2016-04-01

    Full Text Available ydrogenotrophic methanogens are an intriguing group of microorganisms from the domain Archaea. They exhibit extraordinary ecological, biochemical, physiological characteristics colorbox{yellow}{and have a huge biotechnological potential}. Yet, the only possibility to assess the methane (CH$_4$ production potential of hydrogenotrophic methanogens is to apply gas chromatographic quantification of CH$_4$.In order to be able to effectively screen pure cultures of hydrogenotrophic methanogens regarding their CH$_4$ production potential we developed a novel method for indirect quantification of colorbox{yellow}{the} volumetric CH$_4$ production rate by measuring colorbox{yellow}{the} volumetric water production rate. This colorbox{yellow}{ } method was established in serum bottles for cultivation of methanogens in closed batch cultivation mode. Water production was colorbox{yellow}{estimated} by determining the difference in mass increase in an isobaric setting.This novel CH$_4$ quantification method is an accurate and precise analytical technique, colorbox{yellow}{which can be used} to rapidly screen pure cultures of methanogens regarding colorbox{yellow}{their} volumetric CH$_{4}$ evolution rate. colorbox{yellow}{It} is a cost effective alternative colorbox{yellow}{determining} CH$_4$ production of methanogens over CH$_4$ quantification by using gas chromatography, especially if colorbox{yellow}{ } applied as a high throughput quantification method. colorbox{yellow}{Eventually, the} method can be universally applied for quantification of CH$_4$ production from psychrophilic, thermophilic and hyperthermophilic hydrogenotrophic methanogens.

  7. The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes.

    Science.gov (United States)

    Gray, N D; Sherry, A; Grant, R J; Rowan, A K; Hubert, C R J; Callbeck, C M; Aitken, C M; Jones, D M; Adams, J J; Larter, S R; Head, I M

    2011-11-01

    Libraries of 16S rRNA genes cloned from methanogenic oil degrading microcosms amended with North Sea crude oil and inoculated with estuarine sediment indicated that bacteria from the genera Smithella (Deltaproteobacteria, Syntrophaceace) and Marinobacter sp. (Gammaproteobacteria) were enriched during degradation. Growth yields and doubling times (36 days for both Smithella and Marinobacter) were determined using qPCR and quantitative data on alkanes, which were the predominant hydrocarbons degraded. The growth yield of the Smithella sp. [0.020 g(cell-C)/g(alkane-C)], assuming it utilized all alkanes removed was consistent with yields of bacteria that degrade hydrocarbons and other organic compounds in methanogenic consortia. Over 450 days of incubation predominance and exponential growth of Smithella was coincident with alkane removal and exponential accumulation of methane. This growth is consistent with Smithella's occurrence in near surface anoxic hydrocarbon degrading systems and their complete oxidation of crude oil alkanes to acetate and/or hydrogen in syntrophic partnership with methanogens in such systems. The calculated growth yield of the Marinobacter sp., assuming it grew on alkanes, was [0.0005 g(cell-C)/g(alkane-C)] suggesting that it played a minor role in alkane degradation. The dominant methanogens were hydrogenotrophs (Methanocalculus spp. from the Methanomicrobiales). Enrichment of hydrogen-oxidizing methanogens relative to acetoclastic methanogens was consistent with syntrophic acetate oxidation measured in methanogenic crude oil degrading enrichment cultures. qPCR of the Methanomicrobiales indicated growth characteristics consistent with measured rates of methane production and growth in partnership with Smithella. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  8. Energetic and hydrogen limitations of thermophilic and hyperthermophilic methanogens

    Science.gov (United States)

    Stewart, L. C.; Holden, J. F.

    2013-12-01

    Deep-sea hydrothermal vents are a unique ecosystem, based ultimately not on photosynthesis but chemosynthetic primary production. This makes them an excellent analog environment for the early Earth, and for potential extraterrestrial habitable environments, such as those on Mars and Europa. The habitability of given vent systems for chemoautotrophic prokaryotes can be modeled energetically by estimating the available Gibbs energy for specific modes of chemoautotrophy, using geochemical data and mixing models for hydrothermal fluids and seawater (McCollom and Shock, 1997). However, modeling to date has largely not taken into account variation in organisms' energy demands in these environments. Controls on maintenance energies are widely assumed to be temperature-dependent, rising with increasing temperature optima (Tijhuis et al., 1993), and species-independent. The impacts of other environmental stressors and particular energy-gathering strategies on maintenance energies have not been investigated. We have undertaken culture-based studies of growth and maintenance energies in thermophilic and hyperthermophilic methanogenic (hydrogenotrophic) archaea from deep-sea hydrothermal vents to investigate potential controls on energy demands in hydrothermal vent microbes, and to quantify their growth and maintenance energies for future bioenergetic modeling. We have investigated trends in their growth energies over their full temperature range and a range of nitrogen concentrations, and in their maintenance energies at different hydrogen concentrations. Growth energies in these organisms appear to rise with temperature, but do not vary between hyperthermophilic and thermophilic methanogens. Nitrogen availability at tested levels (40μM - 9.4 mM) does not appear to affect growth energies in all but one tested organism. In continuous chemostat culture, specific methane production varied with hydrogen availability but was similar between a thermophilic and a hyperthermophilic

  9. Increased methane production in cyanobacteria and methanogenic microbe co-cultures.

    Science.gov (United States)

    Yeung, Tracey; Kwan, Matthew; Adler, Lewis; Mills, Toby J; Neilan, Brett A; Conibeer, Gavin; Patterson, Robert

    2017-11-01

    A novel light-to-bioenergy system produced 3.5 times the baseline methane output using a co-culture of cyanobacteria (Oscillatoria sp.) and a methanogenic microbial community. Analysis of micronutrients in the system during the growth phase indicated that cobalt, iron, nickel and zinc were not appreciably consumed. The stable consumption and return of macronutrients calcium and magnesium were also observed. Essential macronutrients nitrogen, in the form of nitrate, and phosphorus showed no cycling during the growth phase and were depleted at rates of 0.35mg/L/day and 0.40µg/L/day, respectively. Biofilm formation increased the resilience of biomass to bacterial degradation in an anaerobic digester, as shown by viability assays of cyanobacterial biofilms in the co-culture. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Relating Anaerobic Digestion Microbial Community and Process Function.

    Science.gov (United States)

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

    2015-01-01

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

  11. Methanogenic degradation of petroleum hydrocarbons in subsurface environments remediation, heavy oil formation, and energy recovery.

    Science.gov (United States)

    Gray, N D; Sherry, A; Hubert, C; Dolfing, J; Head, I M

    2010-01-01

    Hydrocarbons are common constituents of surface, shallow, and deep-subsurface environments. Under anaerobic conditions, hydrocarbons can be degraded to methane by methanogenic microbial consortia. This degradation process is widespread in the geosphere. In comparison with other anaerobic processes, methanogenic hydrocarbon degradation is more sustainable over geological time scales because replenishment of an exogenous electron acceptor is not required. As a consequence, this process has been responsible for the formation of the world's vast deposits of heavy oil, which far exceed conventional oil assets such as those found in the Middle East. Methanogenic degradation is also a potentially important component of attenuation in hydrocarbon contamination plumes. Studies of the organisms, syntrophic partnerships, mechanisms, and geochemical signatures associated with methanogenic hydrocarbon degradation have identified common themes and diagnostic markers for this process in the subsurface. These studies have also identified the potential to engineer methanogenic processes to enhance the recovery of energy assets as biogenic methane from residual oils stranded in petroleum systems. Copyright 2010 Elsevier Inc. All rights reserved.

  12. Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales.

    Directory of Open Access Journals (Sweden)

    Sanae Sakai

    Full Text Available We report complete genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultured representative of the order Methanocellales once recognized as an uncultured key archaeal group for methane emission in rice fields. The genome sequence of M. paludicola consists of a single circular chromosome of 2,957,635 bp containing 3004 protein-coding sequences (CDS. Genes for most of the functions known in the methanogenic archaea were identified, e.g. a full complement of hydrogenases and methanogenesis enzymes. The mixotrophic growth of M. paludicola was clarified by the genomic characterization and re-examined by the subsequent growth experiments. Comparative genome analysis with the previously reported genome sequence of RC-I(MRE50, which was metagenomically reconstructed, demonstrated that about 70% of M. paludicola CDSs were genetically related with RC-I(MRE50 CDSs. These CDSs included the genes involved in hydrogenotrophic methane production, incomplete TCA cycle, assimilatory sulfate reduction and so on. However, the genetic components for the carbon and nitrogen fixation and antioxidant system were different between the two Methanocellales genomes. The difference is likely associated with the physiological variability between M. paludicola and RC-I(MRE50, further suggesting the genomic and physiological diversity of the Methanocellales methanogens. Comparative genome analysis among the previously determined methanogen genomes points to the genome-wide relatedness of the Methanocellales methanogens to the orders Methanosarcinales and Methanomicrobiales methanogens in terms of the genetic repertoire. Meanwhile, the unique evolutionary history of the Methanocellales methanogens is also traced in an aspect by the comparative genome analysis among the methanogens.

  13. Correlation between microbial community and granule conductivity in anaerobic bioreactors for brewery wastewater treatment

    DEFF Research Database (Denmark)

    Shrestha, Pravin; Malvankar, Nikhil S.; Werner, Jeffrey

    2014-01-01

    Prior investigation of an upflow anaerobic sludge blanket (UASB) reactor treating brewery wastes suggested that direct interspecies electron transfer (DIET) significantly contributed to interspecies electron transfer to methanogens. To investigate DIET in granules further, the electrical conducti......Prior investigation of an upflow anaerobic sludge blanket (UASB) reactor treating brewery wastes suggested that direct interspecies electron transfer (DIET) significantly contributed to interspecies electron transfer to methanogens. To investigate DIET in granules further, the electrical...... conductivity and bacterial community composition of granules in fourteen samples from four different UASB reactors treating brewery wastes were investigated. All of the UASB granules were electrically conductive whereas control granules from ANAMMOX (ANaerobic AMMonium OXidation) reactors and microbial...... granules from an aerobic bioreactor designed for phosphate removal were not. There was a moderate correlation (r = 0.67) between the abundance of Geobacter species in the UASB granules and granule conductivity, suggesting that Geobacter contributed to granule conductivity. These results, coupled...

  14. Distribution of benthic phototrophs, sulfate reducers, and methanogens in two adjacent saltern evaporation ponds in Eilat, Israel

    Czech Academy of Sciences Publication Activity Database

    Sørensen, K.; Řeháková, Klára; Zapomělová, Eliška; Oren, A.

    2009-01-01

    Roč. 56, 2-3 (2009), s. 275-284 ISSN 0948-3055. [GAP workshop /8./. Eilat, 30.03.2008-08.04.2008] R&D Projects: GA ČR(CZ) GA206/06/0462; GA AV ČR(CZ) KJB600960703; GA AV ČR(CZ) 1QS600170504 Institutional research plan: CEZ:AV0Z60170517; CEZ:AV0Z60050516 Keywords : salterns * microbial community * molecular ecology * phototrohs * sulfate reducers * methanogens Subject RIV: EH - Ecology, Behaviour Impact factor: 1.743, year: 2009

  15. Comparison of microbial communities associated with three Atlantic ultramafic hydrothermal systems.

    Science.gov (United States)

    Roussel, Erwan G; Konn, Cécile; Charlou, Jean-Luc; Donval, Jean-Pierre; Fouquet, Yves; Querellou, Joël; Prieur, Daniel; Bonavita, Marie-Anne Cambon

    2011-09-01

    The distribution of Archaea and methanogenic, methanotrophic and sulfate-reducing communities in three Atlantic ultramafic-hosted hydrothermal systems (Rainbow, Ashadze, Lost City) was compared using 16S rRNA gene and functional gene (mcrA, pmoA and dsrA) clone libraries. The overall archaeal community was diverse and heterogeneously distributed between the hydrothermal sites and the types of samples analyzed (seawater, hydrothermal fluid, chimney and sediment). The Lost City hydrothermal field, characterized by high alkaline warm fluids (pH>11; Tphylum and Methanopyrales order were also retrieved from the Rainbow and Ashadze hydrothermal fluids. However, the methanogenic Methanococcales was the most widely distributed hyper/thermophilic archaeal group among the hot and acidic ultramafic-hosted hydrothermal system environments. Most of the lineages detected are linked to methane and hydrogen cycling, suggesting that in ultramafic-hosted hydrothermal systems, large methanogenic and methanotrophic communities could be fuelled by hydrothermal fluids highly enriched in methane and hydrogen. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  16. Dynamics of two methanogenic microbiomes incubated in polycyclic aromatic hydrocarbons, naphthenic acids, and oil field produced water.

    Science.gov (United States)

    Oko, Bonahis J; Tao, Yu; Stuckey, David C

    2017-01-01

    Oil field produced water (OFPW) is widely produced in large volumes around the world. Transforming the organic matter in OFPW into bioenergy, such as biomethane, is one promising way to sustainability. However, OFPW is difficult to biologically degrade because it contains complex compounds such as naphthenic acids (NAs), or polycyclic aromatic hydrocarbons (PAHs). Although active microbial communities have been found in many oil reservoirs, little is known about how an exotic microbiome, e.g. the one which originates from municipal wastewater treatment plants, would evolve when incubated with OFPW. In this study, we harvested methanogenic biomass from two sources: a full-scale anaerobic digester (AD) treating oil and gas processing wastewater (named O&G sludge), and from a full-scale AD reactor treating multiple fractions of municipal solid wastes (named MS, short for mixed sludge). Both were incubated in replicate microcosms fed with PAHs, NAs, or OFPW. The results showed that the PAHs, NAs, and OFPW feeds could rapidly alter the methanogenic microbiomes, even after 14 days, while the O&G sludge adapted faster than the mixed sludge in all the incubations. Two rarely reported microorganisms, a hydrogenotrophic methanogen Candidatus methanoregula and a saccharolytic fermenter Kosmotoga , were found to be prevalent in the PAHs and OFPW microcosms, and are likely to play an important role in the syntrophic degradation of PAHs and OFPW, cooperating with methanogens such as Methanoregula, Methanosarcina, or Methanobacterium . The dominant phyla varied in certain patterns during the incubations, depending on the biomass source, feed type, and variation in nutrients. The sludge that originated from the oil and gas processing wastewater treatment (O&G) reactor adapted faster than the one from municipal solid waste reactors, almost certainly because the O&G biomass had been "pre-selected" by the environment. This study reveals the importance of biomass selection for other

  17. Decreasing ammonia inhibition in thermophilic methanogenic bioreactors using carbon fiber textiles.

    Science.gov (United States)

    Sasaki, Kengo; Morita, Masahiko; Hirano, Shin-ichi; Ohmura, Naoya; Igarashi, Yasuo

    2011-05-01

    Ammonia accumulation is one of the main causes of the loss of methane production observed during fermentation. We investigated the effect of addition of carbon fiber textiles (CFT) to thermophilic methanogenic bioreactors with respect to ammonia tolerance during the process of degradation of artificial garbage slurry, by comparing the performance of the reactors containing CFT with the performance of reactors without CFT. Under total ammonia-N concentrations of 3,000 mg L(-1), the reactors containing CFT were found to mediate stable removal of organic compounds and methane production. Under these conditions, high levels of methanogenic archaea were retained at the CFT, as determined by 16S rRNA gene analysis for methanogenic archaea. In addition, Methanobacterium sp. was found to be dominant in the suspended fraction, and Methanosarcina sp. was dominant in the retained fraction of the reactors with CFT. However, the reactors without CFT had lower rates of removal of organic compounds and production of methane under total ammonia-N concentrations of 1,500 mg L(-1). Under this ammonia concentration, a significant accumulation of acetate was observed in the reactors without CFT (130.0 mM), relative to the reactors with CFT (4.2 mM). Only Methanobacterium sp. was identified in the reactors without CFT. These results suggest that CFT enables stable proliferation of aceticlastic methanogens by preventing ammonia inhibition. This improves the process of stable garbage degradation and production of methane in thermophilic bioreactors that include high levels of ammonia.

  18. Application of real-time PCR to determination of combined effect of antibiotics on Bacteria, Methanogenic Archaea, Archaea in anaerobic sequencing batch reactors.

    Science.gov (United States)

    Aydin, Sevcan; Ince, Bahar; Ince, Orhan

    2015-06-01

    This study evaluated the long-term effects of erythromycin-tetracycline-sulfamethoxazole (ETS) and sulfamethoxazole-tetracycline (ST) antibiotic combinations on the microbial community and examined the ways in which these antimicrobials impact the performance of anaerobic reactors. Quantitative real-time PCR was used to determine the effect that different antibiotic combinations had on the total and active Bacteria, Archae and Methanogenic Archae. Three primer sets that targeted metabolic genes encoding formylterahydrofolate synthetase, methyl-coenzyme M reductase and acetyl-coA synthetase were also used to determine the inhibition level on the mRNA expression of the homoacetogens, methanogens and specifically acetoclastic methanogens, respectively. These microorganisms play a vital role in the anaerobic degradation of organic waste and targeting these gene expressions offers operators or someone at a treatment plant the potential to control and the improve the anaerobic system. The results of the investigation revealed that acetogens have a competitive advantage over Archaea in the presence of ETS and ST combinations. Although the efficiency with which methane production takes place and the quantification of microbial populations in both the ETS and ST reactors decreased as antibiotic concentrations increased, the ETS batch reactor performed better than the ST batch reactor. According to the expression of genes results, the syntrophic interaction of acetogens and methanogens is critical to the performance of the ETS and ST reactors. Failure to maintain the stability of these microorganisms resulted in a decrease in the performance and stability of the anaerobic reactors. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Microbial community composition affects soil fungistasis.

    Science.gov (United States)

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

    2003-02-01

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

  20. An intertwined evolutionary history of methanogenic archaea and sulfate reduction.

    Directory of Open Access Journals (Sweden)

    Dwi Susanti

    Full Text Available Hydrogenotrophic methanogenesis and dissimilatory sulfate reduction, two of the oldest energy conserving respiratory systems on Earth, apparently could not have evolved in the same host, as sulfite, an intermediate of sulfate reduction, inhibits methanogenesis. However, certain methanogenic archaea metabolize sulfite employing a deazaflavin cofactor (F(420-dependent sulfite reductase (Fsr where N- and C-terminal halves (Fsr-N and Fsr-C are homologs of F(420H(2 dehydrogenase and dissimilatory sulfite reductase (Dsr, respectively. From genome analysis we found that Fsr was likely assembled from freestanding Fsr-N homologs and Dsr-like proteins (Dsr-LP, both being abundant in methanogens. Dsr-LPs fell into two groups defined by following sequence features: Group I (simplest, carrying a coupled siroheme-[Fe(4-S(4] cluster and sulfite-binding Arg/Lys residues; Group III (most complex, with group I features, a Dsr-type peripheral [Fe(4-S(4] cluster and an additional [Fe(4-S(4] cluster. Group II Dsr-LPs with group I features and a Dsr-type peripheral [Fe(4-S(4] cluster were proposed as evolutionary intermediates. Group III is the precursor of Fsr-C. The freestanding Fsr-N homologs serve as F(420H(2 dehydrogenase unit of a putative novel glutamate synthase, previously described membrane-bound electron transport system in methanogens and of assimilatory type sulfite reductases in certain haloarchaea. Among archaea, only methanogens carried Dsr-LPs. They also possessed homologs of sulfate activation and reduction enzymes. This suggested a shared evolutionary history for methanogenesis and sulfate reduction, and Dsr-LPs could have been the source of the oldest (3.47-Gyr ago biologically produced sulfide deposit.

  1. Computational Modeling of Fluctuations in Energy and Metabolic Pathways of Methanogenic Archaea

    Energy Technology Data Exchange (ETDEWEB)

    Luthey-Schulten, Zaida [Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Chemistry; Carl R. Woese Inst. for Genomic Biology

    2017-01-04

    The methanogenic archaea, anaerobic microbes that convert CO2 and H2 and/or other small organic fermentation products into methane, play an unusually large role in the global carbon cycle. As they perform the final step in the anaerobic breakdown of biomass, methanogens are a biogenic source of an estimated one billion tons methane each year. Depending on the location, produced methane can be considered as either a greenhouse gas (agricultural byproduct), sequestered carbon storage (methane hydrate deposits), or a potential energy source (organic wastewater treatment). These microbes therefore represent an important target for biotechnology applications. Computational models of methanogens with predictive power are useful aids in the adaptation of methanogenic systems, but need to connect processes of wide-ranging time and length scales. In this project, we developed several computational methodologies for modeling the dynamic behavior of entire cells that connects stochastic reaction-diffusion dynamics of individual biochemical pathways with genome-scale modeling of metabolic networks. While each of these techniques were in the realm of well-defined computational methods, here we integrated them to develop several entirely new approaches to systems biology. The first scientific aim of the project was to model how noise in a biochemical pathway propagates into cellular phenotypes. Genetic circuits have been optimized by evolution to regulate molecular processes despite stochastic noise, but the effect of such noise on a cellular biochemical networks is currently unknown. An integrated stochastic/systems model of Escherichia coli species was created to analyze how noise in protein expression gives—and therefore noise in metabolic fluxes—gives rise to multiple cellular phenotype in isogenic population. After the initial work developing and validating methods that allow characterization of the heterogeneity in the model organism E. coli, the project shifted toward

  2. Impact of Peat Mining and Restoration on Methane Turnover Potential and Methane-Cycling Microorganisms in a Northern Bog.

    Science.gov (United States)

    Reumer, Max; Harnisz, Monika; Lee, Hyo Jung; Reim, Andreas; Grunert, Oliver; Putkinen, Anuliina; Fritze, Hannu; Bodelier, Paul L E; Ho, Adrian

    2018-02-01

    Ombrotrophic peatlands are a recognized global carbon reservoir. Without restoration and peat regrowth, harvested peatlands are dramatically altered, impairing their carbon sink function, with consequences for methane turnover. Previous studies determined the impact of commercial mining on the physicochemical properties of peat and the effects on methane turnover. However, the response of the underlying microbial communities catalyzing methane production and oxidation have so far received little attention. We hypothesize that with the return of Sphagnum spp. postharvest, methane turnover potential and the corresponding microbial communities will converge in a natural and restored peatland. To address our hypothesis, we determined the potential methane production and oxidation rates in natural (as a reference), actively mined, abandoned, and restored peatlands over two consecutive years. In all sites, the methanogenic and methanotrophic population sizes were enumerated using quantitative PCR (qPCR) assays targeting the mcrA and pmoA genes, respectively. Shifts in the community composition were determined using Illumina MiSeq sequencing of the mcrA gene and a pmoA -based terminal restriction fragment length polymorphism (t-RFLP) analysis, complemented by cloning and sequence analysis of the mmoX gene. Peat mining adversely affected methane turnover potential, but the rates recovered in the restored site. The recovery in potential activity was reflected in the methanogenic and methanotrophic abundances. However, the microbial community composition was altered, being more pronounced for the methanotrophs. Overall, we observed a lag between the recovery of the methanogenic/methanotrophic activity and the return of the corresponding microbial communities, suggesting that a longer duration (>15 years) is needed to reverse mining-induced effects on the methane-cycling microbial communities. IMPORTANCE Ombrotrophic peatlands are a crucial carbon sink, but this environment

  3. Ammonia tolerant enriched methanogenic cultures as bioaugmentation inocula to alleviate ammonia inhibition in continuous anaerobic reactors

    DEFF Research Database (Denmark)

    Fotidis, Ioannis; Wang, Han; Angelidaki, Irini

    Ammonia is the most common inhibitor of anaerobic digestion (AD) process, resulting in suboptimal exploitation of the biogas potential of the feedstocks, causing significant economic losses to the biogas plants. Ammonia is mainly inhibiting the aceticlastic methanogens, while the hydrogenotrophic...... methanogens are more robust to ammonia toxicity effect. It has been shown that bioaugmentation of a pure strain of a hydrogenotrophic methanogen (i.e. Methanoculleus bourgensis) in an ammonia inhibited continuous anaerobic reactor can improve methane production more than 30%. Nevertheless, cultivation...... tolerant methanogenic culture as potential bioaugmentation inoculum in a continuous stirred tank reactor (CSTR) operating under “inhibited steady-state”, triggered by high ammonia levels (5 g NH4+-N L-1). The results of the current study established for the first time that bioaugmentation of an enriched...

  4. Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences

    Directory of Open Access Journals (Sweden)

    Shailendra Yadav

    2015-01-01

    Full Text Available Methanogens, a key contributor in global carbon cycling, methane emission, and alternative energy production, generate methane gas via anaerobic digestion of organic matter. The methane emission potential depends upon methanogenic diversity and activity. Since they are anaerobes and difficult to isolate and culture, their diversity present in the landfill sites of Delhi and marshlands of Southern Assam, India, was analyzed using molecular techniques like 16S rDNA sequencing, DGGE, and qPCR. The sequencing results indicated the presence of methanogens belonging to the seventh order and also the order Methanomicrobiales in the Ghazipur and Bhalsawa landfill sites of Delhi. Sequences, related to the phyla Crenarchaeota (thermophilic and Thaumarchaeota (mesophilic, were detected from marshland sites of Southern Assam, India. Jaccard analysis of DGGE gel using Gel2K showed three main clusters depending on the number and similarity of band patterns. The copy number analysis of hydrogenotrophic methanogens using qPCR indicates higher abundance in landfill sites of Delhi as compared to the marshlands of Southern Assam. The knowledge about “methanogenic archaea composition” and “abundance” in the contrasting ecosystems like “landfill” and “marshland” may reorient our understanding of the Archaea inhabitants. This study could shed light on the relationship between methane-dynamics and the global warming process.

  5. A simple model for simultaneous methanogenic-denitrification systems

    DEFF Research Database (Denmark)

    Garibay-Orijel, C.; Ahring, Birgitte Kiær; Rinderknecht-Seijas, N.

    2006-01-01

    We describe a useful and simple model for studies of simultaneous methanogenic-denitrification (M-D) systems. One equation predicts an inverse relationship between the percentage of electron donor channeled into dissimilatory denitrification and the loading ratio X given by grams degradable COD per...

  6. Native arbuscular mycorrhizal symbiosis alters foliar bacterial community composition.

    Science.gov (United States)

    Poosakkannu, Anbu; Nissinen, Riitta; Kytöviita, Minna-Maarit

    2017-11-01

    The effects of arbuscular mycorrhizal (AM) fungi on plant-associated microbes are poorly known. We tested the hypothesis that colonization by an AM fungus affects microbial species richness and microbial community composition of host plant tissues. We grew the grass, Deschampsia flexuosa in a greenhouse with or without the native AM fungus, Claroideoglomus etunicatum. We divided clonally produced tillers into two parts: one inoculated with AM fungus spores and one without AM fungus inoculation (non-mycorrhizal, NM). We characterized bacterial (16S rRNA gene) and fungal communities (internal transcribed spacer region) in surface-sterilized leaf and root plant compartments. AM fungus inoculation did not affect microbial species richness or diversity indices in leaves or roots, but the AM fungus inoculation significantly affected bacterial community composition in leaves. A total of three OTUs in leaves belonging to the phylum Firmicutes positively responded to the presence of the AM fungus in roots. Another six OTUs belonging to the Proteobacteria (Alpha, Beta, and Gamma) and Bacteroidetes were significantly more abundant in NM plants when compared to AM fungus-inoculated plants. Further, there was a significant correlation between plant dry weight and leaf microbial community compositional shift. Also, there was a significant correlation between leaf bacterial community compositional shift and foliar nitrogen content changes due to AM fungus inoculation. The results suggest that AM fungus colonization in roots has a profound effect on plant physiology that is reflected in leaf bacterial community composition.

  7. Low-temperature (10°C) anaerobic digestion of dilute dairy wastewater in an EGSB bioreactor: microbial community structure, population dynamics, and kinetics of methanogenic populations.

    Science.gov (United States)

    Bialek, Katarzyna; Cysneiros, Denise; O'Flaherty, Vincent

    2013-01-01

    The feasibility of anaerobic digestion of dairy wastewater at 10°C was investigated in a high height : diameter ratio EGSB reactor. Stable performance was observed at an applied organic loading rate (OLR) of 0.5-2 kg COD m(-3) d(-1) with chemical oxygen demand (COD) removal efficiencies above 85%. When applied OLR increased to values above 2 kg COD m(-3) d(-1), biotreatment efficiency deteriorated, with methanogenesis being the rate-limiting step. The bioreactor recovered quickly (3 days) after reduction of the OLR. qPCR results showed a reduction in the abundance of hydrogenotrophic methanogenic Methanomicrobiales and Methanobacteriales throughout the steady state period followed by a sharp increase in their numbers (111-fold) after the load shock. Specific methanogenic activity and maximum substrate utilising rate (A(max)) of the biomass at the end of trial indicated increased activity and preference towards hydrogenotrophic methanogenesis, which correlated well with the increased abundance of hydrogenotrophic methanogens. Acetoclastic Methanosaeta spp. remained at stable levels throughout the trial. However, increased apparent half-saturation constant (K(m)) at the end of the trial indicated a decrease in the specific substrate affinity for acetate of the sludge, suggesting that Methanosaeta spp., which have high substrate affinity, started to be outcompeted in the reactor.

  8. A new methanogen “Methanobrevibacter massiliense” isolated in a case of severe periodontitis

    OpenAIRE

    Huynh, Hong T. T.; Pignoly, Marion; Drancourt, Michel; Aboudharam, Gérard

    2017-01-01

    Background A few methanogens have been previously recovered from periodontitis lesions, yet their repertoire may not be completed. We recovered a previously unreported methanogen species in this situation. Case presentation A 64-year-old Caucasian woman was diagnosed with chronic, severe generalized periodontitis. In the presence of negative controls, an 18-month culture of periodontal pockets in anaerobe Hungate tube yielded “Methanobrevibacter massiliense” and Pyramidobacter piscolens. Conc...

  9. Conductive iron oxide minerals accelerate syntrophic cooperation in methanogenic benzoate degradation

    Energy Technology Data Exchange (ETDEWEB)

    Zhuang, Li; Tang, Jia; Wang, Yueqiang; Hu, Min; Zhou, Shungui, E-mail: sgzhou@soil.gd.cn

    2015-08-15

    Highlights: • Paddy soil contaminated with benzoate incubated with hematite and magnetite. • Iron oxides addition enhanced methanogenic benzoate degradation by 25–53%. • The facilitated syntrophy might involve direct interspecies electron transfer. • Bacillaceae, Peptococcaceae, and Methanobacterium are potentially involved. - Abstract: Recent studies have suggested that conductive iron oxide minerals can facilitate syntrophic metabolism of the methanogenic degradation of organic matter, such as ethanol, propionate and butyrate, in natural and engineered microbial ecosystems. This enhanced syntrophy involves direct interspecies electron transfer (DIET) powered by microorganisms exchanging metabolic electrons through electrically conductive minerals. Here, we evaluated the possibility that conductive iron oxides (hematite and magnetite) can stimulate the methanogenic degradation of benzoate, which is a common intermediate in the anaerobic metabolism of aromatic compounds. The results showed that 89–94% of the electrons released from benzoate oxidation were recovered in CH{sub 4} production, and acetate was identified as the only carbon-bearing intermediate during benzoate degradation. Compared with the iron-free controls, the rates of methanogenic benzoate degradation were enhanced by 25% and 53% in the presence of hematite and magnetite, respectively. This stimulatory effect probably resulted from DIET-mediated methanogenesis in which electrons transfer between syntrophic partners via conductive iron minerals. Phylogenetic analyses revealed that Bacillaceae, Peptococcaceae, and Methanobacterium are potentially involved in the functioning of syntrophic DIET. Considering the ubiquitous presence of iron minerals within soils and sediments, the findings of this study will increase the current understanding of the natural biological attenuation of aromatic hydrocarbons in anaerobic environments.

  10. The nif Gene Operon of the Methanogenic Archaeon Methanococcus maripaludis

    Science.gov (United States)

    Kessler, Peter S.; Blank, Carrine; Leigh, John A.

    1998-01-01

    Nitrogen fixation occurs in two domains, Archaea and Bacteria. We have characterized a nif (nitrogen fixation) gene cluster in the methanogenic archaeon Methanococcus maripaludis. Sequence analysis revealed eight genes, six with sequence similarity to known nif genes and two with sequence similarity to glnB. The gene order, nifH, ORF105 (similar to glnB), ORF121 (similar to glnB), nifD, nifK, nifE, nifN, and nifX, was the same as that found in part in other diazotrophic methanogens and except for the presence of the glnB-like genes, also resembled the order found in many members of the Bacteria. Using transposon insertion mutagenesis, we determined that an 8-kb region required for nitrogen fixation corresponded to the nif gene cluster. Northern analysis revealed the presence of either a single 7.6-kb nif mRNA transcript or 10 smaller mRNA species containing portions of the large transcript. Polar effects of transposon insertions demonstrated that all of these mRNAs arose from a single promoter region, where transcription initiated 80 bp 5′ to nifH. Distinctive features of the nif gene cluster include the presence of the six primary nif genes in a single operon, the placement of the two glnB-like genes within the cluster, the apparent physical separation of the cluster from any other nif genes that might be in the genome, the fragmentation pattern of the mRNA, and the regulation of expression by a repression mechanism described previously. Our study and others with methanogenic archaea reporting multiple mRNAs arising from gene clusters with only a single putative promoter sequence suggest that mRNA processing following transcription may be a common occurrence in methanogens. PMID:9515920

  11. Abundance and diversity of methanogens: potential role in high arsenic groundwater in Hetao Plain of Inner Mongolia, China.

    Science.gov (United States)

    Wang, Y H; Li, P; Dai, X Y; Zhang, R; Jiang, Z; Jiang, D W; Wang, Y X

    2015-05-15

    To investigate the community diversity and abundance of methanogens and their potential role in high arsenic groundwater, 17 groundwater samples from Hetao Plain of Inner Mongolia were investigated with an integrated method including 16S rRNA gene clone library, quantitative polymerase chain reaction and geochemistry analyses. Total arsenic (AsTot) concentrations were 82.7-1088.7 μg/L and arsenite (AsIII) mostly dominated in these samples with percentages of 0.04-0.79. CH₄ concentrations ranged from 0.01 to 292 μg/L and distinctly elevated only when AsTot were relatively high and SO₄(2-) were distinctly low. Principal component analysis indicated that these samples were divided into three groups according to the variations of AsTot, CH₄ and SO₄(2-). AsTot concentrations were distinctly high in the group with high CH₄ and low SO₄(2-) comparing to the other two groups (one with high CH₄ and high SO₄(2-), the other with low CH₄ and SO₄(2-)). The mcrA gene (methyl coenzyme-M reductase gene) based phylogenetic analysis of methanogens population showed that methanogenic archaea was diverse but mainly composed of Methanomicrobiales, Methanosarcinales, Methanobacteria and unidentified groups, with Methanomicrobiales being distinctly dominant (50.6%). The mcrA gene abundance in high arsenic groundwater ranged from 3.01 × 10(3) to 3.80 × 10(6)copies/L and accounted for 0-30.2% of total archaeal 16S rRNA genes. The abundance of mcrA genes was positively correlated with the concentrations of AsTot (R=0.59), AsIII (R=0.57) and FeII (R=0.79), while it was negatively correlated with oxidation-reduction potential (R=-0.66) and SO₄(2-) concentration (R=-0.64). These results implied that methanogenic archaea might accelerate As release in groundwater aquifers in Hetao Plain. Copyright © 2015. Published by Elsevier B.V.

  12. Methanogens Are Major Contributors to Nitrogen Fixation in Soils of the Florida Everglades.

    Science.gov (United States)

    Bae, Hee-Sung; Morrison, Elise; Chanton, Jeffrey P; Ogram, Andrew

    2018-04-01

    The objective of this study was to investigate the interaction of the nitrogen (N) cycle with methane production in the Florida Everglades, a large freshwater wetland. This study provides an initial analysis of the distribution and expression of N-cycling genes in Water Conservation Area 2A (WCA-2A), a section of the marsh that underwent phosphorus (P) loading for many years due to runoff from upstream agricultural activities. The elevated P resulted in increased primary productivity and an N limitation in P-enriched areas. Results from quantitative real-time PCR (qPCR) analyses indicated that the N cycle in WCA-2A was dominated by nifH and nirK / S , with an increasing trend in copy numbers in P-impacted sites. Many nifH sequences (6 to 44% of the total) and nifH transcript sequences (2 to 49%) clustered with the methanogenic Euryarchaeota , in stark contrast to the proportion of core gene sequences representing Archaea (≤0.27% of SSU rRNA genes) for the WCA-2A microbiota. Notably, archaeal nifH gene transcripts were detected at all sites and comprised a significant proportion of total nifH transcripts obtained from the unimpacted site, indicating that methanogens are actively fixing N 2 Laboratory incubations with soils taken from WCA-2A produced nifH transcripts with the production of methane from H 2 plus CO 2 and acetate as electron donors and carbon sources. Methanogenic N 2 fixation is likely to be an important, although largely unrecognized, route through which fixed nitrogen enters the anoxic soils of the Everglades and may have significant relevance regarding methane production in wetlands. IMPORTANCE Wetlands are the most important natural sources of the greenhouse gas methane, and much of that methane emanates from (sub)tropical peatlands. Primary productivity in these peatlands is frequently limited by the availability of nitrogen or phosphorus; however, the response to nutrient limitations of microbial communities that control biogeochemical cycling

  13. A portable anaerobic microbioreactor reveals optimum growth conditions for the methanogen Methanosaeta concilii.

    Science.gov (United States)

    Steinhaus, Benjamin; Garcia, Marcelo L; Shen, Amy Q; Angenent, Largus T

    2007-03-01

    Conventional studies of the optimum growth conditions for methanogens (methane-producing, obligate anaerobic archaea) are typically conducted with serum bottles or bioreactors. The use of microfluidics to culture methanogens allows direct microscopic observations of the time-integrated response of growth. Here, we developed a microbioreactor (microBR) with approximately 1-microl microchannels to study some optimum growth conditions for the methanogen Methanosaeta concilii. The microBR is contained in an anaerobic chamber specifically designed to place it directly onto an inverted light microscope stage while maintaining a N2-CO2 environment. The methanogen was cultured for months inside microchannels of different widths. Channel width was manipulated to create various fluid velocities, allowing the direct study of the behavior and responses of M. concilii to various shear stresses and revealing an optimum shear level of approximately 20 to 35 microPa. Gradients in a single microchannel were then used to find an optimum pH level of 7.6 and an optimum total NH4-N concentration of less than 1,100 mg/liter (<47 mg/liter as free NH3-N) for M. concilii under conditions of the previously determined ideal shear stress and pH and at a temperature of 35 degrees C.

  14. Reducing methane emissions and the methanogen population in the rumen of Tibetan sheep by dietary supplementation with coconut oil.

    Science.gov (United States)

    Ding, Xuezhi; Long, Ruijun; Zhang, Qian; Huang, Xiaodan; Guo, Xusheng; Mi, Jiandui

    2012-10-01

    The objective was to evaluate the effect of dietary coconut oil on methane (CH(4)) emissions and the microbial community in Tibetan sheep. Twelve animals were assigned to receive either a control diet (oaten hay) or a mixture diet containing concentrate (maize meal), in which coconut oil was supplemented at 12 g/day or not for a period of 4 weeks. CH(4) emissions were measured by using the 'tunnel' technique, and microbial communities were examined using quantitative real-time PCR. Daily CH(4) production for the control and forage-to-concentrate ratio of 6:4 was 17.8 and 15.3 g, respectively. Coconut oil was particularly effective at reducing CH(4) emissions from Tibetan sheep. The inclusion of coconut oil for the control decreased CH(4) production (in grams per day) by 61.2%. In addition, there was a positive correlation between the number of methanogens and the daily CH(4) production (R = 0.95, P coconut oil supplemented at 12 g/day decreases the number of methanogens by 77% and a decreases in the ruminal fungal population (85-95%) and Fibrobacter succinogenes (50-98%) but an increase in Ruminococcus flavefaciens (25-70%). The results from our experiment suggest that adding coconut oil to the diet can reduce CH(4) emissions in Tibetan sheep and that these reductions persist for at least the 4-week feeding period.

  15. Soil biodiversity and soil community composition determine ecosystem multifunctionality

    Science.gov (United States)

    Wagg, Cameron; Bender, S. Franz; Widmer, Franco; van der Heijden, Marcel G. A.

    2014-01-01

    Biodiversity loss has become a global concern as evidence accumulates that it will negatively affect ecosystem services on which society depends. So far, most studies have focused on the ecological consequences of above-ground biodiversity loss; yet a large part of Earth’s biodiversity is literally hidden below ground. Whether reductions of biodiversity in soil communities below ground have consequences for the overall performance of an ecosystem remains unresolved. It is important to investigate this in view of recent observations that soil biodiversity is declining and that soil communities are changing upon land use intensification. We established soil communities differing in composition and diversity and tested their impact on eight ecosystem functions in model grassland communities. We show that soil biodiversity loss and simplification of soil community composition impair multiple ecosystem functions, including plant diversity, decomposition, nutrient retention, and nutrient cycling. The average response of all measured ecosystem functions (ecosystem multifunctionality) exhibited a strong positive linear relationship to indicators of soil biodiversity, suggesting that soil community composition is a key factor in regulating ecosystem functioning. Our results indicate that changes in soil communities and the loss of soil biodiversity threaten ecosystem multifunctionality and sustainability. PMID:24639507

  16. Microbial community stratification linked to utilization of carbohydrates and phosphorus limitation in a boreal peatland at Marcell Experimental Forest, Minnesota, USA.

