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

• Published in: The ISME Journal Vol. 13; no. 5; pp. 1269 - 1279
• Main Authors: Boyd, Joel A., Jungbluth, Sean P., Leu, Andy O., Evans, Paul N., Woodcroft, Ben J., Chadwick, Grayson L., Orphan, Victoria J., Amend, Jan P., Rappé, Michael S., Tyson, Gene W.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01-05-2019; Nature Publishing Group
• Subjects: 631/208/212/2142; 631/326/26/2526; 704/158/855; Archaea; Archaeal Proteins - genetics; Archaeal Proteins - metabolism; Archaeoglobi; Bathyarchaeota; Biomedical and Life Sciences; Butane; Butanes - metabolism; Coenzyme M; Ecology; Electron transport; Electron transport chain; ENVIRONMENTAL SCIENCES; Euryarchaeota; Euryarchaeota - classification; Euryarchaeota - enzymology; Euryarchaeota - genetics; Euryarchaeota - metabolism; Evolution, Molecular; Evolutionary Biology; Gene transfer; Genes; Genomes; Life Sciences; Metabolism; Metagenome; Metagenomics; Methane; Methane - metabolism; Methane generation; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; New species; Operons; Oxidation; Oxidation-Reduction; Oxidoreductases - genetics; Oxidoreductases - metabolism; Phylogeny; Polytropus marinifundus; Reductase; Seawater - microbiology; Sulfur; Sulfur compounds; Syntrophoarchaeum
• ISSN: 1751-7362; 1751-7370
• DOI: 10.1038/s41396-018-0343-2

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.