Expanding anaerobic alkane metabolism in the domain of Archaea

Methanogenesis and anaerobic methane oxidation through methyl-coenzyme M reductase (MCR) as a key enzyme have been suggested to be basal pathways of archaea1. How widespread MCR-based alkane metabolism is among archaea, where it occurs and how it evolved remain elusive. Here, we performed a global survey of MCR-encoding genomes based on metagenomic data from various environments. Eleven high-quality mcr-containing metagenomic-assembled genomes were obtained belonging to the Archaeoglobi in the Euryarchaeota, Hadesarchaeota and different TACK superphylum archaea, including the Nezhaarchaeota, Korarchaeota and Verstraetearchaeota. Archaeoglobi WYZ-LMO1 and WYZ-LMO3 and Korarchaeota WYZ-LMO9 encode both the (reverse) methanogenesis and the dissimilatory sulfate reduction pathway, suggesting that they have the genomic potential to couple both pathways in individual organisms. The Hadesarchaeota WYZ-LMO4–6 and Archaeoglobi JdFR42 encode highly divergent MCRs, enzymes that may enable them to thrive on non-methane alkanes. The occurrence of mcr genes in different archaeal phyla indicates that MCR-based alkane metabolism is common in the domain of Archaea.
(Author: Yinzhao Wang, Gunter Wegener , Jialin Hou, Fengping Wang  and Xiang Xiao)

Metabolic schemes of the studied MAGs with novel mcr genes. (a-c) The new MAGs demonstrate the large metabolic diversity of mcr-containing Archaeoglobi. a. WYZ-LMO1 and 2 are likely methane oxidizers capable of sulfate reduction; b. WYZ-LMO2, with a TACK-type mcr gene cluster, is likely a methanogen; c. JdFR-42 contains the multi-carbon-type mcr gene cluster, genes for fatty acid degradation, and genes for nitrate/nitrite reduction. Hence, it is likely a nitrate/nitrite- or partner-bacterium-dependent hydrocarbon oxidizer. d. The bins of Hadesarchaeota archaea WYZ-LMO4-6 encode multi-carbon-compound metabolism; the absence of reductive pathways suggests a need for partner bacteria. e. Nezhaarchaeota archaea WYZ-LMO7-8 contains the genes for hydrogenotrophic methanogenesis. f. Korarchaeota archaeon WYZ-LMO9 is likely a methylotrophic methanogen that uses electrons from sulfide or hydrogen oxidation.