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Sklute EC, Leopo DA, Neat KA, Livi KJT, Dyar MD, Holden JF. Fe(III) (oxyhydr)oxide reduction by the thermophilic iron-reducing bacterium Desulfovulcanus ferrireducens. Front Microbiol 2023; 14:1272245. [PMID: 37928658 PMCID: PMC10622975 DOI: 10.3389/fmicb.2023.1272245] [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: 08/03/2023] [Accepted: 09/19/2023] [Indexed: 11/07/2023] Open
Abstract
Some thermophilic bacteria from deep-sea hydrothermal vents grow by dissimilatory iron reduction, but our understanding of their biogenic mineral transformations is nascent. Mineral transformations catalyzed by the thermophilic iron-reducing bacterium Desulfovulcanus ferrireducens during growth at 55°C were examined using synthetic nanophase ferrihydrite, akaganeite, and lepidocrocite separately as terminal electron acceptors. Spectral analyses using visible-near infrared (VNIR), Fourier-transform infrared attenuated total reflectance (FTIR-ATR), and Mössbauer spectroscopies were complemented with x-ray diffraction (XRD) and transmission electron microscopy (TEM) using selected area electron diffraction (SAED) and energy dispersive X-ray (EDX) analyses. The most extensive biogenic mineral transformation occurred with ferrihydrite, which produced a magnetic, visibly dark mineral with spectral features matching cation-deficient magnetite. Desulfovulcanus ferrireducens also grew on akaganeite and lepidocrocite and produced non-magnetic, visibly dark minerals that were poorly soluble in the oxalate solution. Bioreduced mineral products from akaganeite and lepidocrocite reduction were almost entirely absorbed in the VNIR spectroscopy in contrast to both parent minerals and the abiotic controls. However, FTIR-ATR and Mössbauer spectra and XRD analyses of both biogenic minerals were almost identical to the parent and control minerals. The TEM of these biogenic minerals showed the presence of poorly crystalline iron nanospheres (50-200 nm in diameter) of unknown mineralogy that were likely coating the larger parent minerals and were absent from the controls. The study demonstrated that thermophilic bacteria transform different types of Fe(III) (oxyhydr)oxide minerals for growth with varying mineral products. These mineral products are likely formed through dissolution-reprecipitation reactions but are not easily predictable through chemical equilibrium reactions alone.
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Affiliation(s)
- Elizabeth C Sklute
- Planetary Science Institute, Tucson, AZ, United States
- Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Deborah A Leopo
- Department of Microbiology, University of Massachusetts, Amherst, MA, United States
| | - Kaylee A Neat
- Department of Astronomy, Mount Holyoke College, South Hadley, MA, United States
| | - Kenneth J T Livi
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - M Darby Dyar
- Planetary Science Institute, Tucson, AZ, United States
- Department of Astronomy, Mount Holyoke College, South Hadley, MA, United States
| | - James F Holden
- Department of Microbiology, University of Massachusetts, Amherst, MA, United States
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2
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Sun QL, Xu K, Cao L, Du Z, Wang M, Sun L. Nitrogen and sulfur cycling driven by Campylobacterota in the sediment-water interface of deep-sea cold seep: a case in the South China Sea. mBio 2023; 14:e0011723. [PMID: 37409803 PMCID: PMC10470523 DOI: 10.1128/mbio.00117-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/11/2023] [Indexed: 07/07/2023] Open
Abstract
Chemoautotrophs within Campylobacterota, especially Sulfurovum and Sulfurimonas, are abundant in the seawater-sediment interface of the Formosa cold seep in the South China Sea. However, the in situ activity and function of Campylobacterota are unknown. In this study, the geochemical role of Campylobacterota in the Formosa cold seep was investigated with multiple means. Two members of Sulfurovum and Sulfurimonas were isolated for the first time from deep-sea cold seep. These isolates are new chemoautotrophic species that can use molecular hydrogen as an energy source and CO2 as a sole carbon source. Comparative genomics identified an important hydrogen-oxidizing cluster in Sulfurovum and Sulfurimonas. Metatranscriptomic analysis detected high expression of hydrogen-oxidizing gene in the RS, suggesting that H2 was likely an energy source in the cold seep. Genomic analysis indicated that the Sulfurovum and Sulfurimonas isolates possess a truncated sulfur-oxidizing system, and metatranscriptomic analysis revealed that Sulfurovum and Sulfurimonas with this genotype were active in the surface of RS and likely contributed to thiosulfate production. Furthermore, geochemical and in situ analyses revealed sharply decreased nitrate concentration in the sediment-water interface due to microbial consumption. Consistently, the denitrification genes of Sulfurimonas and Sulfurovum were highly expressed, suggesting an important contribution of these bacteria to nitrogen cycling. Overall, this study demonstrated that Campylobacterota played a significant role in the cycling of nitrogen and sulfur in a deep-sea cold seep. IMPORTANCE Chemoautotrophs within Campylobacterota, in particular Sulfurovum and Sulfurimonas, are ubiquitous in deep-sea cold seeps and hydrothermal vents. However, to date, no Sulfurovum or Sulfurimonas has been isolated from cold seeps, and the ecological roles of these bacteria in cold seeps remain to be investigated. In this study, we obtained two isolates of Sulfurovum and Sulfurimonas from Formosa cold seep, South China Sea. Comparative genomics, metatranscriptomics, geochemical analysis, and in situ experimental study indicated collectively that Campylobacterota played a significant part in nitrogen and sulfur cycling in cold seep and was the cause of thiosulfate accumulation and sharp reduction of nitrate level in the sediment-water interface. The findings of this study promoted our understanding of the in situ function and ecological role of deep-sea Campylobacterota.