    Science.gov (United States)

    Lin, Xueju; Tfaily, Malak M; Steinweg, J Megan; Chanton, Patrick; Esson, Kaitlin; Yang, Zamin K; Chanton, Jeffrey P; Cooper, William; Schadt, Christopher W; Kostka, Joel E

    2014-06-01

    This study investigated the abundance, distribution, and composition of microbial communities at the watershed scale in a boreal peatland within the Marcell Experimental Forest (MEF), Minnesota, USA. Through a close coupling of next-generation sequencing, biogeochemistry, and advanced analytical chemistry, a biogeochemical hot spot was revealed in the mesotelm (30- to 50-cm depth) as a pronounced shift in microbial community composition in parallel with elevated peat decomposition. The relative abundance of Acidobacteria and the Syntrophobacteraceae, including known hydrocarbon-utilizing genera, was positively correlated with carbohydrate and organic acid content, showing a maximum in the mesotelm. The abundance of Archaea (primarily crenarchaeal groups 1.1c and 1.3) increased with depth, reaching up to 60% of total small-subunit (SSU) rRNA gene sequences in the deep peat below the 75-cm depth. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by the Methanosarcinales in the mesotelm, while hydrogen-utilizing methanogens predominated in the deeper catotelm. RNA-derived pyrosequence libraries corroborated DNA sequence data to indicate that the above-mentioned microbial groups are metabolically active in the mid-depth zone. Fungi showed a maximum in rRNA gene abundance above the 30-cm depth, which comprised only an average of 0.1% of total bacterial and archaeal rRNA gene abundance, indicating prokaryotic dominance. Ratios of C to P enzyme activities approached 0.5 at the acrotelm and catotelm, indicating phosphorus limitation. In contrast, P limitation pressure appeared to be relieved in the mesotelm, likely due to P solubilization by microbial production of organic acids and C-P lyases. Based on path analysis and the modeling of community spatial turnover, we hypothesize that P limitation outweighs N limitation at

  17. Evaluation of the vinyl acetate elimination process in methanogenic sludge with oxygen

    International Nuclear Information System (INIS)

    Duran, U.; Monroy, O.; Rendon, B.; Gomez, J.; Ramirez, F.

    2009-01-01

    The vinyl acetate (AV) is a volatile toxic used in the painting manufacture, causing serious problems of contamination in grounds, air and natural bodies of water. Under methanogenic conditions the complete mineralization of the AV has not been obtained, but evidences exist suggesting that with the addition of low oxygen concentrations to methanogenic sludge the elimination of this compound is possible. In this work was studied the respiratory process of elimination of the AV methano genesis and methano genesis with oxygen (1 mg/L-d). (Author)

  18. Microbial community diversity in the gut of the South American termite Cornitermes cumulans (Isoptera: Termitidae).

    Science.gov (United States)

    Grieco, Maria Angela B; Cavalcante, Janaina J V; Cardoso, Alexander M; Vieira, Ricardo P; Machado, Ednildo A; Clementino, Maysa M; Medeiros, Marcelo N; Albano, Rodolpho M; Garcia, Eloi S; de Souza, Wanderley; Constantino, Reginaldo; Martins, Orlando B

    2013-01-01

    Termites inhabit tropical and subtropical areas where they contribute to structure and composition of soils by efficiently degrading biomass with aid of resident gut microbiota. In this study, culture-independent molecular analysis was performed based on bacterial and archaeal 16S rRNA clone libraries to describe the gut microbial communities within Cornitermes cumulans, a South American litter-feeding termite. Our data reveal extensive bacterial diversity, mainly composed of organisms from the phyla Spirochaetes, Bacteroidetes, Firmicutes, Actinobacteria, and Fibrobacteres. In contrast, a low diversity of archaeal 16S rRNA sequences was found, comprising mainly members of the Crenarchaeota phylum. The diversity of archaeal methanogens was further analyzed by sequencing clones from a library for the mcrA gene, which encodes the enzyme methyl coenzyme reductase, responsible for catalyzing the last step in methane production, methane being an important greenhouse gas. The mcrA sequences were diverse and divided phylogenetically into three clades related to uncultured environmental archaea and methanogens found in different termite species. C. cumulans is a litter-feeding, mound-building termite considered a keystone species in natural ecosystems and also a pest in agriculture. Here, we describe the archaeal and bacterial communities within this termite, revealing for the first time its intriguing microbiota.

  19. Abundance and potential metabolic activity of methanogens in well-aerated forest and grassland soils of an alpine region.

    Science.gov (United States)

    Hofmann, Katrin; Praeg, Nadine; Mutschlechner, Mira; Wagner, Andreas O; Illmer, Paul

    2016-02-01

    Although methanogens were recently discovered to occur in aerated soils, alpine regions have not been extensively studied for their presence so far. Here, the abundance of archaea and the methanogenic guilds Methanosarcinales, Methanococcales, Methanobacteriales, Methanomicrobiales and Methanocella spp. was studied at 16 coniferous forest and 14 grassland sites located at the montane and subalpine belts of the Northern Limestone Alps (calcareous) and the Austrian Central Alps (siliceous) using quantitative real-time PCR. Abundance of archaea, methanogens and the methanogenic potentials were significantly higher in grasslands than in forests. Furthermore, methanogenic potentials of calcareous soils were higher due to pH. Methanococcales, Methanomicrobiales and Methanocella spp. were detected in all collected samples, which indicates that they are autochthonous, while Methanobacteriales were absent from 4 out of 16 forest soils. Methanosarcinales were absent from 10 out of 16 forest soils and 2 out of 14 grassland soils. Nevertheless, together with Methanococcales they represented the majority of the 16S rRNA gene copies quantified from the grassland soils. Contrarily, forest soils were clearly dominated by Methanococcales. Our results indicate a higher diversity of methanogens in well-aerated soils than previously believed and that pH mainly influences their abundances and activities. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  20. Microbial community analysis of ambient temperature anaerobic digesters

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-07-01

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

  1. Microbial diversity in methanogenic hydrocarbon-degrading enrichment cultures isolated from a water-flooded oil reservoir (Dagang oil field, China)

    Science.gov (United States)

    Jiménez, Núria; Cai, Minmin; Straaten, Nontje; Yao, Jun; Richnow, Hans H.; Krüger, Martin

    2015-04-01

    Microbial transformation of oil to methane is one of the main degradation processes taking place in oil reservoirs, and it has important consequences as it negatively affects the quality and economic value of the oil. Nevertheless, methane could constitute a recovery method of carbon from exhausted reservoirs. Previous studies combining geochemical and isotopic analysis with molecular methods showed evidence for in situ methanogenic oil degradation in the Dagang oil field, China (Jiménez et al., 2012). However, the main key microbial players and the underlying mechanisms are still relatively unknown. In order to better characterize these processes and identify the main microorganisms involved, laboratory biodegradation experiments under methanogenic conditions were performed. Microcosms were inoculated with production and injection waters from the reservoir, and oil or 13C-labelled single hydrocarbons (e.g. n-hexadecane or 2-methylnaphthalene) were added as sole substrates. Indigenous microbiota were able to extensively degrade oil within months, depleting most of the n-alkanes in 200 days, and producing methane at a rate of 76 ± 6 µmol day-1 g-1 oil added. They could also produce heavy methane from 13C-labeled 2-methylnaphthalene, suggesting that further methanogenesis may occur from the aromatic and polyaromatic fractions of Dagang reservoir fluids. Microbial communities from oil and 2-methyl-naphthalene enrichment cultures were slightly different. Although, in both cases Deltaproteobacteria, mainly belonging to Syntrophobacterales (e.g. Syntrophobacter, Smithella or Syntrophus) and Clostridia, mostly Clostridiales, were among the most represented taxa, Gammaproteobacteria could be only identified in oil-degrading cultures. The proportion of Chloroflexi, exclusively belonging to Anaerolineales (e.g. Leptolinea, Bellilinea) was considerably higher in 2-methyl-naphthalene degrading cultures. Archaeal communities consisted almost exclusively of representatives of

  2. Non-Psychrophilic Methanogens Capable of Growth Following Long-Term Extreme Temperature Changes, with Application to Mars

    Directory of Open Access Journals (Sweden)

    Rebecca L. Mickol

    2018-04-01

    Full Text Available Although the martian environment is currently cold and dry, geomorphological features on the surface of the planet indicate relatively recent (<4 My freeze/thaw episodes. Additionally, the recent detections of near-subsurface ice as well as hydrated salts within recurring slope lineae suggest potentially habitable micro-environments within the martian subsurface. On Earth, microbial communities are often active at sub-freezing temperatures within permafrost, especially within the active layer, which experiences large ranges in temperature. With warming global temperatures, the effect of thawing permafrost communities on the release of greenhouse gases such as carbon dioxide and methane becomes increasingly important. Studies examining the community structure and activity of microbial permafrost communities on Earth can also be related to martian permafrost environments, should life have developed on the planet. Here, two non-psychrophilic methanogens, Methanobacterium formicicum and Methanothermobacter wolfeii, were tested for their ability to survive long-term (~4 year exposure to freeze/thaw cycles varying in both temperature and duration, with implications both for climate change on Earth and possible life on Mars.

  3. Non-Psychrophilic Methanogens Capable of Growth Following Long-Term Extreme Temperature Changes, with Application to Mars.

    Science.gov (United States)

    Mickol, Rebecca L; Laird, Sarah K; Kral, Timothy A

    2018-04-23

    Although the martian environment is currently cold and dry, geomorphological features on the surface of the planet indicate relatively recent (<4 My) freeze/thaw episodes. Additionally, the recent detections of near-subsurface ice as well as hydrated salts within recurring slope lineae suggest potentially habitable micro-environments within the martian subsurface. On Earth, microbial communities are often active at sub-freezing temperatures within permafrost, especially within the active layer, which experiences large ranges in temperature. With warming global temperatures, the effect of thawing permafrost communities on the release of greenhouse gases such as carbon dioxide and methane becomes increasingly important. Studies examining the community structure and activity of microbial permafrost communities on Earth can also be related to martian permafrost environments, should life have developed on the planet. Here, two non-psychrophilic methanogens, Methanobacterium formicicum and Methanothermobacter wolfeii , were tested for their ability to survive long-term (~4 year) exposure to freeze/thaw cycles varying in both temperature and duration, with implications both for climate change on Earth and possible life on Mars.

  4. Illumina sequencing-based analysis of a microbial community enriched under anaerobic methane oxidation condition coupled to denitrification revealed coexistence of aerobic and anaerobic methanotrophs.

    Science.gov (United States)

    Siniscalchi, Luciene Alves Batista; Leite, Laura Rabelo; Oliveira, Guilherme; Chernicharo, Carlos Augusto Lemos; de Araújo, Juliana Calabria

    2017-07-01

    Methane is produced in anaerobic environments, such as reactors used to treat wastewaters, and can be consumed by methanotrophs. The composition and structure of a microbial community enriched from anaerobic sewage sludge under methane-oxidation condition coupled to denitrification were investigated. Denaturing gradient gel electrophoresis (DGGE) analysis retrieved sequences of Methylocaldum and Chloroflexi. Deep sequencing analysis revealed a complex community that changed over time and was affected by methane concentration. Methylocaldum (8.2%), Methylosinus (2.3%), Methylomonas (0.02%), Methylacidiphilales (0.45%), Nitrospirales (0.18%), and Methanosarcinales (0.3%) were detected. Despite denitrifying conditions provided, Nitrospirales and Methanosarcinales, known to perform anaerobic methane oxidation coupled to denitrification (DAMO) process, were in very low abundance. Results demonstrated that aerobic and anaerobic methanotrophs coexisted in the reactor together with heterotrophic microorganisms, suggesting that a diverse microbial community was important to sustain methanotrophic activity. The methanogenic sludge was a good inoculum to enrich methanotrophs, and cultivation conditions play a selective role in determining community composition.

  5. Anaerobic metabolism of nitroaromatic compounds by sulfate-reducing and methanogenic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Boopathy, R. [Argonne National Lab., IL (United States); Kulpa, C.F. [Notre Dame Univ., IN (United States). Dept. of Biological Sciences

    1994-06-01

    Ecological observations suggest that sulfate-reducing and methanogenic bacteria might metabolize nitroaromatic compounds under anaerobic conditions if appropriate electron donors and electron acceptors are present in the environment, but this ability had not been demonstrated until recently. Most studies on the microbial metabolism of nitroaromatic compounds used aerobic microorganisms. In most cases no mineralization of nitroaromatics occurs, and only superficial modifications of the structures are reported. However, under anaerobic sulfate-reducing conditions, the nitroaromatic compounds reportedly undergo a series of reductions with the formation of amino compounds. For example, trinitrotoluene under sulfate-reducing conditions is reduced to triaminotoluene by the enzyme nitrite reductase, which is commonly found in many Desulfovibrio spp. The removal of ammonia from triaminotoluene is achieved by reductive deamination catalyzed by the enzyme reductive deaminase, with the production of ammonia and toluene. Some sulfate reducers can metabolize toluene to CO{sub 2}. Similar metabolic processes could be applied to other nitroaromatic compounds like nitrobenzene, nitrobenzoic acids, nitrophenols, and aniline. Many methanogenic bacteria can reduce nitroaromatic compounds to amino compounds. In this paper we review the anaerobic metabolic processes of nitroaromatic compounds under sulfate-reducing And methanogenic conditions.

  6. Anaerobic metabolism of nitroaromatic compounds by sulfate-reducing and methanogenic bacteria

    International Nuclear Information System (INIS)

    Boopathy, R.; Kulpa, C.F.

    1994-01-01

    Ecological observations suggest that sulfate-reducing and methanogenic bacteria might metabolize nitroaromatic compounds under anaerobic conditions if appropriate electron donors and electron acceptors are present in the environment, but this ability had not been demonstrated until recently. Most studies on the microbial metabolism of nitroaromatic compounds used aerobic microorganisms. In most cases no mineralization of nitroaromatics occurs, and only superficial modifications of the structures are reported. However, under anaerobic sulfate-reducing conditions, the nitroaromatic compounds reportedly undergo a series of reductions with the formation of amino compounds. For example, trinitrotoluene under sulfate-reducing conditions is reduced to triaminotoluene by the enzyme nitrite reductase, which is commonly found in many Desulfovibrio spp. The removal of ammonia from triaminotoluene is achieved by reductive deamination catalyzed by the enzyme reductive deaminase, with the production of ammonia and toluene. Some sulfate reducers can metabolize toluene to CO 2 . Similar metabolic processes could be applied to other nitroaromatic compounds like nitrobenzene, nitrobenzoic acids, nitrophenols, and aniline. Many methanogenic bacteria can reduce nitroaromatic compounds to amino compounds. In this paper we review the anaerobic metabolic processes of nitroaromatic compounds under sulfate-reducing And methanogenic conditions

  7. Low-Temperature (10°C Anaerobic Digestion of Dilute Dairy Wastewater in an EGSB Bioreactor: Microbial Community Structure, Population Dynamics, and Kinetics of Methanogenic Populations

    Directory of Open Access Journals (Sweden)

    Katarzyna Bialek

    2013-01-01

    Full Text Available The feasibility of anaerobic digestion of dairy wastewater at 10°C was investigated in a high height : diameter ratio EGSB reactor. Stable performance was observed at an applied organic loading rate (OLR of 0.5–2 kg COD m−3 d−1 with chemical oxygen demand (COD removal efficiencies above 85%. When applied OLR increased to values above 2 kg COD m−3 d−1, biotreatment efficiency deteriorated, with methanogenesis being the rate-limiting step. The bioreactor recovered quickly (3 days after reduction of the OLR. qPCR results showed a reduction in the abundance of hydrogenotrophic methanogenic Methanomicrobiales and Methanobacteriales throughout the steady state period followed by a sharp increase in their numbers (111-fold after the load shock. Specific methanogenic activity and maximum substrate utilising rate (Amax of the biomass at the end of trial indicated increased activity and preference towards hydrogenotrophic methanogenesis, which correlated well with the increased abundance of hydrogenotrophic methanogens. Acetoclastic Methanosaeta spp. remained at stable levels throughout the trial. However, increased apparent half-saturation constant (Km at the end of the trial indicated a decrease in the specific substrate affinity for acetate of the sludge, suggesting that Methanosaeta spp., which have high substrate affinity, started to be outcompeted in the reactor.

  8. Thermophilic methanogenic Archaea in compost material: occurrence, persistence and possible mechanisms for their distribution to other environments.

    Science.gov (United States)

    Thummes, Kathrin; Schäfer, Jenny; Kämpfer, Peter; Jäckel, Udo

    2007-12-01

    Since compost is widely used as soil amendment and the fact that during the processing of compost material high amounts of microorganisms are released into the air, we investigated whether compost may act as a carrier for thermophilic methanogens to temperate soils. All eight investigated compost materials showed a clear methane production potential between 0.01 and 0.98 micromol CH(4) g dw(-1)h(-1) at 50 degrees C. Single strand conformation polymorphism (SSCP) and cloning analysis indicated the presence of Methanosarcina thermophila, Methanoculleus thermophilus, and Methanobacterium formicicum. Bioaerosols collected during the turning of a compost pile showed both a highly similar SSCP profile compared to the corresponding compost material and clear methane production during anoxic incubation in selective medium at 50 degrees C. Both observations indicated a considerable release of thermophilic methanogens into the air. To analyse the persistence of compost-borne thermophilic methanogens in temperate oxic soils, we therefore studied their potential activity in compost and compost/soil mixtures, which was brought to a meadow soil, as well as in an agricultural soil fertilised with compost. After 24h anoxic incubation at 50 degrees C, all samples containing compost showed a clear methanogenic activity, even 1 year after application. In combination with the in vitro observed resilience of the compost-borne methanogens against desiccation and UV radiation we assume that compost material acts as an effective carrier for the distribution of thermophilic methanogens by fertilisation and wind.

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

    International Nuclear Information System (INIS)

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

    2008-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-04-15

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

  11. An improved enzyme-linked immunosorbent assay for whole-cell determination of methanogens in samples from anaerobic reactors

    DEFF Research Database (Denmark)

    Sørensen, A.H.; Ahring, B.K.

    1997-01-01

    An enzyme-linked immunosorbent assay was developed for the detection of whole cells of methanogens in samples from anaerobic continuously stirred tank digesters treating slurries of solid waste. The assay was found to allow for quantitative analysis of the most important groups of methanogens......-quality microtiter plates and the addition of dilute hydrochloric acid to the samples. In an experiment on different digester samples, the test demonstrated a unique pattern of different methanogenic strains present in each sample. The limited preparatory work required for the assay and the simple assay design make...... in samples from anaerobic digesters in a reproducible manner. Polyclonal antisera against eight strains of methanogens were employed in the test, The specificities of the antisera were increased by adsorption with cross-reacting cells. The reproducibility of the assay depended on the use of high...

  12. Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient.

    Science.gov (United States)

    Mondav, Rhiannon; McCalley, Carmody K; Hodgkins, Suzanne B; Frolking, Steve; Saleska, Scott R; Rich, Virginia I; Chanton, Jeff P; Crill, Patrick M

    2017-08-01

    Biogenic production and release of methane (CH 4 ) from thawing permafrost has the potential to be a strong source of radiative forcing. We investigated changes in the active layer microbial community of three sites representative of distinct permafrost thaw stages at a palsa mire in northern Sweden. The palsa site (intact permafrost and low radiative forcing signature) had a phylogenetically clustered community dominated by Acidobacteria and Proteobacteria. The bog (thawing permafrost and low radiative forcing signature) had lower alpha diversity and midrange phylogenetic clustering, characteristic of ecosystem disturbance affecting habitat filtering. Hydrogenotrophic methanogens and Acidobacteria dominated the bog shifting from palsa-like to fen-like at the waterline. The fen (no underlying permafrost, high radiative forcing signature) had the highest alpha, beta and phylogenetic diversity, was dominated by Proteobacteria and Euryarchaeota and was significantly enriched in methanogens. The Mire microbial network was modular with module cores consisting of clusters of Acidobacteria, Euryarchaeota or Xanthomonodales. Loss of underlying permafrost with associated hydrological shifts correlated to changes in microbial composition, alpha, beta and phylogenetic diversity associated with a higher radiative forcing signature. These results support the complex role of microbial interactions in mediating carbon budget changes and climate feedback in response to climate forcing. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  13. Toxicity assessment of inorganic nanoparticles to acetoclastic and hydrogenotrophic methanogenic activity in anaerobic granular sludge.

    Science.gov (United States)

    Gonzalez-Estrella, Jorge; Sierra-Alvarez, Reyes; Field, James A

    2013-09-15

    Release of engineered nanoparticles (NPs) to municipal wastewater from industrial and residential sources could impact biological systems in wastewater treatment plants. Methanogenic inhibition can cause failure of anaerobic waste(water) treatment. This study investigated the inhibitory effect of a wide array of inorganic NPs (Ag(0), Al₂O₃, CeO₂, Cu(0), CuO, Fe(0), Fe₂O₃, Mn₂O₃, SiO₂, TiO₂, and ZnO supplied up to 1500 mgL(-1)) to acetoclastic and hydrogenotrophic methanogenic activity of anaerobic granular sludge. Of all the NPs tested, only Cu(0) and ZnO caused severe methanogenic inhibition. The 50% inhibiting concentrations determined towards acetoclastic and hydrogenotrophic methanogens were 62 and 68 mgL(-1) for Cu(0) NP; and 87 and 250 mgL(-1) for ZnO NP, respectively. CuO NPs also caused inhibition of acetoclastic methanogens. Cu(2+) and Zn(2+) salts caused similar levels of inhibition as Cu(0) and ZnO NPs based on equilibrium soluble metal concentrations measured during the assays, suggesting that the toxicity was due to the release of metal ions by NP-corrosion. A commercial dispersant, Dispex, intended to increase NP stability did not affect the inhibitory impact of the NPs. The results taken as a whole suggest that Zn- and Cu-containing NPs can release metal ions that are inhibitory for methanogenesis. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Application of Pseudomurein Endoisopeptidase to Fluorescence In Situ Hybridization of Methanogens within the Family Methanobacteriaceae▿

    Science.gov (United States)

    Nakamura, Kohei ; Terada, Takeshi; Sekiguchi, Yuji; Shinzato, Naoya; Meng, Xian-Ying; Enoki, Miho; Kamagata, Yoichi

    2006-01-01

    In situ detection of methanogens within the family Methanobacteriaceae is sometimes known to be unsuccessful due to the difficulty in permeability of oligonucleotide probes. Pseudomurein endoisopeptidase (Pei), a lytic enzyme that specifically acts on their cell walls, was applied prior to 16S rRNA-targeting fluorescence in situ hybridization (FISH). For this purpose, pure cultured methanogens within this family, Methanobacterium bryantii, Methanobrevibacter ruminantium, Methanosphaera stadtmanae, and Methanothermobacter thermautotrophicus together with a Methanothermobacter thermautotrophicus-containing syntrophic acetate-oxidizing coculture, endosymbiotic Methanobrevibacter methanogens within an anaerobic ciliate, and an upflow anaerobic sludge blanket (UASB) granule were examined. Even without the Pei treatment, Methanobacterium bryantii and Methanothermobacter thermautotrophicus cells are relatively well hybridized with oligonucleotide probes. However, almost none of the cells of Methanobrevibacter ruminantium, Methanosphaera stadtmanae, cocultured Methanothermobacter thermautotrophicus, and the endosymbiotic methanogens and the cells within UASB granule were hybridized. Pei treatment was able to increase the probe hybridization ratio in every specimen, particularly in the specimen that had shown little hybridization. Interestingly, the hybridizing signal intensity of Methanothermobacter thermautotrophicus cells in coculture with an acetate-oxidizing H2-producing syntroph was significantly improved by Pei pretreatment, whereas the probe was well hybridized with the cells of pure culture of the same strain. We found that the difference is attributed to the differences in cell wall thicknesses between the two culture conditions. These results indicate that Pei treatment is effective for FISH analysis of methanogens that show impermeability to the probe. PMID:16950902

  15. Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition

    Directory of Open Access Journals (Sweden)

    Jacob D. Hosen

    2017-08-01

    Full Text Available Urbanization strongly influences headwater stream chemistry and hydrology, but little is known about how these conditions impact bacterial community composition. We predicted that urbanization would impact bacterial community composition, but that stream water column bacterial communities would be most strongly linked to urbanization at a watershed-scale, as measured by impervious cover, while sediment bacterial communities would correlate with environmental conditions at the scale of stream reaches. To test this hypothesis, we determined bacterial community composition in the water column and sediment of headwater streams located across a gradient of watershed impervious cover using high-throughput 16S rRNA gene amplicon sequencing. Alpha diversity metrics did not show a strong response to catchment urbanization, but beta diversity was significantly related to watershed impervious cover with significant differences also found between water column and sediment samples. Samples grouped primarily according to habitat—water column vs. sediment—with a significant response to watershed impervious cover nested within each habitat type. Compositional shifts for communities in urbanized streams indicated an increase in taxa associated with human activity including bacteria from the genus Polynucleobacter, which is widespread, but has been associated with eutrophic conditions in larger water bodies. Another indicator of communities in urbanized streams was an OTU from the genus Gallionella, which is linked to corrosion of water distribution systems. To identify changes in bacterial community interactions, bacterial co-occurrence networks were generated from urban and forested samples. The urbanized co-occurrence network was much smaller and had fewer co-occurrence events per taxon than forested equivalents, indicating a loss of keystone taxa with urbanization. Our results suggest that urbanization has significant impacts on the community composition

  16. Exocellular electron transfer in anaerobic microbial communities

    NARCIS (Netherlands)

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

    2006-01-01

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

  17. Molecular Biology and Physiology of Methanogenic Archaebacteria

    Science.gov (United States)

    1989-06-27

    anaerobic food chains, the methanogens contribute to the mineralization of large amounts of organic matter. The end product of their metabolism...of radiolabelled substrate to product [8; Worrell and Nagle, in preparation]. Strain RT103, a formate auxotroph was isolated from the kanamycin...methylmercaptopurine riboside 0. 16 Bacteriocidald 8-aza-2, 6-diaminopurine 0.0011 6-thioguanine 0.0004 8-azaguanine 0.0004 6- mercaptopurine 0 8

  18. Microbial community composition is consistent across anaerobic digesters processing wheat-based fuel ethanol waste streams.

    Science.gov (United States)

    Town, Jennifer; Annand, Holly; Pratt, Dyan; Dumonceaux, Tim; Fonstad, Terrance

    2014-04-01

    Biochemical methane potential (BMP) assays were conducted on byproducts from dry-grind wheat-based ethanol plants amended with feedlot manure at two input ratios. Whole stillage (WST), thin stillage (TST) and wet cake (WCK) were tested alone and with 1:1 and 2:1 ratios (VS basis) of byproduct:feedlot manure in bench-scale batch reactors. The addition of manure increased both the rate and consistency of methane production in triplicate reactors. In addition, digesters co-digesting thin stillage and cattle manure at 1:1 and 2:1 stillage:manure produced 125% and 119% expected methane based on the biomethane potential of each substrate digested individually. Bacterial community analysis using universal target amplification and pyrosequencing indicated there was a numerically dominant core of 42 bacteria that was universally present in the reactors regardless of input material. A smaller-scale analysis of the archaeal community showed that both hydrogenotrophic and acetoclastic methanogens were present in significant quantities. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

  19. Expression of a bacterial catalase in a strictly anaerobic methanogen significantly increases tolerance to hydrogen peroxide but not oxygen

    Science.gov (United States)

    Jennings, Matthew E.; Schaff, Cody W.; Horne, Alexandra J.; Lessner, Faith H.

    2014-01-01

    Haem-dependent catalase is an antioxidant enzyme that degrades H2O2, producing H2O and O2, and is common in aerobes. Catalase is present in some strictly anaerobic methane-producing archaea (methanogens), but the importance of catalase to the antioxidant system of methanogens is poorly understood. We report here that a survey of the sequenced genomes of methanogens revealed that the majority of species lack genes encoding catalase. Moreover, Methanosarcina acetivorans is a methanogen capable of synthesizing haem and encodes haem-dependent catalase in its genome; yet, Methanosarcina acetivorans cells lack detectable catalase activity. However, inducible expression of the haem-dependent catalase from Escherichia coli (EcKatG) in the chromosome of Methanosarcina acetivorans resulted in a 100-fold increase in the endogenous catalase activity compared with uninduced cells. The increased catalase activity conferred a 10-fold increase in the resistance of EcKatG-induced cells to H2O2 compared with uninduced cells. The EcKatG-induced cells were also able to grow when exposed to levels of H2O2 that inhibited or killed uninduced cells. However, despite the significant increase in catalase activity, growth studies revealed that EcKatG-induced cells did not exhibit increased tolerance to O2 compared with uninduced cells. These results support the lack of catalase in the majority of methanogens, since methanogens are more likely to encounter O2 rather than high concentrations of H2O2 in the natural environment. Catalase appears to be a minor component of the antioxidant system in methanogens, even those that are aerotolerant, including Methanosarcina acetivorans. Importantly, the experimental approach used here demonstrated the feasibility of engineering beneficial traits, such as H2O2 tolerance, in methanogens. PMID:24222618

  20. Microbial ecology of methanogenic crude oil biodegradation; from microbial consortia to heavy oil

    Energy Technology Data Exchange (ETDEWEB)

    Head, Ian M.; Maguire, Michael J.; Sherry, Angela; Grant, Russell; Gray, Neil D.; Aitken, Carolyn M.; Martin Jones, D.; Oldenburg, Thomas B.P.; Larter, Stephen R. [Petroleum Research Group, Geosciences, University of Calgary (Canada)

    2011-07-01

    This paper presents the microbial ecology of methanogenic crude oil biodegradation. Biodegraded petroleum reservoirs are one of the most dramatic indications of the deep biosphere. It is estimated that heavy oil and oil sands will account for a considerable amount of energy production in the future. Carbon, a major resource for deep subsurface microorganisms, and energy are contained in large quantities in petroleum reservoirs. The aerobic to anaerobic paradigm shift is explained. A key process for in-situ oil biodegradation in petroleum reservoirs is methanogenesis. New paradigms for in-reservoir crude oil biodegradation are discussed. Variations in anaerobic degradation of crude oil hydrocarbons are also discussed. A graph shows the different patterns of crude oil biodegradation under sulfate-reducing and methanogenic conditions. Alternative anaerobic alkane activation mechanisms are also shown. From the study, it can be concluded that methanogenic crude oil degradation is of global importance and led to the establishment of the world's enormous heavy oil deposits.

  1. Cultivation-independent analysis of archaeal and bacterial communities of the formation water in an Indian coal bed to enhance biotransformation of coal into methane

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Durgesh Narain; Kumar, Ashok; Tripathi, Anil Kumar [Banaras Hindu Univ., Varanasi (India). School of Biotechnolgy; Sarbhai, Munish Prasad [Oil and Natural Gas Commission, Ahmedabad (India). Inst. of Reservoir Studies

    2012-02-15

    Biogenic origin of the significant proportion of coal bed methane has indicated the role of microbial communities in methanogenesis. By using cultivation-independent approach, we have analysed the archaeal and bacterial community present in the formation water of an Indian coal bed at 600-700 m depth to understand their role in methanogenesis. Presence of methanogens in the formation water was inferred by epifluorescence microscopy and PCR amplification of mcrA gene. Archaeal 16S rRNA gene clone library from the formation water metagenome was dominated by methanogens showing similarity to Methanobacterium, Methanothermobacter and Methanolinea whereas the clones of bacterial 16S rRNA gene library were closely related to Azonexus, Azospira, Dechloromonas and Thauera. Thus, microbial community of the formation water consisted of predominantly hydrogenotrophic methanogens and the proteobacteria capable of nitrogen fixation, nitrate reduction and polyaromatic compound degradation. Methanogenic potential of the microbial community present in the formation water was elucidated by the production of methane in the enrichment culture, which contained 16S rRNA gene sequences showing close relatedness to the genus Methanobacterium. Microcosm using formation water as medium as well as a source of inoculum and coal as carbon source produced significant amount of methane which increased considerably by the addition of nitrite. The dominance of Diaphorobacter sp. in nitrite amended microcosm indicated their important role in supporting methanogenesis in the coal bed. This is the first study indicating existence of methanogenic and bacterial community in an Indian coal bed that is capable of in situ biotransformation of coal into methane. (orig.)

  2. Microbial community structure and soil pH correspond to methane production in Arctic Alaska soils.

    Science.gov (United States)

    Wagner, Robert; Zona, Donatella; Oechel, Walter; Lipson, David

    2017-08-01

    While there is no doubt that biogenic methane production in the Arctic is an important aspect of global methane emissions, the relative roles of microbial community characteristics and soil environmental conditions in controlling Arctic methane emissions remains uncertain. Here, relevant methane-cycling microbial groups were investigated at two remote Arctic sites with respect to soil potential methane production (PMP). Percent abundances of methanogens and iron-reducing bacteria correlated with increased PMP, while methanotrophs correlated with decreased PMP. Interestingly, α-diversity of the methanogens was positively correlated with PMP, while β-diversity was unrelated to PMP. The β-diversity of the entire microbial community, however, was related to PMP. Shannon diversity was a better correlate of PMP than Simpson diversity across analyses, while rarefied species richness was a weak correlate of PMP. These results demonstrate the following: first, soil pH and microbial community structure both probably control methane production in Arctic soils. Second, there may be high functional redundancy in the methanogens with regard to methane production. Third, iron-reducing bacteria co-occur with methanogens in Arctic soils, and iron-reduction-mediated effects on methanogenesis may be controlled by α- and β-diversity. And finally, species evenness and rare species abundances may be driving relationships between microbial groups, influencing Arctic methane production. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  3. Different substrates and starter inocula govern microbial community structures in biogas reactors.

    Science.gov (United States)

    Satpathy, Preseela; Steinigeweg, Sven; Cypionka, Heribert; Engelen, Bert

    2016-01-01

    The influence of different starter inocula on the microbial communities in biogas batch reactors fed with fresh maize and maize silage as substrates was investigated. Molecular biological analysis by Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rRNA gene fragments showed that each inoculum bore specific microbial communities with varying predominant phylotypes. Both, bacterial and archaeal DGGE profiles displayed three distinct communities that developed depending on the type of inoculum. Although maize and silage are similar substrates, different communities dominated the lactate-rich silage compared to lactate-free fresh maize. Cluster analysis of DGGE gels showed the communities of the same substrates to be stable with their respective inoculum. Bacteria-specific DGGE analysis revealed a rich diversity with Firmicutes being predominant. The other abundant phylotypes were Bacteroidetes and Synergistetes. Archaea-specific DGGE analysis displayed less diverse community structures, identifying members of the Methanosarcinales as the dominant methanogens present in all the three biogas digesters. In general, the source of inoculum played a significant role in shaping microbial communities. Adaptability of the inoculum to the substrates fed also influenced community compositions which further impacted the rates of biogas production.

  4. Salinity drives archaeal distribution patterns in high altitude lake sediments on the Tibetan Plateau.

    Science.gov (United States)

    Liu, Yongqin; Priscu, John C; Xiong, Jinbo; Conrad, Ralf; Vick-Majors, Trista; Chu, Haiyan; Hou, Juzhi

    2016-03-01

    Archaeal communities and the factors regulating their diversity in high altitude lakes are poorly understood. Here, we provide the first high-throughput sequencing study of Archaea from Tibetan Plateau lake sediments. We analyzed twenty lake sediments from the world's highest and largest plateau and found diverse archaeal assemblages that clustered into groups dominated by methanogenic Euryarchaeota, Crenarchaeota and Halobacteria/mixed euryarchaeal phylotypes. Statistical analysis inferred that salinity was the major driver of community composition, and that archaeal diversity increased with salinity. Sediments with the highest salinities were mostly dominated by Halobacteria. Crenarchaeota dominated at intermediate salinities, and methanogens were present in all lake sediments, albeit most abundant at low salinities. The distribution patterns of the three functional types of methanogens (hydrogenotrophic, acetotrophic and methylotrophic) were also related to changes in salinity. Our results show that salinity is a key factor controlling archaeal community diversity and composition in lake sediments on a spatial scale that spans nearly 2000 km on the Tibetan Plateau. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. Detection of methanogenic archaea in seawater particles and the digestive tract of a marine fish species

    NARCIS (Netherlands)

    van der Maarel, MJEC; Sprenger, W; Haanstra, R; Forney, LJ

    1999-01-01

    A methanogen-specific nested PCR approach was used to detect methanogenic archaea in seawater particles of the North Sea and the feces and the digestive tract of flounder (Platichthys flesus), a fish found in the North Sea. A number of 16S rDNA sequences with 97.6-99.5% similarity to

  6. Hydrogen limitation and syntrophic growth among natural assemblages of thermophilic methanogens at deep-sea hydrothermal vents

    Directory of Open Access Journals (Sweden)

    Begüm D. Topçuoğlu

    2016-08-01

    Full Text Available Thermophilic methanogens are common autotrophs at hydrothermal vents, but their growth constraints and dependence on H2 syntrophy in situ are poorly understood. Between 2012 and 2015, methanogens and H2-producing heterotrophs were detected by growth at 80°C and 55°C at most diffuse (7-40°C hydrothermal vent sites at Axial Seamount. Microcosm incubations of diffuse hydrothermal fluids at 80°C and 55°C demonstrated that growth of thermophilic and hyperthermophilic methanogens is primarily limited by H2 availability. Amendment of microcosms with NH4+ generally had no effect on CH4 production. However, annual variations in abundance and CH4 production were observed in relation to the eruption cycle of the seamount. Microcosm incubations of hydrothermal fluids at 80°C and 55°C supplemented with tryptone and no added H2 showed CH4 production indicating the capacity in situ for methanogenic H2 syntrophy. 16S rRNA genes were found in 80°C microcosms from H2-producing archaea and H2-consuming methanogens, but not for any bacteria. In 55°C microcosms, sequences were found from the H2-producing bacteria and H2-consuming methanogens and sulfate-reducing bacteria. A co-culture of representative organisms showed that Thermococcus paralvinellae supported the syntrophic growth of Methanocaldococcus bathoardescens at 82°C and Methanothermococcus sp. strain BW11 at 60°C. The results demonstrate that modeling of subseafloor methanogenesis should focus primarily on H2 availability and temperature, and that thermophilic H2 syntrophy can support methanogenesis within natural microbial assemblages and may be an important energy source for thermophilic autotrophs in marine geothermal environments.

  7. Methanogenic H2 syntrophy among thermophiles: a model of metabolism, adaptation and survival in the subsurface

    Science.gov (United States)

    Topcuoglu, B. D.; Stewart, L. C.; Butterfield, D. A.; Huber, J. A.; Holden, J. F.

    2016-12-01

    Approximately 1 giga ton (Gt, 1015 g) of CH4 is formed globally per year from H2, CO2 and acetate through methanogenesis, largely by methanogens growing in syntrophic association with anaerobic microbes that hydrolyze and ferment biopolymers. However, our understanding of methanogenesis in hydrothermal regions of the subseafloor and potential syntrophic methanogenesis at thermophilic temperatures (i.e., >50°C) is nascent. In this study, the growth of natural assemblages of thermophilic methanogens from Axial Seamount was primarily limited by H2 availability. Heterotrophs supported thermophilic methanogenesis by H2 syntrophy in microcosm incubations of hydrothermal fluids at 55°C and 80°C supplemented with tryptone only. Based on 16S rRNA gene sequencing, only heterotrophic archaea that produce H2, H2-consuming methanogens, and sulfate reducing archaea were found in 80°C tryptone microcosms from Marker 113 vent. No bacteria were found. In 55°C tryptone microcosms, sequences were found from H2-producing bacteria and H2-consuming methanogens and sulfate-reducing bacteria. In order to model the impact of H2 syntrophy at hyperthemophilic temperatures, a co-culture was established consisting of the H2-producing hyperthermophilic heterotroph Thermococcus paralvinellae and a H2-consuming hyperthermophilic methanogen Methanocaldococcus bathoardescens. When grown alone in a chemostat, the growth rates and steady-state cell concentrations of T. paralvinellae decreased significantly when a high H2 (70 µM) background was present. H2 inhibition was ameliorated by the production of formate, but in silico modeling suggests less energetic yield for the cells. H2 syntrophy relieved H2 inhibition for both the heterotroph and the methanogenic partners. The results demonstrate that thermophilic H2 syntrophy can support methanogenesis within natural microbial assemblages and may be an important alternative energy source for thermophilic autotrophs in marine geothermal environments.

