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Conrad R. Complexity of temperature dependence in methanogenic microbial environments. Front Microbiol 2023; 14:1232946. [PMID: 37485527 PMCID: PMC10359720 DOI: 10.3389/fmicb.2023.1232946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
There is virtually no environmental process that is not dependent on temperature. This includes the microbial processes that result in the production of CH4, an important greenhouse gas. Microbial CH4 production is the result of a combination of many different microorganisms and microbial processes, which together achieve the mineralization of organic matter to CO2 and CH4. Temperature dependence applies to each individual step and each individual microbe. This review will discuss the different aspects of temperature dependence including temperature affecting the kinetics and thermodynamics of the various microbial processes, affecting the pathways of organic matter degradation and CH4 production, and affecting the composition of the microbial communities involved. For example, it was found that increasing temperature results in a change of the methanogenic pathway with increasing contribution from mainly acetate to mainly H2/CO2 as immediate CH4 precursor, and with replacement of aceticlastic methanogenic archaea by thermophilic syntrophic acetate-oxidizing bacteria plus thermophilic hydrogenotrophic methanogenic archaea. This shift is consistent with reaction energetics, but it is not obligatory, since high temperature environments exist in which acetate is consumed by thermophilic aceticlastic archaea. Many studies have shown that CH4 production rates increase with temperature displaying a temperature optimum and a characteristic apparent activation energy (Ea). Interestingly, CH4 release from defined microbial cultures, from environmental samples and from wetland field sites all show similar Ea values around 100 kJ mol-1 indicating that CH4 production rates are limited by the methanogenic archaea rather than by hydrolysis of organic matter. Hence, the final rather than the initial step controls the methanogenic degradation of organic matter, which apparently is rarely in steady state.
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DePoy AN, King GM. Distribution and diversity of anaerobic thermophiles and putative anaerobic nickel-dependent carbon monoxide-oxidizing thermophiles in mesothermal soils and sediments. Front Microbiol 2023; 13:1096186. [PMID: 36699584 PMCID: PMC9868602 DOI: 10.3389/fmicb.2022.1096186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Even though thermophiles are best known from geothermal and other heated systems, numerous studies have demonstrated that they occur ubiquitously in mesothermal and permanently cold soils and sediments. Cultivation based studies of the latter have revealed that the thermophiles within them are mostly spore-forming members of the Firmicutes. Since the geographic distribution of spores is presumably unconstrained by transport through the atmosphere, similar communities (composition and diversity) of thermophiles might be expected to emerge in mesothermal habitats after they are heated. Alternatively, thermophiles might experience environmental selection before or after heating leading to divergent communities. After demonstrating the ubiquity of anaerobic thermophiles and CO uptake in a variety of mesothermal habitats and two hot springs, we used high throughput sequencing of 16S rRNA genes to assess the composition and diversity of populations that emerged after incubation at 60°C with or without headspace CO concentrations of 25%. Anaerobic Firmicutes dominated relative abundances at most sites but anaerobic thermophilic members of the Acidobacteria and Proteobacteria were also common. Nonetheless, compositions at the amplicon sequence variant (ASV) level varied among the sites with no convergence resulting from heating or CO addition as indicated by beta diversity analyses. The distinctions among thermophilic communities paralleled patterns observed for unheated "time zero" mesothermal soils and sediments. Occupancy analyses showed that the number of ASVs occupying each of n sites decreased unimodally with increasing n; no ASV occupied all 14 sites and only one each occupied 11 and 12 sites, while 69.3% of 1873 ASVs occupied just one site. Nonetheless, considerations of distances among the sites occupied by individual ASVs along with details of their distributions indicated that taxa were not dispersal limited but rather were constrained by environmental selection. This conclusion was supported by βMNTD and βNTI analyses, which showed dispersal limitation was only a minor contributor to taxon distributions.
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Wang S, Sun P, Liu J, Xu Y, Dolfing J, Wu Y. Distribution of methanogenic and methanotrophic consortia at soil-water interfaces in rice paddies across climate zones. iScience 2022; 26:105851. [PMID: 36636345 PMCID: PMC9829807 DOI: 10.1016/j.isci.2022.105851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Periphytic biofilms (PB) at the soil-water interface contributes 7-38% of the methane emission from rice paddies, yet the biogeographical mechanism underlying and affecting the process remain elusive. In this study, rice fields along an edapho-vclimatic gradient were sampled, and the environmental drivers affecting distribution of methanogenic and methanotrophic communities were evaluated. The methanogenic and methanotrophic communities at soil-water interface showed less complex inter/intra-generic interactions than those in soil, and their relative abundances were weakly driven by spatial distance, soil organic carbon, soil total nitrogen and pH. The nutrient supply and buffering capacity of extracellular polymeric substance released by PB reduced their interaction and enhanced the resilience on edaphic environment changes. Climate affected soil metal content, extracellular polymeric substance content, and thus the methane-related communities, and caused geographical variation in the impacts of PB on methane emissions from rice paddies. This study facilitates our understanding of geographical differences in the contribution of PB to methane emission.
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Affiliation(s)
- Sichu Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China,Institute of Agricultural Resources and Environment, Jiangsu Academy of Agriculture Sciences (JAAS), 50 Zhongling Road, Nanjing 210014, China,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People’s Republic of China, Shuitianba Zigui, Yichang 443605, China
| | - Pengfei Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People’s Republic of China, Shuitianba Zigui, Yichang 443605, China
| | - Junzhuo Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People’s Republic of China, Shuitianba Zigui, Yichang 443605, China
| | - Ying Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People’s Republic of China, Shuitianba Zigui, Yichang 443605, China
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle upon Tyne NE1 8QH, UK
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People’s Republic of China, Shuitianba Zigui, Yichang 443605, China,Corresponding author
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Blake LI, Sherry A, Mejeha OK, Leary P, Coombs H, Stone W, Head IM, Gray ND. An Unexpectedly Broad Thermal and Salinity-Tolerant Estuarine Methanogen Community. Microorganisms 2020; 8:microorganisms8101467. [PMID: 32987846 PMCID: PMC7600826 DOI: 10.3390/microorganisms8101467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/16/2020] [Accepted: 09/22/2020] [Indexed: 12/21/2022] Open
Abstract
Moderately thermophilic (Tmax, ~55 °C) methanogens are identified after extended enrichments from temperate, tropical and low-temperature environments. However, thermophilic methanogens with higher growth temperatures (Topt ≥ 60 °C) are only reported from high-temperature environments. A microcosm-based approach was used to measure the rate of methane production and methanogen community structure over a range of temperatures and salinities in sediment from a temperate estuary. We report short-term incubations (<48 h) revealing methanogens with optimal activity reaching 70 °C in a temperate estuary sediment (in situ temperature 4–5 °C). While 30 °C enrichments amended with acetate, H2 or methanol selected for corresponding mesophilic trophic groups, at 60 °C, only hydrogenotrophs (genus Methanothermobacter) were observed. Since these methanogens are not known to be active under in situ temperatures, we conclude constant dispersal from high temperature habitats. The likely provenance of the thermophilic methanogens was studied by enrichments covering a range of temperatures and salinities. These enrichments indicated that the estuarine sediment hosted methanogens encompassing the global activity envelope of most cultured species. We suggest that estuaries are fascinating sink and source environments for microbial function study.
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Affiliation(s)
- Lynsay I. Blake
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (A.S.); (O.K.M.); (P.L.); (H.C.); (I.M.H.)
