1
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Engelen B, Nguyen T, Heyerhoff B, Kalenborn S, Sydow K, Tabai H, Peterson RN, Wegener G, Teske A. Microbial Communities of Hydrothermal Guaymas Basin Surficial Sediment Profiled at 2 Millimeter-Scale Resolution. Front Microbiol 2021; 12:710881. [PMID: 34335545 PMCID: PMC8322767 DOI: 10.3389/fmicb.2021.710881] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/22/2021] [Indexed: 01/10/2023] Open
Abstract
The surficial hydrothermal sediments of Guaymas Basin harbor complex microbial communities where oxidative and reductive nitrogen, sulfur, and carbon-cycling populations and processes overlap and coexist. Here, we resolve microbial community profiles in hydrothermal sediment cores of Guaymas Basin on a scale of 2 millimeters, using Denaturing Gradient Gel Electrophoresis (DGGE) to visualize the rapid downcore changes among dominant bacteria and archaea. DGGE analysis of bacterial 16S rRNA gene amplicons identified free-living and syntrophic deltaproteobacterial sulfate-reducing bacteria, fermentative Cytophagales, members of the Chloroflexi (Thermoflexia), Aminicenantes, and uncultured sediment clades. The DGGE pattern indicates a gradually changing downcore community structure where small changes on a 2-millimeter scale accumulate to significantly changing populations within the top 4 cm sediment layer. Functional gene DGGE analyses identified anaerobic methane-oxidizing archaea (ANME) based on methyl-coenzyme M reductase genes, and members of the Betaproteobacteria and Thaumarchaeota based on bacterial and archaeal ammonia monooxygenase genes, respectively. The co-existence and overlapping habitat range of aerobic, nitrifying, sulfate-reducing and fermentative bacteria and archaea, including thermophiles, in the surficial sediments is consistent with dynamic redox and thermal gradients that sustain highly complex microbial communities in the hydrothermal sediments of Guaymas Basin.
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Affiliation(s)
- Bert Engelen
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Tien Nguyen
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Benedikt Heyerhoff
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Saskia Kalenborn
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Katharina Sydow
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Houssem Tabai
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Richard N Peterson
- Department of Coastal and Marine Systems Science, Coastal Carolina University, Conway, SC, United States
| | - Gunter Wegener
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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2
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Zhou Z, Pan J, Wang F, Gu JD, Li M. Bathyarchaeota: globally distributed metabolic generalists in anoxic environments. FEMS Microbiol Rev 2018; 42:639-655. [PMID: 29790926 DOI: 10.1093/femsre/fuy023] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 05/18/2018] [Indexed: 11/12/2022] Open
Abstract
Bathyarchaeota, formerly known as the Miscellaneous Crenarchaeotal Group, is a phylum of global generalists that are widespread in anoxic sediments, which host relatively high abundance archaeal communities. Until now, 25 subgroups have been identified in the Bathyarchaeota. The distinct bathyarchaeotal subgroups diverged to adapt to marine and freshwater environments. Based on the physiological and genomic evidence, acetyl-coenzyme A-centralized heterotrophic pathways of energy conservation have been proposed to function in Bathyarchaeota; these microbes are able to anaerobically utilize (i) detrital proteins, (ii) polymeric carbohydrates, (iii) fatty acids/aromatic compounds, (iv) methane (or short chain alkane) and methylated compounds, and/or (v) potentially other organic matter. Furthermore, bathyarchaeotal members have wide metabolic capabilities, including acetogenesis, methane metabolism, and dissimilatory nitrogen and sulfur reduction, and they also have potential interactions with anaerobic methane-oxidizing archaea, acetoclastic methanogens and heterotrophic bacteria. These results have not only demonstrated multiple and important ecological functions of this archaeal phylum, but also paved the way for a detailed understanding of the evolution and metabolism of archaea as such. This review summarizes the recent findings pertaining to the ecological, physiological and genomic aspects of Bathyarchaeota, highlighting the vital role of this phylum in global carbon cycling.
