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Nat Microbiol. 2019 Apr;4(4):603-613. doi: 10.1038/s41564-019-0363-3. Epub 2019 Mar 4.

Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea.

Author information

1
Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France. guillaume.borrel@pasteur.fr.
2
Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France.
3
Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
4
Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
5
Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA.
6
Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture, Campinas University-UNICAMP, Campinas, Sao Paolo, Brazil.
7
Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
8
Bioinformatics and Biostatistics Hub, C3BI, Institut Pasteur, Paris, France.
9
Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
10
State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
11
Department of Microbiology & Immunology, ECOSCOPE Training Program, Graduate Program in Bioinformatics, and Genome Sciences and Technology Training Program, University of British Columbia, Vancouver, British Columbia, Canada.
12
Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.
13
Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.
14
Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France. simonetta.gribaldo@pasteur.fr.

Abstract

Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth's climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea. Five of these MAGs represent under-sampled (Verstraetearchaeota, Methanonatronarchaeia, ANME-1 and GoM-Arc1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation substantially expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea ('Candidatus Methanoliparia'). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.

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PMID:
30833729
PMCID:
PMC6453112
DOI:
10.1038/s41564-019-0363-3
[Indexed for MEDLINE]
Free PMC Article

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