A global atlas of deep-sea cold seep viruses uncovers extensive genomic novelty and biotechnological potential

Abstract

Cold seeps are globally distributed deep-sea ecosystems harboring diverse chemosynthetic microbial communities, yet their viral components remain poorly understood. Here, we establish the Global Cold Seep Virome, a comprehensive catalog of 191,937 species-level viral operational taxonomic units (vOTUs) and 2.44 million viral protein clusters reconstructed from 314 metagenomes spanning 18 cold seep sites worldwide. Most vOTUs are distinct from those in existing environmental viromes, suggesting that cold seeps harbor a largely unexplored viral reservoir. Host prediction suggests diverse viral associations with key prokaryotes, including anaerobic methanotrophic archaea. Protein annotation reveals that these viruses encode widespread uncharacterized proteins and viral hallmark proteins with divergent physicochemical properties, potentially contributing to their ecological adaptability. We also identify putative auxiliary metabolic genes, anti-defense genes, and lysins, and experimentally validate representative anti-defense proteins and lysins with strong activities. This resource expands current knowledge of deep-sea viral diversity and provides a foundation for studying virus-host interactions, testing biogeochemical hypotheses, and exploring biotechnological potential in cold seep ecosystems.