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Lever MA, Alperin MJ, Hinrichs KU, Teske A. Zonation of the active methane-cycling community in deep subsurface sediments of the Peru trench. Front Microbiol 2023; 14:1192029. [PMID: 37250063 PMCID: PMC10213550 DOI: 10.3389/fmicb.2023.1192029] [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: 03/22/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
The production and anaerobic oxidation of methane (AOM) by microorganisms is widespread in organic-rich deep subseafloor sediments. Yet, the organisms that carry out these processes remain largely unknown. Here we identify members of the methane-cycling microbial community in deep subsurface, hydrate-containing sediments of the Peru Trench by targeting functional genes of the alpha subunit of methyl coenzyme M reductase (mcrA). The mcrA profile reveals a distinct community zonation that partially matches the zonation of methane oxidizing and -producing activity inferred from sulfate and methane concentrations and carbon-isotopic compositions of methane and dissolved inorganic carbon (DIC). McrA appears absent from sulfate-rich sediments that are devoid of methane, but mcrA sequences belonging to putatively methane-oxidizing ANME-1a-b occur from the zone of methane oxidation to several meters into the methanogenesis zone. A sister group of ANME-1a-b, referred to as ANME-1d, and members of putatively aceticlastic Methanothrix (formerly Methanosaeta) occur throughout the remaining methanogenesis zone. Analyses of 16S rRNA and mcrA-mRNA indicate that the methane-cycling community is alive throughout (rRNA to 230 mbsf) and active in at least parts of the sediment column (mRNA at 44 mbsf). Carbon-isotopic depletions of methane relative to DIC (-80 to -86‰) suggest mostly methane production by CO2 reduction and thus seem at odds with the widespread detection of ANME-1 and Methanothrix. We explain this apparent contradiction based on recent insights into the metabolisms of both ANME-1 and Methanothricaceae, which indicate the potential for methanogenetic growth by CO2 reduction in both groups.
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Affiliation(s)
- Mark A. Lever
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, United States
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Marc J. Alperin
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas Teske
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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2
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Differences in the methanogen community between the nearshore and offshore sediments of the South Yellow Sea. J Microbiol 2022; 60:814-822. [DOI: 10.1007/s12275-022-2022-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 10/17/2022]
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Kevorkian RT, Sipes K, Winstead R, Paul R, Lloyd KG. Cryptic Methane-Cycling by Methanogens During Multi-Year Incubation of Estuarine Sediment. Front Microbiol 2022; 13:847563. [PMID: 35369448 PMCID: PMC8969600 DOI: 10.3389/fmicb.2022.847563] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
As marine sediments are buried, microbial communities transition from sulfate-reduction to methane-production after sulfate is depleted. When this biogenic methane diffuses into the overlying sulfate-rich sediments, it forms a sulfate-methane transition zone (SMTZ) because sulfate reducers deplete hydrogen concentrations and make hydrogenotrophic methanogenesis exergonic in the reverse direction, a process called the anaerobic oxidation of methane (AOM). Microbial participation in these processes is often inferred from geochemistry, genes, and gene expression changes with sediment depth, using sedimentation rates to convert depth to time. Less is known about how natural sediments transition through these geochemical states transition in real-time. We examined 16S rRNA gene amplicon libraries and metatranscriptomes in microcosms of anoxic sediment from the White Oak River estuary, NC, with three destructively sampled replicates with methane added (586-day incubations) and three re-sampled un-amended replicates (895-day incubations). Sulfate dropped to a low value (∼0.3 mM) on similar days for both experiments (312 and 320 days, respectively), followed by a peak in hydrogen, intermittent increases in methane-cycling archaea starting on days 375 and 362 (mostly Methanolinea spp. and Methanosaeta spp., and Methanococcoides sp. ANME-3), and a methane peak 1 month later. However, methane δ13C values only show net methanogenesis 6 months after methane-cycling archaea increase and 4 months after the methane peak, when sulfate is consistently below 0.1 mM and hydrogen increases to a stable 0.61 ± 0.13 nM (days 553–586, n = 9). Sulfate-reducing bacteria (mostly Desulfatiglans spp. and Desulfosarcina sp. SEEP-SRB1) increase in relative abundance only during this period of net methane production, suggesting syntrophy with methanogens in the absence of sulfate. The transition from sulfate reduction to methane production in marine sediments occurs through a prolonged period of methane-cycling by methanogens at low sulfate concentrations, and steady growth of sulfate reducers along with methanogens after sulfate is depleted.