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Affiliation(s)
- Zhichao Zhou
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China.,Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China
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3
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Stranghoener M, Schippers A, Dultz S, Behrens H. Experimental Microbial Alteration and Fe Mobilization From Basaltic Rocks of the ICDP HSDP2 Drill Core, Hilo, Hawaii. Front Microbiol 2018; 9:1252. [PMID: 29963022 PMCID: PMC6010528 DOI: 10.3389/fmicb.2018.01252] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/23/2018] [Indexed: 11/25/2022] Open
Abstract
The interaction of a single bacterial species (Burkholderia fungorum) with basaltic rocks from the ICDP HSDP2 drill core and synthetic basaltic glasses was investigated in batch laboratory experiments to better understand the role of microbial activity on rock alteration and Fe mobilization. Incubation experiments were performed with drill core basaltic rock samples to investigate differences in the solution chemistry during biotic and abiotic alteration. Additionally, colonization experiments with synthetic basaltic glasses of different Fe redox states and residual stresses were performed to evaluate their influence on microbial activity and surface attachment of cells. In biotic incubation experiments bacterial growth was observed and the release of Fe and other major elements from drill core basaltic rocks to solution exceeded that of abiotic controls only when the rock sample assay was nutrient depleted. The concentration of dissolved major elements in solution in biotic colonization experiments with synthetic basaltic glasses increased with increasing residual stress and Fe(II) content. Furthermore, the concentration of dissolved Fe and Al increased similarly in biotic colonization experiments indicating that their dissolution might be triggered by microbial activity. Surface morphology imaging by SEM revealed that cells on basaltic rocks in incubation experiments were most abundant on the glass and surfaces with high roughness and almost absent on minerals. In colonization experiments, basaltic glasses with residual stress and high Fe(II) content were intensely covered with a cellular biofilm. In contrast, glasses with high Fe(III) content and no residual stress were sparsely colonized. We therefore conclude that structurally bound Fe is most probably used by B. fungorum as a nutrient. Furthermore, we assume that microbial activity overall increased rock dissolution as soon as the environment becomes nutrient depleted. Our results show that besides compositional effects, other factors such as redox state and residual stress can control microbial alteration of basaltic glasses.
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Affiliation(s)
| | - Axel Schippers
- Geomicrobiology, Federal Institute for Geosciences and Natural Resources, Hanover, Germany
| | - Stefan Dultz
- Institute of Soil Science, Leibniz Universität Hannover, Hanover, Germany
| | - Harald Behrens
- Institute of Mineralogy, Leibniz Universität Hannover, Hanover, Germany
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4
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Callac N, Posth NR, Rattray JE, Yamoah KKY, Wiech A, Ivarsson M, Hemmingsson C, Kilias SP, Argyraki A, Broman C, Skogby H, Smittenberg RH, Fru EC. Modes of carbon fixation in an arsenic and CO 2-rich shallow hydrothermal ecosystem. Sci Rep 2017; 7:14708. [PMID: 29089625 PMCID: PMC5665909 DOI: 10.1038/s41598-017-13910-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 09/29/2017] [Indexed: 01/01/2023] Open
Abstract
The seafloor sediments of Spathi Bay, Milos Island, Greece, are part of the largest arsenic-CO2-rich shallow submarine hydrothermal ecosystem on Earth. Here, white and brown deposits cap chemically distinct sediments with varying hydrothermal influence. All sediments contain abundant genes for autotrophic carbon fixation used in the Calvin-Benson-Bassham (CBB) and reverse tricaboxylic acid (rTCA) cycles. Both forms of RuBisCO, together with ATP citrate lyase genes in the rTCA cycle, increase with distance from the active hydrothermal centres and decrease with sediment depth. Clustering of RuBisCO Form II with a highly prevalent Zetaproteobacteria 16S rRNA gene density infers that iron-oxidizing bacteria contribute significantly to the sediment CBB cycle gene content. Three clusters form from different microbial guilds, each one encompassing one gene involved in CO2 fixation, aside from sulfate reduction. Our study suggests that the microbially mediated CBB cycle drives carbon fixation in the Spathi Bay sediments that are characterized by diffuse hydrothermal activity, high CO2, As emissions and chemically reduced fluids. This study highlights the breadth of conditions influencing the biogeochemistry in shallow CO2-rich hydrothermal systems and the importance of coupling highly specific process indicators to elucidate the complexity of carbon cycling in these ecosystems.