- Department of Biosciences, Durham University, Lower Mount Joy, South Road, Durham DH1 3LE, UK
- Correspondence: (L.I.B.); (N.D.G.)
| | - Angela Sherry
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (A.S.); (O.K.M.); (P.L.); (H.C.); (I.M.H.)
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Obioma K. Mejeha
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (A.S.); (O.K.M.); (P.L.); (H.C.); (I.M.H.)
- Department of Microbiology, Federal University of Technology, Owerri P.M.B. 1526, Nigeria
| | - Peter Leary
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (A.S.); (O.K.M.); (P.L.); (H.C.); (I.M.H.)
| | - Henry Coombs
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (A.S.); (O.K.M.); (P.L.); (H.C.); (I.M.H.)
| | - Wendy Stone
- Water Institute and Department of Microbiology, University of Stellenbosch, Stellenbosch 7602, South Africa;
| | - Ian M. Head
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (A.S.); (O.K.M.); (P.L.); (H.C.); (I.M.H.)
| | - Neil D. Gray
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (A.S.); (O.K.M.); (P.L.); (H.C.); (I.M.H.)
- Correspondence: (L.I.B.); (N.D.G.)
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Gryta A, Frąc M. Methodological Aspects of Multiplex Terminal Restriction Fragment Length Polymorphism-Technique to Describe the Genetic Diversity of Soil Bacteria, Archaea and Fungi. SENSORS 2020; 20:s20113292. [PMID: 32527006 PMCID: PMC7309186 DOI: 10.3390/s20113292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/05/2020] [Accepted: 06/07/2020] [Indexed: 01/24/2023]
Abstract
The molecular fingerprinting methods used to evaluate soil microbial diversity could also be used as effective biosensors for the purposes of monitoring ecological soil status. The biodiversity of microorganisms is a relevant index of soil activity and there is a necessity to develop tools to generate reliable results for an emerging approach in the field of environmental control using microbial diversity biosensors. This work reports a method under development for determining soil microbial diversity using high efficiency Multiplex PCR-Terminal Restriction Fragment Length Polymorphism (M-T-RFLP) for the simultaneous detection of bacteria, archaea and fungi. Three different primer sets were used in the reaction and the analytical conditions were optimized. Optimal analytical conditions were achieved using 0.5 µM of primer for bacteria and 1 µM for archaea and fungi, 4 ng of soil DNA template, and HaeIII restriction enzyme. Comparative tests using the proposed analytical approach and a single analysis of each microorganism group were carried out to indicate that both genetic profiles were similar. The Jaccard similarity coefficient between single and multiplexing approach ranged from 0.773 to 0.850 for bacteria and fungi, and 0.208 to 0.905 for archaea. In conclusion, the multiplexing and pooling approaches significantly reduced the costs and time required to perform the analyses, while maintaining a proper effectiveness.
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Liu P, Klose M, Conrad R. Temperature-Dependent Network Modules of Soil Methanogenic Bacterial and Archaeal Communities. Front Microbiol 2019; 10:496. [PMID: 30915063 PMCID: PMC6422946 DOI: 10.3389/fmicb.2019.00496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/26/2019] [Indexed: 11/13/2022] Open
Abstract
Temperature is an important factor regulating the production of the greenhouse gas CH4. Structure and function of the methanogenic microbial communities are often drastically different upon incubation at 45°C versus 25°C or 35°C, but are also different in different soils. However, the extent of taxonomic redundancy within each functional group and the existence of different temperature-dependent microbial community network modules are unknown. Therefore, we investigated paddy soils from Italy and the Philippines and a desert soil from Utah (United States), which all expressed CH4 production upon flooding and exhibited structural and functional differences upon incubation at three different temperatures. We continued incubation of the pre-incubated soils (Liu et al., 2018) by changing the temperature in a factorial manner. We determined composition, abundance and function of the methanogenic archaeal and bacterial communities using HiSeq Illumina sequencing, qPCR and analysis of activity and stable isotope fractionation, respectively. Heatmap analysis of operational taxonomic units (OTU) from the different incubations gave detailed insights into the community structures and their putative functions. Network analysis showed that the microbial communities in the different soils were all organized within modules distinct for the three incubation temperatures. The diversity of Bacteria and Archaea was always lower at 45°C than at 25 or 35°C. A shift from 45°C to lower temperatures did not recover archaeal diversity, but nevertheless resulted in the establishment of structures and functions that were largely typical for soil at moderate temperatures. At 25 and 35°C and after shifting to one of these temperatures, CH4 was always produced by a combination of acetoclastic and hydrogenotrophic methanogenesis being consistent with the presence of acetoclastic (Methanosarcinaceae, Methanotrichaceae) and hydrogenotrophic (Methanobacteriales, Methanocellales, Methanosarcinaceae) methanogens. At 45°C, however, or after shifting from moderate temperatures to 45°C, only the Philippines soil maintained such combination, while the other soils were devoid of acetoclastic methanogens and consumed acetate instead by syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis. Syntrophic acetate oxidation was apparently achieved by Thermoanaerobacteraceae, which were especially abundant in Italian paddy soil and Utah desert soil when incubated at 45°C. Other bacterial taxa were also differently abundant at 45°C versus moderate temperatures, as seen by the formation of specific network modules. However, the archaeal OTUs with putative function in acetoclastic or hydrogenotrophic methanogenesis as well as the bacterial OTUs were usually not identical across the different soils and incubation conditions, and if they were, they suggested the existence of mesophilic and thermophilic ecotypes within the same OTUs. Overall, methanogenic function was determined by the bacterial and/or archaeal community structures, which in turn were to quite some extent determined by the incubation temperature, albeit largely individually in each soil. There was quite some functional redundancy as seen by different taxonomic community structures in the different soils and at the different temperatures.
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Affiliation(s)
- Pengfei Liu
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Melanie Klose
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Peng J, Wegner CE, Bei Q, Liu P, Liesack W. Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil. MICROBIOME 2018; 6:169. [PMID: 30231929 PMCID: PMC6147125 DOI: 10.1186/s40168-018-0546-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/31/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND The expected increase in global surface temperature due to climate change may have a tremendous effect on the structure and function of the anaerobic food web in flooded rice field soil. Here, we used the metatranscriptomic analysis of total RNA to gain a system-level understanding of this temperature effect on the methanogenic food web. RESULTS Mesophilic (30 °C) and thermophilic (45 °C) food web communities had a modular structure. Family-specific rRNA dynamics indicated that each network module represents a particular function within the food webs. Temperature had a differential effect on all the functional activities, including polymer hydrolysis, syntrophic oxidation of key intermediates, and methanogenesis. This was further evidenced by the temporal expression patterns of total bacterial and archaeal mRNA and of transcripts encoding carbohydrate-active enzymes (CAZymes). At 30 °C, various bacterial phyla contributed to polymer hydrolysis, with Firmicutes decreasing and non-Firmicutes (e.g., Bacteroidetes, Ignavibacteriae) increasing with incubation time. At 45 °C, CAZyme expression was solely dominated by the Firmicutes but, depending on polymer and incubation time, varied on family level. The structural and functional community dynamics corresponded well to process measurements (acetate, propionate, methane). At both temperatures, a major change in food web functionality was linked to the transition from the early to late stage. The mesophilic food web was characterized by gradual polymer breakdown that governed acetoclastic methanogenesis (Methanosarcinaceae) and, with polymer hydrolysis becoming the rate-limiting step, syntrophic propionate oxidation (Christensenellaceae, Peptococcaceae). The thermophilic food web had two activity stages characterized first by polymer hydrolysis and followed by syntrophic oxidation of acetate (Thermoanaerobacteraceae, Heliobacteriaceae, clade OPB54). Hydrogenotrophic Methanocellaceae were the syntrophic methanogen partner, but their population structure differed between the temperatures. Thermophilic temperature promoted proliferation of a new Methanocella ecotype. CONCLUSIONS Temperature had a differential effect on the structural and functional continuum in which the methanogenic food web operates. This temperature-induced change in food web functionality may not only be a near-future scenario for rice paddies but also for natural wetlands in the tropics and subtropics.