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Affiliation(s)
- Qing-lei Sun
- College of Life Science, Qingdao Agricultural University, Qingdao, China
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
| | - Ke Xu
- College of Life Science, Qingdao Agricultural University, Qingdao, China
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Lei Cao
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zengfeng Du
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Minxiao Wang
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- CAS Key Laboratory of Marine Ecology and Environmental Science, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Li Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
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3
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Truong C, Bernard S, Le Pape P, Morin G, Baya C, Merrot P, Gorlas A, Guyot F. Production of carbon-containing pyrite spherules induced by hyperthermophilic Thermococcales: a biosignature? Front Microbiol 2023; 14:1145781. [PMID: 37303784 PMCID: PMC10248028 DOI: 10.3389/fmicb.2023.1145781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023] Open
Abstract
Thermococcales, a major order of hyperthermophilic archaea inhabiting iron- and sulfur-rich anaerobic parts of hydrothermal deep-sea vents, are known to induce the formation of iron phosphates, greigite (Fe3S4) and abundant quantities of pyrite (FeS2), including pyrite spherules. In the present study, we report the characterization of the sulfide and phosphate minerals produced in the presence of Thermococcales using X-ray diffraction, synchrotron-based X ray absorption spectroscopy and scanning and transmission electron microscopies. Mixed valence Fe(II)-Fe(III) phosphates are interpreted as resulting from the activity of Thermococcales controlling phosphorus-iron-sulfur dynamics. The pyrite spherules (absent in abiotic control) consist of an assemblage of ultra-small nanocrystals of a few ten nanometers in size, showing coherently diffracting domain sizes of few nanometers. The production of these spherules occurs via a sulfur redox swing from S0 to S-2 and then to S-1, involving a comproportionation of (-II) and (0) oxidation states of sulfur, as supported by S-XANES data. Importantly, these pyrite spherules sequester biogenic organic compounds in small but detectable quantities, possibly making them good biosignatures to be searched for in extreme environments.
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Affiliation(s)
- Chloé Truong
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), MNHN, CNRS, IRD, Sorbonne Université, Paris, France
| | - Sylvain Bernard
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), MNHN, CNRS, IRD, Sorbonne Université, Paris, France
| | - Pierre Le Pape
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), MNHN, CNRS, IRD, Sorbonne Université, Paris, France
| | - Guillaume Morin
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), MNHN, CNRS, IRD, Sorbonne Université, Paris, France
| | - Camille Baya
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), MNHN, CNRS, IRD, Sorbonne Université, Paris, France
| | - Pauline Merrot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), MNHN, CNRS, IRD, Sorbonne Université, Paris, France
| | - Aurore Gorlas
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay, Gif-sur-Yvette, France
| | - François Guyot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), MNHN, CNRS, IRD, Sorbonne Université, Paris, France
- Institut Universitaire de France (IUF), Paris, France
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Dick JM, Tan J. Chemical Links Between Redox Conditions and Estimated Community Proteomes from 16S rRNA and Reference Protein Sequences. MICROBIAL ECOLOGY 2023; 85:1338-1355. [PMID: 35503575 DOI: 10.1007/s00248-022-01988-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/28/2022] [Indexed: 05/10/2023]
Abstract
Environmental influences on community structure are often assessed through multivariate analyses in order to relate microbial abundances to separately measured physicochemical variables. However, genes and proteins are themselves chemical entities; in combination with genome databases, differences in microbial abundances directly encode for chemical variability. We predicted that the carbon oxidation state of estimated community proteomes, obtained by combining taxonomic abundances from published 16S rRNA gene sequencing datasets with reference microbial proteomes from the NCBI Reference Sequence (RefSeq) database, would reflect environmental oxidation-reduction conditions. Analysis of multiple datasets confirms the geobiochemical predictions for environmental redox gradients in hydrothermal systems, stratified lakes and marine environments, and shale gas wells. The geobiochemical signal is largest for the steep redox gradients associated with hydrothermal systems and between injected water and produced fluids from shale gas wells, demonstrating that microbial community composition can be a chemical proxy for environmental redox gradients. Although estimates of oxidation state from 16S amplicon and metagenomic sequences are correlated, the 16S-based estimates show stronger associations with redox gradients in some environments.