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Affiliation(s)
- Nolwenn Callac
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden.
| | - Nicole R Posth
- Nordcee, Department of Biology-University of Southern Denmark Campusvej 55, 5230, Odense M, Denmark.,Department of Geosciences and Natural Resource Management - IGN University of Copenhagen, Øster Voldgade, 10 1350, København K, Denmark
| | - Jayne E Rattray
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden
| | - Kweku K Y Yamoah
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden
| | - Alan Wiech
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden
| | - Magnus Ivarsson
- Department of Palaeobiology and Nordic Center for Earth Evolution, Swedish Museum of Natural History, Stockholm, Sweden
| | - Christoffer Hemmingsson
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden
| | - Stephanos P Kilias
- Department of Geology and Geoenvironment, Section of Economic Geology and Geochemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zographou, 157 84, Athens, Greece
| | - Ariadne Argyraki
- Department of Geology and Geoenvironment, Section of Economic Geology and Geochemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zographou, 157 84, Athens, Greece
| | - Curt Broman
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden
| | - Henrik Skogby
- Department of Geosciences, Swedish Museum of Natural History, Stockholm, Sweden
| | - Rienk H Smittenberg
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden
| | - Ernest Chi Fru
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden. .,School of Earth and Ocean Sciences, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom.
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5
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Sudek LA, Wanger G, Templeton AS, Staudigel H, Tebo BM. Submarine Basaltic Glass Colonization by the Heterotrophic Fe(II)-Oxidizing and Siderophore-Producing Deep-Sea Bacterium Pseudomonas stutzeri VS-10: The Potential Role of Basalt in Enhancing Growth. Front Microbiol 2017; 8:363. [PMID: 28344573 PMCID: PMC5345036 DOI: 10.3389/fmicb.2017.00363] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 02/21/2017] [Indexed: 11/13/2022] Open
Abstract
Phylogenetically and metabolically diverse bacterial communities have been found in association with submarine basaltic glass surfaces. The driving forces behind basalt colonization are for the most part unknown. It remains ambiguous if basalt provides ecological advantages beyond representing a substrate for surface colonization, such as supplying nutrients and/or energy. Pseudomonas stutzeri VS-10, a metabolically versatile bacterium isolated from Vailulu'u Seamount, was used as a model organism to investigate the physiological responses observed when biofilms are established on basaltic glasses. In Fe-limited heterotrophic media, P. stutzeri VS-10 exhibited elevated growth in the presence of basaltic glass. Diffusion chamber experiments demonstrated that physical attachment or contact of soluble metabolites such as siderophores with the basaltic glass plays a pivotal role in this process. Electrochemical data indicated that P. stutzeri VS-10 is able to use solid substrates (electrodes) as terminal electron donors and acceptors. Siderophore production and heterotrophic Fe(II) oxidation are discussed as potential mechanisms enhancing growth of P. stutzeri VS-10 on glass surfaces. In correlation with that we discuss the possibility that metabolic versatility could represent a common and beneficial physiological trait in marine microbial communities being subject to oligotrophic and rapidly changing deep-sea conditions.
