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ISME J. 2019 May;13(5):1269-1279. doi: 10.1038/s41396-018-0343-2. Epub 2019 Jan 16.

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi.

Author information

1
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.
2
Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA.
3
Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.
4
Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
5
Departments of Earth Sciences and Biological Sciences, University of Southern California, Los Angeles, CA, USA.
6
Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA.
7
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia. g.tyson@uq.edu.au.

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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