1
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Coon GR, Duesing PD, Paul R, Baily JA, Lloyd KG. Biological methane production and accumulation under sulfate-rich conditions at Cape Lookout Bight, NC. Front Microbiol 2023; 14:1268361. [PMID: 37869653 PMCID: PMC10587565 DOI: 10.3389/fmicb.2023.1268361] [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: 07/27/2023] [Accepted: 09/14/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction Anaerobic oxidation of methane (AOM) is hypothesized to occur through reverse hydrogenotrophic methanogenesis in marine sediments because sulfate reducers pull hydrogen concentrations so low that reverse hydrogenotrophic methanogenesis is exergonic. If true, hydrogenotrophic methanogenesis can theoretically co-occur with sulfate reduction if the organic matter is so labile that fermenters produce more hydrogen than sulfate reducers can consume, causing hydrogen concentrations to rise. Finding accumulation of biologically-produced methane in sulfate-containing organic-rich sediments would therefore support the theory that AOM occurs through reverse hydrogenotrophic methanogenesis since it would signal the absence of net AOM in the presence of sulfate. Methods 16S rRNA gene libraries were compared to geochemistry and incubations in high depth-resolution sediment cores collected from organic-rich Cape Lookout Bight, North Carolina. Results We found that methane began to accumulate while sulfate is still abundant (6-8 mM). Methane-cycling archaea ANME-1, Methanosarciniales, and Methanomicrobiales also increased at these depths. Incubations showed that methane production in the upper 16 cm in sulfate-rich sediments was biotic since it could be inhibited by 2-bromoethanosulfonoic acid (BES). Discussion We conclude that methanogens mediate biological methane production in these organic-rich sediments at sulfate concentrations that inhibit methanogenesis in sediments with less labile organic matter, and that methane accumulation and growth of methanogens can occur under these conditions as well. Our data supports the theory that H2 concentrations, rather than the co-occurrence of sulfate and methane, control whether methanogenesis or AOM via reverse hydrogenotrophic methanogenesis occurs. We hypothesize that the high amount of labile organic matter at this site prevents AOM, allowing methane accumulation when sulfate is low but still present in mM concentrations.
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2
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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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3
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Glass JB. What is the role of microbes in gas hydrate formation and stability? Environ Microbiol 2023; 25:45-48. [PMID: 36251262 DOI: 10.1111/1462-2920.16252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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4
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Sahu RP, Kazy SK, Bose H, Mandal S, Dutta A, Saha A, Roy S, Dutta Gupta S, Mukherjee A, Sar P. Microbial diversity and function in crystalline basement beneath the Deccan Traps explored in a 3 km borehole at Koyna, western India. Environ Microbiol 2021; 24:2837-2853. [PMID: 34897962 DOI: 10.1111/1462-2920.15867] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 12/20/2022]
Abstract
Deep terrestrial subsurface represents a huge repository of global prokaryotic biomass. Given its vastness and importance, microbial life within the deep subsurface continental crust remains under-represented in global studies. We characterize the microbial communities of deep, extreme and oligotrophic realm hosted by crystalline Archaean granitic rocks underneath the Deccan Traps, through sampling via 3000 m deep scientific borehole at Koyna, India through metagenomics, amplicon sequencing and cultivation-based analyses. Gene sequences 16S rRNA (7.37 × 106 ) show considerable bacterial diversity and the existence of a core microbiome (5724 operational taxonomic units conserved out of a total 118,064 OTUs) across the depths. Relative abundance of different taxa of core microbiome varies with depth in response to prevailing lithology and geochemistry. Co-occurrence network analysis and cultivation attempt to elucidate close interactions among autotrophic and organotrophic bacteria. Shotgun metagenomics reveals a major role of autotrophic carbon fixation via the Wood-Ljungdahl pathway and genes responsible for energy and carbon metabolism. Deeper analysis suggests the existence of an 'acetate switch', coordinating biosynthesis and cellular homeostasis. We conclude that the microbial life in the nutrient- and energy-limited deep granitic crust is constrained by the depth and managed by a few core members via a close interplay between autotrophy and organotrophy.
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Affiliation(s)
- Rajendra Prasad Sahu
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sufia K Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Himadri Bose
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sunanda Mandal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Avishek Dutta
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Anumeha Saha
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sukanta Roy
- Ministry of Earth Sciences, Borehole Geophysics Research Laboratory, Karad, MH, 415114, India
| | - Srimanti Dutta Gupta
- School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Abhijit Mukherjee
- School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India.,Department of Geology and Geophysics, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
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5
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Kaneko M, Takano Y, Kamo M, Morimoto K, Nunoura T, Ohkouchi N. Insights into the Methanogenic Population and Potential in Subsurface Marine Sediments Based on Coenzyme F430 as a Function-Specific Biomarker. JACS AU 2021; 1:1743-1751. [PMID: 34723277 PMCID: PMC8549059 DOI: 10.1021/jacsau.1c00307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Coenzyme F430, the prosthetic group of methyl coenzyme M reductase (MCR), is a key compound in methane metabolism. We applied coenzyme F430 as a function-specific biomarker of methanogenesis to subsurface marine sediments collected below the sulfate reduction zone to investigate the distribution and activity of methanogens. In addition, we examined the kinetics of the epimerization of coenzyme F430, which is the first stage of the degradation process after cell death, at various temperatures (4, 15, 34, 60 °C) and pH (5, 7, 9) conditions, which cover in situ conditions of drilled sediments used in this study. The degradation experiments revealed that the kinetics of the epimerization well follow the thermodynamic laws, and the half-life of coenzyme F430 is decreasing from 304 days to 11 h with increasing the in situ temperature. It indicates that the native F430 detected in the sediments is derived from living methanogens, because the abiotic degradation of F430 is much faster than the sedimentation rate and will not be fossilized. Based on coenzyme F430 analysis and degradation experiments, the native form of F430 detected in subseafloor sediments off the Shimokita Peninsula originates from living methanogen cells, which is protected from degradation in cells but disappears soon after cell death. The biomass of methanogens calculated from in situ F430 concentration and F430 contents in cultivable methanogen species decreases by 2 orders of magnitude up to a sediment depth of 2.5 km, with a maximum value at ∼70 m below the seafloor (mbsf), while the proportion of methanogens to the total prokaryotic cell abundance increases with the depth, which is 1 to 2 orders of magnitude higher than expected previously. Our results indicate the presence of undetectable methanogens using conventional techniques.
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Affiliation(s)
- Masanori Kaneko
- Geological
Survey of Japan, National Institute of Advanced
Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8567, Japan
- Biogeochemistry
Research Center, Japan Agency for Marine-Earth
Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshinori Takano
- Biogeochemistry
Research Center, Japan Agency for Marine-Earth
Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Masashi Kamo
- Research
Institute of Science for Safety and Sustainability, National Institute of Advanced Industrial Science and Technology
(AIST), 16-1 Onogawa, Tsukuba 305-8569, Japan
| | - Kazuya Morimoto
- Geological
Survey of Japan, National Institute of Advanced
Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8567, Japan
| | - Takuro Nunoura
- Research
Center for Bioscience and Nanoscience, Japan
Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Naohiko Ohkouchi
- Biogeochemistry
Research Center, Japan Agency for Marine-Earth
Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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6
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Emerson JB, Varner RK, Wik M, Parks DH, Neumann RB, Johnson JE, Singleton CM, Woodcroft BJ, Tollerson R, Owusu-Dommey A, Binder M, Freitas NL, Crill PM, Saleska SR, Tyson GW, Rich VI. Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes. Nat Commun 2021; 12:5815. [PMID: 34611153 PMCID: PMC8492752 DOI: 10.1038/s41467-021-25983-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/07/2021] [Indexed: 11/23/2022] Open
Abstract
Northern post-glacial lakes are significant, increasing sources of atmospheric carbon through ebullition (bubbling) of microbially-produced methane (CH4) from sediments. Ebullitive CH4 flux correlates strongly with temperature, reflecting that solar radiation drives emissions. However, here we show that the slope of the temperature-CH4 flux relationship differs spatially across two post-glacial lakes in Sweden. We compared these CH4 emission patterns with sediment microbial (metagenomic and amplicon), isotopic, and geochemical data. The temperature-associated increase in CH4 emissions was greater in lake middles—where methanogens were more abundant—than edges, and sediment communities were distinct between edges and middles. Microbial abundances, including those of CH4-cycling microorganisms and syntrophs, were predictive of porewater CH4 concentrations. Results suggest that deeper lake regions, which currently emit less CH4 than shallower edges, could add substantially to CH4 emissions in a warmer Arctic and that CH4 emission predictions may be improved by accounting for spatial variations in sediment microbiota. Arctic lakes are strong and increasing sources of atmospheric methane, but extreme conditions and limited observations hinder robust understanding. Here the authors show that microbes in the middle of Arctic lakes have elevated methane producing potential, and are poised to release even more in the future.
