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Wu M, Li J, Lai CY, Leu AO, Sun S, Gu R, Erler DV, Liu L, Li L, Tyson GW, Yuan Z, McIlroy SJ, Guo J. Nitrate-driven anaerobic oxidation of ethane and butane by bacteria. ISME J 2024; 18:wrad011. [PMID: 38365228 PMCID: PMC10811727 DOI: 10.1093/ismejo/wrad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 02/18/2024]
Abstract
The short-chain gaseous alkanes (ethane, propane, and butane; SCGAs) are important components of natural gas, yet their fate in environmental systems is poorly understood. Microbially mediated anaerobic oxidation of SCGAs coupled to nitrate reduction has been demonstrated for propane, but is yet to be shown for ethane or butane-despite being energetically feasible. Here we report two independent bacterial enrichments performing anaerobic ethane and butane oxidation, respectively, coupled to nitrate reduction to dinitrogen gas and ammonium. Isotopic 13C- and 15N-labelling experiments, mass and electron balance tests, and metabolite and meta-omics analyses collectively reveal that the recently described propane-oxidizing "Candidatus Alkanivorans nitratireducens" was also responsible for nitrate-dependent anaerobic oxidation of the SCGAs in both these enrichments. The complete genome of this species encodes alkylsuccinate synthase genes for the activation of ethane/butane via fumarate addition. Further substrate range tests confirm that "Ca. A. nitratireducens" is metabolically versatile, being able to degrade ethane, propane, and butane under anoxic conditions. Moreover, our study proves nitrate as an additional electron sink for ethane and butane in anaerobic environments, and for the first time demonstrates the use of the fumarate addition pathway in anaerobic ethane oxidation. These findings contribute to our understanding of microbial metabolism of SCGAs in anaerobic environments.
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Affiliation(s)
- Mengxiong Wu
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Jie Li
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Chun-Yu Lai
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Queensland 4072, Australia
- College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Andy O Leu
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology (QUT), Woolloongabba, Queensland, Australia
| | - Shengjie Sun
- Computational Science Program, The University of Texas at El Paso, El Paso, TX, United States
| | - Rui Gu
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Dirk V Erler
- Faculty of Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Lian Liu
- Metabolomics Australia (Queensland Node), Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lin Li
- Department of Physics, University of Texas at El Paso, El Paso, TX, United States
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology (QUT), Woolloongabba, Queensland, Australia
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Queensland 4072, Australia
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology (QUT), Woolloongabba, Queensland, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Queensland 4072, Australia
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2
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Zhang X, Joyce GH, Leu AO, Zhao J, Rabiee H, Virdis B, Tyson GW, Yuan Z, McIlroy SJ, Hu S. Multi-heme cytochrome-mediated extracellular electron transfer by the anaerobic methanotroph 'Candidatus Methanoperedens nitroreducens'. Nat Commun 2023; 14:6118. [PMID: 37777538 PMCID: PMC10542353 DOI: 10.1038/s41467-023-41847-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/18/2023] [Indexed: 10/02/2023] Open
Abstract
Anaerobic methanotrophic archaea (ANME) carry out anaerobic oxidation of methane, thus playing a crucial role in the methane cycle. Previous genomic evidence indicates that multi-heme c-type cytochromes (MHCs) may facilitate the extracellular electron transfer (EET) from ANME to different electron sinks. Here, we provide experimental evidence supporting cytochrome-mediated EET for the reduction of metals and electrodes by 'Candidatus Methanoperedens nitroreducens', an ANME acclimated to nitrate reduction. Ferrous iron-targeted fluorescent assays, metatranscriptomics, and single-cell imaging suggest that 'Ca. M. nitroreducens' uses surface-localized redox-active cytochromes for metal reduction. Electrochemical and Raman spectroscopic analyses also support the involvement of c-type cytochrome-mediated EET for electrode reduction. Furthermore, several genes encoding menaquinone cytochrome type-c oxidoreductases and extracellular MHCs are differentially expressed when different electron acceptors are used.
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Affiliation(s)
- Xueqin Zhang
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
| | - Georgina H Joyce
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Andy O Leu
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Jing Zhao
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
- Ecological Engineering of Mine Wastes, Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Hesamoddin Rabiee
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
- School of Chemical Engineering, The University of Queensland, Brisbane, QLD, Australia
- Centre for Future Materials, University of Southern Queensland, Springfield, QLD, Australia
| | - Bernardino Virdis
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia.
