PT  - JOURNAL ARTICLE
AU  - Rafael Laso-Pérez
AU  - Fabai Wu
AU  - Antoine Crémière
AU  - Daan R. Speth
AU  - John S. Magyar
AU  - Mart Krupovic
AU  - Victoria J. Orphan
TI  - Evolutionary Diversification of Methanotrophic <em>Ca.</em> Methanophagales (ANME-1) and Their Expansive Virome
AID  - 10.1101/2022.07.04.498658
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.07.04.498658
4099  - http://biorxiv.org/content/early/2022/07/04/2022.07.04.498658.short
4100  - http://biorxiv.org/content/early/2022/07/04/2022.07.04.498658.full
AB  - ‘Candidatus Methanophagales’ (ANME-1) is a major order-level clade of archaea responsible for methane removal in deep-sea sediments through anaerobic oxidation of methane. Yet the extent of their diversity and factors which drive their dynamics and evolution remain poorly understood. Here, by sampling hydrothermal rocks and sediments, we expand their phylogenetic diversity and characterize a new deep-branching, thermophilic ANME-1 family, ‘Candidatus Methanoxibalbaceae’ (ANME-1c). They are phylogenetically closest to the short-chain-alkane oxidizers ‘Candidatus Syntrophoarchaeales’ and ‘Candidatus Alkanophagales’, and encode ancestral features including a methyl coenzyme M reductase chaperone McrD and a hydrogenase complex. Global phylogeny and near-complete genomes clarified that the debated hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Our expanded genomic and metagenomic sampling allowed the discovery of viruses constituting 3 new orders and 16 new families that so far are exclusive to ANME-1 hosts. These viruses represent 4 major archaeal virus assemblages, characterized by tailless icosahedral, head-tailed, rod-shaped, and spindle-shaped virions, but display unique structural and replicative signatures. Exemplified by the analyses of thymidylate synthases that unveiled a virus-mediated ancestral process of host gene displacement, this expansive ANME-1 virome carries a large gene repertoire that can influence their hosts across different timescales. Our study thus puts forth an emerging evolutionary continuum between anaerobic methane and short-chain-alkane oxidizers and opens doors for exploring the impacts of viruses on the dynamics and evolution of the anaerobic methane-driven ecosystems.Competing Interest StatementThe authors have declared no competing interest.