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Affiliation(s)
- Joanne B Emerson
- Department of Microbiology, The Ohio State University, 496W 12th Ave, Columbus, OH, 43210, USA. .,Department of Plant Pathology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.
| | - Ruth K Varner
- Department of Earth Sciences, University of New Hampshire, 56 College Road, Durham, NH, 03824, USA. .,Earth Systems Research Center, Institute for the Study of Earth, Oceans and Space, University of New Hampshire, 8 College Road, Durham, NH, 03824, USA.
| | - Martin Wik
- Department of Geological Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Rebecca B Neumann
- Civil & Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA
| | - Joel E Johnson
- Department of Earth Sciences, University of New Hampshire, 56 College Road, Durham, NH, 03824, USA
| | - Caitlin M Singleton
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia.,Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, 9220, Denmark
| | - Ben J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Rodney Tollerson
- Department of Microbiology, The Ohio State University, 496W 12th Ave, Columbus, OH, 43210, USA.,Department of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91106, USA
| | - Akosua Owusu-Dommey
- Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, USA.,Parkland Hospital, 5200 Harry Hines Blvd., Dallas, TX, 75235, USA
| | - Morgan Binder
- Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, USA.,John C. Lincoln Health Network, 34975N North Valley Pkwy Ste 100, Phoenix, AZ, 85086, USA
| | - Nancy L Freitas
- Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, USA.,Energy and Resources Group, University of California, Berkeley, USA
| | - Patrick M Crill
- Department of Geological Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Scott R Saleska
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia.,Centre for Microbiome Research, Queensland University of Technology, 37 Kent St, Woolloongabba, QLD, 4102, Australia
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, 496W 12th Ave, Columbus, OH, 43210, USA.
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7
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Kong Y, Lei H, Zhang Z, Cheng W, Wang B, Pan F, Huang F, Huang F, Li W. Depth profiles of geochemical features, geochemical activities and biodiversity of microbial communities in marine sediments from the Shenhu area, the northern South China Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146233. [PMID: 34030248 DOI: 10.1016/j.scitotenv.2021.146233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
The biogeochemical processes, anaerobic oxidation of methane (AOM) and methanogenesis, control methane emission and create distinct geochemical profiles with depth in marine sediments. Correlating the capacities and biodiversity of the microbial communities in marine sediments remains challenging. We therefore investigated the geochemical constituents and the capabilities and diversity of microbial communities in sediments at different depths in two cores from the Shenhu area in the northern South China Sea, which is characterized by underlying gas hydrates. The geochemical features, sulfate concentration decreased linearly and the acid volatile sulfur accumulated from 4 m below the seafloor (mbsf) to the bottom, indicating significant sulfate reduction. However, the methane concentration was relatively low and showed irregular trends, indicating that our study cores did not reach the sulfate-methane transition zone (SMTZ). Nevertheless, incubation experiments showed that the microbial groups in sediments performed AOM and methanogenesis in the region where sulfate decreased linearly above the SMTZ. We mapped the diversity and abundance of microbial communities in sediments with depth using high-throughput sequencing. A small proportion of known methanogens (<0.3%) may have been responsible for the methanogenesis during incubation. No classical archaeal anaerobic methanotroph (ANME) sequences were detected across all samples; only a small amount of SEEP-SRB1 were detected, and their abundance did not increase with increasing depth. Thus, unknown or unconventional phylotypes may have participated in AOM during the incubation, and the dominant phylum Bathyarchaeota or the small number of detected methanogens are the most likely performers of AOM.
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Affiliation(s)
- Yuan Kong
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Huaiyan Lei
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China.
| | - Zilian Zhang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Weidong Cheng
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Bin Wang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Fulong Pan
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Fanfan Huang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Fanli Huang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Wenqing Li
- Key Laboratory of Mineral Resources Evaluation in Northeast China, Ministry of Land and Resources, Changchun 130061, PR China
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8
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Ranchou-Peyruse M, Auguet JC, Mazière C, Restrepo-Ortiz CX, Guignard M, Dequidt D, Chiquet P, Cézac P, Ranchou-Peyruse A. Geological gas-storage shapes deep life. Environ Microbiol 2019; 21:3953-3964. [PMID: 31314939 DOI: 10.1111/1462-2920.14745] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/14/2019] [Indexed: 11/28/2022]
Abstract
Around the world, several dozen deep sedimentary aquifers are being used for storage of natural gas. Ad hoc studies of the microbial ecology of some of them have suggested that sulfate reducing and methanogenic microorganisms play a key role in how these aquifers' communities function. Here, we investigate the influence of gas storage on these two metabolic groups by using high-throughput sequencing and show the importance of sulfate-reducing Desulfotomaculum and a new monophyletic methanogenic group. Aquifer microbial diversity was significantly related to the geological level. The distance to the stored natural gas affects the ratio of sulfate-reducing Firmicutes to deltaproteobacteria. In only one aquifer, the methanogenic archaea dominate the sulfate-reducers. This aquifer was used to store town gas (containing at least 50% H2 ) around 50 years ago. The observed decrease of sulfates in this aquifer could be related to stimulation of subsurface sulfate-reducers. These results suggest that the composition of the microbial communities is impacted by decades old transient gas storage activity. The tremendous stability of these gas-impacted deep subsurface microbial ecosystems suggests that in situ biotic methanation projects in geological reservoirs may be sustainable over time.
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Affiliation(s)
- Magali Ranchou-Peyruse
- CNRS/Univ Pau & Pays Adour/E2S-UPPA, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, UMR5254, 000, Pau, France
| | - Jean-Christophe Auguet
- MARBEC, Montpellier University, CNRS, IFREMER, IRD, Place Eugène Bataillon, Montpellier, France
| | - Camille Mazière
- CNRS/Univ Pau & Pays Adour/E2S-UPPA, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, UMR5254, 000, Pau, France.,MARBEC, Montpellier University, CNRS, IFREMER, IRD, Place Eugène Bataillon, Montpellier, France
| | | | - Marion Guignard
- CNRS/Univ Pau & Pays Adour/E2S-UPPA, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, UMR5254, 000, Pau, France
| | - David Dequidt
- STORENGY - Geosciences Department, Bois-Colombes, France
| | | | - Pierre Cézac
- Laboratoire de Thermique, Énergétique et Procédés IPRA, EA1932, Univ Pau & Pays Adour/E2S-UPPA, 000, Pau, France
| | - Anthony Ranchou-Peyruse
- CNRS/Univ Pau & Pays Adour/E2S-UPPA, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, UMR5254, 000, Pau, France
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9
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Abstract
It is increasingly accepted that the microbial symbionts of eukaryotes can have profound effects on host ecology and evolution. However, the relative contribution that they make directly to ecosystem processes, like energy and nutrient flows, is less explicitly acknowledged and, in many cases, only poorly constrained. It is increasingly accepted that the microbial symbionts of eukaryotes can have profound effects on host ecology and evolution. However, the relative contribution that they make directly to ecosystem processes, like energy and nutrient flows, is less explicitly acknowledged and, in many cases, only poorly constrained. Here, I explore the idea that, in some habitats, host-associated microbes may have an outsized role in ecosystem processes relative to functionally equivalent free-living microbes due to key aspects of the physiology, ecology, and evolution of symbiotic interactions. My research quantifying symbiont metabolism has shown that microbial symbionts have the potential to make a substantial impact on carbon and sulfur cycling. It is my perspective that direct measurement of symbiont activity and comparison to free-living counterparts will expand our understanding of the significance of microbial symbioses and, more broadly, the role of microbial processes in ecosystems.
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10
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Forearc carbon sink reduces long-term volatile recycling into the mantle. Nature 2019; 568:487-492. [PMID: 31019327 DOI: 10.1038/s41586-019-1131-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 02/08/2019] [Indexed: 11/08/2022]
Abstract
Carbon and other volatiles in the form of gases, fluids or mineral phases are transported from Earth's surface into the mantle at convergent margins, where the oceanic crust subducts beneath the continental crust. The efficiency of this transfer has profound implications for the nature and scale of geochemical heterogeneities in Earth's deep mantle and shallow crustal reservoirs, as well as Earth's oxidation state. However, the proportions of volatiles released from the forearc and backarc are not well constrained compared to fluxes from the volcanic arc front. Here we use helium and carbon isotope data from deeply sourced springs along two cross-arc transects to show that about 91 per cent of carbon released from the slab and mantle beneath the Costa Rican forearc is sequestered within the crust by calcite deposition. Around an additional three per cent is incorporated into the biomass through microbial chemolithoautotrophy, whereby microbes assimilate inorganic carbon into biomass. We estimate that between 1.2 × 108 and 1.3 × 1010 moles of carbon dioxide per year are released from the slab beneath the forearc, and thus up to about 19 per cent less carbon is being transferred into Earth's deep mantle than previously estimated.
