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Zehnle H, Laso-Pérez R, Lipp J, Riedel D, Benito Merino D, Teske A, Wegener G. Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes. Nat Microbiol 2023:10.1038/s41564-023-01400-3. [PMID: 37264141 DOI: 10.1038/s41564-023-01400-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/28/2023] [Indexed: 06/03/2023]
Abstract
Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C5) and tetradecane (C14) at 70 °C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons released from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.
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Affiliation(s)
- Hanna Zehnle
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
- Faculty of Geosciences, University of Bremen, Bremen, Germany.
| | - Rafael Laso-Pérez
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
- Biogeochemistry and Microbial Ecology Department, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Julius Lipp
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Dietmar Riedel
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - David Benito Merino
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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2
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Molari M, Hassenrueck C, Laso-Pérez R, Wegener G, Offre P, Scilipoti S, Boetius A. A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes. Nat Microbiol 2023; 8:651-665. [PMID: 36894632 PMCID: PMC10066037 DOI: 10.1038/s41564-023-01342-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 02/10/2023] [Indexed: 03/11/2023]
Abstract
Members of the bacterial genus Sulfurimonas (phylum Campylobacterota) dominate microbial communities in marine redoxclines and are important for sulfur and nitrogen cycling. Here we used metagenomics and metabolic analyses to characterize a Sulfurimonas from the Gakkel Ridge in the Central Arctic Ocean and Southwest Indian Ridge, showing that this species is ubiquitous in non-buoyant hydrothermal plumes at Mid Ocean Ridges across the global ocean. One Sulfurimonas species, USulfurimonas pluma, was found to be globally abundant and active in cold (<0-4 °C), oxygen-saturated and hydrogen-rich hydrothermal plumes. Compared with other Sulfurimonas species, US. pluma has a reduced genome (>17%) and genomic signatures of an aerobic chemolithotrophic metabolism using hydrogen as an energy source, including acquisition of A2-type oxidase and loss of nitrate and nitrite reductases. The dominance and unique niche of US. pluma in hydrothermal plumes suggest an unappreciated biogeochemical role for Sulfurimonas in the deep ocean.
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Affiliation(s)
- Massimiliano Molari
- Max Planck Institute for Marine Microbiology, Bremen, Germany. .,Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
| | | | - Rafael Laso-Pérez
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Pierre Offre
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
| | - Stefano Scilipoti
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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3
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Laso-Pérez R, Wu F, Crémière A, Speth DR, Magyar JS, Zhao K, Krupovic M, Orphan VJ. Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome. Nat Microbiol 2023; 8:231-245. [PMID: 36658397 PMCID: PMC9894754 DOI: 10.1038/s41564-022-01297-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/29/2022] [Indexed: 01/21/2023]
Abstract
'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus-host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.
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Affiliation(s)
- Rafael Laso-Pérez
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany.
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
| | - Fabai Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China.
- Ocean College, Zhejiang University, Zhoushan, China.
- Donghai Laboratory, Zhoushan, China.
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
| | - Antoine Crémière
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Daan R Speth
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
| | - John S Magyar
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Kehan Zhao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France.
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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4
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Abstract
Alkanes are saturated apolar hydrocarbons that range from its simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Gunter Wegener
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rafael Laso-Pérez
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Current affiliation: Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Victoria J Orphan
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Division of Geological and Planetary Sciences and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Antje Boetius
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany;
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5
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Chadwick GL, Skennerton CT, Laso-Pérez R, Leu AO, Speth DR, Yu H, Morgan-Lang C, Hatzenpichler R, Goudeau D, Malmstrom R, Brazelton WJ, Woyke T, Hallam SJ, Tyson GW, Wegener G, Boetius A, Orphan VJ. Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biol 2022; 20:e3001508. [PMID: 34986141 PMCID: PMC9012536 DOI: 10.1371/journal.pbio.3001508] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 04/15/2022] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor. A comparative genomics study of anaerobic methanotrophic (ANME) archaea reveals the genetic "parts list" associated with the repeated evolutionary transition between methanogenic and methanotrophic metabolism in the archaeal domain of life.