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Affiliation(s)
- Jingjing Peng
- Research Group Methanotrophic Bacteria and Environmental Genomics/Transcriptomics, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Carl-Eric Wegner
- Institute of Ecology, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Str. 159, 07749, Jena, Germany
| | - Qicheng Bei
- Research Group Methanotrophic Bacteria and Environmental Genomics/Transcriptomics, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Pengfei Liu
- Research Group Methanotrophic Bacteria and Environmental Genomics/Transcriptomics, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Werner Liesack
- Research Group Methanotrophic Bacteria and Environmental Genomics/Transcriptomics, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.
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Chapleur O, Mazeas L, Godon JJ, Bouchez T. Asymmetrical response of anaerobic digestion microbiota to temperature changes. Appl Microbiol Biotechnol 2015; 100:1445-1457. [DOI: 10.1007/s00253-015-7046-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/17/2015] [Accepted: 09/25/2015] [Indexed: 10/22/2022]
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Breidenbach B, Conrad R. Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage. Front Microbiol 2015; 5:752. [PMID: 25620960 PMCID: PMC4288041 DOI: 10.3389/fmicb.2014.00752] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/11/2014] [Indexed: 01/13/2023] Open
Abstract
We studied the resident (16S rDNA) and the active (16S rRNA) members of soil archaeal and bacterial communities during rice plant development by sampling three growth stages (vegetative, reproductive and maturity) under field conditions. Additionally, the microbial community was investigated in two non-flooded fields (unplanted, cultivated with upland maize) in order to monitor the reaction of the microbial communities to non-flooded, dry conditions. The abundance of Bacteria and Archaea was monitored by quantitative PCR showing an increase in 16S rDNA during reproductive stage and stable 16S rRNA copies throughout the growth season. Community profiling by T-RFLP indicated a relatively stable composition during rice plant growth whereas pyrosequencing revealed minor changes in relative abundance of a few bacterial groups. Comparison of the two non-flooded fields with flooded rice fields showed that the community composition of the Bacteria was slightly different, while that of the Archaea was almost the same. Only the relative abundance of Methanosarcinaceae and Soil Crenarchaeotic Group increased in non-flooded vs. flooded soil. The abundance of bacterial and archaeal 16S rDNA copies was highest in flooded rice fields, followed by non-flooded maize and unplanted fields. However, the abundance of ribosomal RNA (active microbes) was similar indicating maintenance of a high level of ribosomal RNA under the non-flooded conditions, which were unfavorable for anaerobic bacteria and methanogenic archaea. This maintenance possibly serves as preparedness for activity when conditions improve. In summary, the analyses showed that the bacterial and archaeal communities inhabiting Philippine rice field soil were relatively stable over the season but reacted upon change in field management.
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Affiliation(s)
| | - Ralf Conrad
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
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Martinez RJ, Wu CH, Beazley MJ, Andersen GL, Conrad ME, Hazen TC, Taillefert M, Sobecky PA. Microbial community responses to organophosphate substrate additions in contaminated subsurface sediments. PLoS One 2014; 9:e100383. [PMID: 24950228 PMCID: PMC4065101 DOI: 10.1371/journal.pone.0100383] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/27/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Radionuclide- and heavy metal-contaminated subsurface sediments remain a legacy of Cold War nuclear weapons research and recent nuclear power plant failures. Within such contaminated sediments, remediation activities are necessary to mitigate groundwater contamination. A promising approach makes use of extant microbial communities capable of hydrolyzing organophosphate substrates to promote mineralization of soluble contaminants within deep subsurface environments. METHODOLOGY/PRINCIPAL FINDINGS Uranium-contaminated sediments from the U.S. Department of Energy Oak Ridge Field Research Center (ORFRC) Area 2 site were used in slurry experiments to identify microbial communities involved in hydrolysis of 10 mM organophosphate amendments [i.e., glycerol-2-phosphate (G2P) or glycerol-3-phosphate (G3P)] in synthetic groundwater at pH 5.5 and pH 6.8. Following 36 day (G2P) and 20 day (G3P) amended treatments, maximum phosphate (PO4(3-)) concentrations of 4.8 mM and 8.9 mM were measured, respectively. Use of the PhyloChip 16S rRNA microarray identified 2,120 archaeal and bacterial taxa representing 46 phyla, 66 classes, 110 orders, and 186 families among all treatments. Measures of archaeal and bacterial richness were lowest under G2P (pH 5.5) treatments and greatest with G3P (pH 6.8) treatments. Members of the phyla Crenarchaeota, Euryarchaeota, Bacteroidetes, and Proteobacteria demonstrated the greatest enrichment in response to organophosphate amendments and the OTUs that increased in relative abundance by 2-fold or greater accounted for 9%-50% and 3%-17% of total detected Archaea and Bacteria, respectively. CONCLUSIONS/SIGNIFICANCE This work provided a characterization of the distinct ORFRC subsurface microbial communities that contributed to increased concentrations of extracellular phosphate via hydrolysis of organophosphate substrate amendments. Within subsurface environments that are not ideal for reductive precipitation of uranium, strategies that harness microbial phosphate metabolism to promote uranium phosphate precipitation could offer an alternative approach for in situ sequestration.
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Affiliation(s)
- Robert J. Martinez
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Cindy H. Wu
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Melanie J. Beazley
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Gary L. Andersen
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Mark E. Conrad
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Terry C. Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Martial Taillefert
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Patricia A. Sobecky
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, United States of America
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Biosynthetic Mechanism forL-Gulose in Main Polar Lipids ofThermoplasma acidophilumand Possible Resemblance to Plant Ascorbic Acid Biosynthesis. Biosci Biotechnol Biochem 2014; 77:2087-93. [DOI: 10.1271/bbb.130442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Molecular phylogenetic analysis of dominant microbial populations in aged refuse. World J Microbiol Biotechnol 2013; 30:1037-45. [DOI: 10.1007/s11274-013-1522-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
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Sims A, Gajaraj S, Hu Z. Nutrient removal and greenhouse gas emissions in duckweed treatment ponds. WATER RESEARCH 2013; 47:1390-8. [PMID: 23276427 DOI: 10.1016/j.watres.2012.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 11/10/2012] [Accepted: 12/06/2012] [Indexed: 05/24/2023]
Abstract
Stormwater treatment ponds provide a variety of functions including sediment retention, organic and nutrient removal, and habitat restoration. The treatment ponds are, however, also a source of greenhouse gases. The objectives of this study were to assess greenhouse gas (CH(4), CO(2) and N(2)O) emissions in duckweed treatment ponds (DWPs) treating simulated stormwater and to determine the role of ammonia-oxidizing organisms in nutrient removal and methanogens in greenhouse gas emissions. Two replicated DWPs operated at a hydraulic retention time (HRT) of 10 days were able to remove 84% (± 4% [standard deviation]) chemical oxygen demand (COD), 79% (± 3%) NH(4)(+)-N, 86% (± 2%) NO(3)(-)-N and 56% (± 7%) orthophosphate. CH(4) emission rates in the DWPs ranged from 502 to 1900 mg CH(4) m(-2) d(-1) while those of nitrous oxide (N(2)O) ranged from 0.63 to 4 mg N(2)O m(-2) d(-1). The CO(2) emission rates ranged from 1700 to 3300 mg CO(2) m(-2) day(-1). Duckweed coverage on water surface along with the continued deposit of duckweed debris in the DWPs and low-nutrient influent water created a low dissolved oxygen environment for the growth of unique ammonia-oxidizing organisms and methanogens. Archaeal and bacterial amoA abundance in the DWPs ranged from (1.5 ± 0.2) × 10(7) to (1.7 ± 0.2) × 10(8) copies/g dry soil and from (1.0 ± 0.3) × 10(3) to (1.5 ± 0.4) × 10(6) copies/g dry soil, respectively. The 16S rRNA acetoclastic and hydrogenotrophic methanogens ranged from (5.2 ± 0.2) × 10(5) to (9.0 ± 0.3) × 10(6) copies/g dry soil and from (1.0 ± 0.1) × 10(2) to (5.5 ± 0.4) × 10(3) copies/g dry soil, respectively. Ammonia-oxidizing archaea (AOA) appeared to be the dominant nitrifiers and acetoclastic Methanosaeta was the major methanogenic genus. The results suggest that methane is the predominant (>90%) greenhouse gas in the DWPs, where the relatively low stormwater nutrient inputs facilitate the growth of K-strategists such as AOA and Methanosaeta that may be responsible for ammonia removal and greenhouse gas emissions, respectively.