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11
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Vishnivetskaya TA, Buongiorno J, Bird J, Krivushin K, Spirina EV, Oshurkova V, Shcherbakova VA, Wilson G, Lloyd KG, Rivkina EM. Methanogens in the Antarctic Dry Valley permafrost. FEMS Microbiol Ecol 2018; 94:5033399. [DOI: 10.1093/femsec/fiy109] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 06/01/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tatiana A Vishnivetskaya
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, 142290, Russia
- University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Jordan Bird
- University of Tennessee, Knoxville, TN, 37996, USA
| | - Kirill Krivushin
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Elena V Spirina
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Victoria Oshurkova
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, 142290, Russia
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Victoria A Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Gary Wilson
- University of Otago, Dunedin, 9054, New Zealand
| | | | - Elizaveta M Rivkina
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, 142290, Russia
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12
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Carr SA, Schubotz F, Dunbar RB, Mills CT, Dias R, Summons RE, Mandernack KW. Acetoclastic Methanosaeta are dominant methanogens in organic-rich Antarctic marine sediments. ISME JOURNAL 2017; 12:330-342. [PMID: 29039843 PMCID: PMC5776447 DOI: 10.1038/ismej.2017.150] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 06/16/2017] [Accepted: 06/24/2017] [Indexed: 01/11/2023]
Abstract
Despite accounting for the majority of sedimentary methane, the physiology and relative abundance of subsurface methanogens remain poorly understood. We combined intact polar lipid and metagenome techniques to better constrain the presence and functions of methanogens within the highly reducing, organic-rich sediments of Antarctica's Adélie Basin. The assembly of metagenomic sequence data identified phylogenic and functional marker genes of methanogens and generated the first Methanosaeta sp. genome from a deep subsurface sedimentary environment. Based on structural and isotopic measurements, glycerol dialkyl glycerol tetraethers with diglycosyl phosphatidylglycerol head groups were classified as biomarkers for active methanogens. The stable carbon isotope (δ13C) values of these biomarkers and the Methanosaeta partial genome suggest that these organisms are acetoclastic methanogens and represent a relatively small (0.2%) but active population. Metagenomic and lipid analyses suggest that Thaumarchaeota and heterotrophic bacteria co-exist with Methanosaeta and together contribute to increasing concentrations and δ13C values of dissolved inorganic carbon with depth. This study presents the first functional insights of deep subsurface Methanosaeta organisms and highlights their role in methane production and overall carbon cycling within sedimentary environments.
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Affiliation(s)
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Robert B Dunbar
- Department of Environmental Earth Systems Science, Stanford University, Stanford, CA, USA
| | | | - Robert Dias
- US Geological Survey, Denver Federal Center, Denver, CO, USA
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kevin W Mandernack
- Department of Earth Sciences, Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA
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13
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Wyss L, Stadinski BD, King CG, Schallenberg S, McCarthy NI, Lee JY, Kretschmer K, Terracciano LM, Anderson G, Surh CD, Huseby ES, Palmer E. Affinity for self antigen selects Treg cells with distinct functional properties. Nat Immunol 2016; 17:1093-101. [PMID: 27478940 PMCID: PMC4994872 DOI: 10.1038/ni.3522] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/27/2016] [Indexed: 12/30/2022]
Abstract
The manner in which regulatory T cells (Treg cells) control lymphocyte homeostasis is not fully understood. We identified two Treg cell populations with differing degrees of self-reactivity and distinct regulatory functions. We found that GITR(hi)PD-1(hi)CD25(hi) (Triple(hi)) Treg cells were highly self-reactive and controlled lympho-proliferation in peripheral lymph nodes. GITR(lo)PD-1(lo)CD25(lo) (Triple(lo)) Treg cells were less self-reactive and limited the development of colitis by promoting the conversion of CD4(+) Tconv cells into induced Treg cells (iTreg cells). Although Foxp3-deficient (Scurfy) mice lacked Treg cells, they contained Triple(hi)-like and Triple(lo)-like CD4(+) T cells zsuper> T cells infiltrated the skin, whereas Scurfy Triple(lo)CD4(+) T cells induced colitis and wasting disease. These findings indicate that the affinity of the T cell antigen receptor for self antigen drives the differentiation of Treg cells into distinct subsets with non-overlapping regulatory activities.
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Affiliation(s)
- Lena Wyss
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
- Department of Nephrology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Brian D Stadinski
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Carolyn G King
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Sonja Schallenberg
- Molecular and Cellular Immunology/Immune Regulation, DFG-Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Nicholas I McCarthy
- MRC Centre for Immune Regulation, Institute for Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Jun Young Lee
- Academy of Immunology and Microbiology, Institute for Basic Science, Pohang, Republic of Korea
- Department of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Karsten Kretschmer
- Molecular and Cellular Immunology/Immune Regulation, DFG-Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden, German Center for Diabetes Research (DZD), Dresden, Germany
| | - Luigi M Terracciano
- Institute of Pathology, Molecular Pathology Division, University Hospital of Basel, Basel, Switzerland
| | - Graham Anderson
- MRC Centre for Immune Regulation, Institute for Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Charles D Surh
- Academy of Immunology and Microbiology, Institute for Basic Science, Pohang, Republic of Korea
- Department of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Eric S Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Ed Palmer
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
- Department of Nephrology, University Hospital Basel and University of Basel, Basel, Switzerland
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14
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Katayama T, Yoshioka H, Takahashi HA, Amo M, Fujii T, Sakata S. Changes in microbial communities associated with gas hydrates in subseafloor sediments from the Nankai Trough. FEMS Microbiol Ecol 2016; 92:fiw093. [DOI: 10.1093/femsec/fiw093] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2016] [Indexed: 01/17/2023] Open
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15
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Honkalas V, Dabir A, Dhakephalkar PK. Life in the Anoxic Sub-Seafloor Environment: Linking Microbial Metabolism and Mega Reserves of Methane Hydrate. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 156:235-262. [DOI: 10.1007/10_2015_5004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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16
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Nunoura T, Takaki Y, Shimamura S, Kakuta J, Kazama H, Hirai M, Masui N, Tomaru H, Morono Y, Imachi H, Inagaki F, Takai K. Variance and potential niche separation of microbial communities in subseafloor sediments off Shimokita Peninsula, Japan. Environ Microbiol 2015; 18:1889-906. [PMID: 26486095 DOI: 10.1111/1462-2920.13096] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/21/2015] [Accepted: 10/05/2015] [Indexed: 01/23/2023]
Abstract
Subseafloor pelagic sediments with high concentrations of organic matter form habitats for diverse microorganisms. Here, we determined depth profiles of genes for SSU rRNA, mcrA, dsrA and amoA from just beneath the seafloor to 363.3 m below the seafloor (mbsf) using core samples obtained from the forearc basin off the Shimokita Peninsula. The molecular profiles were combined with data on lithostratigraphy, depositional age, sedimentation rate and pore-water chemistry. The SSU rRNA gene tag structure and diversity changed at around the sulfate-methane transition zone (SMTZ), whereas the profiles varied further with depth below the SMTZ, probably in connection with the variation in pore-water chemistry. The depth profiles of diversity and abundance of dsrA, a key gene for sulfate reduction, suggested the possible niche separations of sulfate-reducing populations, even below the SMTZ. The diversity and abundance patterns of mcrA, a key gene for methanogenesis/anaerobic methanotrophy, suggested a stratified distribution and separation of anaerobic methanotrophy and hydrogenotrophic or methylotrophic methanogensis below the SMTZ. This study provides novel insights into the relationships between the composition and function of microbial communities and the chemical environment in the nutrient-rich continental margin subseafloor sediments, which may result in niche separation and variability in subseafloor microbial populations.