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Affiliation(s)
- Jeffrey M Dick
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China.
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
| | - Jingqiang Tan
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
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5
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Kashyap S, Sklute EC, Wang P, Tague TJ, Dyar MD, Holden JF. Spectral Detection of Nanophase Iron Minerals Produced by Fe(III)-Reducing Hyperthermophilic Crenarchaea. ASTROBIOLOGY 2023; 23:43-59. [PMID: 36070586 PMCID: PMC9810357 DOI: 10.1089/ast.2022.0042] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Mineral transformations by two hyperthermophilic Fe(III)-reducing crenarchaea, Pyrodictium delaneyi and Pyrobaculum islandicum, were examined using synthetic nanophase ferrihydrite, lepidocrocite, and akaganeite separately as terminal electron acceptors and compared with abiotic mineral transformations under similar conditions. Spectral analyses using visible-near-infrared, Fourier-transform infrared attenuated total reflectance (FTIR-ATR), Raman, and Mössbauer spectroscopies were complementary and revealed formation of various biomineral assemblages distinguishable from abiotic phases. The most extensive biogenic mineral transformation occurred with ferrihydrite, which formed primarily magnetite with spectral features similar to biomagnetite relative to a synthetic magnetite standard. The FTIR-ATR spectra of ferrihydrite bioreduced by P. delaneyi also showed possible cell-associated organics such as exopolysaccharides. Such combined detections of biomineral assemblages and organics might serve as biomarkers for hyperthermophilic Fe(III) reduction. With lepidocrocite, P. delaneyi produced primarily a ferrous carbonate phase reminiscent of siderite, and with akaganeite, magnetite and a ferrous phosphate phase similar to vivianite were formed. P. islandicum showed minor biogenic production of a ferrous phosphate similar to vivianite when grown on lepidocrocite, and a mixed valent phosphate or sulfate mineral when grown on akaganeite. These results expand the range of biogenic mineral transformations at high temperatures and identify spacecraft-relevant spectroscopies suitable for discriminating mineral biogenicity.
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Affiliation(s)
- Srishti Kashyap
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | | | - Peng Wang
- Bruker Optics, Inc., Billerica, Massachusetts, USA
| | | | - M. Darby Dyar
- Planetary Science Institute, Tucson, Arizona, USA
- Department of Astronomy, Mount Holyoke College, South Hadley, Massachusetts, USA
| | - James F. Holden
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
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6
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Holden JF, Sistu H. Formate and hydrogen in hydrothermal vents and their use by extremely thermophilic methanogens and heterotrophs. Front Microbiol 2023; 14:1093018. [PMID: 36950162 PMCID: PMC10025317 DOI: 10.3389/fmicb.2023.1093018] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
Extremely thermophilic methanogens in the Methanococci and heterotrophs in the Thermococci are common in deep-sea hydrothermal vents. All Methanococci use H2 as an electron donor, and a few species can also use formate. Most Methanococci have a coenzyme F420-reducing formate dehydrogenase. All Thermococci reduce S0 but have hydrogenases and produce H2 in the absence of S0. Some Thermococci have formate hydrogenlyase (Fhl) that reversibly converts H2 and CO2 to formate or an NAD(P)+-reducing formate dehydrogenase (Nfd). Questions remain if Methanococci or Thermococci use or produce formate in nature, why only certain species can grow on or produce formate, and what the physiological role of formate is? Formate forms abiotically in hydrothermal fluids through chemical equilibrium with primarily H2, CO2, and CO and is strongly dependent upon H2 concentration, pH, and temperature. Formate concentrations are highest in hydrothermal fluids where H2 concentrations are also high, such as in ultramafic systems where serpentinization reactions occur. In nature, Methanococci are likely to use formate as an electron donor when H2 is limiting. Thermococci with Fhl likely convert H2 and CO2 to formate when H2 concentrations become inhibitory for growth. They are unlikely to grow on formate in nature unless formate is more abundant than H2 in the environment. Nearly all Methanococci and Thermococci have a gene for at least one formate dehydrogenase catalytic subunit, which may be used to provide free formate for de novo purine biosynthesis. However, only species with a membrane-bound formate transporter can grow on or secrete formate. Interspecies H2 transfer occurs between Thermococci and Methanococci. This and putative interspecies formate transfer may support Methanococci in low H2 environments, which in turn may prevent growth inhibition of Thermococci by its own H2. Future research directions include understanding when, where, and how formate is used and produced by these organisms in nature, and how transcription of Thermococci genes encoding formate-related enzymes are regulated.