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Affiliation(s)
- Atreyee Sims
- Department of Civil and Environmental Engineering, University of Missouri, E2509 Lafferre Hall, Columbia, MO 65211, USA
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Tang YQ, Li Y, Zhao JY, Chi CQ, Huang LX, Dong HP, Wu XL. Microbial communities in long-term, water-flooded petroleum reservoirs with different in situ temperatures in the Huabei Oilfield, China. PLoS One 2012; 7:e33535. [PMID: 22432032 PMCID: PMC3303836 DOI: 10.1371/journal.pone.0033535] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Accepted: 02/10/2012] [Indexed: 11/19/2022] Open
Abstract
The distribution of microbial communities in the Menggulin (MGL) and Ba19 blocks in the Huabei Oilfield, China, were studied based on 16S rRNA gene analysis. The dominant microbes showed obvious block-specific characteristics, and the two blocks had substantially different bacterial and archaeal communities. In the moderate-temperature MGL block, the bacteria were mainly Epsilonproteobacteria and Alphaproteobacteria, and the archaea were methanogens belonging to Methanolinea, Methanothermobacter, Methanosaeta, and Methanocella. However, in the high-temperature Ba19 block, the predominant bacteria were Gammaproteobacteria, and the predominant archaea were Methanothermobacter and Methanosaeta. In spite of shared taxa in the blocks, differences among wells in the same block were obvious, especially for bacterial communities in the MGL block. Compared to the bacterial communities, the archaeal communities were much more conserved within blocks and were not affected by the variation in the bacterial communities.
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Affiliation(s)
- Yue-Qin Tang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Yan Li
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Jie-Yu Zhao
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Chang-Qiao Chi
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Li-Xin Huang
- Research Institute of Petroleum Exploration and Development (Langfang), China National Petroleum Corporation (CNPC), Beijing, People's Republic of China
| | - Han-Ping Dong
- Research Institute of Petroleum Exploration and Development (Langfang), China National Petroleum Corporation (CNPC), Beijing, People's Republic of China
| | - Xiao-Lei Wu
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
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Borrel G, Jézéquel D, Biderre-Petit C, Morel-Desrosiers N, Morel JP, Peyret P, Fonty G, Lehours AC. Production and consumption of methane in freshwater lake ecosystems. Res Microbiol 2011; 162:832-47. [DOI: 10.1016/j.resmic.2011.06.004] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 05/09/2011] [Indexed: 10/18/2022]
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Isolation and characterization of Methanothermobacter crinale sp. nov., a novel hydrogenotrophic methanogen from the Shengli oil field. Appl Environ Microbiol 2011; 77:5212-9. [PMID: 21705537 DOI: 10.1128/aem.00210-11] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Syntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis is an alternative methanogenic pathway in certain thermophilic anaerobic environments such as high-temperature oil reservoirs and thermophilic biogas reactors. In these environments, the dominant thermophilic methanogens were generally related to uncultured organisms of the genus Methanothermobacter. Here we isolated two representative strains, Tm2(T) and HMD, from the oil sands and oil production water in the Shengli oil field in the People's Republic of China. The type strain, Tm2(T), was nonmotile and stained Gram positive. The cells were straight to slightly curved rods (0.3 μm in width and 2.2 to 5.9 μm in length), but some of them possessed a coccal shape connecting with the rods at the ends. Strain Tm2(T) grew with H(2)-CO(2), but acetate is required. Optimum growth of strain Tm2(T) occurred in the presence of 0.025 g/liter NaCl at pH 6.9 and a temperature of 65°C. The G+C content of the genomic DNA was 40.1 mol% ± 1.3 mol% (by the thermal denaturation method) or 41.1 mol% (by high-performance liquid chromatography). Analysis of the 16S rRNA gene sequence indicated that Tm2(T) was most closely related to Methanothermobacter thermautotrophicus ΔH(T) and Methanothermobacter wolfeii VKM B-1829(T) (both with a sequence similarity of 96.4%). Based on these phenotypic and phylogenic characteristics, a novel species was proposed and named Methanothermobacter crinale sp. nov. The type strain is Tm2(T) (ACCC 00699(T) = JCM 17393(T)).
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Rui J, Qiu Q, Lu Y. Syntrophic acetate oxidation under thermophilic methanogenic condition in Chinese paddy field soil. FEMS Microbiol Ecol 2011; 77:264-73. [PMID: 21470253 DOI: 10.1111/j.1574-6941.2011.01104.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The aim of the present work was to determine and compare the degradation of acetate in a Chinese rice field soil at 25°C and 50°C, respectively, and to identify specifically the active organisms involved in syntrophic acetate oxidation. Soil was preincubated anaerobically for 30 days to reduce alternative electron acceptors other than CO(2). The [2-(13)C] acetate (99% (13)C) was added twice: 0 day and 19 days after preincubation. Addition of [2-(13)C] acetate resulted in an immediate increase of (13)C labeled CH(4) but non-labeling of CO(2) at 25°C. The methanogen community was dominated by Methanosarcinaceae and Methanocellales at 25°C. In contrast, the addition of [2-(13)C] acetate at 50°C resulted in a rapid increase of (13)CO(2). The (13)C labeling of CH(4) gradually increased and reached a similar value to CO(2) (13% (13)C) at the end of incubation (40 days). Nearly all archaeal 16S rRNA genes detected at 50°C belonged to hydrogenotrophic Methanocellales. DNA-based stable isotope probing analysis revealed that the organisms related to Thermacetogenium lineage and the unclassified Thermoanaerobacteraceae group were intensively labeled with (13)C in the incubations at 50°C. Thus, acetate was converted to CH(4) and CO(2) through aceticlastic methanogenesis at 25°C, while syntrophic acetate oxidation occurred at 50°C.