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Affiliation(s)
- Takuro Nunoura
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshihiro Takaki
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.,Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shigeru Shimamura
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Jungo Kakuta
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Hiromi Kazama
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Miho Hirai
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Noriaki Masui
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Hitoshi Tomaru
- Department of Earth Sciences, Chiba University, Chiba, Inageku, Japan
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Hiroyuki Imachi
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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17
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Carr SA, Orcutt BN, Mandernack KW, Spear JR. Abundant Atribacteria in deep marine sediment from the Adélie Basin, Antarctica. Front Microbiol 2015; 6:872. [PMID: 26379647 PMCID: PMC4549626 DOI: 10.3389/fmicb.2015.00872] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 08/10/2015] [Indexed: 02/01/2023] Open
Abstract
Bacteria belonging to the newly classified candidate phylum “Atribacteria” (formerly referred to as “OP9” and “JS1”) are common in anoxic methane-rich sediments. However, the metabolic functions and biogeochemical role of these microorganisms in the subsurface remains unrealized due to the lack of pure culture representatives. In this study of deep sediment from Antarctica’s Adélie Basin, collected during Expedition 318 of the Integrated Ocean Drilling Program (IODP), Atribacteria-related sequences of the 16S rRNA gene were abundant (up to 51% of the sequences) and steadily increased in relative abundance with depth throughout the methane-rich zones. To better understand the metabolic potential of Atribacteria within this environment, and to compare with phylogenetically distinct Atribacteria from non-deep-sea environments, individual cells were sorted for single cell genomics from sediment collected from 97.41 m below the seafloor from IODP Hole U1357C. As observed for non-marine Atribacteria, a partial single cell genome suggests a heterotrophic metabolism, with Atribacteria potentially producing fermentation products such as acetate, ethanol, and CO2. These products may in turn support methanogens within the sediment microbial community and explain the frequent occurrence of Atribacteria in anoxic methane-rich sediments. This first report of a single cell genome from deep sediment broadens the known diversity within the Atribacteria phylum and highlights the potential role of Atribacteria in carbon cycling in deep sediment.
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Affiliation(s)
- Stephanie A Carr
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden CO, USA
| | - Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay ME, USA
| | - Kevin W Mandernack
- Department of Earth Sciences, Indiana University - Purdue University Indianapolis, Indianapolis IN, USA
| | - John R Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden CO, USA
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18
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Inagaki F, Hinrichs KU, Kubo Y, Bowles MW, Heuer VB, Hong WL, Hoshino T, Ijiri A, Imachi H, Ito M, Kaneko M, Lever MA, Lin YS, Methé BA, Morita S, Morono Y, Tanikawa W, Bihan M, Bowden SA, Elvert M, Glombitza C, Gross D, Harrington GJ, Hori T, Li K, Limmer D, Liu CH, Murayama M, Ohkouchi N, Ono S, Park YS, Phillips SC, Prieto-Mollar X, Purkey M, Riedinger N, Sanada Y, Sauvage J, Snyder G, Susilawati R, Takano Y, Tasumi E, Terada T, Tomaru H, Trembath-Reichert E, Wang DT, Yamada Y. DEEP BIOSPHERE. Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor. Science 2015. [PMID: 26206933 DOI: 10.1126/science.aaa6882] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ~40° to 60°C sediment associated with lignite coal beds at ~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers, cultivation data, and gas compositions. Concentrations of indigenous microbial cells below 1.5 km ranged from <10 to ~10(4) cells cm(-3). Peak concentrations occurred in lignite layers, where communities differed markedly from shallower subseafloor communities and instead resembled organotrophic communities in forest soils. This suggests that terrigenous sediments retain indigenous community members tens of millions of years after burial in the seabed.
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Affiliation(s)
- F Inagaki
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan. Research and Development Center for Marine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - K-U Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, D-28359 Bremen, Germany
| | - Y Kubo
- Center for Deep-Earth Exploration, JAMSTEC, Yokohama 236-0061, Japan. Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama 236-0001, Japan
| | - M W Bowles
- MARUM Center for Marine Environmental Sciences, University of Bremen, D-28359 Bremen, Germany
| | - V B Heuer
- MARUM Center for Marine Environmental Sciences, University of Bremen, D-28359 Bremen, Germany
| | - W-L Hong
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - T Hoshino
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan. Research and Development Center for Marine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - A Ijiri
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan. Research and Development Center for Marine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - H Imachi
- Research and Development Center for Marine Resources, JAMSTEC, Yokosuka 237-0061, Japan. Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
| | - M Ito
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan. Research and Development Center for Marine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - M Kaneko
- Research and Development Center for Marine Resources, JAMSTEC, Yokosuka 237-0061, Japan. Department of Biogeochemistry, JAMSTEC, Yokosuka 237-0061, Japan
| | - M A Lever
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Y-S Lin
- MARUM Center for Marine Environmental Sciences, University of Bremen, D-28359 Bremen, Germany
| | - B A Methé
- Department of Environmental Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - S Morita
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8567, Japan
| | - Y Morono
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan. Research and Development Center for Marine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - W Tanikawa
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan. Research and Development Center for Marine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - M Bihan
- Department of Environmental Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - S A Bowden
- Department of Geology and Petroleum Geology, School of Geosciences, University of Aberdeen, Aberdeen AB2A 3UE, UK
| | - M Elvert
- MARUM Center for Marine Environmental Sciences, University of Bremen, D-28359 Bremen, Germany
| | - C Glombitza
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, DK-8000 Aarhus C, Denmark
| | - D Gross
- Department of Applied Geosciences and Geophysics, Montanuniversität, 8700 Leoben, Austria
| | - G J Harrington
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - T Hori
- Environmental Management Research Institute, AIST, Tsukuba, Ibaraki 305-8569, Japan
| | - K Li
- Department of Environmental Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - D Limmer
- Department of Geology and Petroleum Geology, School of Geosciences, University of Aberdeen, Aberdeen AB2A 3UE, UK
| | - C-H Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, Jiangsu 210093, China
| | - M Murayama
- Center for Advanced Marine Core Research, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - N Ohkouchi
- Research and Development Center for Marine Resources, JAMSTEC, Yokosuka 237-0061, Japan. Department of Biogeochemistry, JAMSTEC, Yokosuka 237-0061, Japan
| | - S Ono
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Y-S Park
- Petroleum and Marine Resources Research Division, Korea Institute of Geoscience and Mineral Resources, Yuseong-gu, Daejeon 305-350, Korea
| | - S C Phillips
- Department of Earth Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - X Prieto-Mollar
- MARUM Center for Marine Environmental Sciences, University of Bremen, D-28359 Bremen, Germany
| | - M Purkey
- Department of Earth and Atmospheric Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - N Riedinger
- Department of Earth Sciences, University of California Riverside, Riverside, CA 92521, USA
| | - Y Sanada
- Center for Deep-Earth Exploration, JAMSTEC, Yokohama 236-0061, Japan. Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama 236-0001, Japan
| | - J Sauvage
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - G Snyder
- Department of Earth Science, Rice University, Houston, TX 77005, USA
| | - R Susilawati
- School of Earth Science, University of Queensland, Brisbane Queensland 4072, Australia
| | - Y Takano
- Research and Development Center for Marine Resources, JAMSTEC, Yokosuka 237-0061, Japan. Department of Biogeochemistry, JAMSTEC, Yokosuka 237-0061, Japan
| | - E Tasumi
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
| | - T Terada
- Marine Works Japan, Yokosuka 237-0063, Japan
| | - H Tomaru
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
| | - E Trembath-Reichert
- Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - D T Wang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Y Yamada
- Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama 236-0001, Japan. Department of Urban Management, Graduate School of Engineering, Kyoto University, Kyoto 615-8540, Japan
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Tucker YT, Kotcon J, Mroz T. Methanogenic archaea in marcellus shale: a possible mechanism for enhanced gas recovery in unconventional shale resources. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:7048-7055. [PMID: 25924080 DOI: 10.1021/acs.est.5b00765] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Marcellus Shale occurs at depths of 1.5-2.5 km (5000 to 8000 feet) where most geologists generally assume that thermogenic processes are the only source of natural gas. However, methanogens in produced fluids and isotopic signatures of biogenic methane in this deep shale have recently been discovered. This study explores whether those methanogens are indigenous to the shale or are introduced during drilling and hydraulic fracturing. DNA was extracted from Marcellus Shale core samples, preinjected fluids, and produced fluids and was analyzed using Miseq sequencing of 16s rRNA genes. Methanogens present in shale cores were similar to methanogens in produced fluids. No methanogens were detected in injected fluids, suggesting that this is an unlikely source and that they may be native to the shale itself. Bench-top methane production tests of shale core and produced fluids suggest that these organisms are alive and active under simulated reservoir conditions. Growth conditions designed to simulate the hydrofracture processes indicated somewhat increased methane production; however, fluids alone produced relatively little methane. Together, these results suggest that some biogenic methane may be produced in these wells and that hydrofracture fluids currently used to stimulate gas recovery could stimulate methanogens and their rate of producing methane.