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Affiliation(s)
- Lisa A Sudek
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla CA, USA
| | - Greg Wanger
- Jet Propulsion Laboratory, California Institute of Technology, University of Southern California, Pasadena CA, USA
| | - Alexis S Templeton
- Department of Geological Sciences, University of Colorado Boulder, Boulder CO, USA
| | - Hubert Staudigel
- Institute of Geophysics and Planetary Physics, Scripps Institution of Oceanography, University of California, San Diego, La Jolla CA, USA
| | - Bradley M Tebo
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla CA, USA
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6
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Mino S, Nakagawa S, Makita H, Toki T, Miyazaki J, Sievert SM, Polz MF, Inagaki F, Godfroy A, Kato S, Watanabe H, Nunoura T, Nakamura K, Imachi H, Watsuji TO, Kojima S, Takai K, Sawabe T. Endemicity of the cosmopolitan mesophilic chemolithoautotroph Sulfurimonas at deep-sea hydrothermal vents. ISME JOURNAL 2017; 11:909-919. [PMID: 28045457 DOI: 10.1038/ismej.2016.178] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/21/2016] [Accepted: 10/31/2016] [Indexed: 11/09/2022]
Abstract
Rich animal and microbial communities have been found at deep-sea hydrothermal vents. Although the biogeography of vent macrofauna is well understood, the corresponding knowledge about vent microbial biogeography is lacking. Here, we apply the multilocus sequence analysis (MLSA) to assess the genetic variation of 109 Sulfurimonas strains with ⩾98% 16S rRNA gene sequence similarity, which were isolated from four different geographical regions (Okinawa Trough (OT), Mariana Volcanic Arc and Trough (MVAT), Central Indian Ridge (CIR) and Mid-Atlantic Ridge (MAR)). Sequence typing based on 11 protein-coding genes revealed high genetic variation, including some allele types that are widespread within regions, resulting in 102 nucleotide sequence types (STs). This genetic variation was predominantly due to mutation rather than recombination. Phylogenetic analysis of the 11 concatenated genes showed a clear geographical isolation corresponding to the hydrothermal regions they originated from, suggesting limited dispersal. Genetic differentiation among Sulfurimonas populations was primarily influenced by geographical distance rather than gas composition of vent fluid or habitat, although in situ environmental conditions of each microhabitat could not be examined. Nevertheless, Sulfurimonas may possess a higher dispersal capability compared with deep-sea hydrothermal vent thermophiles. This is the first report on MLSA of deep-sea hydrothermal vent Epsilonproteobacteria, which is indicative of allopatric speciation.
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Affiliation(s)
- Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.,Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Hiroko Makita
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Tomohiro Toki
- Department of Chemistry, Biology, and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Japan
| | - Junichi Miyazaki
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Stefan M Sievert
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fumio Inagaki
- Kochi Institute for Core Sample Research, JAMSTEC, Nankoku, Japan.,Research and Development Center for Ocean Drilling Science (ODS), JAMSTEC, Yokohama, Japan
| | - Anne Godfroy
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Shingo Kato
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan
| | - Hiromi Watanabe
- Department of Marine Biodiversity Research, JAMSTEC, Yokosuka, Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, JAMSTEC, Yokosuka, Japan
| | - Koichi Nakamura
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Hiroyuki Imachi
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Tomo-O Watsuji
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shigeaki Kojima
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Ken Takai
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
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7
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Teske A, de Beer D, McKay LJ, Tivey MK, Biddle JF, Hoer D, Lloyd KG, Lever MA, Røy H, Albert DB, Mendlovitz HP, MacGregor BJ. The Guaymas Basin Hiking Guide to Hydrothermal Mounds, Chimneys, and Microbial Mats: Complex Seafloor Expressions of Subsurface Hydrothermal Circulation. Front Microbiol 2016; 7:75. [PMID: 26925032 PMCID: PMC4757712 DOI: 10.3389/fmicb.2016.00075] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/15/2016] [Indexed: 11/13/2022] Open
Abstract
The hydrothermal mats, mounds, and chimneys of the southern Guaymas Basin are the surface expression of complex subsurface hydrothermal circulation patterns. In this overview, we document the most frequently visited features of this hydrothermal area with photographs, temperature measurements, and selected geochemical data; many of these distinct habitats await characterization of their microbial communities and activities. Microprofiler deployments on microbial mats and hydrothermal sediments show their steep geochemical and thermal gradients at millimeter-scale vertical resolution. Mapping these hydrothermal features and sampling locations within the southern Guaymas Basin suggest linkages to underlying shallow sills and heat flow gradients. Recognizing the inherent spatial limitations of much current Guaymas Basin sampling calls for comprehensive surveys of the wider spreading region.