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Ozuolmez D, Moore EK, Hopmans EC, Sinninghe Damsté JS, Stams AJM, Plugge CM. Butyrate Conversion by Sulfate-Reducing and Methanogenic Communities from Anoxic Sediments of Aarhus Bay, Denmark. Microorganisms 2020; 8:microorganisms8040606. [PMID: 32331369 PMCID: PMC7232339 DOI: 10.3390/microorganisms8040606] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 11/29/2022] Open
Abstract
The conventional perception that the zone of sulfate reduction and methanogenesis are separated in high- and low-sulfate-containing marine sediments has recently been changed by studies demonstrating their co-occurrence in sediments. The presence of methanogens was linked to the presence of substrates that are not used by sulfate reducers. In the current study, we hypothesized that both groups can co-exist, consuming common substrates (H2 and/or acetate) in sediments. We enriched butyrate-degrading communities in sediment slurries originating from the sulfate, sulfate–methane transition, and methane zone of Aarhus Bay, Denmark. Sulfate was added at different concentrations (0, 3, 20 mM), and the slurries were incubated at 10 °C and 25 °C. During butyrate conversion, sulfate reduction and methanogenesis occurred simultaneously. The syntrophic butyrate degrader Syntrophomonas was enriched both in sulfate-amended and in sulfate-free slurries, indicating the occurrence of syntrophic conversions at both conditions. Archaeal community analysis revealed a dominance of Methanomicrobiaceae. The acetoclastic Methanosaetaceae reached high relative abundance in the absence of sulfate, while presence of acetoclastic Methanosarcinaceae was independent of the sulfate concentration, temperature, and the initial zone of the sediment. This study shows that there is no vertical separation of sulfate reducers, syntrophs, and methanogens in the sediment and that they all participate in the conversion of butyrate.
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Affiliation(s)
- Derya Ozuolmez
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (D.O.); (A.J.M.S.)
| | - Elisha K. Moore
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands; (E.K.M.); (E.C.H.); (J.S.S.D.)
- Department of Environmental Science, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
| | - Ellen C. Hopmans
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands; (E.K.M.); (E.C.H.); (J.S.S.D.)
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands; (E.K.M.); (E.C.H.); (J.S.S.D.)
- Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (D.O.); (A.J.M.S.)
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (D.O.); (A.J.M.S.)
- Correspondence: ; Tel.: +31-317-483116
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Jahnke LL, Des Marais DJ. Carbon isotopic composition of lipid biomarkers from an endoevaporitic gypsum crust microbial mat reveals cycling of mineralized organic carbon. GEOBIOLOGY 2019; 17:643-659. [PMID: 31361088 DOI: 10.1111/gbi.12355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/02/2019] [Accepted: 06/23/2019] [Indexed: 06/10/2023]
Abstract
Microbial mats that inhabit gypsum deposits in ponds at Guerrero Negro, Baja California Sur, Mexico, developed distinct pigmented horizons that provided an opportunity to examine the fixation and flow of carbon through a trophic structure and, in conjunction with previous phylogenetic analyses, to assess the diagenetic fates of molecular δ13 C biosignatures. The δ13 C values of individual biomarker lipids, total carbon, and total organic carbon (TOC) were determined for each of the following horizons: tan-orange (TO) at the surface, green (G), purple (P), and olive-black (OB) at the bottom. δ13 C of individual fatty acids from intact polar lipids (IPFA) in TO were similar to δ13 C of dissolved inorganic carbon (DIC) in the overlying water column, indicating limited discrimination by cyanobacteria during CO2 fixation. δ13 CTOC of the underlying G was 3‰ greater than that of TO. The most δ13 C-depleted acetogenic lipids in the upper horizons were the cyanobacterial biomarkers C17 n-alkanes and polyunsaturated fatty acids. Bishomohopanol was 4 to 7‰ enriched, relative to alkanes and intact polar fatty acids (IPFA), respectively. Acyclic C20 isoprenoids were depleted by 14‰ relative to bishomohopanol. Significantly, ∆[δ13 CTOC - δ13 C∑IPFA ] increased from 6.9‰ in TO to 14.7‰ in OB. This major trend might indicate that 13 C-enriched residual organic matter accumulated at depth. The permanently anoxic P horizon was dominated by anoxygenic phototrophs and sulfate-reducing bacteria. P hosted an active sulfur-dependent microbial community. IPFA and bishomohopanol were 13 C-depleted relative to upper crust by 7 and 4‰, respectively, and C20 isoprenoids were somewhat 13 C-enriched. Synthesis of alkanes in P was evidenced only by 13 C-depleted n-octadecane and 8-methylhexadecane. In OB, the marked increase of total inorganic carbon δ13 C (δ13 CTIC ) of >6‰ perhaps indicated terminal mineralization. This δ13 CTIC increase is consistent with degradation of the osmolyte glycine betaine by methylotrophic methanogens and loss of 13 C-depleted methane from the mat.