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Affiliation(s)
- Grayson L. Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
| | - Connor T. Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Rafael Laso-Pérez
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andy O. Leu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Daan R. Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Roland Hatzenpichler
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Danielle Goudeau
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Rex Malmstrom
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - William J. Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Steven J. Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, University of British Columbia, British Columbia, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, British Columbia, Canada
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Gunter Wegener
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Antje Boetius
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
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6
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Hahn CJ, Laso-Pérez R, Vulcano F, Vaziourakis KM, Stokke R, Steen IH, Teske A, Boetius A, Liebeke M, Amann R, Knittel K, Wegener G. " Candidatus Ethanoperedens," a Thermophilic Genus of Archaea Mediating the Anaerobic Oxidation of Ethane. mBio 2020; 11:e00600-20. [PMID: 32317322 PMCID: PMC7175092 DOI: 10.1128/mbio.00600-20] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 03/23/2020] [Indexed: 01/01/2023] Open
Abstract
Cold seeps and hydrothermal vents deliver large amounts of methane and other gaseous alkanes into marine surface sediments. Consortia of archaea and partner bacteria thrive on the oxidation of these alkanes and its coupling to sulfate reduction. The inherently slow growth of the involved organisms and the lack of pure cultures have impeded the understanding of the molecular mechanisms of archaeal alkane degradation. Here, using hydrothermal sediments of the Guaymas Basin (Gulf of California) and ethane as the substrate, we cultured microbial consortia of a novel anaerobic ethane oxidizer, "Candidatus Ethanoperedens thermophilum" (GoM-Arc1 clade), and its partner bacterium "Candidatus Desulfofervidus auxilii," previously known from methane-oxidizing consortia. The sulfate reduction activity of the culture doubled within one week, indicating a much faster growth than in any other alkane-oxidizing archaea described before. The dominance of a single archaeal phylotype in this culture allowed retrieval of a closed genome of "Ca. Ethanoperedens," a sister genus of the recently reported ethane oxidizer "Candidatus Argoarchaeum." The metagenome-assembled genome of "Ca. Ethanoperedens" encoded a complete methanogenesis pathway including a methyl-coenzyme M reductase (MCR) that is highly divergent from those of methanogens and methanotrophs. Combined substrate and metabolite analysis showed ethane as the sole growth substrate and production of ethyl-coenzyme M as the activation product. Stable isotope probing demonstrated that the enzymatic mechanism of ethane oxidation in "Ca. Ethanoperedens" is fully reversible; thus, its enzymatic machinery has potential for the biotechnological development of microbial ethane production from carbon dioxide.IMPORTANCE In the seabed, gaseous alkanes are oxidized by syntrophic microbial consortia that thereby reduce fluxes of these compounds into the water column. Because of the immense quantities of seabed alkane fluxes, these consortia are key catalysts of the global carbon cycle. Due to their obligate syntrophic lifestyle, the physiology of alkane-degrading archaea remains poorly understood. We have now cultivated a thermophilic, relatively fast-growing ethane oxidizer in partnership with a sulfate-reducing bacterium known to aid in methane oxidation and have retrieved the first complete genome of a short-chain alkane-degrading archaeon. This will greatly enhance the understanding of nonmethane alkane activation by noncanonical methyl-coenzyme M reductase enzymes and provide insights into additional metabolic steps and the mechanisms underlying syntrophic partnerships. Ultimately, this knowledge could lead to the biotechnological development of alkanogenic microorganisms to support the carbon neutrality of industrial processes.
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Affiliation(s)
| | - Rafael Laso-Pérez
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Francesca Vulcano
- K.G. Jebsen Centre for Deep Sea Research and Department of Biological Sciences, University of Bergen, Bergen, Norway
| | | | - Runar Stokke
- K.G. Jebsen Centre for Deep Sea Research and Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ida Helene Steen
- K.G. Jebsen Centre for Deep Sea Research and Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Andreas Teske
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Antje Boetius
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Manuel Liebeke
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katrin Knittel
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gunter Wegener
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
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7
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Laso-Pérez R, Hahn C, van Vliet DM, Tegetmeyer HE, Schubotz F, Smit NT, Pape T, Sahling H, Bohrmann G, Boetius A, Knittel K, Wegener G. Anaerobic Degradation of Non-Methane Alkanes by " Candidatus Methanoliparia" in Hydrocarbon Seeps of the Gulf of Mexico. mBio 2019; 10:e01814-19. [PMID: 31431553 PMCID: PMC6703427 DOI: 10.1128/mbio.01814-19] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 07/24/2019] [Indexed: 11/20/2022] Open
Abstract