  8. Roles of thermophilic thiosulfate-reducing bacteria and methanogenic archaea in the biocorrosion of oil pipelines

    Directory of Open Access Journals (Sweden)

    Renxing eLiang

    2014-03-01

    Full Text Available Thermophilic sulfide-producing microorganisms from an oil pipeline network were enumerated with different sulfur oxyanions as electron acceptors at 55 oC. Most-probable number (MPN analysis showed that thiosulfate-reducing bacteria were the most numerous sulfidogenic microorganisms in pipeline inspection gauge (PIG scrapings. Thiosulfate-reducing and methanogenic enrichments were obtained from the MPN cultures that were able to use yeast extract as the electron donor. Molecular analysis revealed that both enrichments harbored the same dominant bacterium, which belonged to the genus Anaerobaculum. The dominant archaeon in the methanogenic enrichment was affiliated with the genus Methanothermobacter. With yeast extract as the electron donor, the general corrosion rate by the thiosulfate-reducing enrichment (8.43 ± 1.40 milli-inch per year, abbreviated as mpy was about 5.5 times greater than the abiotic control (1.49 ± 0.15 mpy, while the comparable measures for the methanogenic culture were 2.03 ± 0.49 mpy and 0.62 ± 0.07 mpy, respectively. Total iron analysis in the cultures largely accounted for the mass loss of iron measured in the weight loss determinations. Profilometry analysis of polished steel coupons incubated in the presence of the thiosulfate-reducing enrichment revealed 59 pits over an area of 71.16 mm2, while only 6 pits were evident in the corresponding methanogenic incubations. The results show the importance of thiosulfate-utilizing, sulfide-producing fermentative bacteria such as Anaerobaculum sp. in the corrosion of carbon steel, but also suggest that Anaerobaculum sp. are of far less concern when growing syntrophically with methanogens.

  9. Roles of thermophilic thiosulfate-reducing bacteria and methanogenic archaea in the biocorrosion of oil pipelines.

    Science.gov (United States)

    Liang, Renxing; Grizzle, Robert S; Duncan, Kathleen E; McInerney, Michael J; Suflita, Joseph M

    2014-01-01

    Thermophilic sulfide-producing microorganisms from an oil pipeline network were enumerated with different sulfur oxyanions as electron acceptors at 55°C. Most-probable number (MPN) analysis showed that thiosulfate-reducing bacteria were the most numerous sulfidogenic microorganisms in pipeline inspection gauge (PIG) scrapings. Thiosulfate-reducing and methanogenic enrichments were obtained from the MPN cultures that were able to use yeast extract as the electron donor. Molecular analysis revealed that both enrichments harbored the same dominant bacterium, which belonged to the genus Anaerobaculum. The dominant archaeon in the methanogenic enrichment was affiliated with the genus Methanothermobacter. With yeast extract as the electron donor, the general corrosion rate by the thiosulfate-reducing enrichment (8.43 ± 1.40 milli-inch per year, abbreviated as mpy) was about 5.5 times greater than the abiotic control (1.49 ± 0.15 mpy), while the comparable measures for the methanogenic culture were 2.03 ± 0.49 mpy and 0.62 ± 0.07 mpy, respectively. Total iron analysis in the cultures largely accounted for the mass loss of iron measured in the weight loss determinations. Profilometry analysis of polished steel coupons incubated in the presence of the thiosulfate-reducing enrichment revealed 59 pits over an area of 71.16 mm(2), while only 6 pits were evident in the corresponding methanogenic incubations. The results show the importance of thiosulfate-utilizing, sulfide-producing fermentative bacteria such as Anaerobaculum sp. in the corrosion of carbon steel, but also suggest that Anaerobaculum sp. are of far less concern when growing syntrophically with methanogens.

  10. Relating Anaerobic Digestion Microbial Community and Process Function : Supplementary Issue: Water Microbiology

    Directory of Open Access Journals (Sweden)

    Kaushik Venkiteshwaran

    2015-01-01

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

  11. Compositional differences in simulated root exudates elicit a limited functional and compositional response in soil microbial communities.

    Science.gov (United States)

    Strickland, Michael S; McCulley, Rebecca L; Nelson, Jim A; Bradford, Mark A

    2015-01-01

    Inputs of low molecular weight carbon (LMW-C) to soil - primarily via root exudates- are expected to be a major driver of microbial activity and source of stable soil organic carbon. It is expected that variation in the type and composition of LMW-C entering soil will influence microbial community composition and function. If this is the case then short-term changes in LMW-C inputs may alter processes regulated by these communities. To determine if change in the composition of LMW-C inputs influences microbial community function and composition, we conducted a 90 day microcosm experiment whereby soils sourced from three different land covers (meadows, deciduous forests, and white pine stands) were amended, at low concentrations, with one of eight simulated root exudate treatments. Treatments included no addition of LMW-C, and the full factorial combination of glucose, glycine, and oxalic acid. After 90 days, we conducted a functional response assay and determined microbial composition via phospholipid fatty acid analysis. Whereas we noted a statistically significant effect of exudate treatments, this only accounted for ∼3% of the variation observed in function. In comparison, land cover and site explained ∼46 and ∼41% of the variation, respectively. This suggests that exudate composition has little influence on function compared to site/land cover specific factors. Supporting the finding that exudate effects were minor, we found that an absence of LMW-C elicited the greatest difference in function compared to those treatments receiving any LMW-C. Additionally, exudate treatments did not alter microbial community composition and observable differences were instead due to land cover. These results confirm the strong effects of land cover/site legacies on soil microbial communities. In contrast, short-term changes in exudate composition, at meaningful concentrations, may have little impact on microbial function and composition.

  12. New approach to control the methanogenic reactor of a two-phase anaerobic digestion system.

    Science.gov (United States)

    von Sachs, Jürgen; Meyer, Ulrich; Rys, Paul; Feitkenhauer, Heiko

    2003-03-01

    A new control strategy for the methanogenic reactor of a two-phase anaerobic digestion system has been developed and successfully tested on the laboratory scale. The control strategy serves the purpose to detect inhibitory effects and to achieve good conversion. The concept is based on the idea that volatile fatty acids (VFA) can be measured in the influent of the methanogenic reactor by means of titration. Thus, information on the output (methane production) and input of the methanogenic reactor is available, and a (carbon) mass balance can be obtained. The control algorithm comprises a proportional/integral structure with the ratio of (a) the methane production rate measured online and (b) a maximum methane production rate expected (derived from the stoichiometry) as a control variable. The manipulated variable is the volumetric feed rate. Results are shown for an experiment with VFA (feed) concentration ramps and for experiments with sodium chloride as inhibitor.

  13. Invasion of nitrite oxidizer dominated communities: interactions between propagule pressure and community composition

    DEFF Research Database (Denmark)

    Kinnunen, Marta; Dechesne, Arnaud; Albrechtsen, Hans-Jørgen

    consider a broader community ecology framework. For example, the effect of propagule pressure, often studied in macro-ecology, has rarely been examined for microbial communities. Also, the interactions between processes governing community assembly and propagule pressure on invasion success have never been...... by nitrite oxidizer strain (Candidatus Nitrotoga sp. HW29) at 3 different propagule pressures. The reactors were then operated another 2 weeks before analyzing community composition by targeted qPCRs and 16S rRNA gene amplicon analysis. We successfully assembled resident communities with different ratios...

  14. Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens

    Directory of Open Access Journals (Sweden)

    Maryam Rezadehbashi

    2018-02-01

    Full Text Available Biochemical reactors (BCRs based on the stimulation of sulphate-reducing microorganisms (SRM are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations.

  15. Stress management skills in the subsurface: H2 stress on thermophilic heterotrophs and methanogens

    Science.gov (United States)

    Topcuoglu, B. D.; Holden, J. F.

    2017-12-01

    Marine hyperthermophilic heterotrophs and methanogens belonging to the Thermococcales and Methanococcales are often found in subsurface environments such as coal and shale beds, marine sediments, and oil reservoirs where they encounter H2 stress conditions. It is important to study the H2 stress survival strategies of these organisms and their cooperation with one another for survival to better understand their biogeochemical impact in hot subsurface environments. In this study, we have shown that H2 inhibition changed the growth kinetics and the transcriptome of Thermococcus paralvinellae. We observed a significant decrease in batch phase growth rates and cell concentrations with high H2 background. Produced metabolite production measurements, RNA-seq analyses of differentially expressed genes and in silico experiments we performed with the T. paralvinellae metabolic model showed that T. paralvinellae produces formate by a formate hydrogenlyase to survive H2 inhibition. We have also shown that H2 limitation caused a significant decrease in batch phase growth rates and methane production rates of the methanogen, Methanocaldococcus jannaschii. H2 stress of both organisms can be ameliorated by syntrophic growth. H2 syntrophy was demonstrated in microcosm incubations for a natural assemblage of Thermococcus and hyperthermophilic methanogens present in hydrothermal fluid samples. This project aims to describe how a hyperthermophilic heterotroph and a hyperthermophilic methanogen eliminate H2 stress and explore cooperation among thermophiles in the hot subsurface.

  16. Immobilization Patterns and Dynamics of Acetate-Utilizing Methanogens Immobilized in Sterile Granular Sludge in Upflow Anaerobic Sludge Blanket Reactors

    Science.gov (United States)

    Schmidt, Jens Ejbye; Ahring, Birgitte Kjær

    1999-01-01

    Sterile granular sludge was inoculated with either Methanosarcina mazeii S-6, Methanosaeta concilii GP-6, or both species in acetate-fed upflow anaerobic sludge blanket (UASB) reactors to investigate the immobilization patterns and dynamics of aceticlastic methanogens in granular sludge. After several months of reactor operation, the methanogens were immobilized, either separately or together. The fastest immobilization was observed in the reactor containing M. mazeii S-6. The highest effluent concentration of acetate was observed in the reactor with only M. mazeii S-6 immobilized, while the lowest effluent concentration of acetate was observed in the reactor where both types of methanogens were immobilized together. No changes were observed in the kinetic parameters (Ks and μmax) of immobilized M. concilii GP-6 or M. mazeii S-6 compared with suspended cultures, indicating that immobilization does not affect the growth kinetics of these methanogens. An enzyme-linked immunosorbent assay using polyclonal antibodies against either M. concilii GP-6 or M. mazeii S-6 showed significant variations in the two methanogenic populations in the different reactors. Polyclonal antibodies were further used to study the spatial distribution of the two methanogens. M. concilii GP-6 was immobilized only on existing support material without any specific pattern. M. mazeii S-6, however, showed a different immobilization pattern: large clumps were formed when the concentration of acetate was high, but where the acetate concentration was low this strain was immobilized on support material as single cells or small clumps. The data clearly show that the two aceticlastic methanogens immobilize differently in UASB systems, depending on the conditions found throughout the UASB reactor. PMID:10049862

  17. Effect of different ammonia sources on aceticlastic and hydrogenotrophic methanogens

    DEFF Research Database (Denmark)

    Tian, Hailin; Fotidis, Ioannis; Kissas, Konstantinos

    2018-01-01

    Ammonium chloride (NH4Cl) was usually used as a model ammonia source to simulate ammonia inhibition during anaerobic digestion (AD) of nitrogen-rich feedstocks. However, ammonia in AD originates mainly from degradation of proteins, urea and nucleic acids, which is distinct from NH4Cl. Thus......, in this study, the inhibitory effect of a “natural” ammonia source (urea) and NH4Cl, on four pure methanogenic strains (aceticlastic: Methanosarcina thermophila, Methanosarcina barkeri; hydrogenotrophic: Methanoculleus bourgensis, Methanoculleus thermophilus), was assessed under mesophilic (37 °C......) and thermophilic (55 °C) conditions. The results showed that urea hydrolysis increased pH significantly to unsuitable levels for methanogenic growth, while NH4Cl had a negligible effect on pH. After adjusting initial pH to 7 and 8, urea was significantly stronger inhibitor with longer lag phases to methanogenesis...

  18. Antibiotic degradation and microbial community structures during acidification and methanogenesis of swine manure containing chlortetracycline or oxytetracycline.

    Science.gov (United States)

    Yin, Fubin; Dong, Hongmin; Zhang, Wanqin; Zhu, Zhiping; Shang, Bin

    2018-02-01

    Anaerobic digestion (AD) has been applied to animal manure stabilization, and antibiotics is frequently found in animal manure. However, antibiotic degradation and microbial community structures during two-stage AD (acidification and methanogenesis) remain poorly understood. This experiments on two-stage anaerobic swine manure digesters were performed to investigate the degradation mechanisms and effects of chlortetracycline (CTC) and oxytetracycline (OTC) on microbial community structures. Results showed that acidification and methanogenesis showed good degradation performance for manure containing CTC and OTC at 60 and 40 mg/kg·TS, respectively. CTC and OTC were degraded by 59.8% and 41.3% in the acidogenic stage and by 76.3% and 78.3% in the methanogenic stage, respectively. CTC and OTC negatively affected bacterial community in methanogenic and acidogenic stages, respectively. They also adversely influenced the archaeal species in the methanogenic stage. Two-stage AD was proposed to treat manure containing antibiotics and to reduce the negative effects of antibiotics on AD. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. THE EFFECT OF METHANOGENIC INHIBITOR FEED ON PROPIONIC ACID AND LAMB MEAT CHEMICAL QUALITY

    Directory of Open Access Journals (Sweden)

    E. Suryanto

    2012-09-01

    Full Text Available This study aimed to determine the effect of medium chain fatty acids (MCFA on propionic acids and lamb meat chemical quality. The treatment given was R1: feed without medium chain fatty acids (MCFA, while R2 dan R3 were the feed contained 1.0% and 1.5% of MCFA, respectively. The twelve heads of lambs yearling weight of 16-17 kg were used as materials. Biological trial was done for three months and then was slaughtered. Before being slaughtered, the animal was taken rumen fluid to be analyzed for propionic acid. The carcass was sampled to be analyzed for chemical composition, cholesterol and fatty acids content. This study showed that methanogenic inhibitor feed with 1.0-1.5% MCFA could be used as sheep feed, and the results: the propionic acid content in rumen increased 29.59 – 36.11%. The cholesterol content decreased 7.14-10.06%. For the meat fatty acids composition, unsaturated fatty acids increased 9.05 – 17.96%. while saturated fatty acid decreased 6.59 – 11.88%.

  20. Zero-valent iron enhanced methanogenic activity in anaerobic digestion of waste activated sludge after heat and alkali pretreatment.

    Science.gov (United States)

    Zhang, Yaobin; Feng, Yinghong; Quan, Xie

    2015-04-01

    Heat or alkali pretreatment is the effective method to improve hydrolysis of waste sludge and then enhance anaerobic sludge digestion. However the pretreatment may inactivate the methanogens in the sludge. In the present work, zero-valent iron (ZVI) was used to enhance the methanogenic activity in anaerobic sludge digester under two methanogens-suppressing conditions, i.e. heat-pretreatment and alkali condition respectively. With the addition of ZVI, the lag time of methane production was shortened, and the methane yield increased by 91.5% compared to the control group. The consumption of VFA was accelerated by ZVI, especially for acetate, indicating that the acetoclastic methanogenesis was enhanced. In the alkali-condition experiment, the hydrogen produced decreased from 27.6 to 18.8 mL when increasing the ZVI dosage from 0 to 10 g/L. Correspondingly, the methane yield increased from 1.9 to 32.2 mL, which meant that the H2-utilizing methanogenes was enriched. These results suggested that the addition of ZVI into anaerobic digestion of sludge after pretreated by the heat or alkali process could efficiently recover the methanogenic activity and increase the methane production and sludge reduction. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Controls on bacterial and archaeal community structure and greenhouse gas production in natural, mined, and restored Canadian peatlands

    Directory of Open Access Journals (Sweden)

    Nathan eBasiliko

    2013-07-01

    Full Text Available Northern peatlands are important global C reservoirs, largely because of their slow rates of microbial C mineralization. Particularly in sites that are heavily influenced by anthropogenic disturbances, there is scant information about microbial ecology and whether or not microbial community structure influences greenhouse gas production. This work characterized communities of bacteria and archaea using terminal restriction fragment length polymorphism and sequence analysis of 16S rRNA and functional genes across eight natural, mined, or restored peatlands in two locations in eastern Canada. Correlations were explored among chemical properties of peat, bacterial and archaeal community structure, and carbon dioxide and methane production rates under oxic and anoxic conditions. Bacteria and archaea similar to those found in other peat soil environments were detected. In contrast to other reports, methanogen diversity was low in our study, with only 2 groups of known or suspected methanogens. Although mining and restoration affected substrate availability and microbial activity, these land-uses did not consistently affect bacterial or archaeal community composition. In fact, larger differences were observed between the two locations and between oxic and anoxic peat samples than between mined and restored sites, with anoxic samples characterized by less detectable bacterial diversity and stronger dominance by members of the phylum Acidobacteria. There were also no apparent strong linkages between prokaryote community structure and methane or carbon dioxide production, suggesting that different organisms exhibit functional redundancy and/or that the same taxa function at very different rates when exposed to different peat substrates. In contrast to other earlier work focusing on fungal communities across similar mined and restored peatlands, bacterial and archaeal communities appeared to be more resistant or resilient to peat substrate changes brought

  2. Methanogenic population dynamics during startup of a full-scale anaerobic sequencing batch reactor treating swine waste.

    Science.gov (United States)

    Angenent, Largus T; Sung, Shihwu; Raskin, Lutgarde

    2002-11-01

    Changes in methanogenic population levels were followed during startup of a full-scale, farm-based anaerobic sequencing batch reactor (ASBR) and these changes were linked to operational and performance data. The ASBR was inoculated with anaerobic digester sludge from a municipal wastewater treatment facility. During an acclimation period of approximately 3 months, the ASBR content was diluted to maintain a total ammonia-N level of approximately 2000mg l(-1). After this acclimation period, the volatile solids loading rate was increased to its design value of 1.7g l(-1) day(-1) with a 15-day hydraulic retention time, which increased the total ammonia-N level in the ASBR to approximately 3,600 mg l(-1). The 16S ribosomal RNA (rRNA) levels of the acetate-utilizing methanogens of the genus Methanosarcina decreased from 3.8% to 1.2% (expressed as a percentage of the total 16S rRNA levels) during this period, while the 16S rRNA levels of Methanosaeta concilii remained low (below 2.2%). Methane production and reactor performance were not affected as the 16S rRNA levels of the hydrogen-utilizing methanogens of the order Methanomicrobiales increased from 2.3% to 7.0%. Hence, it is likely that during operation with high ammonia levels, the major route of methane production is through a syntrophic relationship between acetate-oxidizing bacteria and hydrogen-utilizing methanogens. Anaerobic digestion at total ammonia-N levels exceeding 3500mg l(-1) was sustainable apparently due to the acclimation of hydrogen-utilizing methanogens to high ammonia levels.

  3. Effects of high salinity wastewater on methanogenic sludge bed systems

    NARCIS (Netherlands)

    Ismail, S.; Gonzalez-Contreras, P.A.; Jeison, D.A.; Lier, van J.B.

    2008-01-01

    The attainable loading potentials of anaerobic sludge bed systems are strongly dependent on the growth of granular biomass with a particular wastewater. Experiments were conducted to determine the effects of high salinity wastewater on the biological and physical properties of methanogenic sludge.

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

    Directory of Open Access Journals (Sweden)

    David eWilkins

    2015-10-01

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

  5. The community ecology of pathogens: coinfection, coexistence and community composition.

    Science.gov (United States)

    Seabloom, Eric W; Borer, Elizabeth T; Gross, Kevin; Kendig, Amy E; Lacroix, Christelle; Mitchell, Charles E; Mordecai, Erin A; Power, Alison G

    2015-04-01

    Disease and community ecology share conceptual and theoretical lineages, and there has been a resurgence of interest in strengthening links between these fields. Building on recent syntheses focused on the effects of host community composition on single pathogen systems, we examine pathogen (microparasite) communities using a stochastic metacommunity model as a starting point to bridge community and disease ecology perspectives. Such models incorporate the effects of core community processes, such as ecological drift, selection and dispersal, but have not been extended to incorporate host-pathogen interactions, such as immunosuppression or synergistic mortality, that are central to disease ecology. We use a two-pathogen susceptible-infected (SI) model to fill these gaps in the metacommunity approach; however, SI models can be intractable for examining species-diverse, spatially structured systems. By placing disease into a framework developed for community ecology, our synthesis highlights areas ripe for progress, including a theoretical framework that incorporates host dynamics, spatial structuring and evolutionary processes, as well as the data needed to test the predictions of such a model. Our synthesis points the way for this framework and demonstrates that a deeper understanding of pathogen community dynamics will emerge from approaches working at the interface of disease and community ecology. © 2015 John Wiley & Sons Ltd/CNRS.

  6. Methanogenic activity tests by Infrared Tunable Diode Laser Absorption Spectroscopy.

    Science.gov (United States)

    Martinez-Cruz, Karla; Sepulveda-Jauregui, Armando; Escobar-Orozco, Nayeli; Thalasso, Frederic

    2012-10-01

    Methanogenic activity (MA) tests are commonly carried out to estimate the capability of anaerobic biomass to treat effluents, to evaluate anaerobic activity in bioreactors or natural ecosystems, or to quantify inhibitory effects on methanogenic activity. These activity tests are usually based on the measurement of the volume of biogas produced by volumetric, pressure increase or gas chromatography (GC) methods. In this study, we present an alternative method for non-invasive measurement of methane produced during activity tests in closed vials, based on Infrared Tunable Diode Laser Absorption Spectroscopy (MA-TDLAS). This new method was tested during model acetoclastic and hydrogenotrophic methanogenic activity tests and was compared to a more traditional method based on gas chromatography. From the results obtained, the CH(4) detection limit of the method was estimated to 60 ppm and the minimum measurable methane production rate was estimated to 1.09(.)10(-3) mg l(-1) h(-1), which is below CH(4) production rate usually reported in both anaerobic reactors and natural ecosystems. Additionally to sensitivity, the method has several potential interests compared to more traditional methods among which short measurements time allowing the measurement of a large number of MA test vials, non-invasive measurements avoiding leakage or external interferences and similar cost to GC based methods. It is concluded that MA-TDLAS is a promising method that could be of interest not only in the field of anaerobic digestion but also, in the field of environmental ecology where CH(4) production rates are usually very low. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Microbiological characterization and specific methanogenic activity of anaerobe sludges used in urban solid waste treatment

    International Nuclear Information System (INIS)

    Sandoval Lozano, Claudia Johanna; Vergara Mendoza, Marisol; Carreno de Arango, Mariela; Castillo Monroy, Edgar Fernando

    2009-01-01

    This study presents the microbiological characterization of the anaerobic sludge used in a two-stage anaerobic reactor for the treatment of organic fraction of urban solid waste (OFUSW). This treatment is one alternative for reducing solid waste in landfills at the same time producing a biogas (CH 4 and CO 2 ) and an effluent that can be used as biofertilizer. The system was inoculated with sludge from a wastewater treatment plant (WWTP) (Rio Frio Plant in Bucaramanga-Colombia) and a methanogenic anaerobic digester for the treatment of pig manure (Mesa de los Santos in Santander). Bacterial populations were evaluated by counting groups related to oxygen sensitivity, while metabolic groups were determined by most probable number (MPN) technique. Specific methanogenic activity (SMA) for acetate, formate, methanol and ethanol substrates was also determined. In the acidogenic reactor (R1), volatile fatty acids (VFA) reached values of 25,000 mg L -1 and a concentration of CO 2 of 90%. In this reactor, the fermentative population was predominant (10 5 -10 6 MPN mL -1 ). The acetogenic population was (10 5 MPN mL -1 ) and the sulphate-reducing population was (10 4 -10 5 MPN mL -1 ). In the methanogenic reactor (R2), levels of CH 4 (70%) were higher than CO 2 (25%), whereas the VFA values were lower than 4000 mg L -1 . Substrate competition between sulphate-reducing (10 4 -10 5 MPN mL -1 ) and methanogenic bacteria (10 5 MPN mL -1 ) was not detected. From the SMA results obtained, acetoclastic (2.39 g COD-CH 4 g -1 VSS -1 day -1 ) and hydrogenophilic (0.94 g COD-CH 4 g -1 VSS -1 day -1 ) transformations as possible metabolic pathways used by methanogenic bacteria is suggested from the SMA results obtained. Methanotrix sp., Methanosarcina sp., Methanoccocus sp. and Methanobacterium sp. were identified

  8. Magnetic resonance microscopy of iron transport in methanogenic granules

    Science.gov (United States)

    Bartacek, Jan; Vergeldt, Frank J.; Gerkema, Edo; Jenicek, Pavel; Lens, Piet N. L.; Van As, Henk

    2009-10-01

    Interactions between anaerobic biofilms and heavy metals such as iron, cobalt or nickel are largely unknown. Magnetic resonance imaging (MRI) is a non-invasive method that allows in situ studies of metal transport within biofilm matrixes. The present study investigates quantitatively the penetration of iron (1.75 mM) bound to ethylenediaminetetraacetate (EDTA) into the methanogenic granules (spherical biofilm). A spatial resolution of 109 × 109 × 218 μm 3 and a temporal resolution of 11 min are achieved with 3D Turbo Spin Echo (TSE) measurements. The longitudinal relaxivity, i.e. the slope the dependence of the relaxation rate (1/ T1) on the concentration of paramagnetic metal ions, was used to measure temporal changes in iron concentration in the methanogenic granules. It took up to 300 min for the iron-EDTA complex ([FeEDTA] 2-) to penetrate into the methanogenic granules (3-4 mm in diameter). The diffusion was equally fast in all directions with irregularities such as diffusion-facilitating channels and diffusion-resistant zones. Despite these irregularities, the overall process could be modeled using Fick's equations for diffusion in a sphere, because immobilization of [FeEDTA] 2- in the granular matrix (or the presence of a reactive barrier) was not observed. The effective diffusion coefficient ( D ejf) of [FeEDTA] 2- was found to be 2.8 × 10 -11 m 2 s -1, i.e. approximately 4% of D ejf of [FeEDTA] 2- in water. The Fickian model did not correspond to the processes taking place in the core of the granule (3-5% of the total volume of the granule), where up to 25% over-saturation by iron (compare to the concentration in the bulk solution) occurred.

  9. Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions.

    Science.gov (United States)

    Hubalek, Valerie; Buck, Moritz; Tan, BoonFei; Foght, Julia; Wendeberg, Annelie; Berry, David; Bertilsson, Stefan; Eiler, Alexander

    2017-01-01

    Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH 4 and CO 2 . Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermentation of alkanes facilitated by energy conservation linked to H 2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and intermediate fermentation products derived from detrital biomass was a common feature. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H 2 -producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocarbon transformation. IMPORTANCE Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an

  10. Bacterial community composition in reclaimed and unreclaimed ...

    African Journals Online (AJOL)

    AJL-021

    2013-07-24

    Jul 24, 2013 ... characteristics, chemical speciation of heavy metals Cu, Cd and Zn were revealed to ... Phylogenetic analysis indicated that bacteria in these two samples fell into 12 ... plant community and the abundance and composition of.

  11. Growth of desulfovibrio in lactate or ethanol media low in sulfate in association with H2-utilizing methanogenic bacteria.

    Science.gov (United States)

    Bryant, M P; Campbell, L L; Reddy, C A; Crabill, M R

    1977-05-01

    In the analysis of an ethanol-CO(2) enrichment of bacteria from an anaerobic sewage digestor, a strain tentatively identified as Desulfovibrio vulgaris and an H(2)-utilizing methanogen resembling Methanobacterium formicicum were isolated, and they were shown to represent a synergistic association of two bacterial species similar to that previously found between S organism and Methanobacterium strain MOH isolated from Methanobacillus omelianskii. In lowsulfate media, the desulfovibrio produced acetate and H(2) from ethanol and acetate, H(2), and, presumably, CO(2) from lactate; but growth was slight and little of the energy source was catabolized unless the organism was combined with an H(2)-utilizing methanogenic bacterium. The type strains of D. vulgaris and Desulfovibrio desulfuricans carried out the same type of synergistic growth with methanogens. In mixtures of desulfovibrio and strain MOH growing on ethanol, lactate, or pyruvate, diminution of methane produced was stoichiometric with the moles of sulfate added, and the desulfovibrios grew better with sulfate addition. The energetics of the synergistic associations and of the competition between the methanogenic system and sulfate-reducing system as sinks for electrons generated in the oxidation of organic materials such as ethanol, lactate, and acetate are discussed. It is suggested that lack of availability of H(2) for growth of methanogens is a major factor in suppression of methanogenesis by sulfate in natural ecosystems. The results with these known mixtures of bacteria suggest that hydrogenase-forming, sulfate-reducing bacteria could be active in some methanogenic ecosystems that are low in sulfate.

  12. Neighboring trees affect ectomycorrhizal fungal community composition in a woodland-forest ecotone.

    Science.gov (United States)

    Hubert, Nathaniel A; Gehring, Catherine A

    2008-09-01

    Ectomycorrhizal fungi (EMF) are frequently species rich and functionally diverse; yet, our knowledge of the environmental factors that influence local EMF diversity and species composition remains poor. In particular, little is known about the influence of neighboring plants on EMF community structure. We tested the hypothesis that the EMF of plants with heterospecific neighbors would differ in species richness and community composition from the EMF of plants with conspecific neighbors. We conducted our study at the ecotone between pinyon (Pinus edulis)-juniper (Juniperus monosperma) woodland and ponderosa pine (Pinus ponderosa) forest in northern Arizona, USA where the dominant trees formed associations with either EMF (P. edulis and P. ponderosa) or arbuscular mycorrhizal fungi (AMF; J. monosperma). We also compared the EMF communities of pinyon and ponderosa pines where their rhizospheres overlapped. The EMF community composition, but not species richness of pinyon pines was significantly influenced by neighboring AM juniper, but not by neighboring EM ponderosa pine. Ponderosa pine EMF communities were different in species composition when growing in association with pinyon pine than when growing in association with a conspecific. The EMF communities of pinyon and ponderosa pines were similar where their rhizospheres overlapped consisting of primarily the same species in similar relative abundance. Our findings suggest that neighboring tree species identity shaped EMF community structure, but that these effects were specific to host-neighbor combinations. The overlap in community composition between pinyon pine and ponderosa pine suggests that these tree species may serve as reservoirs of EMF inoculum for one another.

  13. Methanogens at the top of the world: occurrence and potential activity of methanogens in newly deglaciated soils in high-altitude cold deserts in the Western Himalayas

    Czech Academy of Sciences Publication Activity Database

    Aschenbach, K.; Conrad, R.; Řeháková, Klára; Doležal, Jiří; Janatková, Kateřina; Angel, R.

    2013-01-01

    Roč. 4, Dec 2013 (2013), Ar.359 ISSN 1664-302X R&D Projects: GA ČR GA13-13368S Institutional support: RVO:67985939 Keywords : methanogens * desert areas * cold climate Subject RIV: EH - Ecology, Behaviour Impact factor: 3.941, year: 2013

  14. Factors that control the stable carbon isotopic composition of methane produced in an anoxic marine sediment

    Science.gov (United States)

    Alperin, M. J.; Blair, Neal E.; Albert, D. B.; Hoehler, T. M.; Martens, C. S.

    1993-01-01

    The carbon isotopic composition of methane produced in anoxic marine sediment is controlled by four factors: (1) the pathway of methane formation, (2) the isotopic composition of the methanogenic precursors, (3) the isotope fractionation factors for methane production, and (4) the isotope fractionation associated with methane oxidation. The importance of each factor was evaluated by monitoring stable carbon isotope ratios in methane produced by a sediment microcosm. Methane did not accumulate during the initial 42-day period when sediment contained sulfate, indicating little methane production from 'noncompetitive' substrates. Following sulfate depletion, methane accumulation proceeded in three distinct phases. First, CO2 reduction was the dominant methanogenic pathway and the isotopic composition of the methane produced ranged from -80 to -94 per thousand. The acetate concentration increased during this phase, suggesting that acetoclastic methanogenic bacteria were unable to keep pace with acetate production. Second, acetate fermentation became the dominant methanogenic pathway as bacteria responded to elevated acetate concentrations. The methane produced during this phase was progressively enriched in C-13, reaching a maximum delta(C-13) value of -42 per thousand. Third, the acetate pool experienced a precipitous decline from greater than 5 mM to less than 20 micro-M and methane production was again dominated by CO2 reduction. The delta(C-13) of methane produced during this final phase ranged from -46 to -58 per thousand. Methane oxidation concurrent with methane production was detected throughout the period of methane accumulation, at rates equivalent to 1 to 8 percent of the gross methane production rate. Thus methane oxidation was too slow to have significantly modified the isotopic signature of methane. A comparison of microcosm and field data suggests that similar microbial interactions may control seasonal variability in the isotopic composition of methane

  15. Bacterial community composition and structure in an Urban River impacted by different pollutant sources.

    Science.gov (United States)

    Ibekwe, A Mark; Ma, Jincai; Murinda, Shelton E

    2016-10-01

    Microbial communities in terrestrial fresh water are diverse and dynamic in composition due to different environmental factors. The goal of this study was to undertake a comprehensive analysis of bacterial composition along different rivers and creeks and correlate these to land-use practices and pollutant sources. Here we used 454 pyrosequencing to determine the total bacterial community composition, and bacterial communities that are potentially of fecal origin, and of relevance to water quality assessment. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, and community composition. Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to correlate bacterial composition in streams and creeks to different environmental parameters impacting bacterial communities in the sediment and surface water within the watershed. Bacteria were dominated by the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, with Bacteroidetes significantly (PPCoA and DCA showed that bacterial composition in sediment and surface water was significantly different (Pmicrobial community compositions were influenced by several environmental factors, and pH, NO2, and NH4 were the major environmental factors driving FIB in surface water based on CCA analysis, while NO3 was the only factor in sediment. Published by Elsevier B.V.

  16. Microbial communities involved in methane production from hydrocarbons in oil sands tailings.

    Science.gov (United States)

    Siddique, Tariq; Penner, Tara; Klassen, Jonathan; Nesbø, Camilla; Foght, Julia M

    2012-09-04

    Microbial metabolism of residual hydrocarbons, primarily short-chain n-alkanes and certain monoaromatic hydrocarbons, in oil sands tailings ponds produces large volumes of CH(4) in situ. We characterized the microbial communities involved in methanogenic biodegradation of whole naphtha (a bitumen extraction solvent) and its short-chain n-alkane (C(6)-C(10)) and BTEX (benzene, toluene, ethylbenzene, and xylenes) components using primary enrichment cultures derived from oil sands tailings. Clone libraries of bacterial 16S rRNA genes amplified from these enrichments showed increased proportions of two orders of Bacteria: Clostridiales and Syntrophobacterales, with Desulfotomaculum and Syntrophus/Smithella as the closest named relatives, respectively. In parallel archaeal clone libraries, sequences affiliated with cultivated acetoclastic methanogens (Methanosaetaceae) were enriched in cultures amended with n-alkanes, whereas hydrogenotrophic methanogens (Methanomicrobiales) were enriched with BTEX. Naphtha-amended cultures harbored a blend of these two archaeal communities. The results imply syntrophic oxidation of hydrocarbons in oil sands tailings, with the activities of different carbon flow pathways to CH(4) being influenced by the primary hydrocarbon substrate. These results have implications for predicting greenhouse gas emissions from oil sands tailings repositories.

  17. Compositional differences in simulated root exudates elicit a limited functional and compositional response in soil microbial communities

    Directory of Open Access Journals (Sweden)

    Michael S Strickland

    2015-08-01

    Full Text Available Inputs of low molecular weight carbon (LMW-C to soil −primarily via root exudates− are expected to be a major driver of microbial activity and source of stable soil organic carbon. It is expected that variation in the type and composition of LMW-C entering soil will influence microbial community composition and function. If this is the case then short-term changes in LMW-C inputs may alter processes regulated by these communities. To determine if change in the composition of LMW-C inputs influences microbial community function and composition, we conducted a 90 day microcosm experiment whereby soils sourced from three different land covers (meadows, deciduous forests, and white pine stands were amended, at low concentrations, with one of eight simulated root exudate treatments. Treatments included no addition of LMW-C, and the full factorial combination of glucose, glycine, and oxalic acid. After 90 days, we conducted a functional response assay and determined microbial composition via phospholipid fatty acid analysis. Whereas we noted a statistically significant effect of exudate treatments, this only accounted for ~3% of the variation observed in function. In comparison, land cover and site explained ~46 and ~41% of the variation, respectively. This suggests that exudate composition has little influence on function

  18. A mathematical model for the interactive behavior of sulfate-reducing bacteria and methanogens during anaerobic digestion.

    Science.gov (United States)

    Ahammad, S Ziauddin; Gomes, James; Sreekrishnan, T R

    2011-09-01

    Anaerobic degradation of waste involves different classes of microorganisms, and there are different types of interactions among them for substrates, terminal electron acceptors, and so on. A mathematical model is developed based on the mass balance of different substrates, products, and microbes present in the system to study the interaction between methanogens and sulfate-reducing bacteria (SRB). The performance of major microbial consortia present in the system, such as propionate-utilizing acetogens, butyrate-utilizing acetogens, acetoclastic methanogens, hydrogen-utilizing methanogens, and SRB were considered and analyzed in the model. Different substrates consumed and products formed during the process also were considered in the model. The experimental observations and model predictions showed very good prediction capabilities of the model. Model prediction was validated statistically. It was observed that the model-predicted values matched the experimental data very closely, with an average error of 3.9%.

  19. 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.

  20. Interspecies electron transfer in suspended and aggregated methanogenic propionate-degrading consortia

    NARCIS (Netherlands)

    Bok, de F.A.M.; Plugge, C.M.; Stams, A.J.M.

    2002-01-01

    Propionate is a key intermediate in the conversion of complex organic matter under methanogenic conditions. Oxidation of propionate to acetate is energetically unfavorable under standard conditions. Therefore, micro organisms are only able to gain energy from this conversion if the concentrations of

  1. Reductive decolourisation of azo dyes by mesophilic and thermophilic methanogenic consortia

    NARCIS (Netherlands)

    Cervantes, F.J.; Santos, dos A.B.; Madrid, de M.P.; Stams, A.J.M.; Lier, van J.B.

    2005-01-01

    The contribution of acidogenic bacteria and methanogenic archaea on the reductive decolourisation of azo dyes was assessed in anaerobic granular sludge. Acidogenic bacteria appeared to play an important role in the decolourising processes when glucose was provided as an electron donor; whereas

  2. Genomic analysis of methanogenic archaea reveals a shift towards energy conservation

    DEFF Research Database (Denmark)

    Gilmore, Sean P.; Henske, John K.; Sexton, Jessica A.

    2017-01-01

    Background: The metabolism of archaeal methanogens drives methane release into the environment and is critical to understanding global carbon cycling. Methanogenesis operates at a very low reducing potential compared to other forms of respiration and is therefore critical to many anaerobic enviro...

  3. Changing Feeding Regimes To Demonstrate Flexible Biogas Production: Effects on Process Performance, Microbial Community Structure, and Methanogenesis Pathways

    Science.gov (United States)

    Mulat, Daniel Girma; Jacobi, H. Fabian; Feilberg, Anders; Adamsen, Anders Peter S.; Richnow, Hans-Hermann

    2015-01-01

    Flexible biogas production that adapts biogas output to energy demand can be regulated by changing feeding regimes. In this study, the effect of changes in feeding intervals on process performance, microbial community structure, and the methanogenesis pathway was investigated. Three different feeding regimes (once daily, every second day, and every 2 h) at the same organic loading rate were studied in continuously stirred tank reactors treating distiller's dried grains with solubles. A larger amount of biogas was produced after feeding in the reactors fed less frequently (once per day and every second day), whereas the amount remained constant in the reactor fed more frequently (every 2 h), indicating the suitability of the former for the flexible production of biogas. Compared to the conventional more frequent feeding regimes, a methane yield that was up to 14% higher and an improved stability of the process against organic overloading were achieved by employing less frequent feeding regimes. The community structures of bacteria and methanogenic archaea were monitored by terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA and mcrA genes, respectively. The results showed that the composition of the bacterial community varied under the different feeding regimes, and the observed T-RFLP patterns were best explained by the differences in the total ammonia nitrogen concentrations, H2 levels, and pH values. However, the methanogenic community remained stable under all feeding regimes, with the dominance of the Methanosarcina genus followed by that of the Methanobacterium genus. Stable isotope analysis showed that the average amount of methane produced during each feeding event by acetoclastic and hydrogenotrophic methanogenesis was not influenced by the three different feeding regimes. PMID:26497462

  4. Community size and composition of ammonia oxidizers and denitrifiers in an alluvial intertidal wetland ecosystem

    Directory of Open Access Journals (Sweden)

    Ziye eHu

    2014-07-01

    Full Text Available Global nitrogen cycling is mainly mediated by the activity of microorganisms. Nitrogen cycle processes are mediated by functional groups of microorganisms that are affected by constantly changing environmental conditions and substrate availability. In this study, we investigated the temporal and spatial patterns of nitrifier and denitrifier communities in an intertidal wetland. Soil samples were collected over four distinct seasons from three locations with different vegetative cover. Multiple environmental factors and process rates were measured and analyzed together with the community size and composition profiles. We observed that the community size and composition of the nitrifiers and denitrifiers are affected significantly by seasonal factors, while vegetative cover affected the community composition. The seasonal impacts on the community size of ammonia oxidizing archaea (AOA are much higher than that of ammonia oxidizing bacteria (AOB. The seasonal change was a more important indicator for AOA community composition patterns, while vegetation was more important for the AOB community patterns. The microbial process rates were correlated with both the community size and composition.