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Affiliation(s)
- Linda L Jahnke
- Exobiology Branch, Space Science & Astrobiology Division, NASA-Ames Research Center, Moffett Field, CA, USA
| | - David J Des Marais
- Exobiology Branch, Space Science & Astrobiology Division, NASA-Ames Research Center, Moffett Field, CA, USA
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Prakash D, Chauhan SS, Ferry JG. Life on the thermodynamic edge: Respiratory growth of an acetotrophic methanogen. SCIENCE ADVANCES 2019; 5:eaaw9059. [PMID: 31457094 PMCID: PMC6703866 DOI: 10.1126/sciadv.aaw9059] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/12/2019] [Indexed: 05/20/2023]
Abstract
Although two-thirds of the nearly 1 billion metric tons of methane produced annually in Earth's biosphere derives from acetate, the in situ process has escaped rigorous understanding. The unresolved question concerns the mechanism by which the exceptionally marginal amount of available energy supports acetotrophic growth of methanogenic archaea in the environment. Here, we show that Methanosarcina acetivorans conserves energy by Fe(III)-dependent respiratory metabolism of acetate, augmenting production of the greenhouse gas methane. An extensively revised, ecologically relevant, biochemical pathway for acetotrophic growth is presented, in which the conservation of respiratory energy is maximized by electron bifurcation, a previously unknown mechanism of biological energy coupling. The results transform the ecological and biochemical understanding of methanogenesis and the role of iron in the mineralization of organic matter in anaerobic environments.
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Cetecioglu Z, Dolfing J, Taylor J, Purdy KJ, Eyice Ö. COD/sulfate ratio does not affect the methane yield and microbial diversity in anaerobic digesters. WATER RESEARCH 2019; 155:444-454. [PMID: 30861382 DOI: 10.1016/j.watres.2019.02.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/19/2019] [Accepted: 02/21/2019] [Indexed: 06/09/2023]
Abstract
Anaerobic digestion of organic matter is the major route of biomethane production. However, in the presence of sulfate, sulfate-reducing bacteria (SRB) typically outcompete methanogens, which may reduce or even preclude methane production from sulfate-containing wastewaters. Although sulfate-reduction and methanogenesis can occur simultaneously, our limited understanding of the microbiology of anaerobic digesters treating sulfate-containing wastewaters constrains improvements in the production of methane from these systems. This study tested the effects of carbon sources and chemical oxygen demand-to-sulfate ratio (COD/SO42-) on the diversity and interactions of SRB and methanogens in an anaerobic digester treating a high-sulfate waste stream. Overall, the data showed that sulfate removal and methane generation occurred in varying efficiencies and the carbon source had limited effect on the methane yield. Importantly, the results demonstrated that methanogenic and SRB diversities were only affected by the carbon source and not by the COD/SO42- ratio.
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Affiliation(s)
- Zeynep Cetecioglu
- School of Chemical Science and Engineering, KTH Royal Institute of Technology, SE-100 44, Sweden; School of Life Sciences, University of Warwick, CV4 7AL, UK
| | - Jan Dolfing
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - Jessica Taylor
- School of Life Sciences, University of Warwick, CV4 7AL, UK
| | - Kevin J Purdy
- School of Life Sciences, University of Warwick, CV4 7AL, UK
| | - Özge Eyice
- School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS, UK.
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Community and Proteomic Analysis of Anaerobic Consortia Converting Tetramethylammonium to Methane. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2017; 2017:2170535. [PMID: 29391857 PMCID: PMC5748143 DOI: 10.1155/2017/2170535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/25/2017] [Accepted: 10/31/2017] [Indexed: 11/17/2022]
Abstract
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.