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7
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Gorlas A, Mariotte T, Morey L, Truong C, Bernard S, Guigner JM, Oberto J, Baudin F, Landrot G, Baya C, Le Pape P, Morin G, Forterre P, Guyot F. Precipitation of greigite and pyrite induced by Thermococcales: an advantage to live in Fe- and S-rich environments? Environ Microbiol 2022; 24:626-642. [PMID: 35102700 PMCID: PMC9306673 DOI: 10.1111/1462-2920.15915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/05/2022] [Accepted: 01/17/2022] [Indexed: 11/29/2022]
Abstract
Thermococcales, a major order of archaea inhabiting the iron- and sulfur-rich anaerobic parts of hydrothermal deep-sea vents, have been shown to rapidly produce abundant quantities of pyrite FeS2 in iron-sulfur-rich fluids at 85°C, suggesting that they may contribute to the formation of 'low temperature' FeS2 in their ecosystem. We show that this process operates in Thermococcus kodakarensis only when zero-valent sulfur is directly available as intracellular sulfur vesicles. Whether in the presence or absence of zero-valent sulfur, significant amounts of Fe3 S4 greigite nanocrystals are formed extracellularly. We also show that mineralization of iron sulfides induces massive cell mortality but that concomitantly with the formation of greigite and/or pyrite, a new generation of cells can grow. This phenomenon is observed for Fe concentrations of 5 mM but not higher suggesting that above a threshold in the iron pulse all cells are lysed. We hypothesize that iron sulfides precipitation on former cell materials might induce the release of nutrients in the mineralization medium further used by a fraction of surviving non-mineralized cells allowing production of new alive cells. This suggests that biologically induced mineralization of iron-sulfides could be part of a survival strategy employed by Thermococcales to cope with mineralizing high-temperature hydrothermal environments.
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Affiliation(s)
- A Gorlas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - T Mariotte
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - L Morey
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - C Truong
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 - CNRS, Sorbonne Université, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France
| | - S Bernard
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 - CNRS, Sorbonne Université, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France
| | - J-M Guigner
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 - CNRS, Sorbonne Université, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France
| | - J Oberto
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - F Baudin
- Institut des Sciences de la Terre de Paris, UMR 7193 - Sorbonne Université - CNRS, Paris, 75005, France
| | - G Landrot
- Synchrotron SOLEIL - SAMBA beamline, Saint-Aubin, 91190, France
| | - C Baya
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 - CNRS, Sorbonne Université, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France
| | - P Le Pape
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 - CNRS, Sorbonne Université, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France
| | - G Morin
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 - CNRS, Sorbonne Université, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France
| | - P Forterre
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - F Guyot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 - CNRS, Sorbonne Université, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France.,Institut Universitaire de France (IUF), Paris, France
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8
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Cathalot C, Roussel EG, Perhirin A, Creff V, Donval JP, Guyader V, Roullet G, Gula J, Tamburini C, Garel M, Godfroy A, Sarradin PM. Hydrothermal plumes as hotspots for deep-ocean heterotrophic microbial biomass production. Nat Commun 2021; 12:6861. [PMID: 34824206 PMCID: PMC8617075 DOI: 10.1038/s41467-021-26877-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/19/2021] [Indexed: 11/09/2022] Open
Abstract
Carbon budgets of hydrothermal plumes result from the balance between carbon sinks through plume chemoautotrophic processes and carbon release via microbial respiration. However, the lack of comprehensive analysis of the metabolic processes and biomass production rates hinders an accurate estimate of their contribution to the deep ocean carbon cycle. Here, we use a biogeochemical model to estimate the autotrophic and heterotrophic production rates of microbial communities in hydrothermal plumes and validate it with in situ data. We show how substrate limitation might prevent net chemolithoautotrophic production in hydrothermal plumes. Elevated prokaryotic heterotrophic production rates (up to 0.9 gCm-2y-1) compared to the surrounding seawater could lead to 0.05 GtCy-1 of C-biomass produced through chemoorganotrophy within hydrothermal plumes, similar to the Particulate Organic Carbon (POC) export fluxes reported in the deep ocean. We conclude that hydrothermal plumes must be accounted for as significant deep sources of POC in ocean carbon budgets.