  5. Experimental soil warming shifts the fungal community composition at the alpine treeline.

    Science.gov (United States)

    Solly, Emily F; Lindahl, Björn D; Dawes, Melissa A; Peter, Martina; Souza, Rômulo C; Rixen, Christian; Hagedorn, Frank

    2017-07-01

    Increased CO 2 emissions and global warming may alter the composition of fungal communities through the removal of temperature limitation in the plant-soil system, faster nitrogen (N) cycling and changes in the carbon (C) allocation of host plants to the rhizosphere. At a Swiss treeline featuring Larix decidua and Pinus uncinata, the effects of multiple years of CO 2 enrichment and experimental soil warming on the fungal community composition in the organic horizons were analysed using 454-pyrosequencing of ITS2 amplicons. Sporocarp production and colonization of ectomycorrhizal root tips were investigated in parallel. Fungal community composition was significantly altered by soil warming, whereas CO 2 enrichment had little effect. Tree species influenced fungal community composition and the magnitude of the warming responses. The abundance of ectomycorrhizal fungal taxa was positively correlated with N availability, and ectomycorrhizal taxa specialized for conditions of high N availability proliferated with warming, corresponding to considerable increases in inorganic N in warmed soils. Traits related to N utilization are important in determining the responses of ectomycorrhizal fungi to warming in N-poor cold ecosystems. Shifts in the overall fungal community composition in response to higher temperatures may alter fungal-driven processes with potential feedbacks on ecosystem N cycling and C storage at the alpine treeline. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  6. Spatial variations of community structures and methane cycling across a transect of Lei-Gong-Hou mud volcanoes in eastern Taiwan

    Directory of Open Access Journals (Sweden)

    Pei-Ling eWang

    2014-03-01

    Full Text Available This study analyzed cored sediments retrieved from sites distributed across a transect of the Lei-Gong-Hou mud volcanoes in eastern Taiwan to uncover the spatial distributions of biogeochemical processes and community assemblages involved in methane cycling. The profiles of methane concentration and carbon isotopic composition revealed various orders of the predominance of specific methane-related metabolisms along depth. At a site proximal to the bubbling pool, the methanogenic zone was sandwiched by the anaerobic methanotrophic zones. For two sites distributed toward the topographic depression, the methanogenic zone overlaid the anaerobic methanotrophic zone. The predominance of anaerobic methanotrophy at specific depth intervals is supported by the enhanced copy numbers of the ANME-2a 16S rRNA gene and coincides with high dissolved Fe/Mn concentrations and copy numbers of the Desulfuromonas/Pelobacter 16S rRNA gene. Assemblages of 16S rRNA and mcrA genes revealed that methanogenesis was mediated by Methanococcoides and Methanosarcina. pmoA genes and a few 16S rRNA genes related to aerobic methanotrophs were detected in limited numbers of subsurface samples. While dissolved Fe/Mn signifies the presence of anaerobic metabolisms near the surface, the correlations between geochemical characteristics and gene abundances, and the absence of aerobic methanotrophs in top sediments suggest that anaerobic methanotrophy is potentially dependent on iron/manganese reduction and dominates over aerobic methanotrophy for the removal of methane produced in situ or from a deep source. Near-surface methanogenesis contributes to the methane emissions from mud platform. The alternating arrangements of methanogenic and methanotrophic zones at different sites suggest that the interactions between mud deposition, evaporation, oxidation and fluid transport modulate the assemblages of microbial communities and methane cycling in different compartments of terrestrial

  7. Spatial variations of community structures and methane cycling across a transect of Lei-Gong-Hou mud volcanoes in eastern Taiwan.

    Science.gov (United States)

    Wang, Pei-Ling; Chiu, Yi-Ping; Cheng, Ting-Wen; Chang, Yung-Hsin; Tu, Wei-Xain; Lin, Li-Hung

    2014-01-01

    This study analyzed cored sediments retrieved from sites distributed across a transect of the Lei-Gong-Hou mud volcanoes in eastern Taiwan to uncover the spatial distributions of biogeochemical processes and community assemblages involved in methane cycling. The profiles of methane concentration and carbon isotopic composition revealed various orders of the predominance of specific methane-related metabolisms along depth. At a site proximal to the bubbling pool, the methanogenic zone was sandwiched by the anaerobic methanotrophic zones. For two sites distributed toward the topographic depression, the methanogenic zone overlaid the anaerobic methanotrophic zone. The predominance of anaerobic methanotrophy at specific depth intervals is supported by the enhanced copy numbers of the ANME-2a 16S rRNA gene and coincides with high dissolved Fe/Mn concentrations and copy numbers of the Desulfuromonas/Pelobacter 16S rRNA gene. Assemblages of 16S rRNA and mcrA genes revealed that methanogenesis was mediated by Methanococcoides and Methanosarcina. pmoA genes and a few 16S rRNA genes related to aerobic methanotrophs were detected in limited numbers of subsurface samples. While dissolved Fe/Mn signifies the presence of anaerobic metabolisms near the surface, the correlations between geochemical characteristics and gene abundances, and the absence of aerobic methanotrophs in top sediments suggest that anaerobic methanotrophy is potentially dependent on iron/manganese reduction and dominates over aerobic methanotrophy for the removal of methane produced in situ or from a deep source. Near-surface methanogenesis contributes to the methane emissions from mud platform. The alternating arrangements of methanogenic and methanotrophic zones at different sites suggest that the interactions between mud deposition, evaporation, oxidation and fluid transport modulate the assemblages of microbial communities and methane cycling in different compartments of terrestrial mud volcanoes.

  8. Dosing of anaerobic granular sludge bioreactors with cobalt: Impact of cobalt retention on methanogenic activity

    KAUST Repository

    Fermoso, Fernando G.

    2010-12-01

    The effect of dosing a metal limited anaerobic sludge blanket (UASB) reactor with a metal pulse on the methanogenic activity of granular sludge has thus far not been successfully modeled. The prediction of this effect is crucial in order to optimize the strategy for metal dosage and to prevent unnecessary losses of resources. This paper describes the relation between the initial immobilization of cobalt in anaerobic granular sludge cobalt dosage into the reactor and the evolution of methanogenic activity during the subsequent weeks. An operationally defined parameter (A0· B0) was found to combine the amount of cobalt immobilized instantaneously upon the pulse (B0) and the amount of cobalt immobilized within the subsequent 24. h (A0). In contrast with the individual parameters A0 and B0, the parameter A0· B0 correlated significantly with the methanogenic activity of the sludge during the subsequent 16 or 35. days. This correlation between metal retention and activity evolution is a useful tool to implement trace metal dosing strategies for biofilm-based biotechnological processes. © 2010.

  9. Chemical structure-based predictive model for methanogenic anaerobic biodegradation potential.

    Science.gov (United States)

    Meylan, William; Boethling, Robert; Aronson, Dallas; Howard, Philip; Tunkel, Jay

    2007-09-01

    Many screening-level models exist for predicting aerobic biodegradation potential from chemical structure, but anaerobic biodegradation generally has been ignored by modelers. We used a fragment contribution approach to develop a model for predicting biodegradation potential under methanogenic anaerobic conditions. The new model has 37 fragments (substructures) and classifies a substance as either fast or slow, relative to the potential to be biodegraded in the "serum bottle" anaerobic biodegradation screening test (Organization for Economic Cooperation and Development Guideline 311). The model correctly classified 90, 77, and 91% of the chemicals in the training set (n = 169) and two independent validation sets (n = 35 and 23), respectively. Accuracy of predictions of fast and slow degradation was equal for training-set chemicals, but fast-degradation predictions were less accurate than slow-degradation predictions for the validation sets. Analysis of the signs of the fragment coefficients for this and the other (aerobic) Biowin models suggests that in the context of simple group contribution models, the majority of positive and negative structural influences on ultimate degradation are the same for aerobic and methanogenic anaerobic biodegradation.

  10. Restricted diversity of dental calculus methanogens over five centuries, France.

    Science.gov (United States)

    Huynh, Hong T T; Nkamga, Vanessa D; Signoli, Michel; Tzortzis, Stéfan; Pinguet, Romuald; Audoly, Gilles; Aboudharam, Gérard; Drancourt, Michel

    2016-05-11

    Methanogens are acknowledged archaeal members of modern dental calculus microbiota and dental pathogen complexes. Their repertoire in ancient dental calculus is poorly known. We therefore investigated archaea in one hundred dental calculus specimens collected from individuals recovered from six archaeological sites in France dated from the 14(th) to 19(th) centuries AD. Dental calculus was demonstrated by macroscopic and cone-beam observations. In 56 calculus specimens free of PCR inhibition, PCR sequencing identified Candidatus Methanobrevibacter sp. N13 in 44.6%, Methanobrevibacter oralis in 19.6%, a new Methanomassiliicoccus luminyensis-like methanogen in 12.5%, a Candidatus Nitrososphaera evergladensis-like in one and Methanoculleus bourgensis in one specimen, respectively. One Candidatus Methanobrevibacter sp. N13 dental calculus was further documented by fluorescent in situ hybridization. The prevalence of dental calculus M. oralis was significantly lower in past populations than in modern populations (P = 0.03, Chi-square test). This investigation revealed a previously unknown repertoire of archaea found in the oral cavity of past French populations as reflected in preserved dental calculus.

  11. The microbial community of a passive biochemical reactor treating arsenic, zinc and sulfate-rich seepage

    Directory of Open Access Journals (Sweden)

    Susan Anne Baldwin

    2015-03-01

    Full Text Available Sulfidogenic biochemical reactors for metal removal that use complex organic carbon have been shown to be effective in laboratory studies, but their performance in the field is highly variable. Successful operation depends on the types of microorganisms supported by the organic matrix, and factors affecting the community composition are unknown. A molecular survey of a field-based biochemical reactor that had been removing zinc and arsenic for over six years revealed that the microbial community was dominated by methanogens related to Methanocorpusculum sp. and Methanosarcina sp., which co-occurred with Bacteroidetes environmental groups, such as Vadin HA17, in places where the organic matter was more degraded. The metabolic potential for organic matter decomposition by Ruminococcaceae was prevalent in samples with more pyrolysable carbon. Rhodobium- and Hyphomicrobium-related genera within the Rhizobiales Order that have the metabolic potential for dark hydrogen fermentation and methylotrophy, and unclassified Comamonadaceae were the dominant Proteobacteria. The unclassified environmental group Sh765B-TzT-29 was an important Delta-Proteobacteria group in this BCR, that co-occurred with the dominant Rhizobiales OTUs. Organic matter degradation is one driver for shifting the microbial community composition and therefore possibly the performance of these bioreactors over time.

  12. Isolation and characterization of new strains of methanogens from cold terrestrial habitats.

    Science.gov (United States)

    Simankova, Maria V; Kotsyurbenko, Oleg R; Lueders, Tillmann; Nozhevnikova, Alla N; Wagner, Bianca; Conrad, Ralf; Friedrich, Michael W

    2003-06-01

    Five strains of methanogenic archaea (MT, MS, MM, MSP, ZB) were isolated from permanently and periodically cold terrestrial habitats. Physiological and morphological studies, as well as phylogenetic analyses of the new isolates were performed. Based on sequences of the 16S rRNA and methyl-coenzyme M reductase a-subunit (mcrA) genes all new isolates are closely related to known mesophilic and psychrotolerant methanogens. Both, phylogenetic analyses and phenotypic properties allow to classify strains MT, MS, and MM as members of the genus Methanosarcina. Strain MT is a new ecotype of Methanosarcina mazei, whereas strains MM and MS are very similar to each other and can be assigned to the recently described psychrotolerant species Methanosarcina lacustris. The hydrogenotrophic strain MSP is a new ecotype of the genus Methanocorpusculum. The obligately methylotrophic strain ZB is closely related to Methanomethylovorans hollandica and can be classified as new ecotype of this species. All new isolates, including the strains from permanently cold environments, are not true psychrophiles according to their growth temperature characteristics. In spite of the ability of all isolates to grow at temperatures as low as 1-5 degrees C, all of them have their growth optima in the range of moderate temperatures (25-35 degrees C). Thus, they can be regarded as psychrotolerant organisms. Psychrotolerant methanogens are thought to play an important role in methane production in both, habitats under seasonal temperature variations or from permanently cold areas.

  13. Methanogenic degradation of acetone by an enrichment culture

    OpenAIRE

    Platen, Harald; Schink, Bernhard

    1987-01-01

    An anaerobic enrichment culture degraded 1 mol of acetone to 2 tool of methane and 1 tool of carbon dioxide. Two microorganisms were involved in this process, a filament-forming rod similar to Methanothrix sp. and an unknown rod with round to slightly pointed ends. Both organisms formed aggregates up to 300 gm in diameter. No fluorescing bacteria were observed indicating that hydrogen or formate-utilizing methanogens are not involved in this process. Acetate was utilized in this culture by th...

  14. RUMINANT NUTRITION SYMPOSIUM: Use of genomics and transcriptomics to identify strategies to lower ruminal methanogenesis.

    Science.gov (United States)

    McAllister, T A; Meale, S J; Valle, E; Guan, L L; Zhou, M; Kelly, W J; Henderson, G; Attwood, G T; Janssen, P H

    2015-04-01

    Globally, methane (CH4) emissions account for 40% to 45% of greenhouse gas emissions from ruminant livestock, with over 90% of these emissions arising from enteric fermentation. Reduction of carbon dioxide to CH4 is critical for efficient ruminal fermentation because it prevents the accumulation of reducing equivalents in the rumen. Methanogens exist in a symbiotic relationship with rumen protozoa and fungi and within biofilms associated with feed and the rumen wall. Genomics and transcriptomics are playing an increasingly important role in defining the ecology of ruminal methanogenesis and identifying avenues for its mitigation. Metagenomic approaches have provided information on changes in abundances as well as the species composition of the methanogen community among ruminants that vary naturally in their CH4 emissions, their feed efficiency, and their response to CH4 mitigators. Sequencing the genomes of rumen methanogens has provided insight into surface proteins that may prove useful in the development of vaccines and has allowed assembly of biochemical pathways for use in chemogenomic approaches to lowering ruminal CH4 emissions. Metagenomics and metatranscriptomic analysis of entire rumen microbial communities are providing new perspectives on how methanogens interact with other members of this ecosystem and how these relationships may be altered to reduce methanogenesis. Identification of community members that produce antimethanogen agents that either inhibit or kill methanogens could lead to the identification of new mitigation approaches. Discovery of a lytic archaeophage that specifically lyses methanogens is 1 such example. Efforts in using genomic data to alter methanogenesis have been hampered by a lack of sequence information that is specific to the microbial community of the rumen. Programs such as Hungate1000 and the Global Rumen Census are increasing the breadth and depth of our understanding of global ruminal microbial communities, steps that

  15. Methanogenic biodegradation of paraffinic solvent hydrocarbons in two different oil sands tailings.

    Science.gov (United States)

    Mohamad Shahimin, Mohd Faidz; Siddique, Tariq

    2017-04-01

    Microbial communities drive many biogeochemical processes in oil sands tailings and cause greenhouse gas emissions from tailings ponds. Paraffinic solvent (primarily C 5 -C 6 ; n- and iso-alkanes) is used by some oil sands companies to aid bitumen extraction from oil sands ores. Residues of unrecovered solvent escape to tailings ponds during tailings deposition and sustain microbial metabolism. To investigate biodegradation of hydrocarbons in paraffinic solvent, mature fine tailings (MFT) collected from Albian and CNRL ponds were amended with paraffinic solvent at ~0.1wt% (final concentration: ~1000mgL -1 ) and incubated under methanogenic conditions for ~1600d. Albian and CNRL MFTs exhibited ~400 and ~800d lag phases, respectively after which n-alkanes (n-pentane and n-hexane) in the solvent were preferentially metabolized to methane over iso-alkanes in both MFTs. Among iso-alkanes, only 2-methylpentane was completely biodegraded whereas 2-methylbutane and 3-methylpentane were partially biodegraded probably through cometabolism. 16S rRNA gene pyrosequencing showed dominance of Anaerolineaceae and Methanosaetaceae in Albian MFT and Peptococcaceae and co-domination of "Candidatus Methanoregula" and Methanosaetaceae in CNRL MFT bacterial and archaeal communities, respectively, during active biodegradation of paraffinic solvent. The results are important for developing future strategies for tailings reclamation and management of greenhouse gas emissions. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Rapid decay of tree-community composition in Amazonian forest fragments

    Science.gov (United States)

    Laurance, William F.; Nascimento, Henrique E. M.; Laurance, Susan G.; Andrade, Ana; Ribeiro, José E. L. S.; Giraldo, Juan Pablo; Lovejoy, Thomas E.; Condit, Richard; Chave, Jerome; Harms, Kyle E.; D'Angelo, Sammya

    2006-01-01

    Forest fragmentation is considered a greater threat to vertebrates than to tree communities because individual trees are typically long-lived and require only small areas for survival. Here we show that forest fragmentation provokes surprisingly rapid and profound alterations in Amazonian tree-community composition. Results were derived from a 22-year study of exceptionally diverse tree communities in 40 1-ha plots in fragmented and intact forests, which were sampled repeatedly before and after fragment isolation. Within these plots, trajectories of change in abundance were assessed for 267 genera and 1,162 tree species. Abrupt shifts in floristic composition were driven by sharply accelerated tree mortality and recruitment within ≈100 m of fragment margins, causing rapid species turnover and population declines or local extinctions of many large-seeded, slow-growing, and old-growth taxa; a striking increase in a smaller set of disturbance-adapted and abiotically dispersed species; and significant shifts in tree size distributions. Even among old-growth trees, species composition in fragments is being restructured substantially, with subcanopy species that rely on animal seed-dispersers and have obligate outbreeding being the most strongly disadvantaged. These diverse changes in tree communities are likely to have wide-ranging impacts on forest architecture, canopy-gap dynamics, plant–animal interactions, and forest carbon storage. PMID:17148598

  17. Rapid adjustment of bird community compositions to local climatic variations and its functional consequences.

    Science.gov (United States)

    Gaüzère, Pierre; Jiguet, Frédéric; Devictor, Vincent

    2015-09-01

    The local spatial congruence between climate changes and community changes has rarely been studied over large areas. We proposed one of the first comprehensive frameworks tracking local changes in community composition related to climate changes. First, we investigated whether and how 12 years of changes in the local composition of bird communities were related to local climate variations. Then, we tested the consequences of this climate-induced adjustment of communities on Grinnellian (habitat-related) and Eltonian (function-related) homogenization. A standardized protocol monitoring spatial and temporal trends of birds over France from 2001 to 2012 was used. For each plot and each year, we used the spring temperature and the spring precipitations and calculated three indices reflecting the thermal niche, the habitat specialization, and the functional originality of the species within a community. We then used a moving-window approach to estimate the spatial distribution of the temporal trends in each of these indices and their congruency with local climatic variations. Temperature fluctuations and community dynamics were found to be highly variable in space, but their variations were finely congruent. More interestingly, the community adjustment to temperature variations was nonmonotonous. Instead, unexplained fluctuations in community composition were observed up to a certain threshold of climate change intensity, above which a change in community composition was observed. This shift corresponded to a significant decrease in the relative abundance of habitat specialists and functionally original species within communities, regardless of the direction of temperature change. The investigation of variations in climate and community responses appears to be a central step toward a better understanding of climate change effects on biodiversity. Our results suggest a fine-scale and short-term adjustment of community composition to temperature changes. Moreover

  18. Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time

    Directory of Open Access Journals (Sweden)

    Cody Springer Sheik

    2015-05-01

    Full Text Available Glaciers are geologically important yet transient ecosystems that support diverse, biogeochemically significant microbial communities. During the melt season glaciers undergo dramatic physical, geochemical and biological changes that exert great influence on downstream biogeochemical cycles. Thus, we sought to understand the temporal melt-season dynamics of microbial communities and associated geochemistry at the terminus of Lemon Creek Glacier (LCG in coastal southern Alaska. Due to late season snowfall, sampling of LCG occurred in three interconnected areas: proglacial Lake Thomas, the lower glacial outflow stream and the glacier’s terminus. LCG associated microbial communities were phylogenetically diverse and varied by sampling location. However, Betaproteobacteria, Alphaproteobacteria and Bacteroidetes dominated communities at all sampling locations. Strict anaerobic groups such as methanogens, SR1, and OP11 were also recovered from glacier outflows, indicating anoxic conditions in at least some portions of the LCG subglacial environment. Microbial community structure was significantly correlated with sampling location and sodium concentrations. Microbial communities sampled from terminus outflow waters exhibited day-to-day fluctuation in taxonomy and phylogenetic similarity. However, these communities were not significantly different from randomly constructed communities from all three sites. These results indicate that glacial outflows share a large proportion of phylogenetic overlap with downstream environments and that the observed significant shifts in community structure are driven by changes in relative abundance of different taxa, and not complete restructuring of communities. We conclude that LCG glacial discharge hosts a diverse and relatively stable microbiome that shifts at fine taxonomic scales in response to geochemistry and likely water residence time.

  19. Influence of Martian regolith analogs on the activity and growth of methanogenic archaea, with special regard to long-term desiccation

    Directory of Open Access Journals (Sweden)

    Janosch eSchirmack

    2015-03-01

    Full Text Available Methanogenic archaea have been studied as model organisms for possible life on Mars for several reasons: they can grow lithoautotrophically by using hydrogen and carbon dioxide as energy and carbon sources, respectively; they are anaerobes; and they evolved at a time when conditions on early Earth are believed to have looked similar to those of early Mars. As Mars is currently dry and cold and as water might be available only at certain time intervals, any organism living on this planet would need to cope with desiccation. On Earth there are several regions with low water availability as well, e.g. permafrost environments, desert soils and salt pans. Here, we present the results of a set of experiments investigating the influence of different Martian regolith analogs on the metabolic activity and growth of three methanogenic strains exposed to culture conditions as well as long-term desiccation. In most cases, concentrations below 1 %wt of regolith in the media resulted in an increase of methane production rates, whereas higher concentrations decreased the rates, thus prolonging the lag phase. Further experiments showed that methanogenic archaea are capable of producing methane when incubated on a water-saturated sedimentary matrix of regolith lacking nutrients. Survival of methanogens under these conditions was analyzed with a 400 day desiccation experiment in the presence of regolith analogs. All tested strains of methanogens survived the desiccation period as it was determined through reincubation on fresh medium and via qPCR following propidium monoazide treatment to identify viable cells. The survival of long-term desiccation and the ability of active metabolism on water-saturated MRAs strengthens the possibility of methanogenic archaea or physiologically similar organisms to exist in environmental niches on Mars. The best results were achieved in presence of a phyllosilicate, which provides insights of possible positive effects in habitats

  20. Hydrogen or formate: Alternative key players in methanogenic degradation.

    Science.gov (United States)

    Schink, Bernhard; Montag, Dominik; Keller, Anja; Müller, Nicolai

    2017-06-01

    Hydrogen and formate are important electron carriers in methanogenic degradation in anoxic environments such as sediments, sewage sludge digestors and biogas reactors. Especially in the terminal steps of methanogenesis, they determine the energy budgets of secondary (syntrophically) fermenting bacteria and their methanogenic partners. The literature provides considerable data on hydrogen pool sizes in such habitats, but little data exist for formate concentrations due to technical difficulties in formate determination at low concentration. Recent evidence from biochemical and molecular biological studies indicates that several secondary fermenters can use both hydrogen and formate for electron release, and may do so even simultaneously. Numerous strictly anaerobic bacteria contain enzymes which equilibrate hydrogen and formate pools to energetically equal values, and recent measurements in sewage digestors and biogas reactors indicate that - beyond occasional fluctuations - the pool sizes of hydrogen and formate are indeed energetically nearly equivalent. Nonetheless, a thermophilic archaeon from a submarine hydrothermal vent, Thermococcus onnurineus, can obtain ATP from the conversion of formate to hydrogen plus bicarbonate at 80°C, indicating that at least in this extreme environment the pools of formate and hydrogen are likely to be sufficiently different to support such an unusual type of energy conservation. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  1. Community and Proteomic Analysis of Anaerobic Consortia Converting Tetramethylammonium to Methane

    Directory of Open Access Journals (Sweden)

    Wei-Yu Chen

    2017-01-01

    Full Text Available Tetramethylammonium-degrading methanogenic consortia from a complete-mixing suspended sludge (CMSS and an upflow anaerobic sludge blanket (UASB reactors were studied using multiple PCR-based molecular techniques and shotgun proteomic approach. The prokaryotic 16S rRNA genes of the consortia were analyzed by quantitative PCR, high-throughput sequencing, and DGGE-cloning methods. The results showed that methanogenic archaea were highly predominant in both reactors but differed markedly according to community structure. Community and proteomic analysis revealed that Methanomethylovorans and Methanosarcina were the major players for the demethylation of methylated substrates and methane formation through the reduction pathway of methyl-S-CoM and possibly, acetyl-CoA synthase/decarbonylase-related pathways. Unlike high dominance of one Methanomethylovorans population in the CMSS reactor, diverse methylotrophic Methanosarcina species inhabited in syntrophy-like association with hydrogenotrophic Methanobacterium in the granular sludge of UASB reactor. The overall findings indicated the reactor-dependent community structures of quaternary amines degradation and provided microbial insight for the improved understanding of engineering application.

  2. Community and Proteomic Analysis of Anaerobic Consortia Converting Tetramethylammonium to Methane

    Science.gov (United States)

    Chen, Wei-Yu; Kraková, Lucia; Pangallo, Domenico; Jeszeová, Lenka; Liu, Bing; Yasui, Hidenari

    2017-01-01

    Tetramethylammonium-degrading methanogenic consortia from a complete-mixing suspended sludge (CMSS) and an upflow anaerobic sludge blanket (UASB) reactors were studied using multiple PCR-based molecular techniques and shotgun proteomic approach. The prokaryotic 16S rRNA genes of the consortia were analyzed by quantitative PCR, high-throughput sequencing, and DGGE-cloning methods. The results showed that methanogenic archaea were highly predominant in both reactors but differed markedly according to community structure. Community and proteomic analysis revealed that Methanomethylovorans and Methanosarcina were the major players for the demethylation of methylated substrates and methane formation through the reduction pathway of methyl-S-CoM and possibly, acetyl-CoA synthase/decarbonylase-related pathways. Unlike high dominance of one Methanomethylovorans population in the CMSS reactor, diverse methylotrophic Methanosarcina species inhabited in syntrophy-like association with hydrogenotrophic Methanobacterium in the granular sludge of UASB reactor. The overall findings indicated the reactor-dependent community structures of quaternary amines degradation and provided microbial insight for the improved understanding of engineering application. PMID:29391857

  3. The effect of pectin, corn and wheat starch, inulin and pH on in vitro production of methane, short chain fatty acids and on the microbial community composition in rumen fluid.

    Science.gov (United States)

    Poulsen, Morten; Jensen, Bent Borg; Engberg, Ricarda M

    2012-02-01

    Methane emission from livestock, ruminants in particular, contributes to the build up of greenhouse gases in the atmosphere. Therefore the focus on methane emission from ruminants has increased. The objective of this study was to investigate mechanisms for methanogenesis in a rumen fluid-based in vitro fermentation system as a consequence of carbohydrate source (pectin, wheat and corn starch and inulin) and pH (ranging from 5.5 to 7.0). Effects were evaluated with respect to methane and short chain fatty acid (SCFA) production, and changes in the microbial community in the ruminal fluid as assessed by terminal-restriction fragment length polymorphism (T-RFLP) analysis. Fermentation of pectin resulted in significantly lower methane production rates during the first 10 h of fermentation compared to the other substrates (P = 0.001), although total methane production was unaffected by carbohydrate source (P = 0.531). Total acetic acid production was highest for pectin and lowest for inulin (P Methane production rates were significantly lower for fermentations at pH 5.5 and 7.0 (P = 0.005), sustained as a trend after 48 h (P = 0.059), indicating that there was a general optimum for methanogenic activity in the pH range from 6.0 to 6.5. Decreasing pH from 7.0 to 5.5 significantly favored total butyric acid production (P composition. This study demonstrates that both carbohydrate source and pH affect methane and SCFA production patterns, and the microbial community composition in rumen fluid. Copyright © 2011 Elsevier Ltd. All rights reserved.

  4. Storm-scale dynamics of bacterial community composition in throughfall and stemflow

    Science.gov (United States)

    Van Stan, J. T., II; Teachey, M. E.; Pound, P.; Ottesen, E. A.

    2017-12-01

    Transport of bacteria between ecosystem spheres can significantly affect microbially-mediated biogeochemical processes. During rainfall, there is a large, temporally-concentrated exchange of bacteria between the forest phyllosphere and the pedosphere by rain dripping from canopy surfaces, as throughfall (TF), and draining to the stem, as stemflow (SF). Many phyllosphere bacteria possibly transported by TF and SF have been linked to important litter and soil processes (like cyanobacteria and actinobacteria). Despite this, no work has applied high throughput DNA sequencing to assess the community composition of bacteria transported by TF and SF. We characterized bacterial community composition for TF and SF from an epiphyte-laden (Tillandsia usneoides L., Spanish moss) southern live oak (Quercus virginiana) forest in southeastern Georgia (USA) to address two hypotheses: that bacterial community composition will differ between (1) TF and SF, and (2) TF sampled beneath bare and epiphyte-laden canopy. Variability in family-level bacterial abundance, Bray-Curtis dissimilarity, and Shannon diversity index was greater between storms than between net rainfall fluxes. In fact, TF and SF bacterial communities were relatively similar for individual storms and may be driven by pre-storm atmospheric deposition rather than the communities affixed to leaves, bark, and epiphyte surfaces.

  5. The presence of hydrogenotrophic methanogens in the inoculum improves methane gas production in microbial electrolysis cells.

    KAUST Repository

    Siegert, Michael; Li, Xiu-Fen; Yates, Matthew D; Logan, Bruce E

    2014-01-01

    High current densities in microbial electrolysis cells (MECs) result from the predominance of various Geobacter species on the anode, but it is not known if archaeal communities similarly converge to one specific genus. MECs were examined here on the basis of maximum methane production and current density relative to the inoculum community structure. We used anaerobic digester (AD) sludge dominated by acetoclastic Methanosaeta, and an anaerobic bog sediment where hydrogenotrophic methanogens were detected. Inoculation using solids to medium ratio of 25% (w/v) resulted in the highest methane production rates (0.27 mL mL(-1) cm(-2), gas volume normalized by liquid volume and cathode projected area) and highest peak current densities (0.5 mA cm(-2)) for the bog sample. Methane production was independent of solid to medium ratio when AD sludge was used as the inoculum. 16S rRNA gene community analysis using pyrosequencing and quantitative PCR confirmed the convergence of Archaea to Methanobacterium and Methanobrevibacter, and of Bacteria to Geobacter, despite their absence in AD sludge. Combined with other studies, these findings suggest that Archaea of the hydrogenotrophic genera Methanobacterium and Methanobrevibacter are the most important microorganisms for methane production in MECs and that their presence in the inoculum improves the performance.

  6. Identification of novel potential acetate-oxidizing bacteria in an acetate-fed methanogenic chemostat based on DNA stable isotope probing.

    Science.gov (United States)

    Wang, Hui-Zhong; Gou, Min; Yi, Yue; Xia, Zi-Yuan; Tang, Yue-Qin

    2018-05-11

    Acetate is a significant intermediate of anaerobic fermentation. There are two pathways for converting acetate to CH 4 and CO 2 : acetoclastic methanogenesis by acetoclastic methanogens, and syntrophic acetate oxidation by acetate-oxidizing bacteria (AOB) and hydrogenotrophic methanogens. Detailed investigations of syntrophic acetate-oxidizing bacteria (SAOB) should contribute to the elucidation of the microbial mechanisms of methanogenesis. In this study, we investigated the major phylogenetic groups of acetate-utilizing bacteria (AUB) in a mesophilic methanogenic chemostat fed with acetate as the sole carbon source by using DNA stable isotope probing (SIP) technology. The results indicated that acetoclastic methanogenesis and acetate oxidization/hydrogenotrophic methanogenesis coexisted in the mesophilic chemostat fed with acetate, operated at a dilution rate of 0.1 d -1 . OTU Ace13(9-17) (KU869530), Ace13(9-4) (KU667241), and Ace13(9-23) (KU667236), assigned to the phyla Firmicutes and Bacteroidetes, were probably potential SAOB in the chemostat, which needs further investigation. Species in the phyla Proteobacteria, Deferribacteres, Acidobacteria, Spirochaetes and Actinobacteria were probably capable of utilizing acetate for their growth. Methanoculleus was likely to be the preferred hydrogenotrophic methanogen for syntrophy with AOB in the chemostat.

  7. Specific acyclic isoprenoids as biological markers of methanogenic bacteria in marine sediments.

    Science.gov (United States)

    Brassell, S C; Wardroper, A M; Thomson, I D; Maxwell, J R; Eglinton, G

    1981-04-23

    The widespread occurrence of extended hopanoids in sediments and petroleums illustrates the importance of bacterial lipid contributions to geological materials. In archaebacteria, however, hopanoids are absent; their role as structural components of biomembranes is fulfilled by acyclic isoprenoids. Recent studies of the lipid constituents of archaebacteria have greatly extended the range of acyclic isoprenoid skeletons known in organisms (Fig. 1). In particularly, isoprenoids with head-to-head linkages have been identified, and such compounds (for example, 3,7,11,15,18,22,26,30-octamethyldotriacontane, I) have been recognized in petroleum and as degradation products of Messel shale kerogen. Here we report the first recognition of 2,6,10,15,19-pentamethyleicosane (II), a known component of methanogens, in marine sediments of Recent to Cretaceous age (Table 1) and suggest that it and certain other acyclic isoprenoids may be used as biological markers for methanogens.

  8. The effect of organic loading rate and retention time on hydrogen production from a methanogenic CSTR.

    Science.gov (United States)

    Pakarinen, O; Kaparaju, P; Rintala, J

    2011-10-01

    The possibility of shifting a methanogenic process for hydrogen production by changing the process parameters viz., organic loading rate (OLR) and hydraulic retention time (HRT) was evaluated. At first, two parallel semi-continuously fed continuously stirred tank reactors (CSTR) were operated as methanogenic reactors (M1 and M2) for 78 days. Results showed that a methane yield of 198-218 L/kg volatile solids fed (VS(fed)) was obtained when fed with grass silage at an OLR of 2 kgVS/m³/d and HRT of 30 days. After 78 days of operation, hydrogen production was induced in M2 by increasing the OLR from 2 to 10 kgVS/m³/d and shortening the HRT from 30 to 6 days. The highest H₂ yield of 42 L/kgVS(fed) was obtained with a maximum H₂ content of 24%. The present results thus demonstrate that methanogenic process can be shifted towards hydrogen production by increasing the OLR and decreasing HRT. Copyright © 2011 Elsevier Ltd. All rights reserved.

  9. Changing Feeding Regimes To Demonstrate Flexible Biogas Production: Effects on Process Performance, Microbial Community Structure, and Methanogenesis Pathways.

    Science.gov (United States)

    Mulat, Daniel Girma; Jacobi, H Fabian; Feilberg, Anders; Adamsen, Anders Peter S; Richnow, Hans-Hermann; Nikolausz, Marcell

    2016-01-15

    Flexible biogas production that adapts biogas output to energy demand can be regulated by changing feeding regimes. In this study, the effect of changes in feeding intervals on process performance, microbial community structure, and the methanogenesis pathway was investigated. Three different feeding regimes (once daily, every second day, and every 2 h) at the same organic loading rate were studied in continuously stirred tank reactors treating distiller's dried grains with solubles. A larger amount of biogas was produced after feeding in the reactors fed less frequently (once per day and every second day), whereas the amount remained constant in the reactor fed more frequently (every 2 h), indicating the suitability of the former for the flexible production of biogas. Compared to the conventional more frequent feeding regimes, a methane yield that was up to 14% higher and an improved stability of the process against organic overloading were achieved by employing less frequent feeding regimes. The community structures of bacteria and methanogenic archaea were monitored by terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA and mcrA genes, respectively. The results showed that the composition of the bacterial community varied under the different feeding regimes, and the observed T-RFLP patterns were best explained by the differences in the total ammonia nitrogen concentrations, H2 levels, and pH values. However, the methanogenic community remained stable under all feeding regimes, with the dominance of the Methanosarcina genus followed by that of the Methanobacterium genus. Stable isotope analysis showed that the average amount of methane produced during each feeding event by acetoclastic and hydrogenotrophic methanogenesis was not influenced by the three different feeding regimes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  10. Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil

    Directory of Open Access Journals (Sweden)

    Yendi E. Navarro-Noya

    2015-01-01

    Full Text Available In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic Candidatus Nitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family. Novel phylogenetic branches in the Halobacteriales class were detected in the soil, and more abundantly in soil with the higher pH (10.5, indicating that unknown and uncharacterized Archaea can be found in this soil. Thirteen different genera of the Halobacteriaceae family were identified and were distributed differently between the soils. Halobiforma, Halostagnicola, Haloterrigena, and Natronomonas were found in all soil samples. Methanogenic archaea were found only in soil with pH between 10.0 and 10.3. Retrieved methanogenic archaea belonged to the Methanosarcinales and Methanomicrobiales orders. The comparison of the archaeal community structures considering phylogenetic information (UniFrac distances clearly clustered the communities by pH.

  11. Methane production and methanogenic Archaea in the digestive tracts of millipedes (Diplopoda)

    Czech Academy of Sciences Publication Activity Database

    Šustr, Vladimír; Chroňáková, Alica; Semanová, Stanislava; Tajovský, Karel; Šimek, Miloslav

    2014-01-01

    Roč. 9, č. 7 (2014), e102659 E-ISSN 1932-6203 R&D Projects: GA ČR GA526/09/1570 Institutional support: RVO:60077344 Keywords : methane production * methanogenic Archaea * digestive tracts of millipedes Subject RIV: EG - Zoology Impact factor: 3.234, year: 2014

  12. Does stability in local community composition depend on temporal variation in rates of dispersal and connectivity?

    Science.gov (United States)

    Valanko, Sebastian; Norkko, Joanna; Norkko, Alf

    2015-04-01

    In ecology understanding variation in connectivity is central for how biodiversity is maintained. Field studies on dispersal and temporal dynamics in community regulating processes are, however, rare. We test the short-term temporal stability in community composition in a soft-sediment benthic community by determining among-sampling interval similarity in community composition. We relate stability to in situ measures of connectivity (wind, wave, current energy) and rates of dispersal (quantified in different trap types). Waves were an important predictor of when local community taxa are most likely to disperse in different trap-types, suggesting that wave energy is important for connectivity in a region. Community composition at the site was variable and changed stochastically over time. We found changes in community composition (occurrence, abundance, dominance) to be greater at times when connectivity and rates of dispersal were low. In response to periods of lower connectedness dominant taxa in the local community only exhibited change in their relative abundance. In contrast, locally less abundant taxa varied in both their presence, as well as in relative abundance. Constancy in connectivity and rates of dispersal promotes community stability and persistence, suggesting that local community composition will be impacted by changes in the spatial extent over which immigration and emigration operates in the region. Few empirical studies have actually measured dispersal directly in a multi-species context to demonstrate the role it plays in maintaining local community structure. Even though our study does not evaluate coexistence over demographic time scales, it importantly demonstrates that dispersal is not only important in initial recruitment or following a disturbance, but also key in maintaining local community composition.

  13. Phenotypic properties and microbial diversity of methanogenic granules from a full-scale upflow anaerobic sludge bed reactor treating brewery wastewater.

    Science.gov (United States)

    Díaz, Emiliano E; Stams, Alfons J M; Amils, Ricardo; Sanz, José L

    2006-07-01

    Methanogenic granules from an anaerobic bioreactor that treated wastewater of a beer brewery consisted of different morphological types of granules. In this study, the microbial compositions of the different granules were analyzed by molecular microbiological techniques: cloning, denaturing gradient gel electrophoresis and fluorescent in situ hybridization (FISH), and scanning and transmission electron microscopy. We propose here that the different types of granules reflect the different stages in the life cycle of granules. Young granules were small, black, and compact and harbored active cells. Gray granules were the most abundant granules. These granules have a multilayer structure with channels and void areas. The core was composed of dead or starving cells with low activity. The brown granules, which were the largest granules, showed a loose and amorphous structure with big channels that resulted in fractured zones and corresponded to the older granules. Firmicutes (as determined by FISH) and Nitrospira and Deferribacteres (as determined by cloning and sequencing) were the predominant Bacteria. Remarkably, Firmicutes could not be detected in the brown granules. The methanogenic Archaea identified were Methanosaeta concilii (70 to 90% by FISH and cloning), Methanosarcina mazei, and Methanospirillum spp. The phenotypic appearance of the granules reflected the physiological condition of the granules. This may be valuable to easily select appropriate seed sludges to start up other reactors.