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Estimating Population Turnover Rates by Relative Quantification Methods Reveals Microbial Dynamics in Marine Sediment. Appl Environ Microbiol 2017; 84:AEM.01443-17. [PMID: 29054869 DOI: 10.1128/aem.01443-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/09/2017] [Indexed: 11/20/2022] Open
Abstract
The difficulty involved in quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina, USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentrations consistent with the predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, which stands for "fraction of read abundance times cells"), to estimate the population turnover rates of uncultured clades. Most 16S rRNA reads were from deeply branching uncultured groups, and ∼98% of 16S rRNA genes did not abruptly shift in relative abundance when sulfate reduction gave way to methanogenesis. Uncultured Methanomicrobiales and Methanosarcinales increased at the onset of methanogenesis with population turnover times estimated from qPCR at 9.7 ± 3.9 and 12.6 ± 4.1 days, respectively. These were consistent with FRAxC turnover times of 9.4 ± 5.8 and 9.2 ± 3.5 days, respectively. Uncultured Syntrophaceae, which are possibly fermentative syntrophs of methanogens, and uncultured Kazan-3A-21 archaea also increased at the onset of methanogenesis, with FRAxC turnover times of 14.7 ± 6.9 and 10.6 ± 3.6 days. Kazan-3A-21 may therefore either perform methanogenesis or form a fermentative syntrophy with methanogens. Three genera of sulfate-reducing bacteria, Desulfovibrio, Desulfobacter, and Desulfobacterium, increased in the first 19 days before declining rapidly during sulfate reduction. We conclude that population turnover times on the order of days can be measured robustly in organic-rich marine sediment, and the transition from sulfate-reducing to methanogenic conditions stimulates growth only in a few clades directly involved in methanogenesis, rather than in the whole microbial community.IMPORTANCE Many microbes cannot be isolated in pure culture to determine their preferential growth conditions and predict their response to changing environmental conditions. We created a microcosm of marine sediments that allowed us to simulate a diagenetic profile using a temporal analog for depth. This allowed for the observation of the microbial community population dynamics caused by the natural shift from sulfate reduction to methanogenesis. Our research provides evidence for the population dynamics of uncultured microbes as well as the application of a novel method of turnover rate analysis for individual taxa within a mixed incubation, FRAxC, which stands for "fraction of read abundance times cells," which was verified by quantitative PCR. This allows for the calculation of population turnover times for microbes in a natural setting and the identification of uncultured clades involved in geochemical processes.
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Xiao KQ, Beulig F, Kjeldsen KU, Jørgensen BB, Risgaard-Petersen N. Concurrent Methane Production and Oxidation in Surface Sediment from Aarhus Bay, Denmark. Front Microbiol 2017; 8:1198. [PMID: 28713339 PMCID: PMC5492102 DOI: 10.3389/fmicb.2017.01198] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/12/2017] [Indexed: 12/26/2022] Open
Abstract
Marine surface sediments, which are replete with sulfate, are typically considered to be devoid of endogenous methanogenesis. Yet, methanogenic archaea are present in those sediments, suggesting a potential for methanogenesis. We used an isotope dilution method based on sediment bag incubation and spiking with 13C-CH4 to quantify CH4 turnover rates in sediment from Aarhus Bay, Denmark. In two independent experiments, highest CH4 production and oxidation rates (>200 pmol cm-3 d-1) were found in the top 0-2 cm, below which rates dropped below 100 pmol cm-3 d-1 in all other segments down to 16 cm. This drop in overall methane turnover with depth was accompanied by decreasing rates of organic matter mineralization with depth. Molecular analyses based on quantitative PCR and MiSeq sequencing of archaeal 16S rRNA genes showed that the abundance of methanogenic archaea also peaked in the top 0-2 cm segment. Based on the community profiling, hydrogenotrophic and methylotrophic methanogens dominated among the methanogenic archaea in general, suggesting that methanogenesis in surface sediment could be driven by both CO2 reduction and fermentation of methylated compounds. Our results show the existence of elevated methanogenic activity and a dynamic recycling of CH4 at low concentration in sulfate-rich marine surface sediment. Considering the common environmental conditions found in other coastal systems, we speculate that such a cryptic methane cycling can be ubiquitous.
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Affiliation(s)
- Ke-Qing Xiao
- Center for Geomicrobiology, Department of Bioscience, Aarhus UniversityAarhus, Denmark
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Roussel EG, Cragg BA, Webster G, Sass H, Tang X, Williams AS, Gorra R, Weightman AJ, Parkes RJ. Complex coupled metabolic and prokaryotic community responses to increasing temperatures in anaerobic marine sediments: critical temperatures and substrate changes. FEMS Microbiol Ecol 2015. [PMID: 26207045 PMCID: PMC4629870 DOI: 10.1093/femsec/fiv084] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The impact of temperature (0-80°C) on anaerobic biogeochemical processes and prokaryotic communities in marine sediments (tidal flat) was investigated in slurries for up to 100 days. Temperature had a non-linear effect on biogeochemistry and prokaryotes with rapid changes over small temperature intervals. Some activities (e.g. methanogenesis) had multiple 'windows' within a large temperature range (∼10 to 80°C). Others, including acetate oxidation, had maximum activities within a temperature zone, which varied with electron acceptor [metal oxide (up to ∼34°C) and sulphate (up to ∼50°C)]. Substrates for sulphate reduction changed from predominantly acetate below, and H2 above, a 43°C critical temperature, along with changes in activation energies and types of sulphate-reducing Bacteria. Above ∼43°C, methylamine metabolism ceased with changes in methanogen types and increased acetate concentrations (>1 mM). Abundances of uncultured Archaea, characteristic of deep marine sediments (e.g. MBGD Euryarchaeota, 'Bathyarchaeota') changed, indicating their possible metabolic activity and temperature range. Bacterial cell numbers were consistently higher than archaeal cells and both decreased above ∼15°C. Substrate addition stimulated activities, widened some activity temperature ranges (methanogenesis) and increased bacterial (×10) more than archaeal cell numbers. Hence, additional organic matter input from climate-related eutrophication may amplify the impact of temperature increases on sedimentary biogeochemistry.