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Affiliation(s)
- Yael Tarlovsky Tucker
- †National Energy Technology Laboratory, United States Department of Energy, 3610 Collins Ferry Road, Post Office Box 880, Morgantown, West Virginia 26505, United States
- ‡Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia 26505, United States
| | - James Kotcon
- ‡Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Thomas Mroz
- †National Energy Technology Laboratory, United States Department of Energy, 3610 Collins Ferry Road, Post Office Box 880, Morgantown, West Virginia 26505, United States
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20
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Lever MA, Rogers KL, Lloyd KG, Overmann J, Schink B, Thauer RK, Hoehler TM, Jørgensen BB. Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations. FEMS Microbiol Rev 2015; 39:688-728. [PMID: 25994609 DOI: 10.1093/femsre/fuv020] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2015] [Indexed: 11/13/2022] Open
Abstract
The ability of microorganisms to withstand long periods with extremely low energy input has gained increasing scientific attention in recent years. Starvation experiments in the laboratory have shown that a phylogenetically wide range of microorganisms evolve fitness-enhancing genetic traits within weeks of incubation under low-energy stress. Studies on natural environments that are cut off from new energy supplies over geologic time scales, such as deeply buried sediments, suggest that similar adaptations might mediate survival under energy limitation in the environment. Yet, the extent to which laboratory-based evidence of starvation survival in pure or mixed cultures can be extrapolated to sustained microbial ecosystems in nature remains unclear. In this review, we discuss past investigations on microbial energy requirements and adaptations to energy limitation, identify gaps in our current knowledge, and outline possible future foci of research on life under extreme energy limitation.
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Affiliation(s)
- Mark A Lever
- Center for Geomicrobiology, Institute of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Karyn L Rogers
- Rensselaer Polytechnic Institute, Earth and Environmental Sciences, Jonsson-Rowland Science Center, 1W19, 110 8th Street, Troy, NY 12180, USA
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee at Knoxville, M409 Walters Life Sciences, Knoxville, TN 37996-0845, USA
| | - Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - Bernhard Schink
- Microbial Ecology, Department of Biology, University of Konstanz, P.O. Box 55 60, D-78457 Konstanz, Germany
| | - Rudolf K Thauer
- Max Planck Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße, D-35043 Marburg, Germany
| | - Tori M Hoehler
- NASA Ames Research Center, Mail Stop 239-4, Moffett Field, CA 94035-1000, USA
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Institute of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
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21
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Morono Y, Terada T, Yamamoto Y, Xiao N, Hirose T, Sugeno M, Ohwada N, Inagaki F. Intact preservation of environmental samples by freezing under an alternating magnetic field. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:243-251. [PMID: 25403324 DOI: 10.1111/1758-2229.12238] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/19/2017] [Accepted: 10/10/2014] [Indexed: 06/04/2023]
Abstract
The study of environmental samples requires a preservation system that stabilizes the sample structure, including cells and biomolecules. To address this fundamental issue, we tested the cell alive system (CAS)-freezing technique for subseafloor sediment core samples. In the CAS-freezing technique, an alternating magnetic field is applied during the freezing process to produce vibration of water molecules and achieve a stable, super-cooled liquid phase. Upon further cooling, the temperature decreases further, achieving a uniform freezing of sample with minimal ice crystal formation. In this study, samples were preserved using the CAS and conventional freezing techniques at 4, -20, -80 and -196 (liquid nitrogen) °C. After 6 months of storage, microbial cell counts by conventional freezing significantly decreased (down to 10.7% of initial), whereas that by CAS-freezing resulted in minimal. When Escherichia coli cells were tested under the same freezing conditions and storage for 2.5 months, CAS-frozen E. coli cells showed higher viability than the other conditions. In addition, an alternating magnetic field does not impact on the direction of remanent magnetization in sediment core samples, although slight partial demagnetization in intensity due to freezing was observed. Consequently, our data indicate that the CAS technique is highly useful for the preservation of environmental samples.
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Affiliation(s)
- Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe B200, Nankoku, Kochi, 783-8502, Japan; Geobiotechnology Group, Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe B200, Nankoku, Kochi, 783-8502, Japan
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Matheus Carnevali PB, Rohrssen M, Williams MR, Michaud AB, Adams H, Berisford D, Love GD, Priscu JC, Rassuchine O, Hand KP, Murray AE. Methane sources in arctic thermokarst lake sediments on the North Slope of Alaska. GEOBIOLOGY 2015; 13:181-197. [PMID: 25612141 DOI: 10.1111/gbi.12124] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 12/19/2014] [Indexed: 06/04/2023]
Abstract
The permafrost on the North Slope of Alaska is densely populated by shallow lakes that result from thermokarst erosion. These lakes release methane (CH4 ) derived from a combination of ancient thermogenic pools and contemporary biogenic production. Despite the potential importance of CH4 as a greenhouse gas, the contribution of biogenic CH4 production in arctic thermokarst lakes in Alaska is not currently well understood. To further advance our knowledge of CH4 dynamics in these lakes, we focused our study on (i) the potential for microbial CH4 production in lake sediments, (ii) the role of sediment geochemistry in controlling biogenic CH4 production, and (iii) the temperature dependence of this process. Sediment cores were collected from one site in Siqlukaq Lake and two sites in Sukok Lake in late October to early November. Analyses of pore water geochemistry, sedimentary organic matter and lipid biomarkers, stable carbon isotopes, results from CH4 production experiments, and copy number of a methanogenic pathway-specific gene (mcrA) indicated the existence of different sources of CH4 in each of the lakes chosen for the study. Analysis of this integrated data set revealed that there is biological CH4 production in Siqlukaq at moderate levels, while the very low levels of CH4 detected in Sukok had a mixed origin, with little to no biological CH4 production. Furthermore, methanogenic archaea exhibited temperature-dependent use of in situ substrates for methanogenesis, and the amount of CH4 produced was directly related to the amount of labile organic matter in the sediments. This study constitutes an important first step in better understanding the actual contribution of biogenic CH4 from thermokarst lakes on the coastal plain of Alaska to the current CH4 budgets.
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Affiliation(s)
- P B Matheus Carnevali
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA; Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
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23
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Primers: Functional Genes and 16S rRNA Genes for Methanogens. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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24
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Pathak H, Wölk J, Strey R, Wyslouzil BE. Co-condensation of nonane and D2O in a supersonic nozzle. J Chem Phys 2014; 140:034304. [DOI: 10.1063/1.4861052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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25
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Onstott TC, Magnabosco C, Aubrey AD, Burton AS, Dworkin JP, Elsila JE, Grunsfeld S, Cao BH, Hein JE, Glavin DP, Kieft TL, Silver BJ, Phelps TJ, van Heerden E, Opperman DJ, Bada JL. Does aspartic acid racemization constrain the depth limit of the subsurface biosphere? GEOBIOLOGY 2014; 12:1-19. [PMID: 24289240 DOI: 10.1111/gbi.12069] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 11/06/2013] [Indexed: 06/02/2023]
Abstract
Previous studies of the subsurface biosphere have deduced average cellular doubling times of hundreds to thousands of years based upon geochemical models. We have directly constrained the in situ average cellular protein turnover or doubling times for metabolically active micro-organisms based on cellular amino acid abundances, D/L values of cellular aspartic acid, and the in vivo aspartic acid racemization rate. Application of this method to planktonic microbial communities collected from deep fractures in South Africa yielded maximum cellular amino acid turnover times of ~89 years for 1 km depth and 27 °C and 1-2 years for 3 km depth and 54 °C. The latter turnover times are much shorter than previously estimated cellular turnover times based upon geochemical arguments. The aspartic acid racemization rate at higher temperatures yields cellular protein doubling times that are consistent with the survival times of hyperthermophilic strains and predicts that at temperatures of 85 °C, cells must replace proteins every couple of days to maintain enzymatic activity. Such a high maintenance requirement may be the principal limit on the abundance of living micro-organisms in the deep, hot subsurface biosphere, as well as a potential limit on their activity. The measurement of the D/L of aspartic acid in biological samples is a potentially powerful tool for deep, fractured continental and oceanic crustal settings where geochemical models of carbon turnover times are poorly constrained. Experimental observations on the racemization rates of aspartic acid in living thermophiles and hyperthermophiles could test this hypothesis. The development of corrections for cell wall peptides and spores will be required, however, to improve the accuracy of these estimates for environmental samples.