  14. Biological reductive dechlorination of tetrachloroethylene and trichloroethylene to ethylene under methanogenic conditions

    International Nuclear Information System (INIS)

    Freedman, D.L.; Gossett, J.M.

    1989-01-01

    A biological process for remediation of groundwater contaminated with tetrachloroethylene (PCE) and trichloroethylene (TCE) can only be applied if the transformation products are environmentally acceptable. Studies with enrichment cultures of PCE- and TCE-degrading microorganisms provide evidence that, under methanogenic conditions, mixed cultures are able to completely dechlorinate PCE and TCE to ethylene, a product which is environmentally acceptable. Radiotracer studies with [ 14 C]PCE indicated that [ 14 C]ethylene was the terminal product; significant conversion to 14 CO 2 or 14 CH 4 was not observed. The rate-limiting step in the pathway appeared to be conversion of vinyl chloride to ethylene. To sustain reductive dechlorination of PCE and TCE, it was necessary to supply an electron donor; methanol was the most effective, although hydrogen, formate, acetate, and glucose also served. Studies with the inhibitor 2-bromoethanesulfonate suggested that methanogens played a key role in the observed biotransformations of PCE and TCE

  15. Abiotic and biotic transformations of 1,1,1-trichloroethane under methanogenic conditions

    International Nuclear Information System (INIS)

    Vogel, T.M.; McCarty, P.L.

    1987-01-01

    A common industrial solvent, 1,1,1-trichloroethane (TCA), is one of the most frequently found contaminants in ground water. The fate of TCA in ground water is complicated by the different possible abiotic and biotic transformations that it may undergo. Abiotic transformation of TCA can result in a mixture of 1,1-dichloro-ethylene (1,1-DCE) and acetic acid, as shown by others. This study confirms that TCA can be biotransformed by reductive dehalogenation to 1,1-dichloroethane (1,1-DCA) and chloroethane (CA) under methanogenic conditions. Also, reductive dehalogenation of 1,1-DCE to vinyl chloride (VC) is confirmed. This study demonstrates that these transformations can occur stoichiometrically. In addition, [ 14 C]TCA, [ 14 C]-1,1-DCA, [ 14 C]-1,1-DCE, [ 14 C]CA, and [ 14 C]VC were at least partially mineralized to 14 CO 2 under similar methanogenic conditions.23 references, 3 figures, 4 tables

  16. Acclimation to extremely high ammonia levels in continuous biomethanation process and the associated microbial community dynamics

    DEFF Research Database (Denmark)

    Tian, Hailin; Fotidis, Ioannis; Mancini, Enrico

    2018-01-01

    Acclimatized anaerobic communities to high ammonia levels can offer a solution to the ammonia toxicity problem in biogas reactors. In the current study, a stepwise acclimation strategy up to 10 g NH4+-N L−1, was performed in mesophilic (37 ± 1 °C) continuously stirred tank reactors. The reactors...... change throughout the ammonia acclimation process. Clostridium ultunense, a syntrophic acetate oxidizing bacteria, increased significantly alongside with hydrogenotrophic methanogen Methanoculleus spp., indicating strong hydrogenotrophic methanogenic activity at extreme ammonia levels (>7 g NH4+-N L−1...

  17. Effects of viruses and predators on prokaryotic community composition.

    Science.gov (United States)

    Jardillier, Ludwig; Bettarel, Yvan; Richardot, Mathilde; Bardot, Corinne; Amblard, Christian; Sime-Ngando, Télesphore; Debroas, Didier

    2005-11-01

    Dialysis bags were used to examine the impact of predation and viral lysis on prokaryotic community composition (PCC) over a 5-day experiment in the oligomesotrophic Lake Pavin (France). The impact of the different predator communities (protists and metazoans) of prokaryotes was estimated by water fractionation (protists, which also affected PCC, whereas viruses seemed to be essentially responsible for profound changes in PCC via direct and indirect actions.

  18. Response of Syntrophic Propionate Degradation to pH Decrease and Microbial Community Shifts in an UASB Reactor.

    Science.gov (United States)

    Zhang, Liguo; Ban, Qiaoying; Li, Jianzheng; Jha, Ajay Kumar

    2016-08-28

    The effect of pH on propionate degradation in an upflow anaerobic sludge blanket (UASB) reactor containing propionate as a sole carbon source was studied. Under influent propionate of 2,000 mg/l and 35ºC, propionate removal at pH 7.5-6.8 was above 93.6%. Propionate conversion was significantly inhibited with stepwise pH decrease from pH 6.8 to 6.5, 6.0, 5.5, 5.0, 4.5, and then to 4.0. After long-term operation, the propionate removal at pH 6.5-4.5 maintained an efficiency of 88.5%-70.1%, whereas propionate was hardly decomposed at pH 4.0. Microbial composition analysis showed that propionate-oxidizing bacteria from the genera Pelotomaculum and Smithella likely existed in this system. They were significantly reduced at pH ≤5.5. The methanogens in this UASB reactor belonged to four genera: Methanobacterium, Methanospirillum, Methanofollis, and Methanosaeta. Most detectable hydrogenotrophic methanogens were able to grow at low pH conditions (pH 6.0-4.0), but the acetotrophic methanogens were reduced as pH decreased. These results indicated that propionate-oxidizing bacteria and acetotrophic methanogens were more sensitive to low pH (5.5-4.0) than hydrogenotrophic methanogens.

  19. Predictability of bee community composition after floral removals differs by floral trait group.

    Science.gov (United States)

    Urban-Mead, Katherine R

    2017-11-01

    Plant-bee visitor communities are complex networks. While studies show that deleting nodes alters network topology, predicting these changes in the field remains difficult. Here, a simple trait-based approach is tested for predicting bee community composition following disturbance. I selected six fields with mixed cover of flower species with shallow (open) and deep (tube) nectar access, and removed all flowers or flower heads of species of each trait in different plots paired with controls, then observed bee foraging and composition. I compared the bee community in each manipulated plot with bees on the same flower species in control plots. The bee morphospecies composition in manipulations with only tube flowers remaining was the same as that in the control plots, while the bee morphospecies on only open flowers were dissimilar from those in control plots. However, the proportion of short- and long-tongued bees on focal flowers did not differ between control and manipulated plots for either manipulation. So, bees within some functional groups are more strongly linked to their floral trait partners than others. And, it may be more fruitful to describe expected bee community compositions in terms of relative proportions of relevant ecological traits than species, particularly in species-diverse communities. © 2017 The Author(s).

  20. Hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities.

    Science.gov (United States)

    Somenahally, Anil C; Mosher, Jennifer J; Yuan, Tong; Podar, Mircea; Phelps, Tommy J; Brown, Steven D; Yang, Zamin K; Hazen, Terry C; Arkin, Adam P; Palumbo, Anthony V; Van Nostrand, Joy D; Zhou, Jizhong; Elias, Dwayne A

    2013-01-01

    Microbial reduction of toxic hexavalent chromium (Cr(VI)) in-situ is a plausible bioremediation strategy in electron-acceptor limited environments. However, higher [Cr(VI)] may impose stress on syntrophic communities and impact community structure and function. The study objectives were to understand the impacts of Cr(VI) concentrations on community structure and on the Cr(VI)-reduction potential of groundwater communities at Hanford, WA. Steady state continuous flow bioreactors were used to grow native communities enriched with lactate (30 mM) and continuously amended with Cr(VI) at 0.0 (No-Cr), 0.1 (Low-Cr) and 3.0 (High-Cr) mg/L. Microbial growth, metabolites, Cr(VI), 16S rRNA gene sequences and GeoChip based functional gene composition were monitored for 15 weeks. Temporal trends and 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) levels were below detection from week 1 until week 15. With lactate enrichment, native bacterial diversity substantially decreased as Pelosinus spp., and Sporotalea spp., became the dominant groups, but did not significantly differ between Cr concentrations. The Archaea diversity also substantially decreased after lactate enrichment from Methanosaeta (35%), Methanosarcina (17%) and others, to mostly Methanosarcina spp. (95%). Methane production was lower in High-Cr reactors suggesting some inhibition of methanogens. Several key functional genes were distinct in Low-Cr bioreactors compared to High-Cr. Among the Cr resistant microbes, Burkholderia vietnamiensis, Comamonas testosterone and Ralstonia pickettii proliferated in Cr amended bioreactors. In-situ fermentative conditions facilitated Cr(VI) reduction, and as a result 3.0 mg/L Cr(VI) did not impact the overall bacterial community structure.

  1. Hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities.

    Directory of Open Access Journals (Sweden)

    Anil C Somenahally

    Full Text Available Microbial reduction of toxic hexavalent chromium (Cr(VI in-situ is a plausible bioremediation strategy in electron-acceptor limited environments. However, higher [Cr(VI] may impose stress on syntrophic communities and impact community structure and function. The study objectives were to understand the impacts of Cr(VI concentrations on community structure and on the Cr(VI-reduction potential of groundwater communities at Hanford, WA. Steady state continuous flow bioreactors were used to grow native communities enriched with lactate (30 mM and continuously amended with Cr(VI at 0.0 (No-Cr, 0.1 (Low-Cr and 3.0 (High-Cr mg/L. Microbial growth, metabolites, Cr(VI, 16S rRNA gene sequences and GeoChip based functional gene composition were monitored for 15 weeks. Temporal trends and 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 levels were below detection from week 1 until week 15. With lactate enrichment, native bacterial diversity substantially decreased as Pelosinus spp., and Sporotalea spp., became the dominant groups, but did not significantly differ between Cr concentrations. The Archaea diversity also substantially decreased after lactate enrichment from Methanosaeta (35%, Methanosarcina (17% and others, to mostly Methanosarcina spp. (95%. Methane production was lower in High-Cr reactors suggesting some inhibition of methanogens. Several key functional genes were distinct in Low-Cr bioreactors compared to High-Cr. Among the Cr resistant microbes, Burkholderia vietnamiensis, Comamonas testosterone and Ralstonia pickettii proliferated in Cr amended bioreactors. In-situ fermentative conditions facilitated Cr(VI reduction, and as a result 3.0 mg/L Cr(VI did not impact the overall bacterial community structure.

  2. Hexavalent Chromium Reduction under Fermentative Conditions with Lactate Stimulated Native Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    Somenahally, Anil C [ORNL; Mosher, Jennifer J [ORNL; Yuan, Tong [University of Oklahoma; 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; Van Nostrand, Dr. Joy D. [Oklahoma University; Zhou, Jizhong [University of Oklahoma; Elias, Dwayne A [ORNL

    2013-01-01

    Microbial reduction of toxic hexavalent chromium (Cr(VI)) in-situ is a plausible bioremediation strategy in electron-acceptor limited environments. However, higher [Cr(VI)] may impose stress on syntrophic communities and impact community structure and function. The study objectives were to understand the impacts of Cr(VI) concentrations on community structure and on the Cr(VI)-reduction potential of groundwater communities at Hanford, WA. Steady state continuous flow bioreactors were used to grow native communities enriched with lactate (30 mM) and continuously amended with Cr(VI) at 0.0 (No-Cr), 0.1 (Low-Cr) and 3.0 (High-Cr) mg/L. Microbial growth, metabolites, Cr(VI), 16S rRNA gene sequences and GeoChip based functional gene composition were monitored for 15 weeks. Temporal trends and 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) levels were below detection from week 1 until week 15. With lactate enrichment, native bacterial diversity substantially decreased as Pelosinus spp., and Sporotalea spp., became the dominant groups, but did not significantly differ between Cr concentrations. The Archaea diversity also substantially decreased after lactate enrichment from Methanosaeta (35%), Methanosarcina (17%) and others, to mostly Methanosarcina spp. (95%). Methane production was lower in High-Cr reactors suggesting some inhibition of methanogens. Several key functional genes were distinct in Low-Cr bioreactors compared to High-Cr. Among the Cr resistant microbes, Burkholderia vietnamiensis, Comamonas testosterone and Ralstonia pickettii proliferated in Cr amended bioreactors. In-situ fermentative conditions facilitated Cr(VI) reduction, and as a result 3.0 mg/L Cr(VI) did not impact the overall bacterial community structure.

  3. Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering.

    Science.gov (United States)

    Chroňáková, Alica; Schloter-Hai, Brigitte; Radl, Viviane; Endesfelder, David; Quince, Christopher; Elhottová, Dana; Šimek, Miloslav; Schloter, Michael

    2015-01-01

    Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI) and long-term impact (17 years; LTI), one is regenerating from cattle impact (REG) and a control is unaffected by cattle (CON). Cattle manure (CMN), the source of allochthonous microbes, was collected from the same area. We used pyrosequencing of 16S rRNA genes to assess the composition of archaeal and bacterial communities in each soil type and CMN. Both short- and long- term cattle impact negatively altered archaeal and bacterial diversity, leading to increase of homogenization of microbial communities in overwintering soils over time. Moreover, strong shifts in the prokaryotic communities were observed in response to cattle overwintering, with the greatest impact on archaea. Oligotrophic and acidophilic microorganisms (e.g. Thaumarchaeota, Acidobacteria, and α-Proteobacteria) dominated in CON and expressed strong negative response to increased pH, total C and N. Whereas copiotrophic and alkalophilic microbes (e.g. methanogenic Euryarchaeota, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidetes) were common in LTI showing opposite trends. Crenarchaeota were also found in LTI, though their trophic interactions remain cryptic. Firmicutes, Bacteroidetes, Methanobacteriaceae, and Methanomicrobiaceae indicated the introduction and establishment of faecal microbes into the impacted soils, while Chloroflexi and Methanosarcinaceae suggested increased abundance of soil-borne microbes under altered environmental conditions. The observed changes in prokaryotic community composition may have driven corresponding changes in soil functioning.

  4. Visualization of candidate division OP3 cocci in limonene-degrading methanogenic cultures

    DEFF Research Database (Denmark)

    Rotaru, Amelia-Elena; Schauer, Regina; Probian, Christina

    2012-01-01

    Members of candidate division OP3 were detected in 16S rRNA gene clone libraries from methanogenic enrichment cultures that utilized limonene as a carbon and energy source. We developed probes for the visualization of OP3 cells. In situ hybridization experiments with newly designed OP3-specific...

  5. Selenate removal in methanogenic and sulfate-reducing upflow anaerobic sludge bed reactors

    NARCIS (Netherlands)

    Lenz, M.; Hullebusch, van E.D.; Hommes, G.; Corvini, P.F.X.; Lens, P.N.L.

    2008-01-01

    This paper evaluates the use of upflow anaerobic sludge bed (UASB) bioreactors (30 degrees C, pH = 7.0) to remove selenium oxyanions from contaminated waters (790 mu g Se L-1) under methanogenic and sulfate-reducing conditions using lactate as electron donor. One UASB reactor received sulfate at

  6. Exocellular electron transfer in anaerobic microbial communities.

    Science.gov (United States)

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

    2006-03-01

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

  7. Impact of fulvic acids on bio-methanogenic treatment of municipal solid waste incineration leachate.

    Science.gov (United States)

    Dang, Yan; Lei, Yuqing; Liu, Zhao; Xue, Yiting; Sun, Dezhi; Wang, Li-Ying; Holmes, Dawn E

    2016-12-01

    A considerable amount of leachate with high fulvic acid (FA) content is generated during the municipal solid waste (MSW) incineration process. This incineration leachate is usually processed by downstream bio-methanogenic treatment. However, few studies have examined the impact that these compounds have on methanogenesis and how they are degraded and transformed during the treatment process. In this study, a laboratory-scale expanded granular sludge bed (EGSB) reactor was operated with MSW incineration leachate containing various concentrations of FA (1500 mg/L to 8000 mg/L) provided as the influent. We found that FA degradation rates decreased from 86% to 72% when FA concentrations in the reactor were increased, and that molecular size, level of humification and aromatization of the residual FA macromolecules all increased after bio-methanogenic treatment. Increasing FA influent concentrations also inhibited growth of hydrogenotrophic methanogens from the genus Methanobacterium and syntrophic bacteria from the genus Syntrophomonas, which resulted in a decrease in methane production and a concomitant increase in CO 2 content in the biogas. Sequences most similar to species from the genus Anaerolinea went up as FA concentrations increased. Bacteria from this genus are capable of extracellular electron transfer and may be using FA as an electron acceptor for growth or as a shuttle for syntrophic exchange with other microorganisms in the reactor. In order to determine whether FA could serve as an electron shuttle to promote syntrophy in an anaerobic digester, co-cultures of Geobacter metallireducens and G. sulfurreducens were grown in the presence of FA from raw leachate or from residual bioreactor effluent. While raw FA stimulated electron transfer between these two bacteria, residual FA did not have any electron shuttling abilities, indicating that FA underwent a significant transformation during the bio-methanogenic treatment process. These results are

  8. Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function.

    Science.gov (United States)

    Flues, Sebastian; Bass, David; Bonkowski, Michael

    2017-08-01

    Preferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf-associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation on bacteria. Predation-induced shifts in bacterial community composition could be linked to phenotypic protist traits. Protist reproduction rate, morphological plasticity and cell speed were most important in determining bacterial community composition. Analyses of co-occurrence patterns showed less complex correlations between bacterial taxa in the protist-grazed treatments with a higher proportion of positive correlations than in non-grazed controls, suggesting that predation reduced the influence of strong competitors. Protist predation influenced 14 metabolic core functions including membrane transport from which type VI secretion systems were in particular upregulated. In view of the functional importance of bacterial communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of predator-prey interactions, changes in microbial composition and function, and subsequent repercussions on plant performance are clearly required. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  9. Impact of enzymatic digestion on bacterial community composition in CF airway samples.

    Science.gov (United States)

    Williamson, Kayla M; Wagner, Brandie D; Robertson, Charles E; Johnson, Emily J; Zemanick, Edith T; Harris, J Kirk

    2017-01-01

    Previous studies have demonstrated the importance of DNA extraction methods for molecular detection of Staphylococcus, an important bacterial group in cystic fibrosis (CF). We sought to evaluate the effect of enzymatic digestion (EnzD) prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP) samples from patients with CF. DNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD. Shannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the genera Gemella ( p  microbial community composition. We show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection of Staphylococcus in CF OP samples. The enhanced identification of Staphylococcus aureus is a strong indication to utilize EnzD in studies that use OP swabs to monitor CF airway communities.

  10. Stormwater runoff drives viral community composition changes in inland freshwaters

    Science.gov (United States)

    Williamson, Kurt E.; Harris, Jamie V.; Green, Jasmin C.; Rahman, Faraz; Chambers, Randolph M.

    2014-01-01

    Storm events impact freshwater microbial communities by transporting terrestrial viruses and other microbes to freshwater systems, and by potentially resuspending microbes from bottom sediments. The magnitude of these impacts on freshwater ecosystems is unknown and largely unexplored. Field studies carried out at two discrete sites in coastal Virginia (USA) were used to characterize the viral load carried by runoff and to test the hypothesis that terrestrial viruses introduced through stormwater runoff change the composition of freshwater microbial communities. Field data gathered from an agricultural watershed indicated that primary runoff can contain viral densities approximating those of receiving waters. Furthermore, viruses attached to suspended colloids made up a large fraction of the total load, particularly in early stages of the storm. At a second field site (stormwater retention pond), RAPD-PCR profiling showed that the viral community of the pond changed dramatically over the course of two intense storms while relatively little change was observed over similar time scales in the absence of disturbance. Comparisons of planktonic and particle-associated viral communities revealed two completely distinct communities, suggesting that particle-associated viruses represent a potentially large and overlooked portion of aquatic viral abundance and diversity. Our findings show that stormwater runoff can quickly change the composition of freshwater microbial communities. Based on these findings, increased storms in the coastal mid-Atlantic region predicted by most climate change models will likely have important impacts on the structure and function of local freshwater microbial communities. PMID:24672520

  11. Performance of CSTR-EGSB-SBR system for treating sulfate-rich cellulosic ethanol wastewater and microbial community analysis.

    Science.gov (United States)

    Shan, Lili; Zhang, Zhaohan; Yu, Yanling; Ambuchi, John Justo; Feng, Yujie

    2017-06-01

    Performance and microbial community composition were evaluated in a two-phase anaerobic and aerobic system treating sulfate-rich cellulosic ethanol wastewater (CEW). The system was operated at five different chemical oxygen demand (COD)/SO 4 2- ratios (63.8, 26.3, 17.8, 13.7, and 10.7). Stable performance was obtained for total COD removal efficiency (94.5%), sulfate removal (89.3%), and methane production rate (11.5 L/day) at an organic loading rate of 32.4 kg COD/(m 3 ·day). The acidogenic reactor made a positive contribution to net VFAs production (2318.1 mg/L) and sulfate removal (60.9%). Acidogenic bacteria (Megasphaera, Parabacteroides, unclassified Ruminococcaceae spp., and Prevotella) and sulfate-reducing bacteria (Butyrivibrio, Megasphaera) were rich in the acidogenic reactor. In the methanogenic reactor, high diversity of microorganisms corresponded with a COD removal contribution of 83.2%. Moreover, methanogens (Methanosaeta) were predominant, suggesting that these organisms played an important role in the acetotrophic methanogenesis pathway. The dominant aerobic bacteria (Truepera) appeared to have been responsible for the COD removal of the SBR. These results indicate that dividing the sulfate reduction process could effectively minimize sulfide toxicity, which is important for the successful operation of system treating sulfate-rich CEW.

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

    Science.gov (United States)

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

    2017-12-01

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

  13. Influence of DNA isolation on Q-PCR-based quantification of methanogenic Archaea in biogas fermenters.

    Science.gov (United States)

    Bergmann, I; Mundt, K; Sontag, M; Baumstark, I; Nettmann, E; Klocke, M

    2010-03-01

    Quantitative real-time PCR (Q-PCR) is commonly applied for the detection of certain microorganisms in environmental samples. However, some environments, like biomass-degrading biogas fermenters, are enriched with PCR-interfering substances. To study the impact of the DNA extraction protocol on the results of Q-PCR-based analysis of the methane-producing archaeal community in biogas fermenters, nine different protocols with varying cell disruption and DNA purification approaches were tested. Differences in the quantities of the isolated DNA and the purity parameters were found, with the best cell lysis efficiencies being obtained by a combined lysozyme/SDS-based lysis. When DNA was purified by sephacryl columns, the amount of DNA decreased by one log cycle but PCR inhibitors were eliminated sufficiently. In the case of detection of methanogenic Archaea, the chosen DNA isolation protocol strongly influenced the Q-PCR-based determination of 16S rDNA copy numbers. For example, with protocols including mechanical cell disruption, the 16S rDNA of Methanobacteriales were predominantly amplified (81-90% of the total 16S rDNA copy numbers), followed by the 16S rDNA of Methanomicrobiales (9-18%). In contrast, when a lysozyme/SDS-based cell lysis was applied, the 16S rDNA copy numbers determined for these two orders were the opposite (Methanomicrobiales 82-95%, Methanobacteriales 4-18%). In extreme cases, the DNA isolation method led to discrimination of some groups of methanogens (e.g. members of the Methanosaetaceae). In conclusion, for extraction of high amounts of microbial DNA with high purity from samples of biogas plants, a combined lysozyme/SDS-based cell lysis followed by a purification step with sephacryl columns is recommended. Copyright 2010 Elsevier GmbH. All rights reserved.

  14. Submerged macrophytes modify bacterial community composition in sediments in a large, shallow, freshwater lake.

    Science.gov (United States)

    Zhao, Da-Yong; Liu, Peng; Fang, Chao; Sun, Yi-Meng; Zeng, Jin; Wang, Jian-Qun; Ma, Ting; Xiao, Yi-Hong; Wu, Qinglong L

    2013-04-01

    Submerged aquatic macrophytes are an important part of the lacustrine ecosystem. In this study, the bacterial community compositions in the rhizosphere sediments from three kinds of submerged macrophytes (Ceratophyllum demersum, Potamogeton crispus, and Vallisneria natans) were investigated to determine whether submerged macrophytes could drive the variation of bacterial community in the eutrophic Taihu Lake, China. Molecular techniques, including terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene and clone libraries, were employed to analyze the bacterial community compositions. Remarkable differences of the T-RFLP patterns were observed among the different samples, and the results of LIBSHUFF analysis also confirmed that the bacterial community compositions in the rhizosphere sediments of three kinds of submerged macrophytes were statistically different from that of the unvegetated sediment. Acidobacteria, Deltaproteobacteria, and Betaproteobacteria were the dominant bacterial groups in the rhizosphere sediments of Ceratophyllum demersum, Potamogeton crispus, and Vallisneria natans, respectively, accounting for 15.38%, 29.03%, and 18.00% of the total bacterial abundances. Our study demonstrated that submerged macrophytes could influence the bacterial community compositions in their rhizosphere sediments, suggesting that macrophytes have an effect on the cycling and transportation of nutrients in the freshwater lake ecosystem.

  15. Methanosarcina Play an Important Role in Anaerobic Co-Digestion of the Seaweed Ulva lactuca: Taxonomy and Predicted Metabolism of Functional Microbial Communities.

    Directory of Open Access Journals (Sweden)

    Jamie A FitzGerald

    Full Text Available Macro-algae represent an ideal resource of third generation biofuels, but their use necessitates a refinement of commonly used anaerobic digestion processes. In a previous study, contrasting mixes of dairy slurry and the macro-alga Ulva lactuca were anaerobically digested in mesophilic continuously stirred tank reactors for 40 weeks. Higher proportions of U. lactuca in the feedstock led to inhibited digestion and rapid accumulation of volatile fatty acids, requiring a reduced organic loading rate. In this study, 16S pyrosequencing was employed to characterise the microbial communities of both the weakest (R1 and strongest (R6 performing reactors from the previous work as they developed over a 39 and 27-week period respectively. Comparing the reactor communities revealed clear differences in taxonomy, predicted metabolic orientation and mechanisms of inhibition, while constrained canonical analysis (CCA showed ammonia and biogas yield to be the strongest factors differentiating the two reactor communities. Significant biomarker taxa and predicted metabolic activities were identified for viable and failing anaerobic digestion of U. lactuca. Acetoclastic methanogens were inhibited early in R1 operation, followed by a gradual decline of hydrogenotrophic methanogens. Near-total loss of methanogens led to an accumulation of acetic acid that reduced performance of R1, while a slow decline in biogas yield in R6 could be attributed to inhibition of acetogenic rather than methanogenic activity. The improved performance of R6 is likely to have been as a result of the large Methanosarcina population, which enabled rapid removal of acetic acid, providing favourable conditions for substrate degradation.

  16. Methanosarcina Play an Important Role in Anaerobic Co-Digestion of the Seaweed Ulva lactuca: Taxonomy and Predicted Metabolism of Functional Microbial Communities.

    Science.gov (United States)

    FitzGerald, Jamie A; Allen, Eoin; Wall, David M; Jackson, Stephen A; Murphy, Jerry D; Dobson, Alan D W

    2015-01-01

    Macro-algae represent an ideal resource of third generation biofuels, but their use necessitates a refinement of commonly used anaerobic digestion processes. In a previous study, contrasting mixes of dairy slurry and the macro-alga Ulva lactuca were anaerobically digested in mesophilic continuously stirred tank reactors for 40 weeks. Higher proportions of U. lactuca in the feedstock led to inhibited digestion and rapid accumulation of volatile fatty acids, requiring a reduced organic loading rate. In this study, 16S pyrosequencing was employed to characterise the microbial communities of both the weakest (R1) and strongest (R6) performing reactors from the previous work as they developed over a 39 and 27-week period respectively. Comparing the reactor communities revealed clear differences in taxonomy, predicted metabolic orientation and mechanisms of inhibition, while constrained canonical analysis (CCA) showed ammonia and biogas yield to be the strongest factors differentiating the two reactor communities. Significant biomarker taxa and predicted metabolic activities were identified for viable and failing anaerobic digestion of U. lactuca. Acetoclastic methanogens were inhibited early in R1 operation, followed by a gradual decline of hydrogenotrophic methanogens. Near-total loss of methanogens led to an accumulation of acetic acid that reduced performance of R1, while a slow decline in biogas yield in R6 could be attributed to inhibition of acetogenic rather than methanogenic activity. The improved performance of R6 is likely to have been as a result of the large Methanosarcina population, which enabled rapid removal of acetic acid, providing favourable conditions for substrate degradation.

  17. Bacterial community composition of a wastewater treatment system reliant on N{sub 2} fixation

    Energy Technology Data Exchange (ETDEWEB)

    Reid, N.M.; Bowers, T.H.; Lloyd-Jones, G. [Scion, Rotorua (New Zealand)

    2008-05-15

    The temporal stability and change of the dominant phylogenetic groups of the domain bacteria were studied in a model plant-based industrial wastewater treatment system showing high levels of organic carbon removal supported by high levels of N{sub 2} fixation. Community profiles were obtained through terminal restriction fragment length polymorphism analysis and cloning of 16S rRNA amplicons followed by sequencing. Bacterial community profiles showed that ten common terminal restriction fragments made up approximately 50% of the measured bacterial community. As much as 42% of the measured bacterial community could be monitored by using quantitative PCR and primers that targeted three dominant operational taxonomic units. Despite changes in wastewater composition and dissolved oxygen levels, the bacterial community composition appeared stable and was dominated by {alpha}-Proteobacteria and {beta}-Proteobacteria, with a lesser amount of the highly diverse bacterial phylum Bacteroidetes. A short period of considerable change in the bacterial community composition did not appear to affect treatment performance indicating functional redundancy in this treatment system. (orig.)

  18. Studies on methanogenic consortia associated with mangrove sediments of Ennore.

    Digital Repository Service at National Institute of Oceanography (India)

    Ahila, N.K.; Kannapiran, E.; Ravindran, J.; Ramkumar, V.S.

    page : www.jeb.co.in « E-mail : editor@jeb.co.in Journal of Environmental Biology, Vol. 35, 649-654, July 2014© Triveni Enterprises, Lucknow (India) Journal of Environmental Biology ISSN: 0254-8704 CODEN: JEBIDP Introduction Mangroves are complex...-National Institute of Oceanography, Biological Oceanography Division, Dona Paula, Goa – 403 004, India Abstract Key words In this study, methanogenic consortia were isolated and characterized from eight different sediment samples of mangrove ecosystem located...

  19. Restricted diversity of dental calculus methanogens over five centuries, France

    OpenAIRE

    Hong T. T. Huynh; Vanessa D. Nkamga; Michel Signoli; Stéfan Tzortzis; Romuald Pinguet; Gilles Audoly; Gérard Aboudharam; Michel Drancourt

    2016-01-01

    Methanogens are acknowledged archaeal members of modern dental calculus microbiota and dental pathogen complexes. Their repertoire in ancient dental calculus is poorly known. We therefore investigated archaea in one hundred dental calculus specimens collected from individuals recovered from six archaeological sites in France dated from the 14th to 19th centuries AD. Dental calculus was demonstrated by macroscopic and cone-beam observations. In 56 calculus specimens free of PCR inhibition, PCR...

  20. Does mechanical disturbance affect the performance and species composition of submerged macrophyte communities?

    Science.gov (United States)

    Zhang, Qian; Xu, Ying-Shou; Huang, Lin; Xue, Wei; Sun, Gong-Qi; Zhang, Ming-Xiang; Yu, Fei-Hai

    2014-05-01

    Submerged macrophyte communities are frequently subjected to disturbance of various frequency and strength. However, there is still little experimental evidence on how mechanical disturbance affects the performance and species composition of such plant communities. In a greenhouse experiment, we constructed wetland communities consisting of five co-occurring clonal submerged macrophyte species (Hydrilla verticillata, Elodea canadensis, Ceratophyllum demersum, Chara fragilis, and Myriophyllum spicatum) and subjected these communities to three mechanical disturbance regimes (no, moderate and strong disturbance). Strong mechanical disturbance greatly decreased overall biomass, number of shoot nodes and total shoot length, and increased species diversity (evenness) of the total community. It also substantially decreased the growth of the most abundant species (H. verticillata), but did not affect growth of the other four species. Our data reveal that strong disturbance can have different effects on different submerged macrophyte species and thus alters the performance and species composition of submerged macrophyte communities.

  1. Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest

    Science.gov (United States)

    Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

    2016-01-01

    The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient—namely, Santa Virginia, Picinguaba and Restinga—we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms—ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning. PMID:26752633

  2. Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest.

    Science.gov (United States)

    Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

    2016-01-01

    The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient-namely, Santa Virginia, Picinguaba and Restinga-we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms-ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning.

  3. Spatial variation of bacterial community composition near the Luzon ...

    African Journals Online (AJOL)

    Spatial variation of bacterial community composition near the Luzon strait assessed by polymerase chain reaction-denaturing gradient gel electrophoresis ... chain reaction (PCR)-amplified bacterial 16S ribosomal deoxyribonucleic acid (DNA) gene fragments and interpreted the results; its relationship with physical and ...

  4. Differences in microbial communities and performance between suspended and attached growth anaerobic membrane bioreactors treating synthetic municipal wastewater

    KAUST Repository

    Harb, Moustapha; Xiong, Yanghui; Guest, Jeremy; Amy, Gary L.; Hong, Pei-Ying

    2015-01-01

    operational taxonomic units (OTUs) most closely related to fermentative bacteria (e.g., Microbacter margulisiae) were dominant in the suspended biomass of the CSTR, accounting for 30% of the microbial community. Conversely, methanogenic archaea (e

  5. Impacts of Fertilization Regimes on Arbuscular Mycorrhizal Fungal (AMF) Community Composition Were Correlated with Organic Matter Composition in Maize Rhizosphere Soil.

    Science.gov (United States)

    Zhu, Chen; Ling, Ning; Guo, Junjie; Wang, Min; Guo, Shiwei; Shen, Qirong

    2016-01-01

    The understanding of the response of arbuscular mycorrhizal fungi (AMF) community composition to fertilization is of great significance in sustainable agriculture. However, how fertilization influences AMF diversity and composition is not well-established yet. A field experiment located in northeast China in typical black soil (Chernozem) was conducted and high-throughput sequencing approach was used to investigate the effects of different fertilizations on the variation of AMF community in the rhizosphere soil of maize crop. The results showed that AMF diversity in the maize rhizosphere was significantly altered by different fertilization regimes. As revealed by redundancy analysis, the application of organic manure was the most important factor impacting AMF community composition between samples with and without organic manure, followed by N fertilizer and P fertilizer inputs. Moreover, the organic matter composition in the rhizosphere, determined by GC-MS, was significantly altered by the organic manure amendment. Many of the chemical components displayed significant relationships with the AMF community composition according to the Mantel test, among those, 2-ethylnaphthalene explained the highest percentage (54.2%) of the variation. The relative contents of 2-ethylnaphthalene and 2, 6, 10-trimethyltetradecane had a negative correlation with Glomus relative abundance, while the relative content of 3-methylbiphenyl displayed a positive correlation with Rhizophagus . The co-occurrence patterns in treatments with and without organic manure amendment were analyzed, and more hubs were detected in the network of soils with organic manure amendment. Additionally, three operational taxonomic units (OTUs) belonging to Glomerales were identified as hubs in all treatments, indicating these OTUs likely occupied broad ecological niches and were always active for mediating AMF species interaction in the maize rhizosphere. Taken together, impacts of fertilization regimes on

  6. Impacts of fertilization regimes on arbuscular mycorrhizal fungal (AMF community composition were correlated with organic matter composition in maize rhizosphere soil

    Directory of Open Access Journals (Sweden)

    Chen Zhu

    2016-11-01

    Full Text Available The understanding of the response of arbuscular mycorrhizal fungi (AMF community composition to fertilization is of great significance in sustainable agriculture. However, how fertilization influences AMF diversity and composition is not well established yet. A field experiment located in northeast China in typical black soil (Chernozem was conducted and high-throughput sequencing approach was used to investigate the effects of different fertilizations on the variation of AMF community in the rhizosphere soil of maize crop. The results showed that AMF diversity in the maize rhizosphere was significantly altered by different fertilization regimes. As revealed by redundancy analysis, the application of organic manure was the most important factor impacting AMF community composition between samples with and without organic manure, followed by N fertilizer and P fertilizer inputs. Moreover, the organic matter composition in the rhizosphere, determined by GC-MS, was significantly altered by the organic manure amendment. Many of the chemical components displayed significant relationships with the AMF community composition according to the Mantel test, among those, 2-ethylnaphthalene explained the highest percentage (54.2% of the variation. The relative contents of 2-ethylnaphthalene and 2, 6, 10-trimethyltetradecane had a negative correlation with Glomus relative abundance, while the relative content of 3-methylbiphenyl displayed a positive correlation with Rhizophagus. The co-occurrence patterns in treatments with and without organic manure amendment were analysed, and more hubs were detected in the network of soils with organic manure amendment. Additionally, three OTUs belonging to Glomerales were identified as hubs in all treatments, indicating these OTUs likely occupied broad ecological niches and were always active for mediating AMF species interaction in the maize rhizosphere. Taken together, impacts of fertilization regimes on AMF community

  7. RNA preservation agents and nucleic acid extraction method bias perceived bacterial community composition.

    Directory of Open Access Journals (Sweden)

    Ann McCarthy

    Full Text Available Bias is a pervasive problem when characterizing microbial communities. An important source is the difference in lysis efficiencies of different populations, which vary depending on the extraction protocol used. To avoid such biases impacting comparisons between gene and transcript abundances in the environment, the use of one protocol that simultaneously extracts both types of nucleic acids from microbial community samples has gained popularity. However, knowledge regarding tradeoffs to combined nucleic acid extraction protocols is limited, particularly regarding yield and biases in the observed community composition. Here, we evaluated a commercially available protocol for simultaneous extraction of DNA and RNA, which we adapted for freshwater microbial community samples that were collected on filters. DNA and RNA yields were comparable to other commonly used, but independent DNA and RNA extraction protocols. RNA protection agents benefited RNA quality, but decreased DNA yields significantly. Choice of extraction protocol influenced the perceived bacterial community composition, with strong method-dependent biases observed for specific phyla such as the Verrucomicrobia. The combined DNA/RNA extraction protocol detected significantly higher levels of Verrucomicrobia than the other protocols, and those higher numbers were confirmed by microscopic analysis. Use of RNA protection agents as well as independent sequencing runs caused a significant shift in community composition as well, albeit smaller than the shift caused by using different extraction protocols. Despite methodological biases, sample origin was the strongest determinant of community composition. However, when the abundance of specific phylogenetic groups is of interest, researchers need to be aware of the biases their methods introduce. This is particularly relevant if different methods are used for DNA and RNA extraction, in addition to using RNA protection agents only for RNA

  8. Immobilization patterns and dynamics of acetate-utilizing methanogens in sterile granular sludge from upflow anaerobic sludge blanket (UASB) reactors

    DEFF Research Database (Denmark)

    Schmidt, Jens Ejbye; Ahring, Birgitte Kiær

    1999-01-01

    Sterile granular sludge was inoculated with either Methanosarcina mazeii S-6, Methanosaeta concilii GP-6, or both species in acetate-fea upflow anaerobic sludge blanket (UASB) reactors to investigate the immobilization patterns and dynamics of aceticlastic methanogens in granular sludge. After......, but where the acetate concentration was low this strain was immobilized on support material as single cells or small clumps, The data clearly show that the two aceticlastic methanogens immobilize differently in UASB systems, depending on the conditions found throughout the UASB reactor....

  9. Immobilization patterns and dynamics of acetate-utilizing methanogens immobilized in sterile granular sludge in upflow anaerobic sludge blanket reactors

    DEFF Research Database (Denmark)

    Schmidt, Jens Ejbye; Ahring, Birgitte Kiær

    1999-01-01

    Sterile granular sludge was inoculated with either Methanosarcina mazeii S-6, Methanosaeta concilii GP-6, or both species in acetate-fea upflow anaerobic sludge blanket (UASB) reactors to investigate the immobilization patterns and dynamics of aceticlastic methanogens in granular sludge. After......, but where the acetate concentration was low this strain was immobilized on support material as single cells or small clumps, The data clearly show that the two aceticlastic methanogens immobilize differently in UASB systems, depending on the conditions found throughout the UASB reactor....

  10. Community composition of target vs. non-target fungi in fungicide treated wheat

    DEFF Research Database (Denmark)

    Knorr, Kamilla; Jørgensen, Lise Nistrup; Justesen, Annemarie Fejer

    2012-01-01

    disease in wheat and within the last decade, new aggressive strains of yellow rust has caused severe epidemics that lead to substantial yield losses. This study explored the community composition of target versus non-target fungi in yellow rust infected wheat as affected by treatment timing and dose......Fungicide treatments are common control strategies used to manage fungal pathogens in agricultural fields, however, effects of treatments on the composition of total fungal communities, including non-target fungi, in the phyllosphere is not well known. Yellow rust (Puccinia striiformis) is a common...