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Affiliation(s)
- Cécile Cathalot
- Laboratoire Cycles Géochimiques et ressources - LCG/GM/REM, Ifremer, Plouzané, France.
| | - Erwan G. Roussel
- grid.4825.b0000 0004 0641 9240Laboratoire de Microbiologie des Environnements Extrêmes – LMEE/EEP/REM, Ifremer, Plouzané, France
| | - Antoine Perhirin
- grid.4825.b0000 0004 0641 9240Laboratoire Environnement Profond – LEP/EEP/REM, IFREMER, Plouzané, France
| | - Vanessa Creff
- grid.4825.b0000 0004 0641 9240Laboratoire de Microbiologie des Environnements Extrêmes – LMEE/EEP/REM, Ifremer, Plouzané, France
| | - Jean-Pierre Donval
- grid.4825.b0000 0004 0641 9240Laboratoire Cycles Géochimiques et ressources – LCG/GM/REM, Ifremer, Plouzané, France
| | - Vivien Guyader
- grid.4825.b0000 0004 0641 9240Laboratoire Cycles Géochimiques et ressources – LCG/GM/REM, Ifremer, Plouzané, France
| | - Guillaume Roullet
- Univ Brest, CNRS, IRD, Ifremer, Laboratoire d’Océanographie Physique et Spatiale (LOPS), IUEM, Plouzané, France
| | - Jonathan Gula
- Univ Brest, CNRS, IRD, Ifremer, Laboratoire d’Océanographie Physique et Spatiale (LOPS), IUEM, Plouzané, France ,grid.440891.00000 0001 1931 4817Institut Universitaire de France (IUF), Paris, France
| | - Christian Tamburini
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110 Marseille, France
| | - Marc Garel
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110 Marseille, France
| | - Anne Godfroy
- grid.4825.b0000 0004 0641 9240Laboratoire de Microbiologie des Environnements Extrêmes – LMEE/EEP/REM, Ifremer, Plouzané, France
| | - Pierre-Marie Sarradin
- grid.4825.b0000 0004 0641 9240Laboratoire Environnement Profond – LEP/EEP/REM, IFREMER, Plouzané, France
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9
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Pillot G, Amin Ali O, Davidson S, Shintu L, Godfroy A, Combet-Blanc Y, Bonin P, Liebgott PP. Identification of enriched hyperthermophilic microbial communities from a deep-sea hydrothermal vent chimney under electrolithoautotrophic culture conditions. Sci Rep 2021; 11:14782. [PMID: 34285254 PMCID: PMC8292307 DOI: 10.1038/s41598-021-94135-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
Deep-sea hydrothermal vents are extreme and complex ecosystems based on a trophic chain. We are still unsure of the identities of the first colonizers of these environments and their metabolism, but they are thought to be (hyper)thermophilic autotrophs. Here we investigate whether the electric potential observed across hydrothermal chimneys could serve as an energy source for these first colonizers. Experiments were performed in a two-chamber microbial electrochemical system inoculated with deep-sea hydrothermal chimney samples, with a cathode as sole electron donor, CO2 as sole carbon source, and nitrate, sulfate, or oxygen as electron acceptors. After a few days of culturing, all three experiments showed growth of electrotrophic biofilms consuming the electrons (directly or indirectly) and producing organic compounds including acetate, glycerol, and pyruvate. Within the biofilms, the only known autotroph species retrieved were members of Archaeoglobales. Various heterotrophic phyla also grew through trophic interactions, with Thermococcales growing in all three experiments as well as other bacterial groups specific to each electron acceptor. This electrotrophic metabolism as energy source driving initial microbial colonization of conductive hydrothermal chimneys is discussed.