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Affiliation(s)
- Junpeng Rui
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
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18
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Chemolithotrophic acetogenic H2/CO2 utilization in Italian rice field soil. ISME JOURNAL 2011; 5:1526-39. [PMID: 21368906 DOI: 10.1038/ismej.2011.17] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Acetate oxidation in Italian rice field at 50 °C is achieved by uncultured syntrophic acetate oxidizers. As these bacteria are closely related to acetogens, they may potentially also be able to synthesize acetate chemolithoautotrophically. Labeling studies using exogenous H(2) (80%) and (13)CO(2) (20%), indeed demonstrated production of acetate as almost exclusive primary product not only at 50 °C but also at 15 °C. Small amounts of formate, propionate and butyrate were also produced from (13)CO(2). At 50 °C, acetate was first produced but later on consumed with formation of CH(4). Acetate was also produced in the absence of exogenous H(2) albeit to lower concentrations. The acetogenic bacteria and methanogenic archaea were targeted by stable isotope probing of ribosomal RNA (rRNA). Using quantitative PCR, (13)C-labeled bacterial rRNA was detected after 20 days of incubation with (13)CO(2). In the heavy fractions at 15 °C, terminal restriction fragment length polymorphism, cloning and sequencing of 16S rRNA showed that Clostridium cluster I and uncultured Peptococcaceae assimilated (13)CO(2) in the presence and absence of exogenous H(2), respectively. A similar experiment showed that Thermoanaerobacteriaceae and Acidobacteriaceae were dominant in the (13)C treatment at 50 °C. Assimilation of (13)CO(2) into archaeal rRNA was detected at 15 °C and 50 °C, mostly into Methanocellales, Methanobacteriales and rice cluster III. Acetoclastic methanogenic archaea were not detected. The above results showed the potential for acetogenesis in the presence and absence of exogenous H(2) at both 15 °C and 50 °C. However, syntrophic acetate oxidizers seemed to be only active at 50 °C, while other bacterial groups were active at 15 °C.
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Yashiro Y, Sakai S, Ehara M, Miyazaki M, Yamaguchi T, Imachi H. Methanoregula formicica sp. nov., a methane-producing archaeon isolated from methanogenic sludge. Int J Syst Evol Microbiol 2011; 61:53-59. [DOI: 10.1099/ijs.0.014811-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel methane-producing archaeon, strain SMSPT, was isolated from an anaerobic, propionate-degrading enrichment culture that was originally obtained from granular sludge in a mesophilic upflow anaerobic sludge blanket (UASB) reactor used to treat a beer brewery effluent. Cells were non-motile, blunt-ended, straight rods, 1.0–2.6 μm long by 0.5 μm wide; cells were sometimes up to 7 μm long. Asymmetrical cell division was observed in rod-shaped cells. Coccoid cells (0.5–1.0 μm in diameter) were also observed in mid- to late-exponential phase cultures. Growth was observed between 10 and 40 °C (optimum, 30–33 °C) and pH 7.0 and 7.6 (optimum, pH 7.4). The G+C content of the genomic DNA was 56.2 mol%. The strain utilized formate and hydrogen for growth and methane production. Based on comparative sequence analyses of the 16S rRNA and mcrA (encoding the alpha subunit of methyl-coenzyme M reductase, a key enzyme in the methane-producing pathway) genes, strain SMSPT was affiliated with group E1/E2 within the order Methanomicrobiales. The closest relative based on both 16S rRNA and mcrA gene sequences was Methanoregula boonei 6A8T (96.3 % 16S rRNA gene sequence similarity, 85.4 % deduced McrA amino acid sequence similarity). The percentage of 16S rRNA gene sequence similarity indicates that strain SMSPT and Methanoregula boonei 6A8T represent different species within the same genus. This is supported by our findings of shared phenotypic properties, including cell morphology and growth temperature range, and phenotypic differences in substrate usage and pH range. Based on these genetic and phenotypic properties, we propose that strain SMSPT represents a novel species of the genus Methanoregula, for which we propose the name Methanoregula formicica sp. nov., with the type strain SMSPT (=NBRC 105244T =DSM 22288T).
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Affiliation(s)
- Yuto Yashiro
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
- Subsurface Geobiology Advanced Research (SUGAR) Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Sanae Sakai
- Subsurface Geobiology Advanced Research (SUGAR) Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Masayuki Ehara
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
- Subsurface Geobiology Advanced Research (SUGAR) Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Masayuki Miyazaki
- Subsurface Geobiology Advanced Research (SUGAR) Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Takashi Yamaguchi
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Hiroyuki Imachi
- Subsurface Geobiology Advanced Research (SUGAR) Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
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20
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Yu S, Li S, Tang Y, Wu X. Succession of bacterial community along with the removal of heavy crude oil pollutants by multiple biostimulation treatments in the Yellow River Delta, China. J Environ Sci (China) 2011; 23:1533-1543. [PMID: 22432291 DOI: 10.1016/s1001-0742(10)60585-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Multiple biostimulation treatments were applied to enhance the removal of heavy crude oil pollutants in the saline soil of Yellow River Delta. Changes of the soil bacterial community were monitored using the terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses. The 140-day microcosm experiments showed that low C:N:P ratio, high availability of surfactant and addition of bulking agent significantly enhanced the performance, leading to the highest total petroleum hydrocarbon removal. Meanwhile, the bacterial community was remarkably changed by the multiple biostimulation treatments, with the Deltaproteobacteria, Firmicutes, Actinobacteria, Acidobacteria and Planctomycetes being inhibited and the Alpha- and Beta-proteobacteria and some unknown Gammaproteobacteria bacteria being enriched. In addition, different hydrocarbon-degraders came to power in the following turn. At the first stage, the Alcanivorax-related Gammaproteobacteria bacteria dominated in the biostimulated soil and contributed mainly to the biodegradation of easily degradable portion of the heavy crude oil. Then the bacteria belonging to Alphaproteobacteria, followed by bacteria belonging to Candidate division OD1, became the dominant oil-degraders to degrade the remaining recalcitrant constituents of the heavy crude oil.
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Affiliation(s)
- Sulin Yu
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, China.
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21
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Belila A, Ghrabi A, Hassen A. Molecular analysis of the spatial distribution of sulfate-reducing bacteria in three eutrophicated wastewater stabilization ponds. ANN MICROBIOL 2010. [DOI: 10.1007/s13213-010-0174-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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22
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Liu F, Conrad R. Thermoanaerobacteriaceae oxidize acetate in methanogenic rice field soil at 50°C. Environ Microbiol 2010; 12:2341-54. [PMID: 21966924 DOI: 10.1111/j.1462-2920.2010.02289.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rice field soils contain a thermophilic microbial community. Incubation of Italian rice field soil at 50°C resulted in transient accumulation of acetate, but the microorganisms responsible for methane production from acetate are unknown. Without addition of exogenous acetate, the δ(13)C of CH(4) and CO(2) indicated that CH(4) was exclusively produced by hydrogenotrophic methanogenesis. When exogenous acetate was added, acetoclastic methanogenesis apparently also operated. Nevertheless, addition of [2-(13)C]acetate (99% (13)C) resulted in the production not only of (13)C-labelled CH(4) but also of CO(2), which contained up to 27% (13)C, demonstrating that the methyl group of acetate was also oxidized. Part of the (13)C-labelled acetate was also converted to propionate which contained up to 14% (13)C. The microorganisms capable of assimilating acetate at 50°C were targeted by stable isotope probing (SIP) of ribosomal RNA and rRNA genes using [U-(13)C] acetate. Using quantitative PCR, (13)C-labelled bacterial ribosomal RNA and DNA was detected after 21 and 32 days of incubation with [U-(13)C]acetate respectively. In the heavy fractions of the (13)C treatment, terminal restriction fragments (T-RFs) of 140, 120 and 171 bp length predominated. Cloning and sequencing of 16S rRNA showed that these T-RFs were affiliated with the bacterial genera Thermacetogenium and Symbiobacterium and with members of the Thermoanaerobacteriaceae. Similar experiments targeting archaeal RNA and DNA showed that Methanocellales were the dominant methanogens being consistent with the operation of syntrophic bacterial acetate oxidation coupled to hydrogenotrophic methanogenesis. After 17 days, however, Methanosarcinacea increasingly contributed to the synthesis of rRNA from [U-(13)C]acetate indicating that acetoclastic methanogens were also active in methanogenic Italian rice field soil under thermal conditions.