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Affiliation(s)
- Erwan G Roussel
- School of Earth and Ocean Sciences, Main Building, Park Place, Cardiff University, CF10 3AT Cardiff, UK
| | - Barry A Cragg
- School of Earth and Ocean Sciences, Main Building, Park Place, Cardiff University, CF10 3AT Cardiff, UK
| | - Gordon Webster
- School of Earth and Ocean Sciences, Main Building, Park Place, Cardiff University, CF10 3AT Cardiff, UK Cardiff School of Biosciences, Main Building, Park Place, Cardiff University, CF10 3AT Cardiff, UK
| | - Henrik Sass
- School of Earth and Ocean Sciences, Main Building, Park Place, Cardiff University, CF10 3AT Cardiff, UK
| | - Xiaohong Tang
- School of Earth and Ocean Sciences, Main Building, Park Place, Cardiff University, CF10 3AT Cardiff, UK
| | - Angharad S Williams
- Cardiff School of Biosciences, Main Building, Park Place, Cardiff University, CF10 3AT Cardiff, UK
| | - Roberta Gorra
- DISAFA, University of Turin, Largo P. Baccini 2, 10095 Grugliasco, TO, Italy
| | - Andrew J Weightman
- Cardiff School of Biosciences, Main Building, Park Place, Cardiff University, CF10 3AT Cardiff, UK
| | - R John Parkes
- School of Earth and Ocean Sciences, Main Building, Park Place, Cardiff University, CF10 3AT Cardiff, UK
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12
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Ozuolmez D, Na H, Lever MA, Kjeldsen KU, Jørgensen BB, Plugge CM. Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence? Front Microbiol 2015; 6:492. [PMID: 26074892 PMCID: PMC4445324 DOI: 10.3389/fmicb.2015.00492] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/04/2015] [Indexed: 11/28/2022] Open
Abstract
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.
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Affiliation(s)
- Derya Ozuolmez
- Agrotechnology and Food Sciences, Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Hyunsoo Na
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria
| | - Mark A Lever
- Department of Environmental Sciences, Institute of Biogeochemistry and Pollutant Dynamics, Eidgenössische Technische Hochschule Zurich Zürich, Switzerland
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Caroline M Plugge
- Agrotechnology and Food Sciences, Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
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Bertram S, Blumenberg M, Michaelis W, Siegert M, Krüger M, Seifert R. Methanogenic capabilities of ANME-archaea deduced from13C-labelling approaches. Environ Microbiol 2013; 15:2384-93. [DOI: 10.1111/1462-2920.12112] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/20/2012] [Accepted: 02/16/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Sebastian Bertram
- Institute for Biogeochemistry and Marine Chemistry; University of Hamburg; Bundesstr. 55; 20146; Hamburg; Germany
| | - Martin Blumenberg
- Geobiology Group, Geoscience Centre; Georg-August-University Göttingen; Goldschmidtstr. 3; 37077; Göttingen; Germany
| | - Walter Michaelis
- Institute for Biogeochemistry and Marine Chemistry; University of Hamburg; Bundesstr. 55; 20146; Hamburg; Germany
| | - Michael Siegert
- Pennsylvania State University; 127 Sackett Building; University Park; PA; 16802; USA
| | - Martin Krüger
- Federal Institute for Geosciences and Natural Resources; Section Geomicrobiology; Stilleweg 2; 30655; Hannover; Germany
| | - Richard Seifert
- Institute for Biogeochemistry and Marine Chemistry; University of Hamburg; Bundesstr. 55; 20146; Hamburg; Germany
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14
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Maignien L, Parkes RJ, Cragg B, Niemann H, Knittel K, Coulon S, Akhmetzhanov A, Boon N. Anaerobic oxidation of methane in hypersaline cold seep sediments. FEMS Microbiol Ecol 2012; 83:214-31. [PMID: 22882187 DOI: 10.1111/j.1574-6941.2012.01466.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/28/2012] [Accepted: 08/01/2012] [Indexed: 11/30/2022] Open
Abstract
Life in hypersaline environments is typically limited by bioenergetic constraints. Microbial activity at the thermodynamic edge, such as the anaerobic oxidation of methane (AOM) coupled to sulphate reduction (SR), is thus unlikely to thrive in these environments. In this study, carbon and sulphur cycling was investigated in the extremely hypersaline cold seep sediments of Mercator mud volcano. AOM activity was partially inhibited but still present at salinity levels of 292 g L(-1) (c. eightfold sea water concentration) with rates of 2.3 nmol cm(-3) day(-1) and was even detectable under saturated conditions. Methane and evaporite-derived sulphate comigrated in the ascending geofluids, which, in combination with a partial activity inhibition, resulted in AOM activity being spread over unusually wide depth intervals. Up to 79% of total cells in the AOM zone were identified by fluorescence in situ hybridization (FISH) as anaerobic methanotrophs of the ANME-1. Most ANME-1 cells formed monospecific chains without any attached partner. At all sites, AOM activity co-occurred with SR activity and sometimes significantly exceeded it. Possible causes of these unexpected results are discussed. This study demonstrates that in spite of a very low energy yield of AOM, microorganisms carrying this reaction can thrive in salinity up to halite saturation.
