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.
Highlights
To investigate the microbial diversity within Juan de Fuca Ridge flank boreholes, a metagenome
To determine the taxonomy of the metagenome-assembled genome (MAG), a genome tree was constructed from a concatenated alignment of 122 archaeal single copy marker genes
Phylogenies, the MAG was positioned basal to other members within the class Archaeoglobi with strong bootstrap support (100%; Fig. 1b; Supplementary Figure 7,8), including other Archaeoglobi previously recovered from the Juan de Fuca Ridge [31]
Summary
The similarity in the MCR complexes and inferred metabolism of the Ca. Bathyarchaeota and Ca. Syntrophoarchaeum suggest that the Ca. Bathyarchaeota may oxidize short hydrocarbons. The similarity of the MCR complexes encoded by Ca. Bathyarchaeota and Ca. Syntrophoarchaeum is incongruent with their large phylogenetic distance in the genome tree, suggesting that these genes were acquired via horizontal gene transfer (HGT) [1, 5]. Syntrophoarchaeum is incongruent with their large phylogenetic distance in the genome tree, suggesting that these genes were acquired via horizontal gene transfer (HGT) [1, 5] Both scenarios indicate that further diversity of divergent MCR-encoding lineages remains to be discovered [5], which has been supported by gene-centric metagenomic analyses of deep-sea and terrestrial hydrothermal environments [6, 7]. Phylogenetic analyses support a horizontal gene transfer hypothesis for the distribution of novel MCR complex among the Archaea, and provides insight into the evolution of both the MCR complex and the Archaeoglobi
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