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Affiliation(s)
- Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Dirk de Beer
- Microsensor Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Luke J McKay
- Department of Marine Sciences, University of North Carolina at Chapel HillChapel Hill, NC, USA; Center for Biofilm Engineering and Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA
| | - Margaret K Tivey
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware Lewes, DE, USA
| | - Daniel Hoer
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Karen G Lloyd
- Department of Marine Sciences, University of North Carolina at Chapel HillChapel Hill, NC, USA; Department of Microbiology, University of Tennessee at KnoxvilleKnoxville, TN, USA
| | - Mark A Lever
- Department of Marine Sciences, University of North Carolina at Chapel HillChapel Hill, NC, USA; Department of Environmental Sciences, Eidgenössische Technische HochschuleZurich, Switzerland
| | - Hans Røy
- Center for Geomicrobiology, Aarhus University Aarhus, Denmark
| | - Daniel B Albert
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Howard P Mendlovitz
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Barbara J MacGregor
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
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8
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Dowell F, Cardman Z, Dasarathy S, Kellermann MY, Lipp JS, Ruff SE, Biddle JF, McKay LJ, MacGregor BJ, Lloyd KG, Albert DB, Mendlovitz H, Hinrichs KU, Teske A. Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin. Front Microbiol 2016; 7:17. [PMID: 26858698 PMCID: PMC4731509 DOI: 10.3389/fmicb.2016.00017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 01/11/2016] [Indexed: 12/15/2022] Open
Abstract
The hydrothermal sediments of Guaymas Basin, an active spreading center in the Gulf of California (Mexico), are rich in porewater methane, short-chain alkanes, sulfate and sulfide, and provide a model system to explore habitat preferences of microorganisms, including sulfate-dependent, methane- and short chain alkane-oxidizing microbial communities. In this study, hot sediments (above 60°C) covered with sulfur-oxidizing microbial mats surrounding a hydrothermal mound (termed “Mat Mound”) were characterized by porewater geochemistry of methane, C2–C6 short-chain alkanes, sulfate, sulfide, sulfate reduction rate measurements, in situ temperature gradients, bacterial and archaeal 16S rRNA gene clone libraries and V6 tag pyrosequencing. The most abundantly detected groups in the Mat mound sediments include anaerobic methane-oxidizing archaea of the ANME-1 lineage and its sister clade ANME-1Guaymas, the uncultured bacterial groups SEEP-SRB2 within the Deltaproteobacteria and the separately branching HotSeep-1 Group; these uncultured bacteria are candidates for sulfate-reducing alkane oxidation and for sulfate-reducing syntrophy with ANME archaea. The archaeal dataset indicates distinct habitat preferences for ANME-1, ANME-1-Guaymas, and ANME-2 archaea in Guaymas Basin hydrothermal sediments. The bacterial groups SEEP-SRB2 and HotSeep-1 co-occur with ANME-1 and ANME-1Guaymas in hydrothermally active sediments underneath microbial mats in Guaymas Basin. We propose the working hypothesis that this mixed bacterial and archaeal community catalyzes the oxidation of both methane and short-chain alkanes, and constitutes a microbial community signature that is characteristic for hydrothermal and/or cold seep sediments containing both substrates.