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Affiliation(s)
- T C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, USA; Indiana Princeton Tennessee Astrobiology Initiative (IPTAI), NASA Astrobiology Institute, Indiana University, Bloomington, IN, USA
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26
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Zeleke J, Lu SL, Wang JG, Huang JX, Li B, Ogram AV, Quan ZX. Methyl coenzyme M reductase A (mcrA) gene-based investigation of methanogens in the mudflat sediments of Yangtze River estuary, China. MICROBIAL ECOLOGY 2013; 66:257-267. [PMID: 23306392 DOI: 10.1007/s00248-012-0155-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 12/09/2012] [Indexed: 06/01/2023]
Abstract
Methanogen populations of an intertidal mudflat in the Yangtze River estuary of China were investigated based on the methyl coenzyme M reductase A (mcrA) gene using 454-pyrosequencing and quantitative real-time polymerase chain reaction (qPCR). Samples were collected at six depths from three locations. In the qPCR analyses, a mean depth-wise change of mcrA gene abundance was observed from (1.23 ± 0.13) × 10(7) to (1.16 ± 0.29) × 10(8) per g dried soil, which was inversely correlated with the depletion of sulfate (R(2) = 0.74; α = 0.05) and salinity (R (2) = 0.66; α = 0.05). The copy numbers of mcrA was at least 1 order of magnitude higher than dissimilatory sulfate reductase B (dsrB) genes, likely indicating the importance of methanogenesis at the mudflat. Sequences related to the orders Methanomicrobiales, Methanosarcinales, Methanobacteriales, Methanococcales and the uncultured methanogens; Rice Cluster I (RC-I), Zoige cluster I (ZC-I) and anaerobic methane oxidizing archaeal lineage-1 (ANME-1) were detected. Methanomicrobiales and Methanosarcinales dominated the entire sediment layers, but detectable changes of proportions were observed with depth. The hydrogenotrophic methanogens Methanomicrobiales slightly increased with depth while Methanosarcinales showed the reverse. Chao1 and ACE richness estimators revealed higher diversity of methanogens near the surface (0-10 cm) when compared with the bottom sediments. The near-surface sediments were mainly dominated by the family Methanosarcinaceae (45 %), which has members that can utilize substrates that cannot be used by sulfate-reducing bacteria. Overall, current data indicate that Methanosarcinales and Methanomicrobiales are the most dominant methanogens within the entire depth profile down to 100 cm, with higher abundance and diversity of methanogens in the deeper and upper sediment layers, respectively.
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Affiliation(s)
- Jemaneh Zeleke
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China
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27
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Orcutt BN, Larowe DE, Biddle JF, Colwell FS, Glazer BT, Reese BK, Kirkpatrick JB, Lapham LL, Mills HJ, Sylvan JB, Wankel SD, Wheat CG. Microbial activity in the marine deep biosphere: progress and prospects. Front Microbiol 2013; 4:189. [PMID: 23874326 PMCID: PMC3708129 DOI: 10.3389/fmicb.2013.00189] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 06/20/2013] [Indexed: 11/17/2022] Open
Abstract
The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org).
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Affiliation(s)
- Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
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Marquez GPB, Reichardt WT, Azanza RV, Klocke M, Montaño MNE. Thalassic biogas production from sea wrack biomass using different microbial seeds: cow manure, marine sediment and sea wrack-associated microflora. BIORESOURCE TECHNOLOGY 2013; 133:612-617. [PMID: 23453978 DOI: 10.1016/j.biortech.2013.01.082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/11/2013] [Accepted: 01/16/2013] [Indexed: 06/01/2023]
Abstract
Sea wrack (dislodged sea grasses and seaweeds) was used in biogas production. Fresh water scarcity in island communities where sea wrack could accumulate led to seawater utilization as liquid substrate. Three microbial seeds cow manure (CM), marine sediment (MS), and sea wrack-associated microflora (SWA) were explored for biogas production. The average biogas produced were 2172±156 mL (MS), 1223±308 mL (SWA) and 551±126 mL (CM). Though methane potential (396.9 mL(CH4) g(-1) volatile solid) computed from sea wrack proximate values was comparable to other feedstocks, highest methane yield was low (MS=94.33 mL(CH4) g(-1) VS). Among the microbial seeds, MS proved the best microbial source in utilizing sea wrack biomass and seawater. However, salinity (MS=42‰) observed exceeded average seawater salinity (34‰). Hence, methanogenic activity could have been inhibited. This is the first report on sea wrack biomass utilization for thalassic biogas production.
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Affiliation(s)
- Gian Powell B Marquez
- The Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines.
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29
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Lever MA. Functional gene surveys from ocean drilling expeditions - a review and perspective. FEMS Microbiol Ecol 2013; 84:1-23. [PMID: 23228016 DOI: 10.1111/1574-6941.12051] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 10/18/2012] [Accepted: 11/29/2012] [Indexed: 12/18/2022] Open
Abstract
The vast majority of microbes inhabiting the subseafloor remain uncultivated and their energy sources unknown. Thus, a focus of ocean drilling expeditions over the past decade has been to characterize the distribution of microbes associated with specific metabolic reactions. An important question has been whether microbes involved in key microbial processes, such as sulfate reduction and methanogenesis, differ fundamentally from their counterparts in surface environments. To this end, functional genes of anaerobic methane cycling (mcrA), sulfate reduction (dsrAB), acetogenesis (fhs), and dehalorespiration (rdhA) have been examined. A compilation of existing functional gene data suggests that subseafloor microbes involved in anaerobic methane cycling, sulfate reduction, acetogenesis, and dehalorespiration are not fundamentally different from their counterparts in the surface world. Moreover, quantifications of mcrA and dsrAB suggest that, unless the majority of subseafloor microbes involved in methane cycling and sulfate reduction are too genetically divergent to be detected with conventional methods, these processes only support a small fraction (< 1%) of total microbial biomass in the deep biosphere. Ecological explanations for the observed trends, target processes and methods for future investigations, and strategies for tackling the unresolved issue of microbial contamination in samples obtained by ocean drilling are discussed.
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Affiliation(s)
- Mark A Lever
- Center for Geomicrobiology, Institute of BioScience, Aarhus University, Aarhus, Denmark.
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30
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Potential methane reservoirs beneath Antarctica. Nature 2012; 488:633-7. [PMID: 22932387 DOI: 10.1038/nature11374] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 06/28/2012] [Indexed: 11/09/2022]
Abstract
Once thought to be devoid of life, the ice-covered parts of Antarctica are now known to be a reservoir of metabolically active microbial cells and organic carbon. The potential for methanogenic archaea to support the degradation of organic carbon to methane beneath the ice, however, has not yet been evaluated. Large sedimentary basins containing marine sequences up to 14 kilometres thick and an estimated 21,000 petagrams (1 Pg equals 10(15) g) of organic carbon are buried beneath the Antarctic Ice Sheet. No data exist for rates of methanogenesis in sub-Antarctic marine sediments. Here we present experimental data from other subglacial environments that demonstrate the potential for overridden organic matter beneath glacial systems to produce methane. We also numerically simulate the accumulation of methane in Antarctic sedimentary basins using an established one-dimensional hydrate model and show that pressure/temperature conditions favour methane hydrate formation down to sediment depths of about 300 metres in West Antarctica and 700 metres in East Antarctica. Our results demonstrate the potential for methane hydrate accumulation in Antarctic sedimentary basins, where the total inventory depends on rates of organic carbon degradation and conditions at the ice-sheet bed. We calculate that the sub-Antarctic hydrate inventory could be of the same order of magnitude as that of recent estimates made for Arctic permafrost. Our findings suggest that the Antarctic Ice Sheet may be a neglected but important component of the global methane budget, with the potential to act as a positive feedback on climate warming during ice-sheet wastage.
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31
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Briggs BR, Inagaki F, Morono Y, Futagami T, Huguet C, Rosell-Mele A, Lorenson TD, Colwell FS. Bacterial dominance in subseafloor sediments characterized by methane hydrates. FEMS Microbiol Ecol 2012; 81:88-98. [PMID: 22273405 DOI: 10.1111/j.1574-6941.2012.01311.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 12/23/2011] [Accepted: 01/12/2012] [Indexed: 11/28/2022] Open
Abstract
The degradation of organic carbon in subseafloor sediments on continental margins contributes to the largest reservoir of methane on Earth. Sediments in the Andaman Sea are composed of ~ 1% marine-derived organic carbon and biogenic methane is present. Our objective was to determine microbial abundance and diversity in sediments that transition the gas hydrate occurrence zone (GHOZ) in the Andaman Sea. Microscopic cell enumeration revealed that most sediment layers harbored relatively low microbial abundance (10(3)-10(5) cells cm(-3)). Archaea were never detected despite the use of both DNA- and lipid-based methods. Statistical analysis of terminal restriction fragment length polymorphisms revealed distinct microbial communities from above, within, and below the GHOZ, and GHOZ samples were correlated with a decrease in organic carbon. Primer-tagged pyrosequences of bacterial 16S rRNA genes showed that members of the phylum Firmicutes are predominant in all zones. Compared with other seafloor settings that contain biogenic methane, this deep subseafloor habitat has a unique microbial community and the low cell abundance detected can help to refine global subseafloor microbial abundance.