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Affiliation(s)
- Fanghua Liu
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str.10, 35043 Marburg, Germany
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23
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Yu SL, Tang YQ, Li Y, Zhang H, Wu XL. Gradient decrement of annealing time can improve PCR with fluorescent-labeled primers. J Biosci Bioeng 2010; 110:500-4. [PMID: 20646958 DOI: 10.1016/j.jbiosc.2010.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Revised: 05/08/2010] [Accepted: 05/12/2010] [Indexed: 10/19/2022]
Abstract
The influences of fluorescence labeling on PCR amplification and T-RFLP analysis were examined by the analyses of a soil bacterial and archaeal community using both clone library and T-RFLP methods. The PCR amplification and microbial community structure patterns were compared among the primers labeled with and without fluorescent groups. PCR amplification was negatively affected by the labeling groups of the primers, which may be caused by the increment of primer molecular weight. It is known that thermodynamic movement of molecules will be slowed as molecular weight increased. Therefore it is understandable that the reaction of primer-DNA template hybridization will be inhibited with the fluorescent groups added to the primer(s). An effective "Gradient-Decreasing Annealing Time Program," in which the annealing time was initially set long and reduced cycle by cycle, can improve PCR efficiency under comparable amplification specificity with the fluorescent-labeled primers. No significant negative impact was observed in the altered conditions.
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Affiliation(s)
- Su-Lin Yu
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, China
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Noll M, Klose M, Conrad R. Effect of temperature change on the composition of the bacterial and archaeal community potentially involved in the turnover of acetate and propionate in methanogenic rice field soil. FEMS Microbiol Ecol 2010; 73:215-25. [PMID: 20491920 DOI: 10.1111/j.1574-6941.2010.00883.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The microbial community structure was investigated together with the path of methane production in Italian rice field soil incubated at moderate (35 degrees C) and high (45 degrees C) temperature using terminal restriction fragment length polymorphism and stable isotope fractionation. The structure of both the archaeal and bacterial communities differed at 35 degrees C compared with 45 degrees C, and acetoclastic and hydrogenotrophic methanogenesis dominated, respectively. Changing the incubation of the 45 degrees C soil to different temperatures (25, 30, 35, 40, 45, 50 degrees C) resulted in a dynamic change of both microbial community structure and stable isotope fractionation. In all treatments, acetate first accumulated and then decreased. Propionate was also transiently produced and consumed. It is noteworthy that acetate was also consumed at thermophilic conditions, although archaeal community composition and stable isotope fractionation indicated that acetoclastic methanogenesis did not operate. Instead, acetate must have been consumed by syntrophic acetate oxidizers. The transient accumulation and subsequent consumption of acetate at thermophilic conditions was specifically paralleled by terminal restriction fragments characteristic for clostridial cluster I, whereas those of clostridial clusters I and III, Acidaminococcaceae and Heliobacteraceae, paralleled the thermophilic turnover of both acetate and propionate.
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Affiliation(s)
- Matthias Noll
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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25
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Yuan Y, Conrad R, Lu Y. Responses of methanogenic archaeal community to oxygen exposure in rice field soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:347-354. [PMID: 23765886 DOI: 10.1111/j.1758-2229.2009.00036.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Methanogens are regarded as strict anaerobes and hence sensitive to O2 exposure. It has been demonstrated that CH4 production and emission from rice field soil are substantially reduced when soil is drained or aerated even shortly. However, the response of different methanogenic populations to O2 stress remains unclear. Therefore, we determined CH4 production and structure of the methanogenic community in a Chinese rice field soil after short-term (24 h) and long-term (72 h) exposure to O2 under laboratory conditions. O2 stress strongly inhibited CH4 production, and the inhibitory effect increased with the duration of O2 exposure. O2 exposure also resulted in dramatic increase of ferric iron and sulfate concentrations. H2 partial pressures were significantly reduced, most probably due to the competitive consumption by iron and sulfate-reducing bacteria. However, substrate competition could not explain the inhibition of acetoclastic methanogenesis, since acetate accumulated after O2 exposure compared with the control. Quantitative (real-time) PCR analyses of both archaeal 16S rRNA and mcrA genes (coding for alpha subunit of the methyl coenzyme M reductase) revealed that growth of the methanogenic populations was suppressed after O2 exposure. However, terminal restriction fragment length polymorphism (T-RFLP) analyses of both 16S rDNA and 16S rRNA showed that the structure of the methanogenic archaeal community remained remarkably stable, and that acetoclastic Methanosarcinaceae were always dominant whether with or without O2 exposure. Thus, O2 stress apparently did not differentially affect the various methanogenic populations, but instead inhibited CH4 production by enabling competition, generally suppressing growth and differentially affecting existing enzyme activity.
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Affiliation(s)
- Yanli Yuan
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China. Max-Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str, 35043 Marburg, Germany
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Yuan Q, Lu Y. Response of methanogenic archaeal community to nitrate addition in rice field soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:362-369. [PMID: 23765888 DOI: 10.1111/j.1758-2229.2009.00065.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Addition of nitrate strongly inhibits CH4 production from anoxic soil. The main mechanisms were considered to be the substrate competition and the toxic effect of denitrification intermediates on the methanogenesis. However, it is unclear whether these inhibitory effects are reflected in the structure and dynamics of methanogenic community in the soil. In the present study, the response of methanogenic archaeal community to nitrate addition was determined using terminal restriction fragment length polymorphisms in combination with cloning and sequencing of archaeal 16S rRNA genes. When nitrate was added at the beginning of an anoxic incubation of rice field soil, denitrification occurred rapidly and the denitrification intermediates were detected only for a short time. Total production of CH4 was reduced, but no obvious effect on the structure of methanogenic community was observed. In contrast, when nitrate was added 20 days after the anoxic incubation, the denitrification intermediates obviously accumulated. CH4 production was completely suppressed for 7 and 16 days from treatments of 5 and 10 mM nitrate respectively. The dynamics of methanogenic community also diverged greatly from the control. While the hydrogenotrophic methanogens increased and the acetoclastic methanogens decreased with the incubation in the control soil, the structure and abundance of the methanogenic community remained unchanged after the addition of nitrate. Methanogenesis resumed when the denitrification intermediates were depleted in soil. The analysis of carbon isotopic signals revealed that hydrogenotrophic methanogenesis recovered faster than acetoclastic methanogenesis. Our study suggests that the accumulation of denitrification intermediates has a strong inhibitory effect on the activity but not the structure of methanogenic community.