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Affiliation(s)
- Frederick Dowell
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Zena Cardman
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Srishti Dasarathy
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Matthias Y Kellermann
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of BremenBremen, Germany; Department of Earth Science and Marine Science Institute, University of California at Santa BarbaraSanta Barbara, CA, USA
| | - Julius S Lipp
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen Bremen, Germany
| | - S Emil Ruff
- HGF-MPG Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware Lewes, DE, USA
| | - Luke J McKay
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Barbara J MacGregor
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Karen G Lloyd
- Department of Microbiology, The University of Tennessee Knoxville, TN, USA
| | - Daniel B Albert
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Howard Mendlovitz
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen Bremen, Germany
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
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9
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Henri PA, Rommevaux-Jestin C, Lesongeur F, Mumford A, Emerson D, Godfroy A, Ménez B. Structural Iron (II) of Basaltic Glass as an Energy Source for Zetaproteobacteria in an Abyssal Plain Environment, Off the Mid Atlantic Ridge. Front Microbiol 2016; 6:1518. [PMID: 26834704 PMCID: PMC4720738 DOI: 10.3389/fmicb.2015.01518] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/17/2015] [Indexed: 12/27/2022] Open
Abstract
To explore the capability of basaltic glass to support the growth of chemosynthetic microorganisms, complementary in situ and in vitro colonization experiments were performed. Microbial colonizers containing synthetic tholeitic basaltic glasses, either enriched in reduced or oxidized iron, were deployed off-axis from the Mid Atlantic Ridge on surface sediments of the abyssal plain (35°N; 29°W). In situ microbial colonization was assessed by sequencing of the 16S rRNA gene and basaltic glass alteration was characterized using Scanning Electron Microscopy, micro-X-ray Absorption Near Edge Structure at the Fe-K-edge and Raman microspectroscopy. The colonized surface of the reduced basaltic glass was covered by a rind of alteration made of iron-oxides trapped in a palagonite-like structure with thicknesses up to 150 μm. The relative abundance of the associated microbial community was dominated (39% of all reads) by a single operational taxonomic unit (OTU) that shared 92% identity with the iron-oxidizer Mariprofundus ferrooxydans PV-1. Conversely, the oxidized basaltic glass showed the absence of iron-oxides enriched surface deposits and correspondingly there was a lack of known iron-oxidizing bacteria in the inventoried diversity. In vitro, a similar reduced basaltic glass was incubated in artificial seawater with a pure culture of the iron-oxidizing M. ferrooxydans DIS-1 for 2 weeks, without any additional nutrients or minerals. Confocal Laser Scanning Microscopy revealed that the glass surface was covered by twisted stalks characteristic of this iron-oxidizing Zetaproteobacteria. This result supported findings of the in situ experiments indicating that the Fe(II) present in the basalt was the energy source for the growth of representatives of Zetaproteobacteria in both the abyssal plain and the in vitro experiment. In accordance, the surface alteration rind observed on the reduced basaltic glass incubated in situ could at least partly result from their activity.