  11. Climate Clever Clovers: New Paradigm to Reduce the Environmental Footprint of Ruminants by Breeding Low Methanogenic Forages Utilizing Haplotype Variation

    Directory of Open Access Journals (Sweden)

    Parwinder Kaur

    2017-09-01

    Full Text Available Mitigating methane production by ruminants is a significant challenge to global livestock production. This research offers a new paradigm to reduce methane emissions from ruminants by breeding climate-clever clovers. We demonstrate wide genetic diversity for the trait methanogenic potential in Australia’s key pasture legume, subterranean clover (Trifolium subterraneum L.. In a bi-parental population the broadsense heritability in methanogenic potential was moderate (H2 = 0.4 and allelic variation in a region of Chr 8 accounted for 7.8% of phenotypic variation. In a genome-wide association study we identified four loci controlling methanogenic potential assessed by an in vitro fermentation system. Significantly, the discovery of a single nucleotide polymorphism (SNP on Chr 5 in a defined haplotype block with an upstream putative candidate gene from a plant peroxidase-like superfamily (TSub_g18548 and a downstream lectin receptor protein kinase (TSub_g18549 provides valuable candidates for an assay for this complex trait. In this way haplotype variation can be tracked to breed pastures with reduced methanogenic potential. Of the quantitative trait loci candidates, the DNA-damage-repair/toleration DRT100-like protein (TSub_g26967, linked to avoid the severity of DNA damage induced by secondary metabolites, is considered central to enteric methane production, as are disease resistance (TSub_g26971, TSub_g26972, and TSub_g18549 and ribonuclease proteins (TSub_g26974, TSub_g26975. These proteins are good pointers to elucidate the genetic basis of in vitro microbial fermentability and enteric methanogenic potential in subterranean clover. The genes identified allow the design of a suite of markers for marker-assisted selection to reduce rumen methane emission in selected pasture legumes. We demonstrate the feasibility of a plant breeding approach without compromising animal productivity to mitigate enteric methane emissions, which is one of the most

  12. The influence of substrate transport limitation on porosity and methanogenic activity of anaerobic sludge granules

    Energy Technology Data Exchange (ETDEWEB)

    Alphenaar, P.A. (Agricultural Univ., Wageningen (Netherlands). Dept. of Environmental Technology); Perez, M.C. (Agricultural Univ., Wageningen (Netherlands). Dept. of Environmental Technology); Lettinga, G. (Agricultural Univ., Wageningen (Netherlands). Dept. of Environmental Technology)

    1993-05-01

    The relationship between porosity, diameter and methanogenic activity of anaerobic granules has been investigated. Experiments with different granular sludges revealed that substrate transport limitations increase with the diameter of the granules. As a consequence, autolysis can occur in the core of the granule, producing hollow granules. The porosity measurements revealed that the hollow centre is not available for substrate transport. Possibly as an effect of bacterial lysis, the porosity decreases in the more interior layers of the granules. This results in a inactive inner part of the large granules, which is not involved in the treatment process; the specific methanogenic activity decreases with granule size. No marked difference in substrate affinity is observed between granules of different sizes, which probably indicates that for large granules only the exterior is biological active. (orig.)

  13. Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering.

    Directory of Open Access Journals (Sweden)

    Alica Chroňáková

    Full Text Available Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI and long-term impact (17 years; LTI, one is regenerating from cattle impact (REG and a control is unaffected by cattle (CON. Cattle manure (CMN, the source of allochthonous microbes, was collected from the same area. We used pyrosequencing of 16S rRNA genes to assess the composition of archaeal and bacterial communities in each soil type and CMN. Both short- and long- term cattle impact negatively altered archaeal and bacterial diversity, leading to increase of homogenization of microbial communities in overwintering soils over time. Moreover, strong shifts in the prokaryotic communities were observed in response to cattle overwintering, with the greatest impact on archaea. Oligotrophic and acidophilic microorganisms (e.g. Thaumarchaeota, Acidobacteria, and α-Proteobacteria dominated in CON and expressed strong negative response to increased pH, total C and N. Whereas copiotrophic and alkalophilic microbes (e.g. methanogenic Euryarchaeota, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidetes were common in LTI showing opposite trends. Crenarchaeota were also found in LTI, though their trophic interactions remain cryptic. Firmicutes, Bacteroidetes, Methanobacteriaceae, and Methanomicrobiaceae indicated the introduction and establishment of faecal microbes into the impacted soils, while Chloroflexi and Methanosarcinaceae suggested increased abundance of soil-borne microbes under altered environmental conditions. The observed changes in prokaryotic community composition may have driven corresponding changes in soil functioning.

  14. Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering

    Science.gov (United States)

    Chroňáková, Alica; Schloter-Hai, Brigitte; Radl, Viviane; Endesfelder, David; Quince, Christopher; Elhottová, Dana; Šimek, Miloslav; Schloter, Michael

    2015-01-01

    Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI) and long-term impact (17 years; LTI), one is regenerating from cattle impact (REG) and a control is unaffected by cattle (CON). Cattle manure (CMN), the source of allochthonous microbes, was collected from the same area. We used pyrosequencing of 16S rRNA genes to assess the composition of archaeal and bacterial communities in each soil type and CMN. Both short- and long- term cattle impact negatively altered archaeal and bacterial diversity, leading to increase of homogenization of microbial communities in overwintering soils over time. Moreover, strong shifts in the prokaryotic communities were observed in response to cattle overwintering, with the greatest impact on archaea. Oligotrophic and acidophilic microorganisms (e.g. Thaumarchaeota, Acidobacteria, and α-Proteobacteria) dominated in CON and expressed strong negative response to increased pH, total C and N. Whereas copiotrophic and alkalophilic microbes (e.g. methanogenic Euryarchaeota, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidetes) were common in LTI showing opposite trends. Crenarchaeota were also found in LTI, though their trophic interactions remain cryptic. Firmicutes, Bacteroidetes, Methanobacteriaceae, and Methanomicrobiaceae indicated the introduction and establishment of faecal microbes into the impacted soils, while Chloroflexi and Methanosarcinaceae suggested increased abundance of soil-borne microbes under altered environmental conditions. The observed changes in prokaryotic community composition may have driven corresponding changes in soil functioning. PMID:26274496

  15. Associations between retail food store exterior advertisements and community demographic and socioeconomic composition.

    Science.gov (United States)

    Isgor, Zeynep; Powell, Lisa; Rimkus, Leah; Chaloupka, Frank

    2016-05-01

    This paper examines the association between the prevalence of various types of outdoor food and beverage advertising found on the building exteriors and properties of retail food outlets and community racial/ethnic and socioeconomic composition in a nationwide sample of food outlets in the U.S. Our major finding from multivariable analysis is that food stores in low-income communities have higher prevalence of all food and beverage ads, including those for unhealthy products such as regular soda, controlling for community racial/ethnic composition and other covariates. This adds to growing research pointing to socioeconomic disparities in food and beverage marketing exposure. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. The effect of operational conditions on the sludge specific methanogenic activity and sludge biodegradability

    NARCIS (Netherlands)

    Leitao, R.; Santaellla, S.T.; Haandel, van A.C.; Zeeman, G.; Lettinga, G.

    2009-01-01

    The effects of hydraulic retention time (HRT) and influent COD concentration (CODInf) on Specific Methanogenic Activity (SMA) and the biodegradability of an anaerobic sludge need to be elucidated because of the discordant results available in literature. This information is important for the

  17. 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

    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...... that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide...

  18. Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: Evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak.

    Directory of Open Access Journals (Sweden)

    Julia A F Langer

    Full Text Available The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta. Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 μatm and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2.

  19. Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: Evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak.

    Science.gov (United States)

    Langer, Julia A F; Sharma, Rahul; Schmidt, Susanne I; Bahrdt, Sebastian; Horn, Henriette G; Algueró-Muñiz, María; Nam, Bora; Achterberg, Eric P; Riebesell, Ulf; Boersma, Maarten; Thines, Marco; Schwenk, Klaus

    2017-01-01

    The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 μatm) and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2.

  20. Effects of Biochar Blends on Microbial Community Composition in Two Coastal Plain Soils

    Directory of Open Access Journals (Sweden)

    Thomas F. Ducey

    2015-11-01

    Full Text Available The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure. These impacts are modulated not only by the biochar composition, but also on the soil’s physicochemical characteristics. This indicates that soil characteristics must be considered prior to biochar amendment. A significant portion of the soils of the southeastern coastal plain are severely degraded and, therefore, candidates for biochar amendment to strengthen soil fertility. In this study we focused on two common soil series in the southeastern coastal plain, utilizing feedstocks endemic to the area. We chose feedstocks in four ratios (100% pine chip; 80:20 mixture of pine chip to poultry litter; 50:50 mixture of pine chip to poultry litter; 100% poultry litter prior to pyrolysis and soil amendment as a biochar product. Soil was analyzed for bioavailable nutrients via Mehlich-1 extractions, as well as microbial community composition using phospholipid fatty acid analysis (PLFA. Our results demonstrated significant shifts in microbial community composition in response to biochar amendment, the effects of which were greatest with 100% poultry litter biochar. Strong relationships between PLFAs and several Mehlich-1 extractable nutrients (Al, Cu, Fe, and P were observed.

  1. Patterns of vegetation and grasshopper community composition.

    Science.gov (United States)

    Kemp, W P; Harvey, S J; O'Neill, K M

    1990-06-01

    A study was conducted to evaluate differences in rangeland grasshopper communities over environmental gradients in Gallatin Valley, Montana, USA. The concept of habitat type (Daubenmire 1966) was used as a basis for discriminating between groupings of patches based on vegetation. A total of 39 patches were selected that represented five recognized grassland habitat types (Mueggler and Stewart 1980), as well as two disturbed types (replanting within a known habitat type). Repeated sampling in 1988 of both the insect and plant communities yielded a total of 40 grasshopper (19 664 individuals) and 97 plant species. Detrended Correspondence Analysis (DCA) indicated that patch classifications based on presence and percent cover of plants were appropriate and showed good between-group (habitat type) separation for patches along gradients of precipitation/elevation and plant community complexity. Results from undisturbed habitats showed that plant and grasshopper species composition changed over observed environmental gradients and suggested that habitat type influenced not only species presence, but also relative abundance. Discussion is presented that relates results with patch-use and core and satellite species paradigms.

  2. Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle.

    Science.gov (United States)

    Detman, Anna; Mielecki, Damian; Pleśniak, Łukasz; Bucha, Michał; Janiga, Marek; Matyasik, Irena; Chojnacka, Aleksandra; Jędrysek, Mariusz-Orion; Błaszczyk, Mieczysław K; Sikora, Anna

    2018-01-01

    Anaerobic digestion, whose final products are methane and carbon dioxide, ensures energy flow and circulation of matter in ecosystems. This naturally occurring process is used for the production of renewable energy from biomass. Lactate, a common product of acidic fermentation, is a key intermediate in anaerobic digestion of biomass in the environment and biogas plants. Effective utilization of lactate has been observed in many experimental approaches used to study anaerobic digestion. Interestingly, anaerobic lactate oxidation and lactate oxidizers as a physiological group in methane-yielding microbial communities have not received enough attention in the context of the acetogenic step of anaerobic digestion. This study focuses on metabolic transformation of lactate during the acetogenic and methanogenic steps of anaerobic digestion in methane-yielding bioreactors. Methane-yielding microbial communities instead of pure cultures of acetate producers were used to process artificial lactate-rich media to methane and carbon dioxide in up-flow anaerobic sludge blanket reactors. The media imitated the mixture of acidic products found in anaerobic environments/digesters where lactate fermentation dominates in acidogenesis. Effective utilization of lactate and biogas production was observed. 16S rRNA profiling was used to examine the selected methane-yielding communities. Among Archaea present in the bioreactors, the order Methanosarcinales predominated. The acetoclastic pathway of methane formation was further confirmed by analysis of the stable carbon isotope composition of methane and carbon dioxide. The domain Bacteria was represented by Bacteroidetes , Firmicutes , Proteobacteria , Synergistetes , Actinobacteria , Spirochaetes , Tenericutes , Caldithrix , Verrucomicrobia , Thermotogae , Chloroflexi , Nitrospirae, and Cyanobacteria. Available genome sequences of species and/or genera identified in the microbial communities were searched for genes encoding the lactate

  3. Composition and abundance of the zooplankton community in the ...

    African Journals Online (AJOL)

    The taxonomic composition of the zooplankton community of the Bitter Lakes, Egypt, was examined in 2003–2004 in relation to the spatial and temporal distribution of environmental factors. Copepoda were dominant, forming 49% of the zooplankton, followed by Protista at 37%. During the autumn, zooplankton in Small ...

  4. Bacterial communities from Arctic seasonal sea ice are more compositionally variable than those from multi-year sea ice.

    Science.gov (United States)

    Hatam, Ido; Lange, Benjamin; Beckers, Justin; Haas, Christian; Lanoil, Brian

    2016-10-01

    Arctic sea ice can be classified into two types: seasonal ice (first-year ice, FYI) and multi-year ice (MYI). Despite striking differences in the physical and chemical characteristics of FYI and MYI, and the key role sea ice bacteria play in biogeochemical cycles of the Arctic Ocean, there are a limited number of studies comparing the bacterial communities from these two ice types. Here, we compare the membership and composition of bacterial communities from FYI and MYI sampled north of Ellesmere Island, Canada. Our results show that communities from both ice types were dominated by similar class-level phylogenetic groups. However, at the operational taxonomic unit (OTU) level, communities from MYI and FYI differed in both membership and composition. Communities from MYI sites had consistent structure, with similar membership (presence/absence) and composition (OTU abundance) independent of location and year of sample. By contrast, communities from FYI were more variable. Although FYI bacterial communities from different locations and different years shared similar membership, they varied significantly in composition. Should these findings apply to sea ice across the Arctic, we predict increased compositional variability in sea ice bacterial communities resulting from the ongoing transition from predominantly MYI to FYI, which may impact nutrient dynamics in the Arctic Ocean.

  5. Micro-scale H2-CO2 dynamics in a hydrogenotrophic methanogenic membrane reactor

    Directory of Open Access Journals (Sweden)

    Emilio Garcia-Robledo

    2016-08-01

    Full Text Available Biogas production is a key factor in a sustainable energy supply. It is possible to get biogas with very high methane content if the biogas reactors are supplied with exogenous hydrogen, and one of the technologies for supplying hydrogen is through gas permeable membranes. In this study the activity and stratification of hydrogen consumption above such a membrane was investigated by use of microsensors for hydrogen and pH. A hydrogenotrophic methanogenic community that was able to consume the hydrogen flux within 0.5 mm of the membrane with specific rates of up to 30 m3 H2 m-3 day-1 developed within 3 days in fresh manure and was already established at time zero when analyzing slurry from a biogas plant. The hydrogen consumption was dependent on a simultaneous carbon dioxide supply and was inhibited when carbon dioxide depletion elevated the pH to 9.2. The activity was only partially restored when the carbon dioxide supply was resumed. Bioreactors supplied with hydrogen gas should thus be carefully monitored and either have the hydrogen supply disrupted or be supplemented with carbon dioxide when the pH rises to values about 9.

  6. Physical disturbance to ecological niches created by soil structure alters community composition of methanotrophs.

    Science.gov (United States)

    Kumaresan, Deepak; Stralis-Pavese, Nancy; Abell, Guy C J; Bodrossy, Levente; Murrell, J Colin

    2011-10-01

    Aggregates of different sizes and stability in soil create a composite of ecological niches differing in terms of physico-chemical and structural characteristics. The aim of this study was to identify, using DNA-SIP and mRNA-based microarray analysis, whether shifts in activity and community composition of methanotrophs occur when ecological niches created by soil structure are physically perturbed. Landfill cover soil was subject to three treatments termed: 'control' (minimal structural disruption), 'sieved' (sieved soil using 2 mm mesh) and 'ground' (grinding using mortar and pestle). 'Sieved' and 'ground' soil treatments exhibited higher methane oxidation potentials compared with the 'control' soil treatment. Analysis of the active community composition revealed an effect of physical disruption on active methanotrophs. Type I methanotrophs were the most active methanotrophs in 'sieved' and 'ground' soil treatments, whereas both Type I and Type II methanotrophs were active in the 'control' soil treatment. The result emphasize that changes to a particular ecological niche may not result in an immediate change to the active bacterial composition and change in composition will depend on the ability of the bacterial communities to respond to the perturbation. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  7. Legacy effects of no-analogue disturbances alter plant community diversity and composition in semi-arid sagebrush steppe

    Science.gov (United States)

    Ripplinger, Julie; Franklin, Janet; Edwards, Thomas C.

    2015-01-01

    Questions(i) What role does the type of managed disturbance play in structuring sagebrush steppe plant communities? (ii) How does the composition of post-disturbance plant communities change with time since disturbance? (iii) Does plant community diversity change over time following managed disturbance?LocationField study within the sagebrush steppe ecosystem. Rich County, Utah, USA.MethodsWe developed a chronosequence spanning up to 50 yrs post-treatment to study sagebrush steppe vegetation dynamics. Direct ordination was used to examine plant community composition by managed disturbance type and time since disturbance, and factorial analysis of covariance was used to examine diversity dynamics following disturbance. Indicator species values were calculated in order to identify characteristic species for each disturbance type.ResultsPlant communities experienced a shift toward distinct community composition for each of the three managed disturbance types, and gave no indication of returning to untreated community composition or diversity. Small post-disturbance increases in the number of non-native grass species were observed in the treatments relative to reference, with native forb species making the largest contribution to altered composition. On fire- and chemically-treated sites the proportional native forb species richness increased over time since disturbance, while the proportional contribution of non-native forbs to total species richness decreased. For all three treatment types, native grasses contributed less on average to total richness than on reference sites, while non-native grasses made up a higher proportion of total richness.ConclusionsCommon shrubland management techniques have legacy effects on the composition and diversity of sagebrush steppe plant communities, and no-analogue disturbances, such as chemical or mechanical treatments, have more pronounced legacy effects than treatments similar to natural disturbance regimes (fire). This study

  8. Coral Reef Community Composition in the Context of Disturbance History on the Great Barrier Reef, Australia

    Science.gov (United States)

    Graham, Nicholas A. J.; Chong-Seng, Karen M.; Huchery, Cindy; Januchowski-Hartley, Fraser A.; Nash, Kirsty L.

    2014-01-01

    Much research on coral reefs has documented differential declines in coral and associated organisms. In order to contextualise this general degradation, research on community composition is necessary in the context of varied disturbance histories and the biological processes and physical features thought to retard or promote recovery. We conducted a spatial assessment of coral reef communities across five reefs of the central Great Barrier Reef, Australia, with known disturbance histories, and assessed patterns of coral cover and community composition related to a range of other variables thought to be important for reef dynamics. Two of the reefs had not been extensively disturbed for at least 15 years prior to the surveys. Three of the reefs had been severely impacted by crown-of-thorns starfish outbreaks and coral bleaching approximately a decade before the surveys, from which only one of them was showing signs of recovery based on independent surveys. We incorporated wave exposure (sheltered and exposed) and reef zone (slope, crest and flat) into our design, providing a comprehensive assessment of the spatial patterns in community composition on these reefs. Categorising corals into life history groupings, we document major coral community differences in the unrecovered reefs, compared to the composition and covers found on the undisturbed reefs. The recovered reef, despite having similar coral cover, had a different community composition from the undisturbed reefs, which may indicate slow successional processes, or a different natural community dominance pattern due to hydrology and other oceanographic factors. The variables that best correlated with patterns in the coral community among sites included the density of juvenile corals, herbivore fish biomass, fish species richness and the cover of macroalgae. Given increasing impacts to the Great Barrier Reef, efforts to mitigate local stressors will be imperative to encouraging coral communities to persist into

  9. New steady-state microbial community compositions and process performances in biogas reactors induced by temperature disturbances

    DEFF Research Database (Denmark)

    Luo, Gang; De Francisci, Davide; Kougias, Panagiotis

    2015-01-01

    that stochastic factors had a minor role in shaping the profile of the microbial community composition and activity in biogas reactors. On the contrary, temperature disturbance was found to play an important role in the microbial community composition as well as process performance for biogas reactors. Although...... three different temperature disturbances were applied to each biogas reactor, the increased methane yields (around 10% higher) and decreased volatile fatty acids (VFAs) concentrations at steady state were found in all three reactors after the temperature disturbances. After the temperature disturbance...... in shaping the profile of the microbial community composition and activity in biogas reactors. New steady-state microbial community profiles and reactor performances were observed in all the biogas reactors after the temperature disturbance....

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

    Science.gov (United States)

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

    2015-02-01

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

  11. Dosing of anaerobic granular sludge bioreactors with cobalt: Impact of cobalt retention on methanogenic activity

    KAUST Repository

    Fermoso, Fernando G.; Bartacek, Jan; Manzano, Ramon; van Leeuwen, Herman P.; Lens, Piet N.L.

    2010-01-01

    The effect of dosing a metal limited anaerobic sludge blanket (UASB) reactor with a metal pulse on the methanogenic activity of granular sludge has thus far not been successfully modeled. The prediction of this effect is crucial in order to optimize

  12. Carbon nanotubes accelerate methane production in pure cultures of methanogens and in a syntrophic coculture

    NARCIS (Netherlands)

    Salvador, Andreia F.; Martins, Gilberto; Melle-Franco, Manuel; Serpa, Ricardo; Stams, Alfons J.M.; Cavaleiro, Ana J.; Pereira, M.A.; Alves, M.M.

    2017-01-01

    Carbon materials have been reported to facilitate direct interspecies electron transfer (DIET) between bacteria and methanogens improving methane production in anaerobic processes. In this work, the effect of increasing concentrations of carbon nanotubes (CNT) on the activity of pure cultures of

  13. Effect of UVC Radiation on Hydrated and Desiccated Cultures of Slightly Halophilic and Non-Halophilic Methanogenic Archaea: Implications for Life on Mars.

    Science.gov (United States)

    Sinha, Navita; Kral, Timothy A

    2018-05-12

    Methanogens have been considered models for life on Mars for many years. In order to survive any exposure at the surface of Mars, methanogens would have to endure Martian UVC radiation. In this research, we irradiated hydrated and desiccated cultures of slightly halophilic Methanococcus maripaludis and non-halophilic Methanobacterium formicicum for various time intervals with UVC (254 nm) radiation. The survivability of the methanogens was determined by measuring methane concentrations in the headspace gas samples of culture tubes after re-inoculation of the methanogens into their growth-supporting media following exposure to UVC radiation. Hydrated M. maripaludis survived 24 h of UVC exposure, while in a desiccated condition they endured for 16 h. M. formicicum also survived UVC radiation for 24 h in a liquid state; however, in a desiccated condition, the survivability of M. formicicum was only 12 h. Some of the components of the growth media could have served as shielding agents that protected cells from damage caused by exposure to ultraviolet radiation. Overall, these results suggest that limited exposure (12⁻24 h) to UVC radiation on the surface of Mars would not necessarily be a limiting factor for the survivability of M. maripaludis and M. formicicum .

  14. Effects of biochar blends on microbial community composition in two coastal plain soils

    Science.gov (United States)

    The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure....

  15. The Influence of Loading Rate and Variable Temperatures on Microbial Communities in Anaerobic Digesters

    Directory of Open Access Journals (Sweden)

    Richard J. Ciotola

    2014-02-01

    Full Text Available The relationship between seasonal temperatures, organic loading rate (OLR and the structure of archaeal communities in anaerobic digesters was investigated. Previous studies have often assessed archaeal community structure at fixed temperatures and constant OLRs, or at variable temperatures not characteristic of temperate climates. The goal of this study was to determine the maximum OLR that would maintain a balanced microbial ecosystem during operation in a variable temperature range expected in a temperate climate (27–10 °C. Four-liter laboratory digesters were operated in a semi-continuous mode using dairy cow manure as the feedstock. At OLRs of 1.8 and 0.8 kg VS/m3·day the digesters soured (pH < 6.5 as a result of a decrease in temperature. The structure of the archaeal community in the sour digesters became increasingly similar to the manure feedstock with gains in the relative abundance of hydrogenotrophic methanogens. At an OLR of 0.3 kg VS/m3·day the digesters did not sour, but the archaeal community was primarily hydrogenotrophic methanogens. Recommendations for operating an ambient temperature digester year round in a temperate climate are to reduce the OLR to at least 0.3 kg VS/m3·day in colder temperatures to prevent a shift to the microbial community associated with the sour digesters.

  16. Anthropogenic land use shapes the composition and phylogenetic structure of soil arbuscular mycorrhizal fungal communities.

    Science.gov (United States)

    Moora, Mari; Davison, John; Öpik, Maarja; Metsis, Madis; Saks, Ülle; Jairus, Teele; Vasar, Martti; Zobel, Martin

    2014-12-01

    Arbuscular mycorrhizal (AM) fungi play an important role in ecosystems, but little is known about how soil AM fungal community composition varies in relation to habitat type and land-use intensity. We molecularly characterized AM fungal communities in soil samples (n = 88) from structurally open (permanent grassland, intensive and sustainable agriculture) and forested habitats (primeval forest and spruce plantation). The habitats harboured significantly different AM fungal communities, and there was a broad difference in fungal community composition between forested and open habitats, the latter being characterized by higher average AM fungal richness. Within both open and forest habitats, intensive land use significantly influenced community composition. There was a broad difference in the phylogenetic structure of AM fungal communities between mechanically disturbed and nondisturbed habitats. Taxa from Glomeraceae served as indicator species for the nondisturbed habitats, while taxa from Archaeosporaceae, Claroideoglomeraceae and Diversisporaceae were indicators for the disturbed habitats. The distribution of these indicator taxa among habitat types in the MaarjAM global database of AM fungal diversity was in accordance with their local indicator status. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  17. Lipid Biomarkers for a Hypersaline Microbial Mat Community

    Science.gov (United States)

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

    2003-01-01

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

  18. Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

    Directory of Open Access Journals (Sweden)

    Chris L Dupont

    Full Text Available Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.

  19. Impact of enzymatic digestion on bacterial community composition in CF airway samples

    Directory of Open Access Journals (Sweden)

    Kayla M. Williamson

    2017-05-01

    Full Text Available Background Previous studies have demonstrated the importance of DNA extraction methods for molecular detection of Staphylococcus, an important bacterial group in cystic fibrosis (CF. We sought to evaluate the effect of enzymatic digestion (EnzD prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP samples from patients with CF. Methods DNA from 81 samples (39 sputum and 42 OP collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA of individual genera for paired samples with and without EnzD. Results Shannon Diversity Index (alpha-diversity decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn, whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the genera Gemella (p < 0.01, Streptococcus (p < 0.01, and Rothia (p < 0.01. Staphylococcus (p < 0.01 was the only genus with a significant increase in RA from sputum, whereas the following genera decreased in RA with EnzD: Veillonella (p < 0.01, Granulicatella (p < 0.01, Prevotella (p < 0.01, and Gemella (p = 0.02. In OP samples, higher RA of Gram-positive taxa was associated with larger changes in microbial community composition. Discussion We show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection of Staphylococcus in CF OP

  20. Organic carbon and nitrogen availability determine bacterial community composition in paddy fields of the Indo-Gangetic plain.

    Science.gov (United States)

    Kumar, Arvind; Rai, Lal Chand

    2017-07-01

    Soil quality is an important factor and maintained by inhabited microorganisms. Soil physicochemical characteristics determine indigenous microbial population and rice provides food security to major population of the world. Therefore, this study aimed to assess the impact of physicochemical variables on bacterial community composition and diversity in conventional paddy fields which could reflect a real picture of the bacterial communities operating in the paddy agro-ecosystem. To fulfill the objective; soil physicochemical characterization, bacterial community composition and diversity analysis was carried out using culture-independent PCR-DGGE method from twenty soils distributed across eight districts. Bacterial communities were grouped into three clusters based on UPGMA cluster analysis of DGGE banding pattern. The linkage of measured physicochemical variables with bacterial community composition was analyzed by canonical correspondence analysis (CCA). CCA ordination biplot results were similar to UPGMA cluster analysis. High levels of species-environment correlations (0.989 and 0.959) were observed and the largest proportion of species data variability was explained by total organic carbon (TOC), available nitrogen, total nitrogen and pH. Thus, results suggest that TOC and nitrogen are key regulators of bacterial community composition in the conventional paddy fields. Further, high diversity indices and evenness values demonstrated heterogeneity and co-abundance of the bacterial communities.

  1. Vertical distribution and community composition of anammox bacteria in sediments of a eutrophic shallow lake.

    Science.gov (United States)

    Qin, H; Han, C; Jin, Z; Wu, L; Deng, H; Zhu, G; Zhong, W

    2018-07-01

    The aim of this study was to explore the vertical distribution traits of anaerobic ammonium-oxidizing (anammox) bacterial relative abundance and community composition along the oxic/anoxic sediment profiles in a shallow lake. The Illumina Miseq-based sequencing and quantitative polymerase chain reactions were utilized to analyse relative abundance of anammox hydrazine synthase (hzsB) gene in comparison with bacterial 16S rRNA genes, anammox bacterial relative abundance (the number of anammox sequences divided by total number of sequences), community composition and diversity in sediments. The relative abundance of hzsB gene at the low-nitrogen (LN) site in the lake sediments showed that the vertical distribution of anammox bacteria increased to a peak, then decreased with increasing depth. Moreover, the relative abundance of hzsB gene at the high-nitrogen site was significantly lower than that at the LN site. Additionally, the community composition results showed that Candidatus Brocadia sp. was the dominant genus. In addition, the anammox bacterial diversity was also site specific. Redundancy analysis showed that the total N and the NH 4 + -N content might be the most important factors affecting anammox bacterial community composition in the studied sites. The results revealed the specific vertical variance of anammox bacterial distribution and community composition in oxic/anoxic sediments of a eutrophic shallow lake. This is the first study to demonstrate that anammox bacteria displayed the particular distribution in freshwater sediments, which implied a strong response to the anthropogenic eutrophication. © 2018 The Society for Applied Microbiology.

  2. Microbial community composition and endolith colonization at an Arctic thermal spring are driven by calcite precipitation

    Science.gov (United States)

    Starke, Verena; Kirshtein, Julie; Fogel, Marilyn L.; Steele, Andrew

    2013-01-01

    Environmental conditions shape community composition. Arctic thermal springs provide an opportunity to study how environmental gradients can impose strong selective pressures on microbial communities and provide a continuum of niche opportunities. We use microscopic and molecular methods to conduct a survey of microbial community composition at Troll Springs on Svalbard, Norway, in the high Arctic. Microorganisms there exist under a wide range of environmental conditions: in warm water as periphyton, in moist granular materials, and in cold, dry rock as endoliths. Troll Springs has two distinct ecosystems, aquatic and terrestrial, together in close proximity, with different underlying environmental factors shaping each microbial community. Periphyton are entrapped during precipitation of calcium carbonate from the spring's waters, providing microbial populations that serve as precursors for the development of endolithic communities. This process differs from most endolith colonization, in which the rock predates the communities that colonize it. Community composition is modulated as environmental conditions change within the springs. At Troll, the aquatic environments show a small number of dominant operational taxonomic units (OTUs) that are specific to each sample. The terrestrial environments show a more even distribution of OTUs common to multiple samples.

  3. Variability in Parasites' Community Structure and Composition in Cat ...

    African Journals Online (AJOL)

    This study investigated the composition and structure of the parasite communities in Cat fish with respect to levels of water pollution in Lake Victoria. A total of 1071 Clarias gariepinus with mean TL range of 19 to 27 cm were analyzed from three localities in Mwanza Gulf (Kirumba, 298 fish infected with 15 parasite species), ...

  4. 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

  5. Soil biochar amendment shapes the composition of N2O-reducing microbial communities.

    Science.gov (United States)

    Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H; Kappler, Andreas; Behrens, Sebastian

    2016-08-15

    Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N2O) emissions. N2O is a potent greenhouse gas. The main sources of N2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N2O emission mitigation and the abundance and activity of N2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described 'atypical' nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Receding Water Line and Interspecific Competition Determines Plant Community Composition and Diversity in Wetlands in Beijing

    Science.gov (United States)

    Wang, Zhengjun; Gong, Huili; Zhang, Jing

    2015-01-01

    Climate and human-induced wetland degradation has accelerated in recent years, not only resulting in reduced ecosystem services but also greatly affecting the composition and diversity of wetland plant communities. To date, the knowledge of the differences in community parameters and their successional trends in degraded wetlands remains scarce. Here based on remote sensing images, geographic information system technology, and statistical methods, we produced a successional gradient map of the Yeyahu Wetland Nature Reserve in Beijing, which has experienced a steady decline in water level in recent decades. In addition, we analyzed community composition and diversity along with each identified gradient. The results showed that community diversity decreases while dominance increases with the progress of succession, with the highest diversity occurring during the early stage of succession. Moreover, the community demonstrates greater similarity among subareas during later successional stages, and the similarity coefficients calculated from the important value (IV) of each species are more accurate. Correlation analysis showed that the impact of soil factors on diversity was not significant at a subarea scale, although these nutrients showed an increasing trend with the community succession. Furthermore, the IVs of the dominant species had a particularly significant impact on diversity, showing a significantly negative correlation with diversity indices and a significantly positive correlation with dominance indices. Further analysis showed that the retreat of water level resulted from sustained drought and local human activities was a major extrinsic driving force resulting in observed differences in the community successional stages, which resulted in differences in community composition and diversity. On the other hand, interspecific competition was the main intrinsic mechanism, which significantly influenced the IVs of the dominant species and community diversity

  7. Draft Genome Sequence of an Obligately Methylotrophic Methanogen, Methanococcoides methylutens, Isolated from Marine Sediment

    KAUST Repository

    Guan, Yue

    2014-11-20

    Methanococcoides methylutens, the type species of the genus Methanococcoides, is a slightly halophilic methanogenic archaeon with a methylotrophic metabolism. Here, we present the annotated draft genome sequence of M. methylutens, which comprises 2,508,511 bp with 2,482 coding sequences, 51 tRNA genes, and a G+C content of 42.5%.

  8. Draft Genome Sequence of an Obligately Methylotrophic Methanogen, Methanococcoides methylutens, Isolated from Marine Sediment

    KAUST Repository

    Guan, Yue; Ngugi, David; Blom, J.; Ali, Shahjahan; Ferry, J. G.; Stingl, Ulrich

    2014-01-01

    Methanococcoides methylutens, the type species of the genus Methanococcoides, is a slightly halophilic methanogenic archaeon with a methylotrophic metabolism. Here, we present the annotated draft genome sequence of M. methylutens, which comprises 2,508,511 bp with 2,482 coding sequences, 51 tRNA genes, and a G+C content of 42.5%.

  9. Fractionation of carbon isotopes by thermophilic methanogenic bacteria

    International Nuclear Information System (INIS)

    Ivanov, M.V.; Belyaev, S.S.; Zyakun, A.M.; Bondar, V.A.; Shipin, O.P.; Laurinavichus, K.S.

    1985-01-01

    The authors investigated the pattern of fractionation of stable carbon isotopes by the thermophilic methane-forming bacteria under different growth conditions and at various rates of formation of methane. A pure culture of Methanobacterium thermoautotrophicum was used in the experiments under the following growth conditions: temperature 65-70 0 C; pH 7.2-7.6; NaCl content 0-0.9 g/liter. The methanogenic bacteria were cultivated in 0.15 liter flasks in mineral medium. A mixture of CO 2 and H 2 in a 1:4 ratio by volume served as the sole carbon and energy source. In all experiments, not more than 5% of the initial CO 2 level was utilized. The rate of methane generation was altered by adjusting the physicochemical growth parameters (temperature from 45-70 0 C, salinity from 0.9 to 40 g/liter NaCl, pH from 6.3 to 7.2). Methane in the samples was quantitatively determined in a chromatograph which had a flame-ionization detector and a column containing Porapak Q sorbent at T = 120 0 C. The carrier gas was CO 2 . The average specific rate of methane formation was calculated as ml CH 4 per mg dry biomass of bacteria per h. Soluble mineral carbon was isolated form the acidified culture liquid in the form of CO 2 and was quantitatively determined in a Chrom-4 chromatography provided with a katharometer and a column containing activated charcoal at T = 150 0 . The gas carrier was helium. The isotopic composition of carbon was determined in a CH-7 mass-spectrometer and was expressed in 13 C values (per thousand) with respect to the international PDB standard

  10. Microbial communities and greenhouse gas emissions associated with the biodegradation of specified risk material in compost

    International Nuclear Information System (INIS)

    Xu, Shanwei; Reuter, Tim; Gilroyed, Brandon H.; Tymensen, Lisa; Hao, Yongxin; Hao, Xiying; Belosevic, Miodrag; Leonard, Jerry J.; McAllister, Tim A.

    2013-01-01

    Highlights: ► Addition of feathers altered bacterial and fungal communities in compost. ► Microbial communities degrading SRM and compost matrix were distinct. ► Addition of feathers may enrich for microbial communities that degrade SRM. ► Inclusion of feather in compost increased both CH 4 and N 2 O emissions from compost. ► Density of methanogens and methanotrophs were weakly associated with CH 4 emissions. - Abstract: Provided that infectious prions (PrP Sc ) are inactivated, composting of specified risk material (SRM) may be a viable alternative to rendering and landfilling. In this study, bacterial and fungal communities as well as greenhouse gas emissions associated with the degradation of SRM were examined in laboratory composters over two 14 day composting cycles. Chicken feathers were mixed into compost to enrich for microbial communities involved in the degradation of keratin and other recalcitrant proteins such as prions. Feathers altered the composition of bacterial and fungal communities primarily during the first cycle. The bacterial genera Saccharomonospora, Thermobifida, Thermoactinomycetaceae, Thiohalospira, Pseudomonas, Actinomadura, and Enterobacter, and the fungal genera Dothideomycetes, Cladosporium, Chaetomium, and Trichaptum were identified as candidates involved in SRM degradation. Feathers increased (P 4 primarily during the early stages of the first cycle and N 2 O during the second. Although inclusion of feathers in compost increases greenhouse gas emissions, it may promote the establishment of microbial communities that are more adept at degrading SRM and recalcitrant proteins such as keratin and PrP Sc

  11. Herbivory of an invasive slug is affected by earthworms and the composition of plant communities.

    Science.gov (United States)

    Zaller, Johann G; Parth, Myriam; Szunyogh, Ilona; Semmelrock, Ines; Sochurek, Susanne; Pinheiro, Marcia; Frank, Thomas; Drapela, Thomas

    2013-05-13

    Biodiversity loss and species invasions are among the most important human-induced global changes. Moreover, these two processes are interlinked as ecosystem invasibility is considered to increase with decreasing biodiversity. In temperate grasslands, earthworms serve as important ecosystem engineers making up the majority of soil faunal biomass. Herbivore behaviour has been shown to be affected by earthworms, however it is unclear whether these effects differ with the composition of plant communities. To test this we conducted a mesocosm experiment where we added earthworms (Annelida: Lumbricidae) to planted grassland communities with different plant species composition (3 vs. 12 plant spp.). Plant communities had equal plant densities and ratios of the functional groups grasses, non-leguminous forbs and legumes. Later, Arion vulgaris slugs (formerly known as A. lusitanicus; Gastropoda: Arionidae) were added and allowed to freely choose among the available plant species. This slug species is listed among the 100 worst alien species in Europe. We hypothesized that (i) the food choice of slugs would be altered by earthworms' specific effects on the growth and nutrient content of plant species, (ii) slug herbivory will be less affected by earthworms in plant communities containing more plant species than in those with fewer plant species because of a more readily utilization of plant resources making the impacts of earthworms less pronounced. Slug herbivory was significantly affected by both earthworms and plant species composition. Slugs damaged 60% less leaves when earthworms were present, regardless of the species composition of the plant communities. Percent leaf area consumed by slugs was 40% lower in communities containing 12 plant species; in communities containing only three species earthworms increased slug leaf area consumption. Grasses were generally avoided by slugs. Leaf length and number of tillers was increased in mesocosms containing more plant

  12. Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles

    Directory of Open Access Journals (Sweden)

    Maaike evan Agtmaal

    2015-07-01

    Full Text Available There is increasing evidence that microbial volatiles (VOCs play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD, a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are

  13. History of adaptation determines short-term shifts in performance and community structure of hydrogen-producing microbial communities degrading wheat straw.

    Science.gov (United States)

    Valdez-Vazquez, Idania; Morales, Ana L; Escalante, Ana E

    2017-11-01

    This study addresses the question of ecological interest for the determination of structure and diversity of microbial communities that degrade lignocellulosic biomasses to produce biofuels. Two microbial consortia with different history, native of wheat straw (NWS) and from a methanogenic digester (MD) fed with cow manure, were contrasted in terms of hydrogen performance, substrate disintegration and microbial diversity. NWS outperformed the hydrogen production rate of MD. Microscopic images revealed that NWS acted on the cuticle and epidermis, generating cellulose strands with high crystallinity, while MD degraded deeper layers, equally affecting all polysaccharides. The bacterial composition markedly differed according to the inocula origin. NWS almost solely comprised hydrogen producers of the phyla Firmicutes and Proteobacteria, with 38% members of Enterococcus. After hydrogen fermentation, NWS comprised 8% Syntrophococcus, an acetogen that cleaves aryl ethers of constituent groups on the aromatic components of lignin. Conversely, MD comprised thirteen phyla, primarily including Firmicutes with H 2 -producing members, and Bacteroidetes with non-H 2 -producing members, which reduced the hydrogen performance. Overall, the results of this study provide clear evidence that the history of adaptation of NWS enhanced the hydrogen performance from untreated wheat straw. Further, native wheat straw communities have the potential to refine cellulose fibers and produce biofuels simultaneously. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  14. Effect of the anode feeding composition on the performance of a continuous-flow methane-producing microbial electrolysis cell.