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32
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Schippers A, Kock D, Höft C, Köweker G, Siegert M. Quantification of Microbial Communities in Subsurface Marine Sediments of the Black Sea and off Namibia. Front Microbiol 2012; 3:16. [PMID: 22319518 PMCID: PMC3268179 DOI: 10.3389/fmicb.2012.00016] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 01/09/2012] [Indexed: 12/04/2022] Open
Abstract
Organic-rich subsurface marine sediments were taken by gravity coring up to a depth of 10 m below seafloor at six stations from the anoxic Black Sea and the Benguela upwelling system off Namibia during the research cruises Meteor 72-5 and 76-1, respectively. The quantitative microbial community composition at various sediment depths was analyzed using total cell counting, catalyzed reporter deposition – fluorescence in situ hybridization (CARD–FISH) and quantitative real-time PCR (Q-PCR). Total cell counts decreased with depths from 109 to 1010 cells/mL at the sediment surface to 107–109 cells/mL below one meter depth. Based on CARD–FISH and Q-PCR analyses overall similar proportions of Bacteria and Archaea were found. The down-core distribution of prokaryotic and eukaryotic small subunit ribosomal RNA genes (16S and 18S rRNA) as well as functional genes involved in different biogeochemical processes was quantified using Q-PCR. Crenarchaeota and the bacterial candidate division JS-1 as well as the classes Anaerolineae and Caldilineae of the phylum Chloroflexi were highly abundant. Less abundant but detectable in most of the samples were Eukarya as well as the metal and sulfate-reducing Geobacteraceae (only in the Benguela upwelling influenced sediments). The functional genes cbbL, encoding for the large subunit of RuBisCO, the genes dsrA and aprA, indicative of sulfate-reducers as well as the mcrA gene of methanogens were detected in the Benguela upwelling and Black Sea sediments. Overall, the high organic carbon content of the sediments goes along with high cell counts and high gene copy numbers, as well as an equal abundance of Bacteria and Archaea.
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Affiliation(s)
- Axel Schippers
- Geomicrobiology, Federal Institute for Geosciences and Natural Resources Hannover, Germany
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33
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Liu D, Ding W, Jia Z, Cai Z. The impact of dissolved organic carbon on the spatial variability of methanogenic archaea communities in natural wetland ecosystems across China. Appl Microbiol Biotechnol 2012; 96:253-63. [DOI: 10.1007/s00253-011-3842-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 12/07/2011] [Accepted: 12/09/2011] [Indexed: 10/14/2022]
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Carbon and nitrogen assimilation in deep subseafloor microbial cells. Proc Natl Acad Sci U S A 2011; 108:18295-300. [PMID: 21987801 DOI: 10.1073/pnas.1107763108] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Remarkable numbers of microbial cells have been observed in global shallow to deep subseafloor sediments. Accumulating evidence indicates that deep and ancient sediments harbor living microbial life, where the flux of nutrients and energy are extremely low. However, their physiology and energy requirements remain largely unknown. We used stable isotope tracer incubation and nanometer-scale secondary ion MS to investigate the dynamics of carbon and nitrogen assimilation activities in individual microbial cells from 219-m-deep lower Pleistocene (460,000 y old) sediments from the northwestern Pacific off the Shimokita Peninsula of Japan. Sediment samples were incubated in vitro with (13)C- and/or (15)N-labeled glucose, pyruvate, acetate, bicarbonate, methane, ammonium, and amino acids. Significant incorporation of (13)C and/or (15)N and growth occurred in response to glucose, pyruvate, and amino acids (∼76% of total cells), whereas acetate and bicarbonate were incorporated without fostering growth. Among those substrates, a maximum substrate assimilation rate was observed at 67 × 10(-18) mol/cell per d with bicarbonate. Neither carbon assimilation nor growth was evident in response to methane. The atomic ratios between nitrogen incorporated from ammonium and the total cellular nitrogen consistently exceeded the ratios of carbon, suggesting that subseafloor microbes preferentially require nitrogen assimilation for the recovery in vitro. Our results showed that the most deeply buried subseafloor sedimentary microbes maintain potentials for metabolic activities and that growth is generally limited by energy but not by the availability of C and N compounds.
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Narihiro T, Sekiguchi Y. Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea. Microb Biotechnol 2011; 4:585-602. [PMID: 21375721 PMCID: PMC3819009 DOI: 10.1111/j.1751-7915.2010.00239.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 11/12/2010] [Indexed: 11/28/2022] Open
Abstract
For the identification and quantification of methanogenic archaea (methanogens) in environmental samples, various oligonucleotide probes/primers targeting phylogenetic markers of methanogens, such as 16S rRNA, 16S rRNA gene and the gene for the α-subunit of methyl coenzyme M reductase (mcrA), have been extensively developed and characterized experimentally. These oligonucleotides were designed to resolve different groups of methanogens at different taxonomic levels, and have been widely used as hybridization probes or polymerase chain reaction primers for membrane hybridization, fluorescence in situ hybridization, rRNA cleavage method, gene cloning, DNA microarray and quantitative polymerase chain reaction for studies in environmental and determinative microbiology. In this review, we present a comprehensive list of such oligonucleotide probes/primers, which enable us to determine methanogen populations in an environment quantitatively and hierarchically, with examples of the practical applications of the probes and primers.
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Affiliation(s)
- Takashi Narihiro
- International Patent Organism Depositary (IPOD), Tsukuba, Ibaraki 305‐8566, Japan
| | - Yuji Sekiguchi
- Bio‐medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305‐8566, Japan
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Nunoura T, Inagaki F, Delwiche ME, Colwell FS, Takai K. Subseafloor microbial communities in methane hydrate-bearing sediment at two distinct locations (ODP Leg204) in the cascadia margin. Microbes Environ 2011; 23:317-25. [PMID: 21558725 DOI: 10.1264/jsme2.me08514] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The prokaryotic communities in deep subseafloor sediment collected during Ocean Drilling Program (ODP) Leg 204 from the South Hydrate Ridge (SHR) on the Cascadia Margin were analyzed by 16S rRNA gene clone sequencing and a fluorescent quantitative PCR technique. The microbial communities came from sites with contrasting geological characteristics on the SHR: sites 1244 and 1245 (located on the flank of the ridge, hydrate-rich sediment) and site 1251 (located on the slope basin of SHR, hydrate-poor sediment). The overall copy numbers of the 16S rRNA gene, and the proportion of archaeal 16S rRNA gene in all 16S rRNA gene community in sediment were larger on the slope basin than on the flank of the SHR. Archaeal community structure around the sulfate-methane transition zone at site 1251 (4.5 mbsf) was intensively investigated using two different PCR primer sets. A relatively abundant distribution of the 16S rRNA gene sequences related to mesophilic methanogen of the genus Methanoculleus was identified at a depth of 43.2 mbsf, and suggested that the methanogens occur in relatively shallow zones of sediment. This study demonstrated that the subseafloor microbial communities shown by 16S rRNA gene clone analyses were not directly associated with subseafloor methane hydrate deposits.
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Affiliation(s)
- Takuro Nunoura
- Subground Animalcule Retrieval (SUGAR) Program, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science & Technology (JAMSTEC) 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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37
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Imachi H, Aoi K, Tasumi E, Saito Y, Yamanaka Y, Saito Y, Yamaguchi T, Tomaru H, Takeuchi R, Morono Y, Inagaki F, Takai K. Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor. ISME JOURNAL 2011; 5:1913-25. [PMID: 21654849 DOI: 10.1038/ismej.2011.64] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial methanogenesis in subseafloor sediments is a key process in the carbon cycle on the Earth. However, the cultivation-dependent evidences have been poorly demonstrated. Here we report the cultivation of a methanogenic microbial consortium from subseafloor sediments using a continuous-flow-type bioreactor with polyurethane sponges as microbial habitats, called down-flow hanging sponge (DHS) reactor. We anaerobically incubated methane-rich core sediments collected from off Shimokita Peninsula, Japan, for 826 days in the reactor at 10 °C. Synthetic seawater supplemented with glucose, yeast extract, acetate and propionate as potential energy sources was provided into the reactor. After 289 days of operation, microbiological methane production became evident. Fluorescence in situ hybridization analysis revealed the presence of metabolically active microbial cells with various morphologies in the reactor. DNA- and RNA-based phylogenetic analyses targeting 16S rRNA indicated the successful growth of phylogenetically diverse microbial components during cultivation in the reactor. Most of the phylotypes in the reactor, once it made methane, were more closely related to culture sequences than to the subsurface environmental sequence. Potentially methanogenic phylotypes related to the genera Methanobacterium, Methanococcoides and Methanosarcina were predominantly detected concomitantly with methane production, while uncultured archaeal phylotypes were also detected. Using the methanogenic community enrichment as subsequent inocula, traditional batch-type cultivations led to the successful isolation of several anaerobic microbes including those methanogens. Our results substantiate that the DHS bioreactor is a useful system for the enrichment of numerous fastidious microbes from subseafloor sediments and will enable the physiological and ecological characterization of pure cultures of previously uncultivated subseafloor microbial life.
