4.5 Article

Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome

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NATURE MICROBIOLOGY
卷 8, 期 2, 页码 231-+

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NATURE PORTFOLIO
DOI: 10.1038/s41564-022-01297-4

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This study characterizes a family of ANME-1 archaea and its virome using metagenomics on hydrothermal samples from the Gulf of California. It reveals the diversity, ecology, and evolution of ANME-1 and uncovers the effect of virus-host dynamics. The study also discovers 16 undescribed virus families exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures.
ANME-1 archaea are important because of their ability to metabolize methane through anaerobic oxidation. Here the authors use metagenomics on hydrothermal samples from the Gulf of California to characterize a family of ANME-1 and its virome. 'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus-host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.

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