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Affiliation(s)
- Pauline A Henri
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Univ Paris Diderot, Centre National de la Recherche Scientifique Paris, France
| | - Céline Rommevaux-Jestin
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Univ Paris Diderot, Centre National de la Recherche Scientifique Paris, France
| | - Françoise Lesongeur
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS/UMR 6197 Plouzané, France
| | - Adam Mumford
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
| | - Anne Godfroy
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS/UMR 6197 Plouzané, France
| | - Bénédicte Ménez
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Univ Paris Diderot, Centre National de la Recherche Scientifique Paris, France
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10
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Teske A, Reysenbach AL. Editorial: Hydrothermal microbial ecosystems. Front Microbiol 2015; 6:884. [PMID: 26388842 PMCID: PMC4555087 DOI: 10.3389/fmicb.2015.00884] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/12/2015] [Indexed: 11/16/2022] Open
Affiliation(s)
- Andreas Teske
- Department of Marine Sciences, University of North Carolina Chapel Hill, NC, USA
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11
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Gulmann LK, Beaulieu SE, Shank TM, Ding K, Seyfried WE, Sievert SM. Bacterial diversity and successional patterns during biofilm formation on freshly exposed basalt surfaces at diffuse-flow deep-sea vents. Front Microbiol 2015; 6:901. [PMID: 26441852 PMCID: PMC4564720 DOI: 10.3389/fmicb.2015.00901] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/17/2015] [Indexed: 11/13/2022] Open
Abstract
Many deep-sea hydrothermal vent systems are regularly impacted by volcanic eruptions, leaving fresh basalt where abundant animal and microbial communities once thrived. After an eruption, microbial biofilms are often the first visible evidence of biotic re-colonization. The present study is the first to investigate microbial colonization of newly exposed basalt surfaces in the context of vent fluid chemistry over an extended period of time (4-293 days) by deploying basalt blocks within an established diffuse-flow vent at the 9°50' N vent field on the East Pacific Rise. Additionally, samples obtained after a recent eruption at the same vent field allowed for comparison between experimental results and those from natural microbial re-colonization. Over 9 months, the community changed from being composed almost exclusively of Epsilonproteobacteria to a more diverse assemblage, corresponding with a potential expansion of metabolic capabilities. The process of biofilm formation appears to generate similar surface-associated communities within and across sites by selecting for a subset of fluid-associated microbes, via species sorting. Furthermore, the high incidence of shared operational taxonomic units over time and across different vent sites suggests that the microbial communities colonizing new surfaces at diffuse-flow vent sites might follow a predictable successional pattern.
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Affiliation(s)
- Lara K Gulmann
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole MA, USA
| | - Stace E Beaulieu
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole MA, USA
| | - Timothy M Shank
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole MA, USA
| | - Kang Ding
- Department of Earth Sciences, University of Minnesota, Minneapolis MN, USA
| | - William E Seyfried
- Department of Earth Sciences, University of Minnesota, Minneapolis MN, USA
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole MA, USA
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12
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Callac N, Rouxel O, Lesongeur F, Liorzou C, Bollinger C, Pignet P, Chéron S, Fouquet Y, Rommevaux-Jestin C, Godfroy A. Biogeochemical insights into microbe-mineral-fluid interactions in hydrothermal chimneys using enrichment culture. Extremophiles 2015; 19:597-617. [PMID: 25778451 DOI: 10.1007/s00792-015-0742-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/01/2015] [Indexed: 10/23/2022]
Abstract
Active hydrothermal chimneys host diverse microbial communities exhibiting various metabolisms including those involved in various biogeochemical cycles. To investigate microbe-mineral-fluid interactions in hydrothermal chimney and the driver of microbial diversity, a cultural approach using a gas-lift bioreactor was chosen. An enrichment culture was performed using crushed active chimney sample as inoculum and diluted hydrothermal fluid from the same vent as culture medium. Daily sampling provided time-series access to active microbial diversity and medium composition. Active archaeal and bacterial communities consisted mainly of sulfur, sulfate and iron reducers and hydrogen oxidizers with the detection of Thermococcus, Archaeoglobus, Geoglobus, Sulfurimonas and Thermotoga sequences. The simultaneous presence of active Geoglobus sp. and Archaeoglobus sp. argues against competition for available carbon sources and electron donors between sulfate and iron reducers at high temperature. This approach allowed the cultivation of microbial populations that were under-represented in the initial environmental sample. The microbial communities are heterogeneously distributed within the gas-lift bioreactor; it is unlikely that bulk mineralogy or fluid chemistry is the drivers of microbial community structure. Instead, we propose that micro-environmental niche characteristics, created by the interaction between the mineral grains and the fluid chemistry, are the main drivers of microbial diversity in natural systems.