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Affiliation(s)
- Loïs Maignien
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Ghent, Belgium.
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15
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Detection methanogens in newly settled sediments from Xuanwu Lake in Nanjing, China. Curr Microbiol 2012; 64:539-44. [PMID: 22392597 DOI: 10.1007/s00284-012-0103-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 02/07/2012] [Indexed: 10/28/2022]
Abstract
Sediments from Xuanwu Lake have been dredged in the past 3 years to improve the water quality, but methanogenesis should still exist in the newly settled sediment. Methane production, methanogens, and physiochemical parameters were detected in the surface sediments (0-5 cm) and/or vertical sediments (0-21 cm, segmented at interval of 3 cm). Methane flux at water-air interface varied among five detected sites. Principal component analysis showed that CH(4) flux, content of water and the concentration of total nitrogen (TN), CH(4) and organic matters (OM) weighed most heavily on the component I in surface sediments while different patterns were observed for vertical sediments. The copy number of the 16S rRNA gene for bacteria was lower in the surface sediment (0-6 cm) than that in deeper sediments (12-21 cm), while 16S rRNA genes of Archaea were almost evenly distributed in the vertical sediments. Representatives belonging to the orders Methanobacteriales, Methanomicrobiales, and Methanosarcinales were detected in all samples of the vertical sediments, except that no members of the Methanococcales were detected in the samples at 0-6 cm. The level of Methanobacteriales reached a highest density at 18.1 × 10(4) copies g(-1) dry weight (dw) at 6-9 cm; for Methanosarcinales (76.89 × 10(6) copies g(-1) dw) and Methanococcales (82.70 × 10(3) copies g(-1) dw) at 12-15 cm, whereas for Methanomicrobiales (43.37 × 10(6) copies g(-1) dw) at 9-12 cm. Methanosarcinaceae and Methanosaetaceae reached to their highest densities at 6-9 and 9-12 cm, respectively. These data provided useful information for better understanding the methanogenesis in the newly settled sediments of a recently dredged lake.
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16
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Thauer RK. Anaerobic oxidation of methane with sulfate: on the reversibility of the reactions that are catalyzed by enzymes also involved in methanogenesis from CO2. Curr Opin Microbiol 2011; 14:292-9. [DOI: 10.1016/j.mib.2011.03.003] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 03/13/2011] [Accepted: 03/15/2011] [Indexed: 11/16/2022]
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17
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Plugge CM, Zhang W, Scholten JCM, Stams AJM. Metabolic flexibility of sulfate-reducing bacteria. Front Microbiol 2011; 2:81. [PMID: 21734907 PMCID: PMC3119409 DOI: 10.3389/fmicb.2011.00081] [Citation(s) in RCA: 165] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 04/05/2011] [Indexed: 11/13/2022] Open
Abstract
Dissimilatory sulfate-reducing prokaryotes (SRB) are a very diverse group of anaerobic bacteria that are omnipresent in nature and play an imperative role in the global cycling of carbon and sulfur. In anoxic marine sediments sulfate reduction accounts for up to 50% of the entire organic mineralization in coastal and shelf ecosystems where sulfate diffuses several meters deep into the sediment. As a consequence, SRB would be expected in the sulfate-containing upper sediment layers, whereas methanogenic archaea would be expected to succeed in the deeper sulfate-depleted layers of the sediment. Where sediments are high in organic matter, sulfate is depleted at shallow sediment depths, and biogenic methane production will occur. In the absence of sulfate, many SRB ferment organic acids and alcohols, producing hydrogen, acetate, and carbon dioxide, and may even rely on hydrogen- and acetate-scavenging methanogens to convert organic compounds to methane. SRB can establish two different life styles, and these can be termed as sulfidogenic and acetogenic, hydrogenogenic metabolism. The advantage of having different metabolic capabilities is that it raises the chance of survival in environments when electron acceptors become depleted. In marine sediments, SRB and methanogens do not compete but rather complement each other in the degradation of organic matter. Also in freshwater ecosystems with sulfate concentrations of only 10-200 μM, sulfate is consumed efficiently within the top several cm of the sediments. Here, many of the δ-Proteobacteria present have the genetic machinery to perform dissimilatory sulfate reduction, yet they have an acetogenic, hydrogenogenic way of life. In this review we evaluate the physiology and metabolic mode of SRB in relation with their environment.