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Affiliation(s)
- Quan Yuan
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
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27
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Conrad R, Klose M, Noll M. Functional and structural response of the methanogenic microbial community in rice field soil to temperature change. Environ Microbiol 2009; 11:1844-53. [PMID: 19508556 DOI: 10.1111/j.1462-2920.2009.01909.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microbial community in anoxic rice field soil produces CH(4) over a wide temperature range up to 55°C. However, at temperatures higher than about 40°C, the methanogenic path changes from CH(4) production by hydrogenotrophic plus acetoclastic methanogenesis to exclusively hydrogenotrophic methanogenesis and simultaneously, the methanogenic community consisting of Methanosarcinaceae, Methanoseataceae, Methanomicrobiales, Methanobacteriales and Rice Cluster I (RC-1) changes to almost complete dominance of RC-1. We studied changes in structure and function of the methanogenic community with temperature to see whether microbial members of the community were lost or their function impaired by exposure to high temperature. We characterized the function of the community by the path of CH(4) production measuring δ(13)C in CH(4) and CO(2) and calculating the apparent fractionation factor (α(app)) and the structure of the community by analysis of the terminal restriction fragment length polymorphism (T-RFLP) of the microbial 16S rRNA genes. Shift of the temperature from 45°C to 35°C resulted in a corresponding shift of function and structure, especially when some 35°C soil was added to the 45°C soil. The bacterial community (T-RFLP patterns), which was much more diverse than the archaeal community, changed in a similar manner upon temperature shift. Incubation of a mixture of 35°C and 50°C pre-incubated methanogenic rice field soil at different temperatures resulted in functionally and structurally well-defined communities. Although function changed from a mixture of acetoclastic and hydrogenotrophic methanogenesis to exclusively hydrogenotrophic methanogenesis over a rather narrow temperature range of 42-46°C, each of these temperatures also resulted in only one characteristic function and structure. Our study showed that temperature conditions defined structure and function of the methanogenic microbial community.
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Affiliation(s)
- Ralf Conrad
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str., 35043 Marburg, Germany.
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Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Appl Microbiol Biotechnol 2008; 80:365-80. [PMID: 18648804 DOI: 10.1007/s00253-008-1565-4] [Citation(s) in RCA: 218] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Revised: 05/29/2008] [Accepted: 06/01/2008] [Indexed: 10/21/2022]
Abstract
Terminal restriction fragment length polymorphism (T-RFLP) analysis is a popular high-throughput fingerprinting technique used to monitor changes in the structure and composition of microbial communities. This approach is widely used because it offers a compromise between the information gained and labor intensity. In this review, we discuss the progress made in T-RFLP analysis of 16S rRNA genes and functional genes over the last 10 years and evaluate the performance of this technique when used in conjunction with different statistical methods. Web-based tools designed to perform virtual polymerase chain reaction and restriction enzyme digests greatly facilitate the choice of primers and restriction enzymes for T-RFLP analysis. Significant improvements have also been made in the statistical analysis of T-RFLP profiles such as the introduction of objective procedures to distinguish between signal and noise, the alignment of T-RFLP peaks between profiles, and the use of multivariate statistical methods to detect changes in the structure and composition of microbial communities due to spatial and temporal variation or treatment effects. The progress made in T-RFLP analysis of 16S rRNA and genes allows researchers to make methodological and statistical choices appropriate for the hypotheses of their studies.
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Guermazi S, Daegelen P, Dauga C, Rivière D, Bouchez T, Godon JJ, Gyapay G, Sghir A, Pelletier E, Weissenbach J, Le Paslier D. Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach. Environ Microbiol 2008; 10:2111-23. [PMID: 18459975 PMCID: PMC2702496 DOI: 10.1111/j.1462-2920.2008.01632.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We have constructed a large fosmid library from a mesophilic anaerobic digester and explored its 16S rDNA diversity using a high-density filter DNA–DNA hybridization procedure. We identified a group of 16S rDNA sequences forming a new bacterial lineage named WWE3 (Waste Water of Evry 3). Only one sequence from the public databases shares a sequence identity above 80% with the WWE3 group which hence cannot be affiliated to any known or candidate prokaryotic division. Despite representing a non-negligible fraction (5% of the 16S rDNA sequences) of the bacterial population of this digester, the WWE3 bacteria could not have been retrieved using the conventional 16S rDNA amplification procedure due to their unusual 16S rDNA gene sequence. WWE3 bacteria were detected by polymerase chain reaction (PCR) in various environments (anaerobic digesters, swine lagoon slurries and freshwater biofilms) using newly designed specific PCR primer sets. Fluorescence in situ hybridization (FISH) analysis of sludge samples showed that WWE3 microorganisms are oval-shaped and located deep inside sludge flocs. Detailed phylogenetic analysis showed that WWE3 bacteria form a distinct monophyletic group deeply branching apart from all known bacterial divisions. A new bacterial candidate division status is proposed for this group.
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Affiliation(s)
- Sonda Guermazi
- CEA/Genoscope, CNRS-UMR 8030 and Université d'Val d'Essonne, 91057 Evry, France
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Dynamics of the methanogenic archaeal community during plant residue decomposition in an anoxic rice field soil. Appl Environ Microbiol 2008; 74:2894-901. [PMID: 18344350 DOI: 10.1128/aem.00070-08] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Incorporation of plant residues strongly enhances the methane production and emission from flooded rice fields. Temperature and residue type are important factors that regulate residue decomposition and CH(4) production. However, the response of the methanogenic archaeal community to these factors in rice field soil is not well understood. In the present experiment, the structure of the archaeal community was determined during the decomposition of rice root and straw residues in anoxic rice field soil incubated at three temperatures (15 degrees C, 30 degrees C, and 45 degrees C). More CH(4) was produced in the straw treatment than root treatment. Increasing the temperature from 15 degrees C to 45 degrees C enhanced CH(4) production. Terminal restriction fragment length polymorphism analyses in combination with cloning and sequencing of 16S rRNA genes showed that Methanosarcinaceae developed early in the incubations, whereas Methanosaetaceae became more abundant in the later stages. Methanosarcinaceae and Methanosaetaceae seemed to be better adapted at 15 degrees C and 30 degrees C, respectively, while the thermophilic Methanobacteriales and rice cluster I methanogens were significantly enhanced at 45 degrees C. Straw residues promoted the growth of Methanosarcinaceae, whereas the root residues favored Methanosaetaceae. In conclusion, our study revealed a highly dynamic structure of the methanogenic archaeal community during plant residue decomposition. The in situ concentration of acetate (and possibly of H(2)) seems to be the key factor that regulates the shift of methanogenic community.
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Thummes K, Schäfer J, Kämpfer P, Jäckel U. Thermophilic methanogenic Archaea in compost material: Occurrence, persistence and possible mechanisms for their distribution to other environments. Syst Appl Microbiol 2007; 30:634-43. [DOI: 10.1016/j.syapm.2007.08.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Accepted: 08/23/2007] [Indexed: 10/22/2022]
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Moissl C, Bruckner JC, Venkateswaran K. Archaeal diversity analysis of spacecraft assembly clean rooms. ISME JOURNAL 2007; 2:115-9. [DOI: 10.1038/ismej.2007.98] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Thummes K, Kämpfer P, Jäckel U. Temporal change of composition and potential activity of the thermophilic archaeal community during the composting of organic material. Syst Appl Microbiol 2007; 30:418-29. [PMID: 17336478 DOI: 10.1016/j.syapm.2007.01.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Indexed: 11/28/2022]
Abstract
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 during the maturation process, presumably due to altered pile conditions. Likewise, compost may act as a potential carrier for thermophilic methanogens in temperate soils because it is widely used as a soil amendment.