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Affiliation(s)
- Guillaume Pillot
- Aix Marseille Université, Université de Toulon, IRD, CNRS, MIO UM 110, 13288, Marseille Cedex 09, France
| | - Oulfat Amin Ali
- Aix Marseille Université, Université de Toulon, IRD, CNRS, MIO UM 110, 13288, Marseille Cedex 09, France
| | - Sylvain Davidson
- Aix Marseille Université, Université de Toulon, IRD, CNRS, MIO UM 110, 13288, Marseille Cedex 09, France
| | - Laetitia Shintu
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Anne Godfroy
- IFREMER, CNRS, Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes-UMR6197, Ifremer, Centre de Brest CS10070, Plouzané, France
| | - Yannick Combet-Blanc
- Aix Marseille Université, Université de Toulon, IRD, CNRS, MIO UM 110, 13288, Marseille Cedex 09, France
| | - Patricia Bonin
- Aix Marseille Université, Université de Toulon, IRD, CNRS, MIO UM 110, 13288, Marseille Cedex 09, France
| | - Pierre-Pol Liebgott
- Aix Marseille Université, Université de Toulon, IRD, CNRS, MIO UM 110, 13288, Marseille Cedex 09, France.
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10
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François DX, Godfroy A, Mathien C, Aubé J, Cathalot C, Lesongeur F, L'Haridon S, Philippon X, Roussel EG. Persephonella atlantica sp. nov.: How to adapt to physico-chemical gradients in high temperature hydrothermal habitats. Syst Appl Microbiol 2020; 44:126176. [PMID: 33422731 DOI: 10.1016/j.syapm.2020.126176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
A novel thermophilic, microaerophilic and anaerobic, hydrogen- sulphur- and thiosulphate-oxidising bacterium, designated MO1340T, was isolated from a deep-sea hydrothermal chimney collected from the Lucky Strike hydrothermal vent field on the Mid-Atlantic Ridge. Cells were short, motile rods of 1.4-2.2μm length and 0.5-0.8μm width. Optimal growth was observed for a NaCl concentration of 2.5 % (w/v) at pH 6.5. As for other members of the genus Persephonella, strain MO1340T was strictly chemolithoautotrophic and could oxidise hydrogen, elemental sulphur or thiosulphate using oxygen as electron acceptor. Anaerobic nitrate reduction using hydrogen could also be performed. Each catabolic reaction had a different optimal growth temperature (65 to 75°C) and an optimal dissolved oxygen concentration (11.4 to 119.7 μM at 70°C for aerobic reactions) that varied according to the electron donors utilised. These experimental results are consistent with the distribution of these catabolic substrates along the temperature gradient observed in active hydrothermal systems. They strongly suggest that this adaptive strategy could confer a selective advantage for strain MO1340T in the dynamic part of the ecosystem where hot, reduced hydrothermal fluid mixes with cold, oxygenated seawater. Phylogenetic analysis indicated that strain MO1340T was a member of the genus Persephonella within the order Hydrogenothermales as it shared a 16S rRNA gene sequence similarity <95.5 % and ANI respectively 75.66 % with closest described Persephonella (P. hydrogeniphila 29WT). On the basis of the physiological and genomic properties of the new isolate, the name Persephonella atlantica sp. nov. is proposed. The type strain is MO1340T (=UBOCC-M-3359T =JCM 34026T).
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Affiliation(s)
- David X François
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Anne Godfroy
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Clémentine Mathien
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Johanne Aubé
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Cécile Cathalot
- Ifremer, Laboratoire Cycle Géochimique et Ressources (LCG/GM/REM), F-29280, Plouzané, France
| | - Françoise Lesongeur
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Stéphane L'Haridon
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Xavier Philippon
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Erwan G Roussel
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France.
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11
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Dahle H, Le Moine Bauer S, Baumberger T, Stokke R, Pedersen RB, Thorseth IH, Steen IH. Energy Landscapes in Hydrothermal Chimneys Shape Distributions of Primary Producers. Front Microbiol 2018; 9:1570. [PMID: 30061874 PMCID: PMC6055050 DOI: 10.3389/fmicb.2018.01570] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 06/25/2018] [Indexed: 11/25/2022] Open
Abstract
Hydrothermal systems are excellent natural laboratories for the study of how chemical energy landscapes shape microbial communities. Yet, only a few attempts have been made to quantify relationships between energy availability and microbial community structure in these systems. Here, we have investigated how microbial communities and chemical energy availabilities vary along cross-sections of two hydrothermal chimneys from the Soria Moria Vent Field and the Bruse Vent Field. Both vent fields are located on the Arctic Mid-Ocean Ridge, north of the Jan Mayen Island and the investigated chimneys were venting fluids with markedly different H2S:CH4 ratios. Energy landscapes were inferred from a stepwise in silico mixing of hydrothermal fluids (HFs) with seawater, where Gibbs energies of relevant redox-reactions were calculated at each step. These calculations formed the basis for simulations of relative abundances of primary producers in microbial communities. The simulations were compared with an analysis of 24 samples from chimney wall transects by sequencing of 16S rRNA gene amplicons using 454 sequencing. Patterns in relative abundances of sulfide oxidizing Epsilonproteobacteria and methane oxidizing Methylococcales and ANME-1, were consistent with simulations. However, even though H2 was present in HFs from both chimneys, the observed abundances of putative hydrogen oxidizing anaerobic sulfate reducers (Archaeoglobales) and methanogens (Methanococcales) in the inner parts of the Soria Moria Chimney were considerably higher than predicted by simulations. This indicates biogenic production of H2 in the chimney wall by fermentation, and suggests that biological activity inside the chimneys may modulate energy landscapes significantly. Our results are consistent with the notion that energy landscapes largely shape the distribution of primary producers in hydrothermal systems. Our study demonstrates how a combination of modeling and field observations can be useful in deciphering connections between chemical energy landscapes and metabolic networks within microbial communities.