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3
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McIlroy SJ, Leu AO, Zhang X, Newell R, Woodcroft BJ, Yuan Z, Hu S, Tyson GW. Anaerobic methanotroph 'Candidatus Methanoperedens nitroreducens' has a pleomorphic life cycle. Nat Microbiol 2023; 8:321-331. [PMID: 36635574 DOI: 10.1038/s41564-022-01292-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/21/2022] [Indexed: 01/14/2023]
Abstract
'Candidatus Methanoperedens' are anaerobic methanotrophic (ANME) archaea with global importance to methane cycling. Here meta-omics and fluorescence in situ hybridization (FISH) were applied to characterize a bioreactor dominated by 'Candidatus Methanoperedens nitroreducens' performing anaerobic methane oxidation coupled to nitrate reduction. Unexpectedly, FISH revealed the stable co-existence of two 'Ca. M. nitroreducens' morphotypes: the archetypal coccobacilli microcolonies and previously unreported planktonic rods. Metagenomic analysis showed that the 'Ca. M. nitroreducens' morphotypes were genomically identical but had distinct gene expression profiles for proteins associated with carbon metabolism, motility and cell division. In addition, a third distinct phenotype was observed, with some coccobacilli 'Ca. M. nitroreducens' storing carbon as polyhydroxyalkanoates. The phenotypic variation of 'Ca. M. nitroreducens' probably aids their survival and dispersal in the face of sub-optimal environmental conditions. These findings further demonstrate the remarkable ability of members of the 'Ca. Methanoperedens' to adapt to their environment.
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Affiliation(s)
- Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia.
| | - Andy O Leu
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Xueqin Zhang
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
| | - Rhys Newell
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Ben J Woodcroft
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
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4
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Ou YF, Dong HP, McIlroy SJ, Crowe SA, Hallam SJ, Han P, Kallmeyer J, Simister RL, Vuillemin A, Leu AO, Liu Z, Zheng YL, Sun QL, Liu M, Tyson GW, Hou LJ. Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis. ISME J 2022; 16:2373-2387. [PMID: 35810262 PMCID: PMC9478090 DOI: 10.1038/s41396-022-01281-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 05/28/2023]
Abstract
Methane produced by methanogenic archaea has an important influence on Earth's changing climate. Methanogenic archaea are phylogenetically diverse and widespread in anoxic environments. These microorganisms can be divided into two subgroups based on whether or not they use b-type cytochromes for energy conservation. Methanogens with b-type cytochromes have a wider substrate range and higher growth yields than those without them. To date, methanogens with b-type cytochromes were found exclusively in the phylum "Ca. Halobacteriota" (formerly part of the phylum Euryarchaeota). Here, we present the discovery of metagenome-assembled genomes harboring methyl-coenzyme M reductase genes reconstructed from mesophilic anoxic sediments, together with the previously reported thermophilic "Ca. Methylarchaeum tengchongensis", representing a novel archaeal order, designated the "Ca. Methylarchaeales", of the phylum Thermoproteota (formerly the TACK superphylum). These microorganisms contain genes required for methyl-reducing methanogenesis and the Wood-Ljundahl pathway. Importantly, the genus "Ca. Methanotowutia" of the "Ca. Methylarchaeales" encode a cytochrome b-containing heterodisulfide reductase (HdrDE) and methanophenazine-reducing hydrogenase complex that have similar gene arrangements to those found in methanogenic Methanosarcinales. Our results indicate that members of the "Ca. Methylarchaeales" are methanogens with cytochromes and can conserve energy via membrane-bound electron transport chains. Phylogenetic and amalgamated likelihood estimation analyses indicate that methanogens with cytochrome b-containing electron transfer complexes likely evolved before diversification of Thermoproteota or "Ca. Halobacteriota" in the early Archean Eon. Surveys of public sequence databases suggest that members of the lineage are globally distributed in anoxic sediments and may be important players in the methane cycle.
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Affiliation(s)
- Ya-Fei Ou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
| | - Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Sean A Crowe
- Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Ping Han
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Rachel L Simister
- Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Aurele Vuillemin
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Andy O Leu
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Zhanfei Liu
- Marine Science Institute, The University of Texas at Austin, Port Aransas, TX, 78373, USA
| | - Yan-Ling Zheng
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Qian-Li Sun
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
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5
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Luo E, Leu AO, Eppley JM, Karl DM, DeLong EF. Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean. ISME J 2022; 16:1627-1635. [PMID: 35236926 PMCID: PMC9122931 DOI: 10.1038/s41396-022-01202-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 11/15/2022]
Abstract
Sinking particles and particle-associated microbes influence global biogeochemistry through particulate matter export from the surface to the deep ocean. Despite ongoing studies of particle-associated microbes, viruses in these habitats remain largely unexplored. Whether, where, and which viruses might contribute to particle production and export remain open to investigation. In this study, we analyzed 857 virus population genomes associated with sinking particles collected over three years in sediment traps moored at 4000 m in the North Pacific Subtropical Gyre. Particle-associated viruses here were linked to cellular hosts through matches to bacterial and archaeal metagenome-assembled genome (MAG)-encoded prophages or CRISPR spacers, identifying novel viruses infecting presumptive deep-sea bacteria such as Colwellia, Moritella, and Shewanella. We also identified lytic viruses whose abundances correlated with particulate carbon flux and/or were exported from the photic to abyssal ocean, including cyanophages. Our data are consistent with some of the predicted outcomes of the viral shuttle hypothesis, and further suggest that viral lysis of both autotrophic and heterotrophic prokaryotes may play a role in carbon export. Our analyses revealed the diversity and origins of prevalent viruses found on deep-sea sinking particles and identified prospective viral groups for future investigation into processes that govern particle export in the open ocean.