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Affiliation(s)
- Kathrin Thummes
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
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Sakai S, Imachi H, Sekiguchi Y, Ohashi A, Harada H, Kamagata Y. Isolation of key methanogens for global methane emission from rice paddy fields: a novel isolate affiliated with the clone cluster rice cluster I. Appl Environ Microbiol 2007; 73:4326-31. [PMID: 17483259 PMCID: PMC1932770 DOI: 10.1128/aem.03008-06] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2006] [Accepted: 05/01/2007] [Indexed: 11/20/2022] Open
Abstract
Despite the fact that rice paddy fields (RPFs) are contributing 10 to 25% of global methane emissions, the organisms responsible for methane production in RPFs have remained uncultivated and thus uncharacterized. Here we report the isolation of a methanogen (strain SANAE) belonging to an abundant and ubiquitous group of methanogens called rice cluster I (RC-I) previously identified as an ecologically important microbial component via culture-independent analyses. To enrich the RC-I methanogens from rice paddy samples, we attempted to mimic the in situ conditions of RC-I on the basis of the idea that methanogens in such ecosystems should thrive by receiving low concentrations of substrate (H(2)) continuously provided by heterotrophic H(2)-producing bacteria. For this purpose, we developed a coculture method using an indirect substrate (propionate) in defined medium and a propionate-oxidizing, H(2)-producing syntroph, Syntrophobacter fumaroxidans, as the H(2) supplier. By doing so, we significantly enriched the RC-I methanogens and eventually obtained a methanogen within the RC-I group in pure culture. This is the first report on the isolation of a methanogen within RC-I.
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Affiliation(s)
- Sanae Sakai
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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Poplawski AB, Mårtensson L, Wartiainen I, Rasmussen U. Archaeal diversity and community structure in a Swedish barley field: Specificity of the EK510R/(EURY498) 16S rDNA primer. J Microbiol Methods 2006; 69:161-73. [PMID: 17289189 DOI: 10.1016/j.mimet.2006.12.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2006] [Revised: 12/15/2006] [Accepted: 12/15/2006] [Indexed: 11/27/2022]
Abstract
The aim of this study was to analyze a total euryarchaeal community at DNA and RNA levels in a Swedish barley field with relation to soil depth (0-10 and 20-30 cm layers), soil fraction (bulk soil and rhizosphere) and time (August and November sample collection). Amplification of 16S rRNA gene using the archaeal universal A2F and Euryarchaea specific EK510R/(EURY498) primer pair, combined with denaturing gradient gel electrophoresis (DGGE), revealed distinct differences between rDNA and rRNA DGGE profiles. The soil depth, time, or rhizosphere effects did not significantly influence Archaeal community structure. Surprisingly, sequence analysis of DGGE-derived amplicons revealed the presence of Euryarchaea as well as uncultured soil Crenarchaea affiliated with group 1. In agreement, sequence comparison analyses showed that the majority of uncultured Crenarchaea group 1 had almost 100% sequence complementarity to the 3' end of the EK510R/(EURY498) primer. Therefore, we propose that EK510R/(EURY498R) is a universal archaeal primer rather than a Euryarchaea specific SSUrRNA primer. Hence, considerable care should be taken during application of this primer in studies of euryarchaeal biodiversity in soil environments.
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Abstract
Although allopatric divergence is a well-accepted mechanism of speciation for eukaryotic macro-organisms, the importance of geographical barriers to divergence in microbial populations is a subject of great debate. Do geographically separated populations of micro-organisms diverge independently, or does their structure fit the often quoted Bass-Becking description 'everything is everywhere; the environment selects'? Aided by high-resolution genetic and genomic tools, the search for 'microbial marsupials' has revealed that in fact both are true; some species of micro-organisms demonstrate allopatric divergence, while others do not. This discovery opens the door for comparative analyses, where questions about the differences in evolutionary and ecological mechanisms that drive divergence and speciation in different microbial species can begin to be explored. Investigating these differences in evolutionary mechanisms will greatly enhance interest in, and understanding of, the dynamic processes that create and maintain the vast diversity of the microbial world.
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Affiliation(s)
- Rachel J Whitaker
- Department of Microbiology, University of Illinois, 601 South Goodwin Avenue, Urbana, IL 61801, USA.
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Hori T, Noll M, Igarashi Y, Friedrich MW, Conrad R. Identification of acetate-assimilating microorganisms under methanogenic conditions in anoxic rice field soil by comparative stable isotope probing of RNA. Appl Environ Microbiol 2006; 73:101-9. [PMID: 17071795 PMCID: PMC1797110 DOI: 10.1128/aem.01676-06] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acetate is the most abundant intermediate of organic matter degradation in anoxic rice field soil and is converted to CH(4) and/or CO(2). Aceticlastic methanogens are the primary microorganisms dissimilating acetate in the absence of sulfate and reducible ferric iron. In contrast, very little is known about bacteria capable of assimilating acetate under methanogenic conditions. Here, we identified active acetate-assimilating microorganisms by using a combined approach of frequent label application at a low concentration and comparative RNA-stable isotope probing with (13)C-labeled and unlabeled acetate. Rice field soil was incubated anaerobically at 25 degrees C for 12 days, during which (13)C-labeled acetate was added at a concentration of 500 muM every 3 days. (13)C-labeled CH(4) and CO(2) were produced from the beginning of the incubation and accounted for about 60% of the supplied acetate (13)C. RNA was extracted from the cells in each sample taken and separated by isopycnic centrifugation according to molecular weight. Bacterial and archaeal populations in each density fraction were screened by reverse transcription-PCR-mediated terminal restriction fragment polymorphism analysis. No differences in the bacterial populations were observed throughout the density fractions of the unlabeled treatment. However, in the heavy fractions of the (13)C treatment, terminal restriction fragments (T-RFs) of 161 bp and 129 bp in length predominated. These T-RFs were identified by cloning and sequencing of 16S rRNA as from a Geobacter sp. and an Anaeromyxobacter sp., respectively. Apparently these bacteria, which are known as dissimilatory iron reducers, were able to assimilate acetate under methanogenic conditions, i.e., when CO(2) was the predominant electron acceptor. We hypothesize that ferric iron minerals with low bioavailability might have served as electron acceptors for Geobacter spp. and Anaeromyxobacter spp. under these conditions.
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Affiliation(s)
- Tomoyuki Hori
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany
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Conrad R, Erkel C, Liesack W. Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil. Curr Opin Biotechnol 2006; 17:262-7. [PMID: 16621512 DOI: 10.1016/j.copbio.2006.04.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2006] [Revised: 03/25/2006] [Accepted: 04/04/2006] [Indexed: 10/24/2022]
Abstract
Methane, which is an important greenhouse gas, is to a large part produced by methanogenic archaea in anoxic soils and sediments. Rice Cluster I methanogens have been characterized on the basis of their 16S rRNA and mcrA gene sequences, and were found to form a separate lineage within the phylogenetic radiation of Methanosarcinales and Methanomicrobiales. As isolation has not been achieved until recently, our knowledge of distribution, physiology and environmental significance of Rice Cluster I is solely based on molecular biology techniques. Rice Cluster I seems to be widely distributed, particularly in rice fields, possibly occupying different niches among the methane producers. One niche seems to be methane production on roots driven by plant photosynthesis, contributing substantially to the release of methane from rice fields into the atmosphere.
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Affiliation(s)
- Ralf Conrad
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany.
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