    Science.gov (United States)

    Zeppilli, Marco; Villano, Marianna; Aulenta, Federico; Lampis, Silvia; Vallini, Giovanni; Majone, Mauro

    2015-05-01

    A methane-producing microbial electrolysis cell (MEC) was continuously fed at the anode with a synthetic solution of soluble organic compounds simulating the composition of the soluble fraction of a municipal wastewater. The MEC performance was assessed at different anode potentials in terms of chemical oxygen demand (COD) removal efficiency, methane production, and energy efficiency. As a main result, about 72-80% of the removed substrate was converted into current at the anode, and about 84-86% of the current was converted into methane at the cathode. Moreover, even though both COD removed and methane production slightly decreased as the applied anode potential decreased, the energy efficiency (i.e., the energy recovered as methane with respect to the energy input into the system) increased from 54 to 63%. Denaturing gradient gel electrophoresis (DGGE) analyses revealed a high diversity in the anodic bacterial community with the presence of both fermentative (Proteiniphilum acetatigenes and Petrimonas sulphurifila) and aerobic (Rhodococcus qingshengii) microorganisms, whereas only two microorganisms (Methanobrevibacter arboriphilus and Methanosarcina mazei), both assignable to methanogens, were observed in the cathodic community.

  15. Synergistic function of four novel thermostable glycoside hydrolases from a long-term enriched thermophilic methanogenic digester

    Directory of Open Access Journals (Sweden)

    Meng eWang

    2015-05-01

    Full Text Available In biofuel production from lignocellulose, low thermostability and product inhibition strongly restrict the enzyme activities and production process. Application of multiple thermostable glycoside hydrolases, forming an enzyme cocktail, can result in a synergistic action and therefore improve production efficiency and reduce operational costs. Therefore, increasing enzyme thermostabilities and compatibility are important for the biofuel industry. In this study, we reported the screening, cloning and biochemical characterization of four novel thermostable lignocellulose hydrolases from a metagenomic library of a long-term dry thermophilic methanogenic digester community, which were highly compatible with optimal conditions and specific activities. The optimal temperatures of the four enzymes, β-xylosidase, xylanase, β-glucosidase, and cellulase ranged from 60°C to 75°C, and over 80% residual activities were observed after 2 h incubation at 50°C. Mixtures of these hydrolases retained high residual synergistic activities after incubation with cellulose, xylan, and steam-exploded corncob at 50°C for 72 h. In addition, about 55% dry weight of steam-exploded corncob was hydrolyzed to glucose and xylose by the synergistic action of the four enzymes at 50°C for 48 h. This work suggested that since different enzymes from a same ecosystem could be more compatible, screening enzymes from a long-term enriching community could be a favorable strategy.

  16. Biotransformation of tetrachloroethylene to trichloroethylene, dichloroethylene, vinyl chloride, and carbon dioxide under methanogenic conditions

    International Nuclear Information System (INIS)

    Vogel, T.M.; McCarty, P.L.

    1985-01-01

    Tetrachloroethylene (PCE) and trichloroethylene (TCE), common industrial solvents, are among the most frequent contaminants found in groundwater supplies. Due to the potential toxicity and carcinogenicity of chlorinated ethylenes, knowledge about their transformation potential is important in evaluating their environmental fate. The results of this study confirm that PCE can be transformed by reductive dehalogenation to TCE, dichloroethylene, and vinyl chloride (VC) under anaerobic conditions. In addition, [ 14 C]PCE was at least partially mineralized to CO 2 . Mineralization of 24% of the PCE occurred in a continuous-flow fixed-film methanogenic column with a liquid detention time of 4 days. TCE was the major intermediate formed, but traces of dichloroethylene isomers and VC were also found. In other column studies under a different set of methanogenic conditions, nearly quantitative conversion of PCE to VC was found. These studies clearly demonstrate that TCE and VC are major intermediates in PCE biotransformation under anaerobic conditions and suggest that the potential exists for the complete mineralization of PCE to CO 2 in soil and aquifer systems and in biological treatment processes

  17. Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing

    Science.gov (United States)

    Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

    2016-12-01

    Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing’s built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

  18. Progressive biogeochemical transformation of placer gold particles drives compositional changes in associated biofilm communities.

    Science.gov (United States)

    Rea, Maria Angelica; Standish, Christopher D; Shuster, Jeremiah; Bissett, Andrew; Reith, Frank

    2018-05-03

    Biofilms on placer gold (Au)-particle surfaces drive Au solubilization and re-concentration thereby progressively transforming the particles. Gold solubilization induces Au-toxicity; however, Au-detoxifying community members ameliorates Au-toxicity by precipitating soluble Au to metallic Au. We hypothesize that Au-dissolution and re-concentration (precipitation) places selective pressures on associated microbial communities, leading to compositional changes and subsequent Au-particle transformation. We analyzed Au-particles from eight United Kingdom sites using next generation sequencing, electron microscopy and micro-analyses. Gold particles contained biofilms composed of prokaryotic cells and extracellular polymeric substances intermixed with (bio)minerals. Across all sites communities were dominated by Proteobacteria (689, 97% Operational Taxonomic Units, 59.3% of total reads), with β-Proteobacteria being the most abundant. A wide range of Au-morphotypes including nanoparticles, micro-crystals, sheet-like Au and secondary rims, indicated that dissolution and re-precipitation occurred, and from this transformation indices were calculated. Multivariate statistical analyses showed a significant relationship between the extent of Au-particle transformation and biofilm community composition, with putative metal-resistant Au-cycling taxa linked to progressive Au transformation. These included the genera Pseudomonas, Leptothrix and Acinetobacter. Additionally, putative exoelectrogenic genera Rhodoferax and Geobacter were highly abundant. In conclusion, biogeochemical Au-cycling and Au-particle transformation occurred at all sites and exerted a strong influence on biofilm community composition.

  19. Metals other than uranium affected microbial community composition in a historical uranium-mining site.

    Science.gov (United States)

    Sitte, Jana; Löffler, Sylvia; Burkhardt, Eva-Maria; Goldfarb, Katherine C; Büchel, Georg; Hazen, Terry C; Küsel, Kirsten

    2015-12-01

    To understand the links between the long-term impact of uranium and other metals on microbial community composition, ground- and surface water-influenced soils varying greatly in uranium and metal concentrations were investigated at the former uranium-mining district in Ronneburg, Germany. A soil-based 16S PhyloChip approach revealed 2358 bacterial and 35 archaeal operational taxonomic units (OTU) within diverse phylogenetic groups with higher OTU numbers than at other uranium-contaminated sites, e.g., at Oak Ridge. Iron- and sulfate-reducing bacteria (FeRB and SRB), which have the potential to attenuate uranium and other metals by the enzymatic and/or abiotic reduction of metal ions, were found at all sites. Although soil concentrations of solid-phase uranium were high, ranging from 5 to 1569 μg·g (dry weight) soil(-1), redundancy analysis (RDA) and forward selection indicated that neither total nor bio-available uranium concentrations contributed significantly to the observed OTU distribution. Instead, microbial community composition appeared to be influenced more by redox potential. Bacterial communities were also influenced by bio-available manganese and total cobalt and cadmium concentrations. Bio-available cadmium impacted FeRB distribution while bio-available manganese and copper as well as solid-phase zinc concentrations in the soil affected SRB composition. Archaeal communities were influenced by the bio-available lead as well as total zinc and cobalt concentrations. These results suggest that (i) microbial richness was not impacted by heavy metals and radionuclides and that (ii) redox potential and secondary metal contaminants had the strongest effect on microbial community composition, as opposed to uranium, the primary source of contamination.

  20. Fire effects on the composition of a bird community in an amazonian Savanna (Brazil

    Directory of Open Access Journals (Sweden)

    R. Cintra

    Full Text Available The effects of fire on the composition of a bird community were investigated in an Amazonian savanna near Alter-do-Chão, Pará (Brazil. Mist-net captures and visual counts were used to assess species richness and bird abundance pre- and post-fire in an approximately 20 ha area. Visual counts along transects were used to survey birds in an approximately 2000 ha area in a nearby area. Results using the same method of ordination analysis (multidimensional scaling showed significant effects of fire in the 20 ha and 2000 ha areas and strongly suggest direct effects on bird community composition. However, the effects were different at different spatial scales and/or in different years, indicating that the effects of fire vary spatially and/or temporally. Bird community composition pre-fire was significantly different from that found post-fire. Using multiple regression analysis it was found that the numbers of burned and unburned trees were not significantly related to either bird species richness or bird abundance. Two months after the fire, neither bird species richness nor bird abundance was significantly related to the number of flowering trees (Lafoensia pacari or fruiting trees (Byrsonima crassifolia. Since fire is an annual event in Alter-do-Chão and is becoming frequent in the entire Amazon, bird community composition in affected areas could be constantly changing in time and space.

  1. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    Directory of Open Access Journals (Sweden)

    Yao Zhang

    Full Text Available To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4 concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4 was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4 concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  2. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    Science.gov (United States)

    Zhang, Yao; Zhao, Zihao; Chen, Chen-Tung Arthur; Tang, Kai; Su, Jianqiang; Jiao, Nianzhi

    2012-01-01

    To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4)) concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4) was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4) concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  3. Self-adaption of methane-producing communities to pH disturbance at different acetate concentrations by shifting pathways and population interaction.

    Science.gov (United States)

    Hao, Liping; Lü, Fan; Li, Lei; Wu, Qing; Shao, Liming; He, Pinjing

    2013-07-01

    To investigate the competition among acetate-utilizing microorganisms at different acetate levels, bioconversion processes of 50, 100, 150 and 200 mM acetate in the presence and absence of methanogenic inhibitor CH3F were monitored in thermophilic methanogenic system. The successive response of methane-producing community during the deteriorative and recovery phases caused by pH disturbance was analyzed. High acetate concentration (>50mM) inhibited the activity of acetoclastic methanogenesis (AM). The increasing pH (>7.5) enhanced this inhibition. The syntrophic acetate oxidizing (SAO) bacteria and hydrogenotrophic methanogens including Methanomicrobiales and Methanobacteirales were more tolerant to the stress from high acetate concentration and high pH. Resumption from alkali condition to normal pH stimulated the growth of acetate oxidizing syntrophs. The reaction rate of SAO-HM was lower than that of AM. These results point to the possibility to regenerate the deteriorated anaerobic digesters by addition of acclimatized inocula rich in acetate-oxidizing syntrophs. Copyright © 2013 Elsevier Ltd. All rights reserved.

  4. tRNA-dependent cysteine biosynthetic pathway represents a strategy to increase cysteine contents by preventing it from thermal degradation: thermal adaptation of methanogenic archaea ancestor.

    Science.gov (United States)

    Qu, Ge; Wang, Wei; Chen, Ling-Ling; Qian, Shao-Song; Zhang, Hong-Yu

    2009-10-01

    Although cysteine (Cys) is beneficial to stabilize protein structures, it is not prevalent in thermophiles. For instance, the Cys contents in most thermophilic archaea are only around 0.7%. However, methanogenic archaea, no matter thermophilic or not, contain relatively abundant Cys, which remains elusive for a long time. Recently, Klipcan et al. correlated this intriguing property of methanogenic archaea with their unique tRNA-dependent Cys biosynthetic pathway. But, the deep reasons underlying the correlation are ambiguous. Considering the facts that free Cys is thermally labile and the tRNA-dependent Cys biosynthesis avoids the use of free Cys, we speculate that the unique Cys biosynthetic pathway represents a strategy to increase Cys contents by preventing it from thermal degradation, which may be relevant to the thermal adaptation of methanogenic archaea ancestor.

  5. Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale.

    Directory of Open Access Journals (Sweden)

    Nicolas Chemidlin Prévost-Bouré

    Full Text Available Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2: i to examine their spatial structuring; ii to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landescommunities' composition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at

  6. Thioredoxin-linked redox control of metabolism in Methanocaldococcus jannaschii, an evolutionarily deeply-rooted hyperthermophilic methanogenic archaeon

    Science.gov (United States)

    Thioredoxin (Trx), a small redox protein, controls multiple processes in eukaryotes and bacteria by changing the thiol redox status of selected proteins. We have investigated this aspect in methanarchaea. These ancient methanogens produce methane almost exclusively from H2 plus CO2 carried approxima...

  7. Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale.

    Science.gov (United States)

    Chemidlin Prévost-Bouré, Nicolas; Dequiedt, Samuel; Thioulouse, Jean; Lelièvre, Mélanie; Saby, Nicolas P A; Jolivet, Claudy; Arrouays, Dominique; Plassart, Pierre; Lemanceau, Philippe; Ranjard, Lionel

    2014-01-01

    Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landescommunities' composition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at coarse (80 to 120 km radius) and/or medium (40 to 65 km radius) spatial scales, suggesting dispersal limitations at these scales.

  8. Biodegradation and reversible inhibitory impact of sulfamethoxazole on the utilization of volatile fatty acids during anaerobic treatment of pharmaceutical industry wastewater

    International Nuclear Information System (INIS)

    Cetecioglu, Zeynep; Ince, Bahar; Gros, Meritxell; Rodriguez-Mozaz, Sara; Barceló, Damia; Ince, Orhan; Orhon, Derin

    2015-01-01

    This study evaluated the chronic impact and biodegradability of sulfamethoxazole under anaerobic conditions. For this purpose, a lab-scale anaerobic sequencing batch reactor was operated in a sequence of different phases with gradually increasing sulfamethoxazole doses of 1 to 45 mg/L. Conventional parameters, such as COD, VFA, and methane generation, were monitored with corresponding antimicrobial concentrations in the reactor and the methanogenic activity of the sludge. The results revealed that anaerobic treatment was suitable for pharmaceutical industry wastewater with concentrations of up to 40 mg/L of sulfamethoxazole. Higher levels exerted toxic effects on the microbial community under anaerobic conditions, causing the inhibition of substrate/COD utilization and biogas generation and leading to a total collapse of the reactor. The adverse long-term impact was quite variable for fermentative bacteria and methanogenic achaea fractions of the microbial community based on changes inflicted on the composition of the residual organic substrate and mRNA expression of the key enzymes. - Highlights: • Chronic impact of sulfamethoxazole was lethal at 45 mg/L on the microbial community. • Sulfamethoxazole was highly biodegradable under anaerobic conditions. • While the COD removal stopped, the sorption of sulfamethoxazole into the sludge increased. • Sulfamethoxazole has a reversible inhibitory effect on acetoclastic methanogens

  9. Biodegradation and reversible inhibitory impact of sulfamethoxazole on the utilization of volatile fatty acids during anaerobic treatment of pharmaceutical industry wastewater

    Energy Technology Data Exchange (ETDEWEB)

    Cetecioglu, Zeynep, E-mail: cetecioglu@itu.edu.tr [Istanbul Technical University, Environmental Engineering Department, 34469 Maslak, Istanbul (Turkey); Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003 Girona (Spain); Ince, Bahar [Bogazici University, Institute of Environmental Sciences, Rumelihisarustu - Bebek, 34342 Istanbul (Turkey); Gros, Meritxell; Rodriguez-Mozaz, Sara; Barceló, Damia [Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003 Girona (Spain); Ince, Orhan; Orhon, Derin [Istanbul Technical University, Environmental Engineering Department, 34469 Maslak, Istanbul (Turkey)

    2015-12-01

    This study evaluated the chronic impact and biodegradability of sulfamethoxazole under anaerobic conditions. For this purpose, a lab-scale anaerobic sequencing batch reactor was operated in a sequence of different phases with gradually increasing sulfamethoxazole doses of 1 to 45 mg/L. Conventional parameters, such as COD, VFA, and methane generation, were monitored with corresponding antimicrobial concentrations in the reactor and the methanogenic activity of the sludge. The results revealed that anaerobic treatment was suitable for pharmaceutical industry wastewater with concentrations of up to 40 mg/L of sulfamethoxazole. Higher levels exerted toxic effects on the microbial community under anaerobic conditions, causing the inhibition of substrate/COD utilization and biogas generation and leading to a total collapse of the reactor. The adverse long-term impact was quite variable for fermentative bacteria and methanogenic achaea fractions of the microbial community based on changes inflicted on the composition of the residual organic substrate and mRNA expression of the key enzymes. - Highlights: • Chronic impact of sulfamethoxazole was lethal at 45 mg/L on the microbial community. • Sulfamethoxazole was highly biodegradable under anaerobic conditions. • While the COD removal stopped, the sorption of sulfamethoxazole into the sludge increased. • Sulfamethoxazole has a reversible inhibitory effect on acetoclastic methanogens.

  10. Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters.

    Science.gov (United States)

    Ozbayram, Emine Gozde; Ince, Orhan; Ince, Bahar; Harms, Hauke; Kleinsteuber, Sabine

    2018-02-14

    Cattle manure is frequently used as an inoculum for the start-up of agricultural biogas plants or as a co-substrate in the anaerobic digestion of lignocellulosic feedstock. Ruminal microbiota are considered to be effective plant fiber degraders, but the microbes contained in manure do not necessarily reflect the rumen microbiome. The aim of this study was to compare the microbial community composition of cow rumen and manure with respect to plant fiber-digesting microbes. Bacterial and methanogenic communities of rumen and manure samples were examined by 454 amplicon sequencing of bacterial 16S rRNA genes and mcrA genes, respectively. Rumen fluid samples were dominated by Prevotellaceae (29%), whereas Ruminococcaceae was the most abundant family in the manure samples (31%). Fibrobacteraceae (12%) and Bacteroidaceae (13%) were the second most abundant families in rumen fluid and manure, respectively. The high abundances of fiber-degrading bacteria belonging to Prevotellaceae and Fibrobacteraceae might explain the better performance of anaerobic digesters inoculated with rumen fluid. Members of the genus Methanobrevibacter were the predominant methanogens in the rumen fluid, whereas methanogenic communities of the manure samples were dominated by the candidate genus Methanoplasma . Our results suggest that inoculation or bioaugmentation with fiber-digesting rumen microbiota can enhance the anaerobic digestion of lignocellulosic biomass.

  11. Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters

    Directory of Open Access Journals (Sweden)

    Emine Gozde Ozbayram

    2018-02-01

    Full Text Available Cattle manure is frequently used as an inoculum for the start-up of agricultural biogas plants or as a co-substrate in the anaerobic digestion of lignocellulosic feedstock. Ruminal microbiota are considered to be effective plant fiber degraders, but the microbes contained in manure do not necessarily reflect the rumen microbiome. The aim of this study was to compare the microbial community composition of cow rumen and manure with respect to plant fiber-digesting microbes. Bacterial and methanogenic communities of rumen and manure samples were examined by 454 amplicon sequencing of bacterial 16S rRNA genes and mcrA genes, respectively. Rumen fluid samples were dominated by Prevotellaceae (29%, whereas Ruminococcaceae was the most abundant family in the manure samples (31%. Fibrobacteraceae (12% and Bacteroidaceae (13% were the second most abundant families in rumen fluid and manure, respectively. The high abundances of fiber-degrading bacteria belonging to Prevotellaceae and Fibrobacteraceae might explain the better performance of anaerobic digesters inoculated with rumen fluid. Members of the genus Methanobrevibacter were the predominant methanogens in the rumen fluid, whereas methanogenic communities of the manure samples were dominated by the candidate genus Methanoplasma. Our results suggest that inoculation or bioaugmentation with fiber-digesting rumen microbiota can enhance the anaerobic digestion of lignocellulosic biomass.

  12. Structure and Composition of Leachfield Bacterial Communities: Role of Soil Texture, Depth and Septic Tank Effluent Inputs

    Directory of Open Access Journals (Sweden)

    Janet A. Atoyan

    2012-09-01

    Full Text Available Although groundwater quality depends on microbial processes in the soil treatment area (STA of onsite wastewater treatment systems (OWTS, our understanding of the development of these microbial communities is limited. We examined the bacterial communities of sand, sandy loam, and clay STAs at different depths in response to septic tank effluent (STE addition using mesocosms. Terminal restriction fragment length polymorphism (TRFLP analysis was used to compare the bacterial community structure and composition of STE, native soil prior to STE addition (UNX and soil exposed to STE (EXP. Principal component analysis separated communities with depth in sand but not in sandy loam or clay. Indices of richness, diversity, and evenness followed the order: sandy loam > sand > clay. Analysis of TRF peaks indicated that STE contributed least to the composition of STA bacterial communities (5%–16%, followed by UNX soil (18%–48%, with the highest proportion of the community made up of TRFs not detected previously in either UNX or STE (50%–82% for all three soils. Soil type and depth can have a marked effect on the structure and composition of STA bacterial communities, and on the relative contribution of native soil and STE to these communities.

  13. Soil biochar amendment shapes the composition of N_2O-reducing microbial communities

    International Nuclear Information System (INIS)

    Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H.; Kappler, Andreas; Behrens, Sebastian

    2016-01-01

    Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N_2O) emissions. N_2O is a potent greenhouse gas. The main sources of N_2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N_2O emission mitigation and the abundance and activity of N_2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described ‘atypical’ nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N_2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N_2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N_2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. - Highlights: • Biochar promoted anaerobic, alkalinity-adapted, and polymer-degrading microbial taxa. • Biochar fostered the development of distinct N_2O-reducing microbial taxa. • Taxonomic shifts among N_2O-reducing microbes might explain lower N_2O emissions.

  14. The effect of pH profiles in methanogenic aggregates on the kinetics of acetate conversion

    NARCIS (Netherlands)

    Beer, de D.; Huisman, J.W.; Heuvel, van den J.C.; Ottengraf, S.P.P.

    1993-01-01

    Due to the conversion of acetic acid into the weaker carbonic acid and CH4, the pH inside methanogenic aggregates is higher than in the bulk liq. The pH profiles in aggregates were measured with pH microelectrodes. These profiles strongly det. the macro-kinetics of the aggregate, by their influence

  15. Methanomethylovorans thermophila sp. nov., a thermophilic, methylotrophic methanogen form an anaerobic reactor fed with methanol

    NARCIS (Netherlands)

    Jiang, B.; Parshina, S.N.; Doesburg, van W.C.J.; Lomans, B.P.; Stams, A.J.M.

    2005-01-01

    A novel thermophilic, obligately methylotrophic, methanogenic archaeon, strain L2FAWT, was isolated from a thermophilic laboratory-scale upflow anaerobic sludge blanket reactor fed with methanol as the carbon and energy source. Cells of strain L2FAWT were non-motile, irregular cocci, 0·7¿1·5 µm in

  16. Rice Cluster I, an Important Group of Archaea Producing Methane in Rice Fields

    Science.gov (United States)

    Conrad, R.

    2006-12-01

    Rice fields are an important source for the greenhouse gas methane. Methane is a major degradation product of organic matter in the anoxic soil, is partially oxidized in the rhizosphere and is emitted into the atmosphere through the aerenchyma system of the plants. Anaerobic degradation of organic matter by fermenting bacteria eventually results in the production of acetate and hydrogen, the two major substrates for microbial methanogenesis. The community of methanogenic archaea consists of several major orders or families including hydrogen-utilizing Rice Cluster-I (RC-I). Environmental conditions affect the methanogenic degradation process and the community structure of the methanogenic archaea in soil and rhizosphere. For example, populations of acetoclastic Methanosaetaceae and Methanosarcinaceae are enhanced by low and high acetate concentrations, respectively. Stable isotope probing of 16S rRNA showed that RC-I methanogens are mainly active on rice roots and at low H2 concentrations. Growth and population size is largely consistent with energetic conditions. RC-I methanogens on roots seem to be responsible for methane production from plant photosynthates that account for a major part of the emitted methane. Populations of RC-I methanogens in rice field soil are also enhanced at elevated temperatures (40-50°C). Moderately thermophilic members of RC-I methanogens or other methanogenic families were found to be ubiquitously present in soils from rice fields and river marshes. The genome of a RC-I methanogen was completely sequenced out of an enrichment culture using a metagenome approach. Genes found are consistent with life in the rhizosphere and in temporarily drained, oxic soil. We found that the methanogenic community structure on the rice roots is mainly determined by the respective community structure of the soil, but is in addition affected by the rice cultivar. Rice microcosms in which soil and rice roots are mainly colonized by RC-I methanogens produce

  17. Low strength ultrasonication positively affects the methanogenic granules toward higher AD performance. Part I: Physico-chemical characteristics

    DEFF Research Database (Denmark)

    Cho, S. K.; Hwang, Yuhoon; Kim, D. H.

    2013-01-01

    To elucidate the correlation between enhanced biogas production and changed physico-chemical properties of methanogenic granules after low strength ultrasonication, in this study, the effects of low strength ultrasonication on the settling velocity, permeability, porosity, and fluid collection ef...

  18. Effect of soil properties and hydrology on Archaeal community composition in three temperate grasslands on peat

    DEFF Research Database (Denmark)

    Görres, Carolyn-Monika; Conrad, Ralf; Petersen, Søren O

    2013-01-01

    Grasslands established on drained peat soils are regarded as negligible methane (CH4) sources; however, they can still exhibit considerable soil CH4 dynamics. We investigated archaeal community composition in two different fen peat soils and one bog peat soil under permanent grassland in Denmark........ Overall, there seemed to be a significant coupling between peat type and archaeal community composition, with local hydrology modifying the strength of this coupling....

  19. Carbon dioxide and submersed macrophytes in lakes: linking functional ecology to community composition.

    Science.gov (United States)

    Titus, John E; Pagano, Angela M

    2017-12-01

    Evaluating plant community response to atmospheric CO 2 rise is critical to predicting ecosystem level change. Freshwater lakes offer a model system for examining CO 2 effects as submersed macrophyte species differ greatly in their growth responses to CO 2 enrichment, and free CO 2 concentrations among these habitats show a wide range of natural, spatial variation. We determined free CO 2 concentrations in the water column and sediment porewater in littoral zones with pH macrophyte communities coupled with greenhouse-derived growth responses to CO 2 enrichment of constituent species to test two hypotheses: (1) CCRI, which is higher for communities dominated by species with greater growth responses to CO 2 enrichment, is positively correlated to free [CO 2 ] in the water column, and (2) in natural communities, the percent of sediment CO 2 -using species, which are relatively unresponsive to CO 2 enrichment, is negatively correlated to free [CO 2 ]. A significant positive correlation (P = 0.003) between our physiologically based CCRI and the concentration of free CO 2 in the water column supported our primary hypothesis that sites with higher levels of free CO 2 are dominated by species with greater growth responses to CO 2 enrichment. Our CCRI is also highly significantly correlated (P macrophyte community composition. Further, we demonstrate the utility of a physiologically-based index of community composition, our CCRI, as an ecologically valid measure of community response to CO 2 . © 2017 by the Ecological Society of America.

  20. Stratification of Diversity and Activity of Methanogenic and Methanotrophic Microorganisms in a Nitrogen-Fertilized Italian Paddy Soil

    Directory of Open Access Journals (Sweden)

    Annika Vaksmaa

    2017-11-01

    Full Text Available Paddy fields are important ecosystems, as rice is the primary food source for about half of the world’s population. Paddy fields are impacted by nitrogen fertilization and are a major anthropogenic source of methane. Microbial diversity and methane metabolism were investigated in the upper 60 cm of a paddy soil by qPCR, 16S rRNA gene amplicon sequencing and anoxic 13C-CH4 turnover with a suite of electron acceptors. The bacterial community consisted mainly of Acidobacteria, Chloroflexi, Proteobacteria, Planctomycetes, and Actinobacteria. Among archaea, Euryarchaeota and Bathyarchaeota dominated over Thaumarchaeota in the upper 30 cm of the soil. Bathyarchaeota constituted up to 45% of the total archaeal reads in the top 5 cm. In the methanogenic community, Methanosaeta were generally more abundant than the versatile Methanosarcina. The measured maximum methane production rate was 444 nmol gdwh-1, and the maximum rates of nitrate-, nitrite-, and iron-dependent anaerobic oxidation of methane (AOM were 57 nmol, 55 nmol, and 56 nmol gdwh-1, respectively, at different depths. qPCR revealed a higher abundance of ‘Candidatus Methanoperedens nitroreducens’ than methanotrophic NC10 phylum bacteria at all depths, except at 60 cm. These results demonstrate that there is substantial potential for AOM in fertilized paddy fields, with ‘Candidatus Methanoperedens nitroreducens’ archaea as a potential important contributor.

  1. Spatial patterns and links between microbial community composition and function in cyanobacterial mats

    KAUST Repository

    Alnajjar, Mohammad Ahmad; Ramette, Alban; Kü hl, Michael; Hamza, Waleed; Klatt, Judith M.; Polerecky, Lubos

    2014-01-01

    We imaged reflectance and variable fluorescence in 25 cyanobacterial mats from four distant sites around the globe to assess, at different scales of resolution, spatial variabilities in the physiological parameters characterizing their photosynthetic capacity, including the absorptivity by chlorophyll a (Achl), maximum quantum yield of photosynthesis (Ymax), and light acclimation irradiance (Ik). Generally, these parameters significantly varied within individual mats on a sub-millimeter scale, with about 2-fold higher variability in the vertical than in the horizontal direction. The average vertical profiles of Ymax and Ik decreased with depth in the mat, while Achl exhibited a sub-surface maximum. The within-mat variability was comparable to, but often larger than, the between-sites variability, whereas the within-site variabilities (i.e., between samples from the same site) were generally lowest. When compared based on averaged values of their photosynthetic parameters, mats clustered according to their site of origin. Similar clustering was found when the community composition of the mats' cyanobacterial layers were compared by automated ribosomal intergenic spacer analysis (ARISA), indicating a significant link between the microbial community composition and function. Although this link is likely the result of community adaptation to the prevailing site-specific environmental conditions, our present data is insufficient to identify the main factors determining these patterns. Nevertheless, this study demonstrates that the spatial variability in the photosynthetic capacity and light acclimation of benthic phototrophic microbial communities is at least as large on a sub-millimeter scale as it is on a global scale, and suggests that this pattern of variability scaling is similar for the microbial community composition. © 2014 Al-Najjar, Ramette, Kühl, Hamza, Klatt and Polerecky.

  2. Spatial patterns and links between microbial community composition and function in cyanobacterial mats

    KAUST Repository

    Alnajjar, Mohammad Ahmad

    2014-08-06

    We imaged reflectance and variable fluorescence in 25 cyanobacterial mats from four distant sites around the globe to assess, at different scales of resolution, spatial variabilities in the physiological parameters characterizing their photosynthetic capacity, including the absorptivity by chlorophyll a (Achl), maximum quantum yield of photosynthesis (Ymax), and light acclimation irradiance (Ik). Generally, these parameters significantly varied within individual mats on a sub-millimeter scale, with about 2-fold higher variability in the vertical than in the horizontal direction. The average vertical profiles of Ymax and Ik decreased with depth in the mat, while Achl exhibited a sub-surface maximum. The within-mat variability was comparable to, but often larger than, the between-sites variability, whereas the within-site variabilities (i.e., between samples from the same site) were generally lowest. When compared based on averaged values of their photosynthetic parameters, mats clustered according to their site of origin. Similar clustering was found when the community composition of the mats\\' cyanobacterial layers were compared by automated ribosomal intergenic spacer analysis (ARISA), indicating a significant link between the microbial community composition and function. Although this link is likely the result of community adaptation to the prevailing site-specific environmental conditions, our present data is insufficient to identify the main factors determining these patterns. Nevertheless, this study demonstrates that the spatial variability in the photosynthetic capacity and light acclimation of benthic phototrophic microbial communities is at least as large on a sub-millimeter scale as it is on a global scale, and suggests that this pattern of variability scaling is similar for the microbial community composition. © 2014 Al-Najjar, Ramette, Kühl, Hamza, Klatt and Polerecky.

  3. Plankton community composition and vertical migration during polar night in Kongsfjorden

    DEFF Research Database (Denmark)

    Grenvald, Julie Cornelius; Callesen, Trine Abraham; Daase, Malin

    2016-01-01

    characterize the plankton community composition during the polar night using water samplers and zooplankton net samples (50, 64, 200, 1500 lm), supplemented by acoustics (ADCPs, 300 kHz), to address a previously unresolved question–which species of zooplankton perform diel vertical migration during the polar...

  4. Stability of a biogas-producing bacterial, archaeal and fungal community degrading food residues.

    Science.gov (United States)

    Bengelsdorf, Frank R; Gerischer, Ulrike; Langer, Susanne; Zak, Manuel; Kazda, Marian

    2013-04-01

    The resident microbiota was analyzed in a mesophilic, continuously operating biogas plant predominantly utilizing food residues, stale bread, and other waste cosubstrates together with pig manure and maize silage. The dominating bacterial, archaeal, and eukaryotic community members were characterized by two different 16S/18S rRNA gene culture-independent approaches. Prokaryotic 16S rRNA gene and eukaryotic 18S rRNA gene clone libraries were constructed and further analyzed by restriction fragment length polymorphism (RFLP), 16S/18S rRNA gene sequencing, and phylogenetic tree reconstruction. The most dominant bacteria belonged to the phyla Bacteriodetes, Chloroflexus, and Firmicutes. On the family level, the bacterial composition confirmed high differences among biogas plants studied so fare. In contrast, the methanogenic archaeal community was similar to that of other studied biogas plants. Furthermore, it was possible to identify fungi at the genus level, namely Saccharomyces and Mucor. Both genera, which are important for microbial degradation of complex compounds, were up to now not found in biogas plants. The results revealed their long-term presence as indicated by denaturating gradient gel electrophoresis (DGGE). The DGGE method confirmed that the main members of the microbial community were constantly present over more than one-year period. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  5. The contribution of fermentative bacteria and methanogenic archaea to azo dye reduction by a thermophilic anaerobic consortium

    NARCIS (Netherlands)

    Santos, dos A.B.; Cervantes, F.J.; Madrid, de M.P.; Bok, de F.A.M.; Stams, A.J.M.; Lier, van J.B.

    2006-01-01

    The contribution of fermentative bacteria and methanogenic archaea to azo dye reduction by a thermophilic anaerobic consortium was studied. Additionally, the effects of different electron-donating substrates and the redox mediator riboflavin on dye reduction were assessed by using either a

  6. Toxic effects exerted on methanogenic, nitrifying and denitrifying bacteria by chemicals used in a milk analysis laboratory

    NARCIS (Netherlands)

    Lopez-Fiuza, J.; Buys, B.; Mosquera-Corral, A.; Omil, F.; Mendez, R.

    2002-01-01

    The toxic effects caused by the chemicals contained in wastewaters generated by laboratories involved in raw milk analyses were assessed using batch assays. These assays were carried out separately with methanogenic, ammonium-oxidizing, nitrite-oxidizing and denitrifying bacteria. Since sodium azide

  7. Abundance, diversity and community composition of free-living protozoa on vegetable sprouts.

    Science.gov (United States)

    Chavatte, N; Lambrecht, E; Van Damme, I; Sabbe, K; Houf, K

    2016-05-01

    Interactions with free-living protozoa (FLP) have been implicated in the persistence of pathogenic bacteria on food products. In order to assess the potential involvement of FLP in this contamination, detailed knowledge on their occurrence, abundance and diversity on food products is required. In the present study, enrichment and cultivation methods were used to inventory and quantify FLP on eight types of commercial vegetable sprouts (alfalfa, beetroot, cress, green pea, leek, mung bean, red cabbage and rosabi). In parallel, total aerobic bacteria and Escherichia coli counts were performed. The vegetable sprouts harbored diverse communities of FLP, with Tetrahymena (ciliate), Bodo saltans and cercomonads (flagellates), and Acanthamoeba and Vannella (amoebae) as the dominant taxa. Protozoan community composition and abundance significantly differed between the sprout types. Beetroot harbored the most abundant and diverse FLP communities, with many unique species such as Korotnevella sp., Vannella sp., Chilodonella sp., Podophrya sp. and Sphaerophrya sp. In contrast, mung bean sprouts were species-poor and had low FLP numbers. Sampling month and company had no significant influence, suggesting that seasonal and local factors are of minor importance. Likewise, no significant relationship between protozoan community composition and bacterial load was observed. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Enterotypes in the landscape of gut microbial community composition

    DEFF Research Database (Denmark)

    Costea, Paul I.; Hildebrand, Falk; Manimozhiyan, Arumugam

    2017-01-01

    Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met...... with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical...... contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept....

  9. Microbial community assembly patterns under incipient conditions in a basaltic soil system

    Science.gov (United States)

    Sengupta, A.; Stegen, J.; Alves Meira Neto, A.; Wang, Y.; Chorover, J.; Troch, P. A. A.; Maier, R. M.

    2017-12-01

    In sub-surface environments, the biotic components are critically linked to the abiotic processes. However, there is limited understanding of community establishment, functional associations, and community assembly processes of such microbes in sub-surface environments. This study presents the first analysis of microbial signatures in an incipient terrestrial basalt soil system conducted under controlled conditions. A sub-meter scale sampling of a soil mesocosm revealed the contrasting distribution patterns of simple soil parameters such as bulk density and electrical conductivity. Phylogenetic analysis of 16S rRNA gene indicated the presence of a total 40 bacterial and archaeal phyla, with high relative abundance of Actinobacteria on the surface and highest abundance of Proteobacteria throughout the system. Community diversity patterns were inferred to be dependent on depth profile and average water content in the system. Predicted functional gene analysis suggested mixotrophy lifestyles with both autotrophic and heterotrophic metabolisms, likelihood of a unique salt tolerant methanogenic pathway with links to novel Euryarchea, signatures of an incomplete nitrogen cycle, and predicted enzymes of extracellular iron (II) to iron (III) conversion followed by intracellular uptake, transport and regulation. Null modeling revealed microbial community assembly was predominantly governed by variable selection, but the influence of the variable selection did not show systematic spatial structure. The presence of significant heterogeneity in predicted functions and ecologically deterministic shifts in community composition in a homogeneous incipient basalt highlights the complexity exhibited by microorganisms even in the simplest of environmental systems. This presents an opportunity to further develop our understanding of how microbial communities establish, evolve, impact, and respond in sub-surface environments.

  10. Effect of didecyl dimethyl ammonium chloride on nitrate reduction in a mixed methanogenic culture.

    Science.gov (United States)

    Tezel, U; Pierson, J A; Pavlostathis, S G

    2008-01-01

    The effect of the quaternary ammonium compound, didecyl dimethyl ammonium chloride (DDAC), on nitrate reduction was investigated at concentrations up to 100 mg/L in a batch assay using a mixed, mesophilic (35 degrees C) methanogenic culture. Glucose was used as the carbon and energy source and the initial nitrate concentration was 70 mg N/L. Dissimilatory nitrate reduction to ammonia (DNRA) and to dinitrogen (denitrification) were observed at DDAC concentrations up to 25 mg/L. At and above 50 mg DDAC/L, DNRA was inhibited and denitrification was incomplete resulting in accumulation of nitrous oxide. At DDAC concentrations above 10 mg/L, production of nitrous oxide, even transiently, resulted in complete, long-term inhibition of methanogenesis and accumulation of volatile fatty acids. Fermentation was inhibited at and above 75 mg DDAC/L. DDAC suppressed microbial growth and caused cell lysis at a concentration 50 mg/L or higher. Most of the added DDAC was adsorbed on the biomass. Over 96% of the added DDAC was recovered from all cultures at the end of the 100-days incubation period, indicating that DDAC did not degrade in the mixed methanogenic culture under the conditions of this study.

  11. Distribution, Community Composition, and Potential Metabolic Activity of Bacterioplankton in an Urbanized Mediterranean Sea Coastal Zone.

    Science.gov (United States)

    Richa, Kumari; Balestra, Cecilia; Piredda, Roberta; Benes, Vladimir; Borra, Marco; Passarelli, Augusto; Margiotta, Francesca; Saggiomo, Maria; Biffali, Elio; Sanges, Remo; Scanlan, David J; Casotti, Raffaella

    2017-09-01

    Bacterioplankton are fundamental components of marine ecosystems and influence the entire biosphere by contributing to the global biogeochemical cycles of key elements. Yet, there is a significant gap in knowledge about their diversity and specific activities, as well as environmental factors that shape their community composition and function. Here, the distribution and diversity of surface bacterioplankton along the coastline of the Gulf of Naples (GON; Italy) were investigated using flow cytometry coupled with high-throughput sequencing of the 16S rRNA gene. Heterotrophic bacteria numerically dominated the bacterioplankton and comprised mainly Alphaproteobacteria , Gammaproteobacteria , and Bacteroidetes Distinct communities occupied river-influenced, coastal, and offshore sites, as indicated by Bray-Curtis dissimilarity, distance metric (UniFrac), linear discriminant analysis effect size (LEfSe), and multivariate analyses. The heterogeneity in diversity and community composition was mainly due to salinity and changes in environmental conditions across sites, as defined by nutrient and chlorophyll a concentrations. Bacterioplankton communities were composed of a few dominant taxa and a large proportion (92%) of rare taxa (here defined as operational taxonomic units [OTUs] accounting for coastal zones is of critical importance, considering that these areas are highly productive and anthropogenically impacted. Their richness and evenness, as well as their potential activity, are very important to assess ecosystem health and functioning. Here, we investigated bacterial distribution, community composition, and potential metabolic activity in the GON, which is an ideal test site due to its heterogeneous environment characterized by a complex hydrodynamics and terrestrial inputs of varied quantities and quality. Our study demonstrates that bacterioplankton communities in this region are highly diverse and strongly regulated by a combination of different environmental

  12. Morphology and Phylogeny of a New Species of Anaerobic Ciliate, Trimyema finlayi n. sp., with Endosymbiotic Methanogens.