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Affiliation(s)
- Håkon Dahle
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Sven Le Moine Bauer
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Tamara Baumberger
- Pacific Marine Environmental Laboratory (NOAA), Newport, OR, United States
| | - Runar Stokke
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Rolf B. Pedersen
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Ingunn H. Thorseth
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Ida H. Steen
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
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12
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Kashyap S, Sklute EC, Dyar MD, Holden JF. Reduction and Morphological Transformation of Synthetic Nanophase Iron Oxide Minerals by Hyperthermophilic Archaea. Front Microbiol 2018; 9:1550. [PMID: 30050524 PMCID: PMC6050373 DOI: 10.3389/fmicb.2018.01550] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/21/2018] [Indexed: 11/24/2022] Open
Abstract
Fe(III) (oxyhydr)oxides are electron acceptors for some hyperthermophilic archaea in mildly reducing geothermal environments. However, the kinds of iron oxides that can be used, growth rates, extent of iron reduction, and the morphological changes that occur to minerals are poorly understood. The hyperthermophilic iron-reducing crenarchaea Pyrodictium delaneyi and Pyrobaculum islandicum were grown separately on six different synthetic nanophase Fe(III) (oxyhydr)oxides. For both organisms, growth on ferrihydrite produced the highest growth rates and the largest amounts of Fe(II), although P. delaneyi produced four times more Fe(II) (25 mM) than P. islandicum (6 mM). Both organisms grew on lepidocrocite and akaganéite and produced 2 and 3 mM Fe(II). Modest growth occurred for both organisms on goethite, hematite, and maghemite where ≤1 mM Fe(II) was produced. The diameters of the spherical mineral end-products following P. delaneyi growth increased by 30 nm for ferrihydrite and 50–150 nm for lepidocrocite relative to heated abiotic controls. For akaganéite, spherical particle sizes were the same for P. delaneyi-reacted samples and heated abiotic controls, but the spherical particles were more numerous in the P. delaneyi samples. For P. islandicum, there was no increase in grain size for the mineral end-products following growth on ferrihydrite, lepidocrocite, or akaganéite relative to the heated abiotic controls. High-resolution transmission electron microscopy of lattice fringes and selected-area electron diffraction of the minerals produced by both organisms when grown on ferrihydrite showed that magnetite and/or possibly maghemite were the end-products while the heated abiotic controls only contained ferrihydrite. These results expand the current view of bioavailable Fe(III) (oxyhydr)oxides for reduction by hyperthermophilic archaea when presented as synthetic nanophase minerals. They show that growth and reduction rates are inversely correlated with the iron (oxyhydr)oxide crystallinity and that iron (oxyhydr)oxide mineral transformation takes different forms for these two organisms.