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Affiliation(s)
- Nolwenn Callac
- Laboratoire de Microbiologie des Environnements Extrêmes, Université de Bretagne Occidentale, UEB, IUEM, UMR 6197, Place Nicolas Copernic, 29280, Plouzané, France,
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13
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Noffke N. Ancient sedimentary structures in the <3.7 Ga Gillespie Lake Member, Mars, that resemble macroscopic morphology, spatial associations, and temporal succession in terrestrial microbialites. ASTROBIOLOGY 2015; 15:169-92. [PMID: 25495393 DOI: 10.1089/ast.2014.1218] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Sandstone beds of the <3.7 Ga Gillespie Lake Member on Mars have been interpreted as evidence of an ancient playa lake environment. On Earth, such environments have been sites of colonization by microbial mats from the early Archean to the present time. Terrestrial microbial mats in playa lake environments form microbialites known as microbially induced sedimentary structures (MISS). On Mars, three lithofacies of the Gillespie Lake Member sandstone display centimeter- to meter-scale structures similar in macroscopic morphology to terrestrial MISS that include "erosional remnants and pockets," "mat chips," "roll-ups," "desiccation cracks," and "gas domes." The microbially induced sedimentary-like structures identified in Curiosity rover mission images do not have a random distribution. Rather, they were found to be arranged in spatial associations and temporal successions that indicate they changed over time. On Earth, if such MISS occurred with this type of spatial association and temporal succession, they would be interpreted as having recorded the growth of a microbially dominated ecosystem that thrived in pools that later dried completely: erosional pockets, mat chips, and roll-ups resulted from water eroding an ancient microbial mat-covered sedimentary surface; during the course of subsequent water recess, channels would have cut deep into the microbial mats, leaving erosional remnants behind; desiccation cracks and gas domes would have occurred during a final period of subaerial exposure of the microbial mats. In this paper, the similarities of the macroscopic morphologies, spatial associations, and temporal succession of sedimentary structures on Mars to MISS preserved on Earth has led to the following hypothesis: The sedimentary structures in the <3.7 Ga Gillespie Lake Member on Mars are ancient MISS produced by interactions between microbial mats and their environment. Proposed here is a strategy for detecting, identifying, confirming, and differentiating possible MISS during current and future Mars missions.
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Affiliation(s)
- Nora Noffke
- Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University , Norfolk, Virginia
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14
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Vigneron A, Cruaud P, Roussel EG, Pignet P, Caprais JC, Callac N, Ciobanu MC, Godfroy A, Cragg BA, Parkes JR, Van Nostrand JD, He Z, Zhou J, Toffin L. Phylogenetic and functional diversity of microbial communities associated with subsurface sediments of the Sonora Margin, Guaymas Basin. PLoS One 2014; 9:e104427. [PMID: 25099369 PMCID: PMC4123917 DOI: 10.1371/journal.pone.0104427] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/08/2014] [Indexed: 12/14/2022] Open
Abstract
Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments.
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Affiliation(s)
- Adrien Vigneron
- Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
| | - Perrine Cruaud
- Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
| | - Erwan G. Roussel
- School of Earth and Ocean Sciences, Cardiff University, Cardiff, United Kingdom
| | - Patricia Pignet
- Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
| | - Jean-Claude Caprais
- Ifremer, Laboratoire Etude des Environnements Profonds, UMR6197, ZI de la pointe du Diable, Plouzané, France
| | - Nolwenn Callac
- Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- Université de Brest, Domaines Océaniques IUEM, UMR6538, Place Nicolas Copernic, Plouzané, France
| | - Maria-Cristina Ciobanu
- Ifremer, Géosciences Marines, Laboratoire des Environnements Sédimentaires, ZI de la pointe du Diable, Plouzané, France
| | - Anne Godfroy
- Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
| | - Barry A. Cragg
- School of Earth and Ocean Sciences, Cardiff University, Cardiff, United Kingdom
| | - John R. Parkes
- School of Earth and Ocean Sciences, Cardiff University, Cardiff, United Kingdom
| | - Joy D. Van Nostrand
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Zhili He
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Laurent Toffin
- Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
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