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Affiliation(s)
- Caroline M Plugge
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
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18
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Plugge CM, Zhang W, Scholten JCM, Stams AJM. Metabolic flexibility of sulfate-reducing bacteria. Front Microbiol 2011. [PMID: 21734907 DOI: 10.3389/fmicb.2011.00081/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Dissimilatory sulfate-reducing prokaryotes (SRB) are a very diverse group of anaerobic bacteria that are omnipresent in nature and play an imperative role in the global cycling of carbon and sulfur. In anoxic marine sediments sulfate reduction accounts for up to 50% of the entire organic mineralization in coastal and shelf ecosystems where sulfate diffuses several meters deep into the sediment. As a consequence, SRB would be expected in the sulfate-containing upper sediment layers, whereas methanogenic archaea would be expected to succeed in the deeper sulfate-depleted layers of the sediment. Where sediments are high in organic matter, sulfate is depleted at shallow sediment depths, and biogenic methane production will occur. In the absence of sulfate, many SRB ferment organic acids and alcohols, producing hydrogen, acetate, and carbon dioxide, and may even rely on hydrogen- and acetate-scavenging methanogens to convert organic compounds to methane. SRB can establish two different life styles, and these can be termed as sulfidogenic and acetogenic, hydrogenogenic metabolism. The advantage of having different metabolic capabilities is that it raises the chance of survival in environments when electron acceptors become depleted. In marine sediments, SRB and methanogens do not compete but rather complement each other in the degradation of organic matter. Also in freshwater ecosystems with sulfate concentrations of only 10-200 μM, sulfate is consumed efficiently within the top several cm of the sediments. Here, many of the δ-Proteobacteria present have the genetic machinery to perform dissimilatory sulfate reduction, yet they have an acetogenic, hydrogenogenic way of life. In this review we evaluate the physiology and metabolic mode of SRB in relation with their environment.
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Affiliation(s)
- Caroline M Plugge
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
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19
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Tarasov AL, Borzenkov IA, Belyayev SS. Investigation of the trophic relations between anaerobic microorganisms from an underground gas repository during methanol utilization. Microbiology (Reading) 2011. [DOI: 10.1134/s0026261711020159] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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20
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Biological fate of Diuron and Sea-nine® 211 and their effect on primary microbial activities in slurries of a contaminated sediment from Venice Lagoon. ANN MICROBIOL 2010. [DOI: 10.1007/s13213-010-0044-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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21
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Stams AJM, Plugge CM. Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat Rev Microbiol 2009; 7:568-77. [PMID: 19609258 DOI: 10.1038/nrmicro2166] [Citation(s) in RCA: 691] [Impact Index Per Article: 46.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Interspecies electron transfer is a key process in methanogenic and sulphate-reducing environments. Bacteria and archaea that live in syntrophic communities take advantage of the metabolic abilities of their syntrophic partner to overcome energy barriers and break down compounds that they cannot digest by themselves. Here, we review the transfer of hydrogen and formate between bacteria and archaea that helps to sustain growth in syntrophic methanogenic communities. We also describe the process of reverse electron transfer, which is a key requirement in obligately syntrophic interactions. Anaerobic methane oxidation coupled to sulphate reduction is also carried out by syntrophic communities of bacteria and archaea but, as we discuss, the exact mechanism of this syntrophic interaction is not yet understood.