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Affiliation(s)
- Hiroyuki Imachi
- Subsurface Geobiology Advanced Research (SUGAR) Project, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.
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38
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Kolukirik M, Ince O, Ince BK. Increment in anaerobic hydrocarbon degradation activity of Halic Bay sediments via nutrient amendment. MICROBIAL ECOLOGY 2011; 61:871-884. [PMID: 21390532 DOI: 10.1007/s00248-011-9825-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 02/08/2011] [Indexed: 05/30/2023]
Abstract
In this study, hydrocarbon (HC) degradation activity of a HC-rich marine sediment was assessed in anaerobic microcosms during a 224 days incubation period. Natural TOC/N/P ratio of the sediment porewater (1,000/5/1) was gradually decreased to 1,000/40/6 which resulted in approximately ninefold increase in gas production (CH(4)+CO(2)) and HC removal. Addition of external HCs to the microcosms was also resulted in approximately twofold higher gas production and HC removal. A high proportion (92%) of aromatic HCs and all n-alkanes were removed from the microcosms under unlimited nutrient supply conditions without external HC addition. The microorganisms of the sediment degraded a wide range of aliphatic (n-C(9-31) alkanes and acyclic isoprenoids) and aromatic (18 different one- to five-ring aromatics) HCs. Monitoring functional gene and transcript abundances revealed that methanogenesis and dissimilatory sulfate reduction took place simultaneously during the first 126 days, afterwards, only the syntrophic methanogenic consortium was active. Genes and transcripts related to initial activation of HCs were highly abundant throughout the incubation period showing that fumarate addition was the main pathway of anaerobic HC degradation. In conclusion, biostimulation of highly polluted anoxic marine sediments via nutrient amendment is effective and may constitute a suitable and cost-effective field-scale bioremediation strategy.
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Affiliation(s)
- Mustafa Kolukirik
- Department of Molecular Biology and Genetics, Istanbul Technical University, 34469 Istanbul, Turkey.
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Abstract
Our knowledge of physical, chemical, geological and biological processes affecting methane in the ocean and in underlying sediments is expanding at a rapid pace. On first inspection, marine methane biogeochemistry appears simple: Methane distribution in sediment is set by the deposition pattern of organic material, and the balance of sources and sinks keeps its concentration low in most waters. However, recent research reveals that methane is affected by complex biogeochemical processes whose interactions are understood only at a superficial level. Such processes span the deep-subsurface, near subsurface, and ocean waters, and relate primarily to the production, consumption, and transport of methane. The purpose of this synthesis is to examine select processes within the framework of methane biogeochemistry, to formulate hypotheses on how they might operate and interact with one another, and to consider their controls.
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Affiliation(s)
- David L Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, California 93106, USA.
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Boyd ES, Skidmore M, Mitchell AC, Bakermans C, Peters JW. Methanogenesis in subglacial sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2010; 2:685-692. [PMID: 23766256 DOI: 10.1111/j.1758-2229.2010.00162.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Methanogenic archaea have a unique role in Earth's global carbon cycle as producers of the greenhouse gas methane (CH4 ). However, despite the fact that ice covers 11% of Earth's continental landmass, evidence for methanogenic activity in subglacial environments has yet to be clearly demonstrated. Here we present genetic, biochemical and geochemical evidence indicative of an active population of methanogens associated with subglacial sediments from Robertson Glacier (RG), Canadian Rockies. Porewater CH4 was quantified in two subglacial sediment cores at concentrations of 16 and 29 ppmv. Coenzyme M (CoM), a metabolic biomarker for methanogens, was detected at a concentration of 1.3 nmol g sediment(-1) corresponding to ∼3 × 10(3) active cells g sediment(-1) . Genetic characterization of communities associated with subglacial sediments indicated the presence of several archaeal 16S rRNA and methyl CoM reductase subunit A (mcrA) gene phylotypes, all of which were affiliated with the euryarchaeal order Methanosarcinales. Further, CH4 was produced at 9-51 fmol g dry weight sediment(-1) h(-1) in enrichment cultures of RG sediments incubated at 4°C. Collectively, these findings have important implications for the global carbon cycle in light of recent estimates indicating that the Earth's subglacial biome ranges from 10(4) to 10(6) km(3) sediment.
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Affiliation(s)
- Eric S Boyd
- Department of Chemistry and Biochemistry, The Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, USA. Department of Earth Sciences and Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA
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Methane production by Methanothermobacter thermautotrophicus to recover energy from carbon dioxide sequestered in geological reservoirs. J Biosci Bioeng 2010; 110:106-8. [DOI: 10.1016/j.jbiosc.2010.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 01/04/2010] [Accepted: 01/05/2010] [Indexed: 11/23/2022]
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Correlation of methane production and functional gene transcriptional activity in a peat soil. Appl Environ Microbiol 2009; 75:6679-87. [PMID: 19749064 DOI: 10.1128/aem.01021-09] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transcription dynamics of subunit A of the key gene in methanogenesis (methyl coenzyme M reductase; mcrA) was studied to evaluate the relationship between process rate (methanogenesis) and gene transcription dynamics in a peat soil ecosystem. Soil methanogen process rates were determined during incubation of peat slurries at temperatures from 4 to 37 degrees C, and real-time quantitative PCR was applied to quantify the abundances of mcrA genes and transcripts; corresponding transcriptional dynamics were calculated from mcrA transcript/gene ratios. Internal standards suggested unbiased recovery of mRNA abundances in comparison to DNA levels. In comparison to those in pure-culture studies, mcrA transcript/gene ratios indicated underestimation by 1 order of magnitude, possibly due to high proportions of inactive or dead methanogens. Methane production rates were temperature dependent, with maxima at 25 degrees C, but changes in abundance and transcription of the mcrA gene showed no correlation with temperature. However, mcrA transcript/gene ratios correlated weakly (regression coefficient = 0.76) with rates of methanogenesis. Methanogen process rates increased over 3 orders of magnitude, while the corresponding maximum transcript/gene ratio increase was only 18-fold. mcrA transcript dynamics suggested steady-state expression in peat soil after incubation for 24 and 48 h, similar to that in stationary-phase cultures. mcrA transcript/gene ratios are therefore potential in situ indicators of methanogen process rate changes in complex soil systems.
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Nunoura T, Soffientino B, Blazejak A, Kakuta J, Oida H, Schippers A, Takai K. Subseafloor microbial communities associated with rapid turbidite deposition in the Gulf of Mexico continental slope (IODP Expedition 308). FEMS Microbiol Ecol 2009; 69:410-24. [DOI: 10.1111/j.1574-6941.2009.00718.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Sulfur isotope enrichment during maintenance metabolism in the thermophilic sulfate-reducing bacterium Desulfotomaculum putei. Appl Environ Microbiol 2009; 75:5621-30. [PMID: 19561180 DOI: 10.1128/aem.02948-08] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Values of Delta(34)S (=delta(34)S(HS)-delta(34)S(SO(4)), where delta(34)S(HS) and delta(34)S(SO(4)) indicate the differences in the isotopic compositions of the HS(-) and SO(4)(2-) in the eluent, respectively) for many modern marine sediments are in the range of -55 to -75 per thousand, much greater than the -2 to -46 per thousand epsilon(34)S (kinetic isotope enrichment) values commonly observed for microbial sulfate reduction in laboratory batch culture and chemostat experiments. It has been proposed that at extremely low sulfate reduction rates under hypersulfidic conditions with a nonlimited supply of sulfate, isotopic enrichment in laboratory culture experiments should increase to the levels recorded in nature. We examined the effect of extremely low sulfate reduction rates and electron donor limitation on S isotope fractionation by culturing a thermophilic, sulfate-reducing bacterium, Desulfotomaculum putei, in a biomass-recycling culture vessel, or "retentostat." The cell-specific rate of sulfate reduction and the specific growth rate decreased progressively from the exponential phase to the maintenance phase, yielding average maintenance coefficients of 10(-16) to 10(-18) mol of SO(4) cell(-1) h(-1) toward the end of the experiments. Overall S mass and isotopic balance were conserved during the experiment. The differences in the delta(34)S values of the sulfate and sulfide eluting from the retentostat were significantly larger, attaining a maximum Delta(34)S of -20.9 per thousand, than the -9.7 per thousand observed during the batch culture experiment, but differences did not attain the values observed in marine sediments.
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