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Affiliation(s)
- Srishti Kashyap
- Department of Microbiology, University of Massachusetts, Amherst, MA, United States
| | - Elizabeth C Sklute
- Department of Astronomy, Mount Holyoke College, South Hadley, MA, United States.,Planetary Science Institute, Tucson, AZ, United States
| | - M Darby Dyar
- Department of Astronomy, Mount Holyoke College, South Hadley, MA, United States.,Planetary Science Institute, Tucson, AZ, United States
| | - James F Holden
- Department of Microbiology, University of Massachusetts, Amherst, MA, United States
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13
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Pjevac P, Meier DV, Markert S, Hentschker C, Schweder T, Becher D, Gruber-Vodicka HR, Richter M, Bach W, Amann R, Meyerdierks A. Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys. Front Microbiol 2018; 9:680. [PMID: 29696004 PMCID: PMC5904459 DOI: 10.3389/fmicb.2018.00680] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 03/22/2018] [Indexed: 11/15/2022] Open
Abstract
At hydrothermal vent sites, chimneys consisting of sulfides, sulfates, and oxides are formed upon contact of reduced hydrothermal fluids with oxygenated seawater. The walls and surfaces of these chimneys are an important habitat for vent-associated microorganisms. We used community proteogenomics to investigate and compare the composition, metabolic potential and relative in situ protein abundance of microbial communities colonizing two actively venting hydrothermal chimneys from the Manus Basin back-arc spreading center (Papua New Guinea). We identified overlaps in the in situ functional profiles of both chimneys, despite differences in microbial community composition and venting regime. Carbon fixation on both chimneys seems to have been primarily mediated through the reverse tricarboxylic acid cycle and fueled by sulfur-oxidation, while the abundant metabolic potential for hydrogen oxidation and carbon fixation via the Calvin–Benson–Bassham cycle was hardly utilized. Notably, the highly diverse microbial community colonizing the analyzed black smoker chimney had a highly redundant metabolic potential. In contrast, the considerably less diverse community colonizing the diffusely venting chimney displayed a higher metabolic versatility. An increased diversity on the phylogenetic level is thus not directly linked to an increased metabolic diversity in microbial communities that colonize hydrothermal chimneys.
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Affiliation(s)
- Petra Pjevac
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Dimitri V Meier
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Stephanie Markert
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | | | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Harald R Gruber-Vodicka
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Symbiosis, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Michael Richter
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Ribocon GmbH, Bremen, Germany
| | - Wolfgang Bach
- MARUM Center for Marine Environmental Sciences, Department of Geosciences, University of Bremen, Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Anke Meyerdierks
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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14
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Topçuoğlu BD, Stewart LC, Morrison HG, Butterfield DA, Huber JA, Holden JF. Hydrogen Limitation and Syntrophic Growth among Natural Assemblages of Thermophilic Methanogens at Deep-sea Hydrothermal Vents. Front Microbiol 2016; 7:1240. [PMID: 27547206 PMCID: PMC4974244 DOI: 10.3389/fmicb.2016.01240] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/26/2016] [Indexed: 11/13/2022] Open
Abstract
Thermophilic methanogens are common autotrophs at hydrothermal vents, but their growth constraints and dependence on H2 syntrophy in situ are poorly understood. Between 2012 and 2015, methanogens and H2-producing heterotrophs were detected by growth at 80°C and 55°C at most diffuse (7-40°C) hydrothermal vent sites at Axial Seamount. Microcosm incubations of diffuse hydrothermal fluids at 80°C and 55°C demonstrated that growth of thermophilic and hyperthermophilic methanogens is primarily limited by H2 availability. Amendment of microcosms with NH4 (+) generally had no effect on CH4 production. However, annual variations in abundance and CH4 production were observed in relation to the eruption cycle of the seamount. Microcosm incubations of hydrothermal fluids at 80°C and 55°C supplemented with tryptone and no added H2 showed CH4 production indicating the capacity in situ for methanogenic H2 syntrophy. 16S rRNA genes were found in 80°C microcosms from H2-producing archaea and H2-consuming methanogens, but not for any bacteria. In 55°C microcosms, sequences were found from H2-producing bacteria and H2-consuming methanogens and sulfate-reducing bacteria. A co-culture of representative organisms showed that Thermococcus paralvinellae supported the syntrophic growth of Methanocaldococcus bathoardescens at 82°C and Methanothermococcus sp. strain BW11 at 60°C. The results demonstrate that modeling of subseafloor methanogenesis should focus primarily on H2 availability and temperature, and that thermophilic H2 syntrophy can support methanogenesis within natural microbial assemblages and may be an important energy source for thermophilic autotrophs in marine geothermal environments.
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Affiliation(s)
| | - Lucy C. Stewart
- Department of Microbiology, University of Massachusetts, AmherstMA, USA
| | - Hilary G. Morrison
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods HoleMA, USA
| | - David A. Butterfield
- Joint Institute for the Study of Atmosphere and Ocean, University of Washington, SeattleWA, USA
- Pacific Marine Environmental Laboratory, National Oceanic and Atmospheric Administration, SeattleWA, USA
| | - Julie A. Huber
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods HoleMA, USA
| | - James F. Holden
- Department of Microbiology, University of Massachusetts, AmherstMA, USA
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