    Science.gov (United States)

    Lewis, William H; Sendra, Kacper M; Embley, T Martin; Esteban, Genoveva F

    2018-01-01

    Many anaerobic ciliated protozoa contain organelles of mitochondrial ancestry called hydrogenosomes. These organelles generate molecular hydrogen that is consumed by methanogenic Archaea, living in endosymbiosis within many of these ciliates. Here we describe a new species of anaerobic ciliate, Trimyema finlayi n. sp., by using silver impregnation and microscopy to conduct a detailed morphometric analysis. Comparisons with previously published morphological data for this species, as well as the closely related species, Trimyema compressum , demonstrated that despite them being similar, both the mean cell size and the mean number of somatic kineties are lower for T. finlayi than for T. compressum , which suggests that they are distinct species. This was also supported by analysis of the 18S rRNA genes from these ciliates, the sequences of which are 97.5% identical (6 substitutions, 1479 compared bases), and in phylogenetic analyses these sequences grouped with other 18S rRNA genes sequenced from previous isolates of the same respective species. Together these data provide strong evidence that T. finlayi is a novel species of Trimyema , within the class Plagiopylea. Various microscopic techniques demonstrated that T. finlayi n. sp. contains polymorphic endosymbiotic methanogens, and analysis of the endosymbionts' 16S rRNA gene showed that they belong to the genus Methanocorpusculum , which was confirmed using fluorescence in situ hybridization with specific probes. Despite the degree of similarity and close relationship between these ciliates, T. compressum contains endosymbiotic methanogens from a different genus, Methanobrevibacter . In phylogenetic analyses of 16S rRNA genes, the Methanocorpusculum endosymbiont of T. finlayi n. sp. grouped with sequences from Methanomicrobia, including the endosymbiont of an earlier isolate of the same species, ' Trimyema sp.,' which was sampled approximately 22 years earlier, at a distant (∼400 km) geographical location

  13. Morphology and Phylogeny of a New Species of Anaerobic Ciliate, Trimyema finlayi n. sp., with Endosymbiotic Methanogens

    Directory of Open Access Journals (Sweden)

    William H. Lewis

    2018-02-01

    Full Text Available Many anaerobic ciliated protozoa contain organelles of mitochondrial ancestry called hydrogenosomes. These organelles generate molecular hydrogen that is consumed by methanogenic Archaea, living in endosymbiosis within many of these ciliates. Here we describe a new species of anaerobic ciliate, Trimyema finlayi n. sp., by using silver impregnation and microscopy to conduct a detailed morphometric analysis. Comparisons with previously published morphological data for this species, as well as the closely related species, Trimyema compressum, demonstrated that despite them being similar, both the mean cell size and the mean number of somatic kineties are lower for T. finlayi than for T. compressum, which suggests that they are distinct species. This was also supported by analysis of the 18S rRNA genes from these ciliates, the sequences of which are 97.5% identical (6 substitutions, 1479 compared bases, and in phylogenetic analyses these sequences grouped with other 18S rRNA genes sequenced from previous isolates of the same respective species. Together these data provide strong evidence that T. finlayi is a novel species of Trimyema, within the class Plagiopylea. Various microscopic techniques demonstrated that T. finlayi n. sp. contains polymorphic endosymbiotic methanogens, and analysis of the endosymbionts’ 16S rRNA gene showed that they belong to the genus Methanocorpusculum, which was confirmed using fluorescence in situ hybridization with specific probes. Despite the degree of similarity and close relationship between these ciliates, T. compressum contains endosymbiotic methanogens from a different genus, Methanobrevibacter. In phylogenetic analyses of 16S rRNA genes, the Methanocorpusculum endosymbiont of T. finlayi n. sp. grouped with sequences from Methanomicrobia, including the endosymbiont of an earlier isolate of the same species, ‘Trimyema sp.,’ which was sampled approximately 22 years earlier, at a distant (∼400 km

  14. Microbial communities and greenhouse gas emissions associated with the biodegradation of specified risk material in compost

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Shanwei [Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5 (Canada); Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta, Canada T1J 4B1 (Canada); Reuter, Tim [Alberta Agriculture and Rural Development, Lethbridge, Alberta, Canada T1J 4V6 (Canada); Gilroyed, Brandon H. [Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta, Canada T1J 4B1 (Canada); Tymensen, Lisa [Alberta Agriculture and Rural Development, Lethbridge, Alberta, Canada T1J 4V6 (Canada); Hao, Yongxin; Hao, Xiying [Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta, Canada T1J 4B1 (Canada); Belosevic, Miodrag [Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada T6G 2E9 (Canada); Leonard, Jerry J. [Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5 (Canada); McAllister, Tim A., E-mail: tim.mcallister@agr.gc.ca [Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta, Canada T1J 4B1 (Canada)

    2013-06-15

    Highlights: ► Addition of feathers altered bacterial and fungal communities in compost. ► Microbial communities degrading SRM and compost matrix were distinct. ► Addition of feathers may enrich for microbial communities that degrade SRM. ► Inclusion of feather in compost increased both CH{sub 4} and N{sub 2}O emissions from compost. ► Density of methanogens and methanotrophs were weakly associated with CH{sub 4} emissions. - Abstract: Provided that infectious prions (PrP{sup Sc}) are inactivated, composting of specified risk material (SRM) may be a viable alternative to rendering and landfilling. In this study, bacterial and fungal communities as well as greenhouse gas emissions associated with the degradation of SRM were examined in laboratory composters over two 14 day composting cycles. Chicken feathers were mixed into compost to enrich for microbial communities involved in the degradation of keratin and other recalcitrant proteins such as prions. Feathers altered the composition of bacterial and fungal communities primarily during the first cycle. The bacterial genera Saccharomonospora, Thermobifida, Thermoactinomycetaceae, Thiohalospira, Pseudomonas, Actinomadura, and Enterobacter, and the fungal genera Dothideomycetes, Cladosporium, Chaetomium, and Trichaptum were identified as candidates involved in SRM degradation. Feathers increased (P < 0.05) headspace concentrations of CH{sub 4} primarily during the early stages of the first cycle and N{sub 2}O during the second. Although inclusion of feathers in compost increases greenhouse gas emissions, it may promote the establishment of microbial communities that are more adept at degrading SRM and recalcitrant proteins such as keratin and PrP{sup Sc}.

  15. How microbial community composition regulates coral disease development.

    Directory of Open Access Journals (Sweden)

    Justin Mao-Jones

    2010-03-01

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

  16. How microbial community composition regulates coral disease development.

    Science.gov (United States)

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

    2010-03-30

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

  17. Thermophilic anaerobic acetate-utilizing methanogens and their metabolism

    DEFF Research Database (Denmark)

    Mladenovska, Zuzana

    Six strains of thermophilic anaerobic acetate-utilizing methanogens were isolated from different full-scale thermophilic biogas plants in China and Denmark. The strain isolated from the Chinese biogas plant was designated KN-6P and the isolates from the Danish full-scale biogas plants were......, utilizing the substrates acetate, methanol and methylamines but not hydrogen/carbon dioxide. Strain Methanosarcina sp. SO-2P was able to grow mixotrophically on methanol and hydrogen/carbon dioxide with methane formation from hydrogen and carbon dioxide occurring after methanol depletion. All six...... designated HG-1P, LVG-4P R1-1P, SO-2P and V-1P. The isolates were characterized morphologically and physiologically, and their immunological and phylogenetic relatedness to already known isolated strains were established. All isolated strains were identified as organisms belonging to genus Methanosarcina...

  18. Relative importance of methylotrophic methanogenesis in sediments of the Western Mediterranean Sea

    Science.gov (United States)

    Zhuang, Guang-Chao; Heuer, Verena B.; Lazar, Cassandre S.; Goldhammer, Tobias; Wendt, Jenny; Samarkin, Vladimir A.; Elvert, Marcus; Teske, Andreas P.; Joye, Samantha B.; Hinrichs, Kai-Uwe

    2018-03-01

    Microbial production of methane is an important terminal metabolic process during organic matter degradation in marine sediments. It is generally acknowledged that hydrogenotrophic and acetoclastic methanogenesis constitute the dominant pathways of methane production; the importance of methanogenesis from methylated compounds remains poorly understood. We conducted various biogeochemical and molecular genetic analyses to characterize substrate availability, rates of methanogenesis, and methanogen community composition, and further evaluated the contribution of different substrates and pathways for methane production in deltaic surface and subsurface sediments of the Western Mediterranean Sea. Major substrates representing three methanogenic pathways, including H2, acetate, and methanol, trimethylamine (TMA), and dimethylsulfide (DMS), were detected in the pore waters and sediments, and exhibited variability over depth and between sites. In accompanying incubation experiments, methanogenesis rates from various 14C labeled substrates varied as well, suggesting that environmental factors, such as sulfate concentration and organic matter quality, could significantly influence the relative importance of individual pathway. In particular, methylotrophic and hydrogenotrophic methanogenesis contributed to the presence of micromolar methane concentrations in the sulfate reduction zone, with methanogenesis from methanol accounting for up to 98% of the total methane production in the topmost surface sediment. In the sulfate-depleted zone, hydrogenotrophic methanogenesis was the dominant methanogenic pathway (67-98%), and enhanced methane production from acetate was observed in organic-rich sediment (up to 31%). Methyl coenzyme M reductase gene (mcrA) analysis revealed that the composition of methanogenic communities was generally consistent with the distribution of methanogenic activity from different substrates. This study provides the first quantitative assessment of

  19. Biofouling of reverse-osmosis membranes during tertiary wastewater desalination: microbial community composition.

    Science.gov (United States)

    Al Ashhab, Ashraf; Herzberg, Moshe; Gillor, Osnat

    2014-03-01

    Reverse-osmosis (RO) desalination is frequently used for the production of high-quality water from tertiary treated wastewater (TTWW). However, the RO desalination process is often hampered by biofouling, including membrane conditioning, microbial adhesion, and biofilm growth. The vast majority of biofilm exploration concentrated on the role of bacteria in biofouling neglecting additional microbial contributors, i.e., fungi and archaea. To better understand the RO biofouling process, bacterial, archaeal and fungal diversity was characterized in a laboratory-scale RO desalination plant exploring the TTWW (RO feed), the RO membrane and the RO feed tube biofilms. We sequenced 77,400 fragments of the ribosome small subunit-encoding gene (16S and 18S rRNA) to identify the microbial community members in these matrices. Our results suggest that the bacterial, archaeal but not fungal community significantly differ from the RO membrane biofouling layer to the feedwater and tube biofilm (P < 0.01). Moreover, the RO membrane supported a more diverse community compared to the communities monitored in the feedwater and the biofilm attached to the RO feedwater tube. The tube biofilm was dominated by Actinobacteria (91.2 ± 4.6%), while the Proteobacteria phylum dominated the feedwater and RO membrane (at relative abundance of 92.3 ± 4.4% and 71.5 ± 8.3%, respectively), albeit comprising different members. The archaea communities were dominated by Crenarchaeota (53.0 ± 6.9%, 32.5 ± 7.2% and 69%, respectively) and Euryarchaeota (43.3 ± 6.3%, 23.2 ± 4.8% and 24%, respectively) in all three matrices, though the communities' composition differed. But the fungal communities composition was similar in all matrices, dominated by Ascomycota (97.6 ± 2.7%). Our results suggest that the RO membrane is a selective surface, supporting unique bacterial, and to a lesser extent archaeal communities, yet it does not select for a fungal community. Copyright © 2013

  20. Do Honeybees Shape the Bacterial Community Composition in Floral Nectar?

    Science.gov (United States)

    Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

    2013-01-01

    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. PMID:23844027

  1. Microbial community of high arsenic groundwater in agricultural irrigation area of Hetao Plain, Inner Mongolia

    Directory of Open Access Journals (Sweden)

    Yanhong Wang

    2016-12-01

    Full Text Available 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 gene. 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 TOC. Sequencing results revealed that a total of 329-2823 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 As-rich aquifers of Hetao Plain and other high As 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 analysis and co-inertia analysis. Other geochemical

  2. Modeling plant composition as community continua in a forest landscape with LiDAR and hyperspectral remote sensing.

    Science.gov (United States)

    Hakkenberg, C R; Peet, R K; Urban, D L; Song, C

    2018-01-01

    In light of the need to operationalize the mapping of forest composition at landscape scales, this study uses multi-scale nested vegetation sampling in conjunction with LiDAR-hyperspectral remotely sensed data from the G-LiHT airborne sensor to map vascular plant compositional turnover in a compositionally and structurally complex North Carolina Piedmont forest. Reflecting a shift in emphasis from remotely sensing individual crowns to detecting aggregate optical-structural properties of forest stands, predictive maps reflect the composition of entire vascular plant communities, inclusive of those species smaller than the resolution of the remotely sensed imagery, intertwined with proximate taxa, or otherwise obscured from optical sensors by dense upper canopies. Stand-scale vascular plant composition is modeled as community continua: where discrete community-unit classes at different compositional resolutions provide interpretable context for continuous gradient maps that depict n-dimensional compositional complexity as a single, consistent RGB color combination. In total, derived remotely sensed predictors explain 71%, 54%, and 48% of the variation in the first three components of vascular plant composition, respectively. Among all remotely sensed environmental gradients, topography derived from LiDAR ground returns, forest structure estimated from LiDAR all returns, and morphological-biochemical traits determined from hyperspectral imagery each significantly correspond to the three primary axes of floristic composition in the study site. Results confirm the complementarity of LiDAR and hyperspectral sensors for modeling the environmental gradients constraining landscape turnover in vascular plant composition and hold promise for predictive mapping applications spanning local land management to global ecosystem modeling. © 2017 by the Ecological Society of America.

  3. Thalassiosira spp. community composition shifts in response to chemical and physical forcing in the northeast Pacific Ocean.

    Directory of Open Access Journals (Sweden)

    Phoebe Dreux Chappell

    2013-09-01

    Full Text Available Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a three-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., the ARISA method is a useful screening tool to identify changes in the relative abundance and distribution of specific species. The method also enabled us to assess changes in Thalassiosira community composition in response to chemical and physical forcing. Thalassiosira spp. community composition in the core of a three-month-old Haida eddy remained largely (>80% similar over a two-week period, despite moving 24 km southwestward. Shifts in Thalassiosira species correlated with changes in dissolved iron (Fe and temperature throughout the sampling period. Simultaneously tracking community composition and relative abundance of Thalassiosira species within the physical and chemical context they occurred allowed us to identify quantitative linkages between environmental conditions and community response.

  4. Abundance and composition of indigenous bacterial communities in a multi-step biofiltration-based drinking water treatment plant.

    Science.gov (United States)

    Lautenschlager, Karin; Hwang, Chiachi; Ling, Fangqiong; Liu, Wen-Tso; Boon, Nico; Köster, Oliver; Egli, Thomas; Hammes, Frederik

    2014-10-01

    Indigenous bacterial communities are essential for biofiltration processes in drinking water treatment systems. In this study, we examined the microbial community composition and abundance of three different biofilter types (rapid sand, granular activated carbon, and slow sand filters) and their respective effluents in a full-scale, multi-step treatment plant (Zürich, CH). Detailed analysis of organic carbon degradation underpinned biodegradation as the primary function of the biofilter biomass. The biomass was present in concentrations ranging between 2-5 × 10(15) cells/m(3) in all filters but was phylogenetically, enzymatically and metabolically diverse. Based on 16S rRNA gene-based 454 pyrosequencing analysis for microbial community composition, similar microbial taxa (predominantly Proteobacteria, Planctomycetes, Acidobacteria, Bacteriodetes, Nitrospira and Chloroflexi) were present in all biofilters and in their respective effluents, but the ratio of microbial taxa was different in each filter type. This change was also reflected in the cluster analysis, which revealed a change of 50-60% in microbial community composition between the different filter types. This study documents the direct influence of the filter biomass on the microbial community composition of the final drinking water, particularly when the water is distributed without post-disinfection. The results provide new insights on the complexity of indigenous bacteria colonizing drinking water systems, especially in different biofilters of a multi-step treatment plant. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. The impact of road salt runoff on methanogens and other lacustrine prokaryotes

    Science.gov (United States)

    Sprague, E.; Dupuis, D.; Koretsky, C.; Docherty, K. M.

    2017-12-01

    Road salt deicers are widely used in regions that experience icy winters. The resulting saline runoff can negatively impact freshwater lake ecosystems. Saline runoff can cause density stratification, resulting in persistently anoxic hypolimnia. This may result in a shift in the structure of the hypolimnetic prokaryotic community, with potential increases in anaerobic and halotolerant taxa. Specifically, anoxia creates a habitat suitable for the proliferation of obligately anaerobic Archaeal methanogens. As a result, more persistent and expanded anoxic zones due to road salt runoff have the potential to increase hypolimnetic methane concentrations. If a portion of this methane is released to the atmosphere, it could be a currently uncharacterized contributor to atmospheric greenhouse gas emissions. This study examines two urban, eutrophic lakes with significant road salt influx and one rural, eutrophic lake with little road salt influx. All three lakes are located in southwest Michigan. Samples were taken from the water column at every meter at the deepest part of each lake, with a sample from the sediment-water interface, in May, August, and November 2016 and February 2017. The V4 and V5 hypervariable regions of the 16S rRNA gene in Bacteria and Archaea were amplified and sequenced using an Illumina MiSeq approach. Abundance of the mcrA gene, a marker for Archaeal methyl coenzyme A reductase, was quantified using qPCR. Water column methane levels, sediment methane production, water surface methane flux and a suite of supporting geochemical parameters were measured to determine changes in redox stratification in each lake and across seasons. Results indicate significant changes in the 16S rRNA-based community associated with depth, season, salinity and lake. Cyanobacteria, Actinobacteria, and Proteobacteria were among the phyla with the highest overall relative abundance. Sediment samples had more copies of the mcrA gene than the water column samples. In most

  6. Enriched ammonia-tolerant methanogenic cultures as bioaugmentation inocula in continuous biomethanation processes

    DEFF Research Database (Denmark)

    Fotidis, Ioannis; Treu, Laura; Angelidaki, Irini

    2017-01-01

    reactor (CSTR), resulted in up to 90% recovery of the methane production compared to the uninhibited production. However, cultivation of pure strains has practical difficulties due to the need of special growth media and sterile conditions. In contrast, acclimatized enriched cultures have minor sterility...... requirements. In the current study, an enriched ammonia-tolerant methanogenic culture was bioaugmented in a CSTR reactor operating under ammonia-induced, inhibited-steady-state. The results demonstrated that bioaugmentation, completely counteracted the ammonia toxicity effect. This indicates that a commercial...

  7. Methanol induces low temperature resilient methanogens and improves methane generation from domestic wastewater at low to moderate temperatures.

    Science.gov (United States)

    Saha, Shaswati; Badhe, Neha; De Vrieze, Jo; Biswas, Rima; Nandy, Tapas

    2015-01-01

    Low temperature (methanol is a preferred substrate by methanogens in cold habitats. The study hypothesizes that methanol can induce the growth of low-temperature resilient, methanol utilizing, hydrogenotrophs in UASB reactor. The hypothesis was tested in field conditions to evaluate the impact of seasonal temperature variations on methane yield in the presence and absence of methanol. Results show that 0.04% (v/v) methanol increased methane up to 15 times and its effect was more pronounced at lower temperatures. The qPCR analysis showed the presence of Methanobacteriales along with Methanosetaceae in large numbers. This indicates methanol induced the growth of both the hydrogenotrophic and acetoclastic groups through direct and indirect routes, respectively. This study thus demonstrated that methanol can impart resistance in methanogenic biomass to low temperature and can improve performance of UASB reactor. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Shifts in the microbial community composition of Gulf Coast beaches following beach oiling.

    Directory of Open Access Journals (Sweden)

    Ryan J Newton

    Full Text Available Microorganisms associated with coastal sands serve as a natural biofilter, providing essential nutrient recycling in nearshore environments and acting to maintain coastal ecosystem health. Anthropogenic stressors often impact these ecosystems, but little is known about whether these disturbances can be identified through microbial community change. The blowout of the Macondo Prospect reservoir on April 20, 2010, which released oil hydrocarbons into the Gulf of Mexico, presented an opportunity to examine whether microbial community composition might provide a sensitive measure of ecosystem disturbance. Samples were collected on four occasions, beginning in mid-June, during initial beach oiling, until mid-November from surface sand and surf zone waters at seven beaches stretching from Bay St. Louis, MS to St. George Island, FL USA. Oil hydrocarbon measurements and NOAA shoreline assessments indicated little to no impact on the two most eastern beaches (controls. Sequence comparisons of bacterial ribosomal RNA gene hypervariable regions isolated from beach sands located to the east and west of Mobile Bay in Alabama demonstrated that regional drivers account for markedly different bacterial communities. Individual beaches had unique community signatures that persisted over time and exhibited spatial relationships, where community similarity decreased as horizontal distance between samples increased from one to hundreds of meters. In contrast, sequence analyses detected larger temporal and less spatial variation among the water samples. Superimposed upon these beach community distance and time relationships, was increased variability in bacterial community composition from oil hydrocarbon contaminated sands. The increased variability was observed among the core, resident, and transient community members, indicating the occurrence of community-wide impacts rather than solely an overprinting of oil hydrocarbon-degrading bacteria onto otherwise

  9. Local environment rather than past climate determines community composition of mountain stream macroinvertebrates across Europe.

    Science.gov (United States)

    Múrria, Cesc; Bonada, Núria; Vellend, Mark; Zamora-Muñoz, Carmen; Alba-Tercedor, Javier; Sainz-Cantero, Carmen Elisa; Garrido, Josefina; Acosta, Raul; El Alami, Majida; Barquín, Jose; Derka, Tomáš; Álvarez-Cabria, Mario; Sáinz-Bariain, Marta; Filipe, Ana F; Vogler, Alfried P

    2017-11-01

    Community assembly is determined by a combination of historical events and contemporary processes that are difficult to disentangle, but eco-evolutionary mechanisms may be uncovered by the joint analysis of species and genetic diversity across multiple sites. Mountain streams across Europe harbour highly diverse macroinvertebrate communities whose composition and turnover (replacement of taxa) among sites and regions remain poorly known. We studied whole-community biodiversity within and among six mountain regions along a latitudinal transect from Morocco to Scandinavia at three levels of taxonomic hierarchy: genus, species and haplotypes. Using DNA barcoding of four insect families (>3100 individuals, 118 species) across 62 streams, we found that measures of local and regional diversity and intraregional turnover generally declined slightly towards northern latitudes. However, at all hierarchical levels we found complete (haplotype) or high (species, genus) turnover among regions (and even among sites within regions), which counters the expectations of Pleistocene postglacial northward expansion from southern refugia. Species distributions were mostly correlated with environmental conditions, suggesting a strong role of lineage- or species-specific traits in determining local and latitudinal community composition, lineage diversification and phylogenetic community structure (e.g., loss of Coleoptera, but not Ephemeroptera, at northern sites). High intraspecific genetic structure within regions, even in northernmost sites, reflects species-specific dispersal and demographic histories and indicates postglacial migration from geographically scattered refugia, rather than from only southern areas. Overall, patterns were not strongly concordant across hierarchical levels, but consistent with the overriding influence of environmental factors determining community composition at the species and genus levels. © 2017 John Wiley & Sons Ltd.

  10. Impact of different antibiotics on methane production using waste-activated sludge: mechanisms and microbial community dynamics.

    Science.gov (United States)

    Mustapha, Nurul Asyifah; Sakai, Kenji; Shirai, Yoshihito; Maeda, Toshinari

    2016-11-01

    Anaerobic digestion is an effective method for reducing the by-product of waste-activated sludge (WAS) from wastewater treatment plants and for producing bioenergy from WAS. However, only a limited number of studies have attempted to improve anaerobic digestion by targeting the microbial interactions in WAS. In this study, we examined whether different antibiotics positively, negatively, or neutrally influence methane fermentation by evaluating changes in the microbial community and functions in WAS. Addition of azithromycin promoted the microbial communities related to the acidogenic and acetogenic stages, and a high concentration of soluble proteins and a high activity of methanogens were detected. Chloramphenicol inhibited methane production but did not affect the bacteria that contribute to the hydrolysis, acidogenesis, and acetogenesis digestion stages. The addition of kanamycin, which exhibits the same methane productivity as a control (antibiotic-free WAS), did not affect all of the microbial communities during anaerobic digestion. This study demonstrates the simultaneous functions and interactions of diverse bacteria and methanogenic Archaea in different stages of the anaerobic digestion of WAS. The ratio of Caldilinea, Methanosarcina, and Clostridium may correspond closely to the trend of methane production in each antibiotic. The changes in microbial activities and function by antibiotics facilitate a better understanding of bioenergy production.

  11. Distribution of Archaeal Communities along the Coast of the Gulf of Finland and Their Response to Oil Contamination

    Science.gov (United States)

    Yan, Lijuan; Yu, Dan; Hui, Nan; Naanuri, Eve; Viggor, Signe; Gafarov, Arslan; Sokolov, Sergei L.; Heinaru, Ain; Romantschuk, Martin

    2018-01-01

    The Baltic Sea is vulnerable to environmental changes. With the increasing shipping activities, the risk of oil spills remains high. Archaea are widely distributed in many environments. However, the distribution and the response of archaeal communities to oil contamination have rarely been investigated in brackish habitats. Hence, we conducted a survey to investigate the distribution, diversity, composition, and species interactions of indigenous archaeal communities at oil-contaminated sites along the coast of the Gulf of Finland (GoF) using high-throughput sequencing. Surface water and littoral sediment samples were collected at presumably oil-contaminated (oil distribution facilities) and clean sites along the coastline of the GoF in the winter 2015 and the summer 2016. Another three samples of open sea surface water were taken as offshore references. Of Archaea, Euryarchaeota dominated in the surface water and the littoral sediment of the coast of the GoF, followed by Crenarchaeota (including Thaumarchaeota, Thermoprotei, and Korarchaeota based on the Greengenes database used). The unclassified sequences accounted for 5.62% of the total archaeal sequences. Our study revealed a strong dependence of the archaeal community composition on environmental variables (e.g., salinity, pH, oil concentration, TOM, electrical conductivity, and total DNA concentration) in both littoral sediment and coastal water in the GoF. The composition of archaeal communities was season and ecosystem dependent. Archaea was highly diverse in the three ecosystems (littoral sediment, coastal water, and open sea water). Littoral sediment harbored the highest diversity of archaea. Oil was often detected in the littoral sediment but rarely detected in water at those presumably contaminated sites. Although the composition of archaeal community in the littoral sediment was sensitive to low-input oil contamination, the unchanged putative functional profiles and increased interconnectivity of the

  12. Microbial diversity and dynamics during methane production from municipal solid waste

    Energy Technology Data Exchange (ETDEWEB)

    Bareither, Christopher A., E-mail: christopher.bareither@colostate.edu [Civil and Environmental Engineering, Colorado State University, Ft. Collins, CO 80532 (United States); Geological Engineering, University of Wisconsin-Madison, Madison, WI 53706 (United States); Wolfe, Georgia L., E-mail: gwolfe@wisc.edu [Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 (United States); McMahon, Katherine D., E-mail: tmcmahon@engr.wisc.edu [Bacteriology, Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI 53706 (United States); Benson, Craig H., E-mail: chbenson@wisc.edu [Civil and Environmental Engineering, Geological Engineering, University of Wisconsin-Madison, Madison, WI 53706 (United States)

    2013-10-15

    Highlights: ► Similar bacterial communities developed following different start-up operation. ► Total methanogens in leachate during the decelerated methane phase reflected overall methane yield. ► Created correlations between methanogens, methane yield, and available substrate. ► Predominant bacteria identified with syntrophic polysaccharide degraders. ► Hydrogenotrophic methanogens were dominant in the methane generation process. - Abstract: The objectives of this study were to characterize development of bacterial and archaeal populations during biodegradation of municipal solid waste (MSW) and to link specific methanogens to methane generation. Experiments were conducted in three 0.61-m-diameter by 0.90-m-tall laboratory reactors to simulate MSW bioreactor landfills. Pyrosequencing of 16S rRNA genes was used to characterize microbial communities in both leachate and solid waste. Microbial assemblages in effluent leachate were similar between reactors during peak methane generation. Specific groups within the Bacteroidetes and Thermatogae phyla were present in all samples and were particularly abundant during peak methane generation. Microbial communities were not similar in leachate and solid fractions assayed at the end of reactor operation; solid waste contained a more abundant bacterial community of cellulose-degrading organisms (e.g., Firmicutes). Specific methanogen populations were assessed using quantitative polymerase chain reaction. Methanomicrobiales, Methanosarcinaceae, and Methanobacteriales were the predominant methanogens in all reactors, with Methanomicrobiales consistently the most abundant. Methanogen growth phases coincided with accelerated methane production, and cumulative methane yield increased with increasing total methanogen abundance. The difference in methanogen populations and corresponding methane yield is attributed to different initial cellulose and hemicellulose contents of the MSW. Higher initial cellulose and

  13. Microbial diversity and dynamics during methane production from municipal solid waste

    International Nuclear Information System (INIS)

    Bareither, Christopher A.; Wolfe, Georgia L.; McMahon, Katherine D.; Benson, Craig H.

    2013-01-01

    Highlights: ► Similar bacterial communities developed following different start-up operation. ► Total methanogens in leachate during the decelerated methane phase reflected overall methane yield. ► Created correlations between methanogens, methane yield, and available substrate. ► Predominant bacteria identified with syntrophic polysaccharide degraders. ► Hydrogenotrophic methanogens were dominant in the methane generation process. - Abstract: The objectives of this study were to characterize development of bacterial and archaeal populations during biodegradation of municipal solid waste (MSW) and to link specific methanogens to methane generation. Experiments were conducted in three 0.61-m-diameter by 0.90-m-tall laboratory reactors to simulate MSW bioreactor landfills. Pyrosequencing of 16S rRNA genes was used to characterize microbial communities in both leachate and solid waste. Microbial assemblages in effluent leachate were similar between reactors during peak methane generation. Specific groups within the Bacteroidetes and Thermatogae phyla were present in all samples and were particularly abundant during peak methane generation. Microbial communities were not similar in leachate and solid fractions assayed at the end of reactor operation; solid waste contained a more abundant bacterial community of cellulose-degrading organisms (e.g., Firmicutes). Specific methanogen populations were assessed using quantitative polymerase chain reaction. Methanomicrobiales, Methanosarcinaceae, and Methanobacteriales were the predominant methanogens in all reactors, with Methanomicrobiales consistently the most abundant. Methanogen growth phases coincided with accelerated methane production, and cumulative methane yield increased with increasing total methanogen abundance. The difference in methanogen populations and corresponding methane yield is attributed to different initial cellulose and hemicellulose contents of the MSW. Higher initial cellulose and

  14. Stable acetate production in extreme-thermophilic (70ºC) mixed culture fermentation by selective enrichment of hydrogenotrophic methanogens

    NARCIS (Netherlands)

    Zhang, F.; Zhang, Y.; Ding, J.; Dai, K.; Van Loosdrecht, M.C.M.; Zeng, R.J.

    2014-01-01

    The control of metabolite production is difficult in mixed culture fermentation. This is particularly related to hydrogen inhibition. In this work, hydrogenotrophic methanogens were selectively enriched to reduce the hydrogen partial pressure and to realize efficient acetate production in

  15. Microbial community analysis of anaerobic reactors treating soft drink wastewater.

    Directory of Open Access Journals (Sweden)

    Takashi Narihiro

    Full Text Available The anaerobic packed-bed (AP and hybrid packed-bed (HP reactors containing methanogenic microbial consortia were applied to treat synthetic soft drink wastewater, which contains polyethylene glycol (PEG and fructose as the primary constituents. The AP and HP reactors achieved high COD removal efficiency (>95% after 80 and 33 days of the operation, respectively, and operated stably over 2 years. 16S rRNA gene pyrotag analyses on a total of 25 biofilm samples generated 98,057 reads, which were clustered into 2,882 operational taxonomic units (OTUs. Both AP and HP communities were predominated by Bacteroidetes, Chloroflexi, Firmicutes, and candidate phylum KSB3 that may degrade organic compound in wastewater treatment processes. Other OTUs related to uncharacterized Geobacter and Spirochaetes clades and candidate phylum GN04 were also detected at high abundance; however, their relationship to wastewater treatment has remained unclear. In particular, KSB3, GN04, Bacteroidetes, and Chloroflexi are consistently associated with the organic loading rate (OLR increase to 1.5 g COD/L-d. Interestingly, KSB3 and GN04 dramatically decrease in both reactors after further OLR increase to 2.0 g COD/L-d. These results indicate that OLR strongly influences microbial community composition. This suggests that specific uncultivated taxa may take central roles in COD removal from soft drink wastewater depending on OLR.

  16. The Effects of Disturbance History on Ground-Layer Plant Community Composition in British Columbia

    Directory of Open Access Journals (Sweden)

    Michael Ton

    2016-05-01

    Full Text Available Plant communities are sensitive to perturbations and may display alternative recovery pathways depending on disturbance history. In sub-boreal lodgepole pine forests of central interior British Columbia, Canada, fire and logging are two widespread landscape disturbances that overlap in many regions. We asked whether cumulative, short-interval disturbance from logging and fire resulted in different ground-layer plant communities than resulted from fire alone. Using field-collected data, we compared the taxonomic composition and functional traits of 3-year old plant communities that were either harvested 6-to-13 years prior, or not harvested prior to being burned in a large stand-replacing fire. The taxonomic composition diverged between the two treatments, driven primarily by differences in a few key indicator species such as Petasites frigidus and Vaccinium membranaceum. Analysis of individual species’ morphological traits indicated that only a few species vary in size in relation to disturbance history. Our data suggest that a history of forest harvest leaves a subtle footprint on post-fire ground-layer plant communities at early stages of succession.

  17. Assessment of Zooplankton Community Composition along a Depth Profile in the Central Red Sea

    KAUST Repository

    Pearman, John K.

    2015-07-17

    The composition of zooplankton in the water column has received limited attention in the main body of the Red Sea and this study investigates the change in the community both spatially and temporally across 11 stations in the central Red Sea. Using molecular methods to target the v9 region of the 18S rRNA gene a total of approximately 11.5 million reads were sequenced resulting in 2528 operational taxonomic units (OTUs) at 97% similarity. The phylum Arthropoda dominated in terms of reads accounting for on average 86.2% and 65.3% for neuston nets and vertical multinets respectively. A reduction in the number of OTUs was noticed with depth for both total metazoa and Maxillopoda whilst there was also a significant change in the composition of the Maxillopoda community. The genus Corycaeus had a higher proportion of reads in the epipelagic zone with Pleuromamma becoming increasingly dominant with depth. No significant difference was observed in the community between night and day sampling however there was a significant difference in the zooplankton community between two sampling periods separated by 10 days.

  18. Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere.

    Science.gov (United States)

    Knief, Claudia; Ramette, Alban; Frances, Lisa; Alonso-Blanco, Carlos; Vorholt, Julia A

    2010-06-01

    The plant phyllosphere constitutes a habitat for numerous microorganisms; among them are members of the genus Methylobacterium. Owing to the ubiquitous occurrence of methylobacteria on plant leaves, they represent a suitable target for studying plant colonization patterns. The influence of the factor site, host plant species, time and the presence of other phyllosphere bacteria on Methylobacterium community composition and population size were evaluated in this study. Leaf samples were collected from Arabidopsis thaliana or Medicago truncatula plants and from the surrounding plant species at several sites. The abundance of cultivable Methylobacterium clearly correlated with the abundance of other phyllosphere bacteria, suggesting that methylobacteria constitute a considerable and rather stable fraction of the phyllosphere microbiota under varying environmental conditions. Automated ribosomal intergenic spacer analysis (ARISA) was applied to characterize the Methylobacterium community composition and showed the presence of similar communities on A. thaliana plants at most sites in 2 consecutive years of sampling. A substantial part of the observed variation in the community composition was explained by site and plant species, especially in the case of the plants collected at the Arabidopsis sites (50%). The dominating ARISA peaks that were detected on A. thaliana plants were found on other plant species grown at the same site, whereas some different peaks were detected on A. thaliana plants from other sites. This indicates that site-specific factors had a stronger impact on the Methylobacterium community composition than did plant-specific factors and that the Methylobacterium-plant association is not highly host plant species specific.

  19. Defining microbial community composition and seasonal variation in a sewage treatment plant in India using a down-flow hanging sponge reactor.

    Science.gov (United States)

    Nomoto, Naoki; Hatamoto, Masashi; Hirakata, Yuga; Ali, Muntjeer; Jayaswal, Komal; Iguchi, Akinori; Okubo, Tsutomu; Takahashi, Masanobu; Kubota, Kengo; Tagawa, Tadashi; Uemura, Shigeki; Yamaguchi, Takashi; Harada, Hideki

    2018-05-01

    The characteristics of the microbial community in a practical-scale down-flow hanging sponge (DHS) reactor, high in organic matter and sulfate ion concentration, and the seasonal variation of the microbial community composition were investigated. Microorganisms related to sulfur oxidation and reduction (2-27%), as well as Leucobacter (7.50%), were abundant in the reactor. Anaerobic bacteria (27-38% in the first layer) were also in abundance and were found to contribute to the removal of organic matter from the sewage in the reactor. By comparing the Simpson index, the abundance-based coverage estimator (ACE) index, and the species composition of the microbial community across seasons (summer/dry, summer/rainy, autumn/dry, and winter/dry), the microbial community was found to change in composition only during the winter season. In addition to the estimation of seasonal variation, the difference in the microbial community composition along the axes of the DHS reactor was investigated for the first time. Although the abundance of each bacterial species differed along both axes of the reactor, the change of the community composition in the reactor was found to be greater along the vertical axis than the horizontal axis of the DHS reactor.

  20. Microbial Community Composition of Polyhydroxyalkanoate-Accumulating Organisms in Full-Scale Wastewater Treatment Plants Operated in Fully Aerobic Mode

    Science.gov (United States)

    Oshiki, Mamoru; Onuki, Motoharu; Satoh, Hiroyasu; Mino, Takashi

    2013-01-01

    The removal of biodegradable organic matter is one of the most important objectives in biological wastewater treatments. Polyhydroxyalkanoate (PHA)-accumulating organisms (PHAAOs) significantly contribute to the removal of biodegradable organic matter; however, their microbial community composition is mostly unknown. In the present study, the microbial community composition of PHAAOs was investigated at 8 full-scale wastewater treatment plants (WWTPs), operated in fully aerobic mode, by fluorescence in situ hybridization (FISH) analysis and post-FISH Nile blue A (NBA) staining techniques. Our results demonstrated that 1) PHAAOs were in the range of 11–18% in the total number of cells, and 2) the microbial community composition of PHAAOs was similar at the bacterial domain/phylum/class/order level among the 8 full-scale WWTPs, and dominant PHAAOs were members of the class Alphaproteobacteria and Betaproteobacteria. The microbial community composition of α- and β-proteobacterial PHAAOs was examined by 16S rRNA gene clone library analysis and further by applying a set of newly designed oligonucleotide probes targeting 16S rRNA gene sequences of α- or β-proteobacterial PHAAOs. The results demonstrated that the microbial community composition of PHAAOs differed in the class Alphaproteobacteria and Betaproteobacteria, which possibly resulted in a different PHA accumulation capacity among the WWTPs (8.5–38.2 mg-C g-VSS−1 h−1). The present study extended the knowledge of the microbial diversity of PHAAOs in full-scale WWTPs operated in fully aerobic mode. PMID:23257912

  1. Soil biochar amendment shapes the composition of N{sub 2}O-reducing microbial communities

    Energy Technology Data Exchange (ETDEWEB)

    Harter, Johannes; Weigold, Pascal [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); El-Hadidi, Mohamed; Huson, Daniel H. [Algorithms in Bioinformatics, Center for Bioinformatics, University of Tuebingen, Sand 14, 72076 Tuebingen (Germany); Kappler, Andreas [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); Behrens, Sebastian, E-mail: sbehrens@umn.edu [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Drive S.E., Minneapolis, MN 55455-0116 (United States); BioTechnology Institute, 140 Gortner Labs, 1479 Gortner Avenue, St. Paul, MN 55108-6106 (United States)

    2016-08-15

    Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N{sub 2}O) emissions. N{sub 2}O is a potent greenhouse gas. The main sources of N{sub 2}O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N{sub 2}O emission mitigation and the abundance and activity of N{sub 2}O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described ‘atypical’ nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N{sub 2}O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N{sub 2}O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N{sub 2}O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. - Highlights: • Biochar promoted anaerobic, alkalinity-adapted, and polymer-degrading microbial taxa. • Biochar fostered the development of distinct N{sub 2}O-reducing microbial taxa. • Taxonomic shifts among N{sub 2}O-reducing microbes