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Affiliation(s)
- Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA.
- Woods Hole Oceanographic Institution, 266 Woods Hole Road, MS 51, Woods Hole MA, 02543, Falmouth, USA.
| | - Andy O Leu
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
- Australia Center for Ecogenomics, University of Queensland, St. Lucia QLD, 4072, Australia
| | - John M Eppley
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
| | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA.
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6
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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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7
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Leu AO, Cai C, McIlroy SJ, Southam G, Orphan VJ, Yuan Z, Hu S, Tyson GW. Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae. ISME J 2020; 14:1030-1041. [PMID: 31988473 PMCID: PMC7082337 DOI: 10.1038/s41396-020-0590-x] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [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] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/10/2019] [Accepted: 01/16/2020] [Indexed: 11/09/2022]
Abstract
Anaerobic oxidation of methane (AOM) is a major biological process that reduces global methane emission to the atmosphere. Anaerobic methanotrophic archaea (ANME) mediate this process through the coupling of methane oxidation to different electron acceptors, or in concert with a syntrophic bacterial partner. Recently, ANME belonging to the archaeal family Methanoperedenaceae (formerly known as ANME-2d) were shown to be capable of AOM coupled to nitrate and iron reduction. Here, a freshwater sediment bioreactor fed with methane and Mn(IV) oxides (birnessite) resulted in a microbial community dominated by two novel members of the Methanoperedenaceae, with biochemical profiling of the system demonstrating Mn(IV)-dependent AOM. Genomic and transcriptomic analyses revealed the expression of key genes involved in methane oxidation and several shared multiheme c-type cytochromes (MHCs) that were differentially expressed, indicating the likely use of different extracellular electron transfer pathways. We propose the names "Candidatus Methanoperedens manganicus" and "Candidatus Methanoperedens manganireducens" for the two newly described Methanoperedenaceae species. This study demonstrates the ability of members of the Methanoperedenaceae to couple AOM to the reduction of Mn(IV) oxides, which suggests their potential role in linking methane and manganese cycling in the environment.
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Affiliation(s)
- Andy O Leu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Chen Cai
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia
| | - Simon J McIlroy
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Gordon Southam
- School of Earth & Environmental Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Victoria J Orphan
- Department of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91106, USA
| | - Zhiguo Yuan
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia
| | - Shihu Hu
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia.
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
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8
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Boyd JA, Jungbluth SP, Leu AO, Evans PN, Woodcroft BJ, Chadwick GL, Orphan VJ, Amend JP, Rappé MS, Tyson GW. Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. ISME J 2019; 13:1269-1279. [PMID: 30651609 PMCID: PMC6474303 DOI: 10.1038/s41396-018-0343-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/29/2018] [Accepted: 12/11/2018] [Indexed: 12/28/2022]
Abstract
The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane, and potentially propane. The number of archaeal clades encoding the MCR continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; Ca. Polytropus marinifundus gen. nov. sp. nov.) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found in Ca. Bathyarchaeota and Ca. Syntrophoarchaeum MAGs. Ca. P. marinifundus is basal to members of the class Archaeoglobi, and encodes the genes for β-oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed for Ca. Syntrophoarchaeum. Ca. P. marinifundus also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. Phylogenetic analysis suggests that the Ca. P. marinifundus MCR operons were horizontally transferred, changing our understanding of the evolution and distribution of this complex in the Archaea.
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Affiliation(s)
- Joel A Boyd
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Sean P Jungbluth
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Andy O Leu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Paul N Evans
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Ben J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Grayson L Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Jan P Amend
- Departments of Earth Sciences and Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Michael S Rappé
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.
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Leu AO, Pavli P, Gordon DM, Cave J, Gowzdz JM, Linden N, Rawlin G, Allison GE, O'Brien CL. Relative abundance of Mycobacterium in ovine Johne's disease. Microbiol Aust 2015. [DOI: 10.1071/ma15010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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