Crude oil and gases in the seabed provide an important energy source for subsurface microorganisms. We investigated the role of archaea in the anaerobic degradation of non-methane alkanes in deep-sea oil seeps from the Gulf of Mexico. We identified microscopically the ethane and short-chain alkane oxidizers "Candidatus Argoarchaeum" and "Candidatus Syntrophoarchaeum" forming consortia with bacteria. Moreover, we found that the sediments contain large numbers of cells from the archaeal clade "Candidatus Methanoliparia," which was previously proposed to perform methanogenic alkane degradation. "Ca. Methanoliparia" occurred abundantly as single cells attached to oil droplets in sediments without apparent bacterial or archaeal partners. Metagenome-assembled genomes of "Ca. Methanoliparia" encode a complete methanogenesis pathway including a canonical methyl-coenzyme M reductase (MCR) but also a highly divergent MCR related to those of alkane-degrading archaea and pathways for the oxidation of long-chain alkyl units. Its metabolic genomic potential and its global detection in hydrocarbon reservoirs suggest that "Ca. Methanoliparia" is an important methanogenic alkane degrader in subsurface environments, producing methane by alkane disproportionation as a single organism.IMPORTANCE Oil-rich sediments from the Gulf of Mexico were found to contain diverse alkane-degrading groups of archaea. The symbiotic, consortium-forming "Candidatus Argoarchaeum" and "Candidatus Syntrophoarchaeum" are likely responsible for the degradation of ethane and short-chain alkanes, with the help of sulfate-reducing bacteria. "Ca. Methanoliparia" occurs as single cells associated with oil droplets. These archaea encode two phylogenetically different methyl-coenzyme M reductases that may allow this organism to thrive as a methanogen on a substrate of long-chain alkanes. Based on a library survey, we show that "Ca. Methanoliparia" is frequently detected in oil reservoirs and may be a key agent in the transformation of long-chain alkanes to methane. Our findings provide evidence for the important and diverse roles of archaea in alkane-rich marine habitats and support the notion of a significant functional versatility of the methyl coenzyme M reductase.
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Affiliation(s)
- Rafael Laso-Pérez
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Cedric Hahn
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
| | - Daan M van Vliet
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Halina E Tegetmeyer
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Florence Schubotz
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Nadine T Smit
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Thomas Pape
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Heiko Sahling
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Gerhard Bohrmann
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Antje Boetius
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Katrin Knittel
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gunter Wegener
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
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8
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Laso-Pérez R, Wegener G, Knittel K, Widdel F, Harding KJ, Krukenberg V, Meier DV, Richter M, Tegetmeyer HE, Riedel D, Richnow HH, Adrian L, Reemtsma T, Lechtenfeld OJ, Musat F. Thermophilic archaea activate butane via alkyl-coenzyme M formation. Nature 2016; 539:396-401. [PMID: 27749816 DOI: 10.1038/nature20152] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/11/2016] [Indexed: 12/25/2022]
Abstract
The anaerobic formation and oxidation of methane involve unique enzymatic mechanisms and cofactors, all of which are believed to be specific for C1-compounds. Here we show that an anaerobic thermophilic enrichment culture composed of dense consortia of archaea and bacteria apparently uses partly similar pathways to oxidize the C4 hydrocarbon butane. The archaea, proposed genus 'Candidatus Syntrophoarchaeum', show the characteristic autofluorescence of methanogens, and contain highly expressed genes encoding enzymes similar to methyl-coenzyme M reductase. We detect butyl-coenzyme M, indicating archaeal butane activation analogous to the first step in anaerobic methane oxidation. In addition, Ca. Syntrophoarchaeum expresses the genes encoding β-oxidation enzymes, carbon monoxide dehydrogenase and reversible C1 methanogenesis enzymes. This allows for the complete oxidation of butane. Reducing equivalents are seemingly channelled to HotSeep-1, a thermophilic sulfate-reducing partner bacterium known from the anaerobic oxidation of methane. Genes encoding 16S rRNA and methyl-coenzyme M reductase similar to those identifying Ca. Syntrophoarchaeum were repeatedly retrieved from marine subsurface sediments, suggesting that the presented activation mechanism is naturally widespread in the anaerobic oxidation of short-chain hydrocarbons.
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Affiliation(s)
- Rafael Laso-Pérez
- Max-Planck Institute for Marine Microbiology, 28359 Bremen, Germany.,Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Gunter Wegener
- Max-Planck Institute for Marine Microbiology, 28359 Bremen, Germany.,Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, 27570 Bremerhaven, Germany.,MARUM, Center for Marine Environmental Sciences, University Bremen, 28359 Bremen, Germany
| | - Katrin Knittel
- Max-Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Friedrich Widdel
- Max-Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Katie J Harding
- Max-Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Viola Krukenberg
- Max-Planck Institute for Marine Microbiology, 28359 Bremen, Germany.,Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Dimitri V Meier
- Max-Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Michael Richter
- Max-Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Halina E Tegetmeyer
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, 27570 Bremerhaven, Germany.,Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dietmar Riedel
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | | | - Lorenz Adrian
- Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Thorsten Reemtsma
- Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | | | - Florin Musat
- Max-Planck Institute for Marine Microbiology, 28359 Bremen, Germany.,Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
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