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Affiliation(s)
- Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
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22
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Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 2008; 6:579-91. [PMID: 18587410 DOI: 10.1038/nrmicro1931] [Citation(s) in RCA: 1083] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most methanogenic archaea can reduce CO(2) with H(2) to methane, and it is generally assumed that the reactions and mechanisms of energy conservation that are involved are largely the same in all methanogens. However, this does not take into account the fact that methanogens with cytochromes have considerably higher growth yields and threshold concentrations for H(2) than methanogens without cytochromes. These and other differences can be explained by the proposal outlined in this Review that in methanogens with cytochromes, the first and last steps in methanogenesis from CO(2) are coupled chemiosmotically, whereas in methanogens without cytochromes, these steps are energetically coupled by a cytoplasmic enzyme complex that mediates flavin-based electron bifurcation.
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Affiliation(s)
- Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany.
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23
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Response of fermentation and sulfate reduction to experimental temperature changes in temperate and Arctic marine sediments. ISME JOURNAL 2008; 2:815-29. [DOI: 10.1038/ismej.2008.20] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Goffredi SK, Wilpiszeski R, Lee R, Orphan VJ. Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale-fall in Monterey Canyon, California. ISME JOURNAL 2008; 2:204-20. [PMID: 18219285 DOI: 10.1038/ismej.2007.103] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Whale-falls represent localized areas of extreme organic enrichment in an otherwise oligotrophic deep-sea environment. Anaerobic remineralization within these habitats is typically portrayed as sulfidogenic; however, we demonstrate that these systems are also favorable for diverse methane-producing archaeal assemblages, representing up to 40% of total cell counts. Chemical analyses revealed elevated methane and depleted sulfate concentrations in sediments under the whale-fall, as compared to surrounding sediments. Carbon was enriched (up to 3.5%) in whale-fall sediments, as well as the surrounding sea floor to at least 10 m, forming a 'bulls eye' of elevated carbon. The diversity of sedimentary archaea associated with the 2893 m whale-fall in Monterey Canyon (California) varied both spatially and temporally. 16S rRNA diversity, determined by both sequencing and terminal restriction fragment length polymorphism analysis, as well as quantitative PCR of the methyl-coenzyme M reductase gene, revealed that methanogens, including members of the Methanomicrobiales and Methanosarcinales, were the dominant archaea (up to 98%) in sediments immediately beneath the whale-fall. Temporal changes in this archaeal community included the early establishment of methylotrophic methanogens followed by development of methanogens thought to be hydrogenotrophic, as well as members related to the newly described methanotrophic lineage, ANME-3. In comparison, archaeal assemblages in 'reference' sediments collected 10 m from the whale-fall primarily consisted of Crenarchaeota affiliated with marine group I and marine benthic group B. Overall, these results indicate that whale-falls can favor the establishment of metabolically and phylogenetically diverse methanogen assemblages, resulting in an active near-seafloor methane cycle in the deep sea.
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Affiliation(s)
- Shana K Goffredi
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA.
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25
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Smith JM, Green SJ, Kelley CA, Prufert-Bebout L, Bebout BM. Shifts in methanogen community structure and function associated with long-term manipulation of sulfate and salinity in a hypersaline microbial mat. Environ Microbiol 2007; 10:386-94. [PMID: 18177370 DOI: 10.1111/j.1462-2920.2007.01459.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Methanogenesis was characterized in hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico both in situ and after long-term manipulation in a greenhouse environment. Substrate addition experiments indicate methanogenesis to occur primarily through the catabolic demethylation of non-competitive substrates, under field conditions. However, evidence for the coexistence of other metabolic guilds of methanogens was obtained during a previous manipulation of sulfate concentrations. To fully characterize methanogenesis in these mats, in the absence of competition for reducing equivalents with sulfate-reducing microorganisms, we maintained microbial mats for longer than 1 year under conditions of lowered sulfate and salinity levels. The goal of this study was to assess whether observed differences in methane production during sulfate and salinity manipulation were accompanied by shifts in the composition of methanogen communities. Culture-independent techniques targeting methyl coenzyme M reductase genes (mcrA) were used to assess the dynamics of methanogen assemblages. Clone libraries from mats sampled in situ or maintained at field-like conditions in the greenhouse were exclusively composed of sequences related to methylotrophic members of the Methanosarcinales. Increases in pore water methane concentrations under conditions of low sulfate correlated with an observed increase in the abundance of putatively hydrogenotrophic mcrA, related to Methanomicrobiales. Geochemical and molecular data provide evidence of a significant shift in the metabolic pathway of methanogenesis from a methylotroph-dominated system in high-sulfate environments to a mixed community of methylotrophic and hydrogenotrophic methanogens under low sulfate conditions.
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Affiliation(s)
- Jason M Smith
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
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