Deep-sea polymetallic nodule provinces host distinct benthic prokaryotic communities, yet viruses that regulate them remain largely unknown. Here, we established the viral genome dataset of the Clarion-Clipperton Fracture Zone, the world's largest deep-sea mineral exploration region, to investigate viral diversity and ecological functions. Protein-sharing network and phylogenetic analyses showed extensive benthic viral diversity, with over 99% of viral clusters not represented in current reference databases. Inferred virus-host associations suggest that viral infections span a broad range of prokaryotic lineages involved in carbon, nitrogen, phosphorus, sulfur, and metal cycling. By infecting key functional microbes and encoding auxiliary metabolic genes, viruses may modulate host metabolism and survival during infection, with potential implications for biogeochemical processes in polymetallic nodule field sediments. Moreover, gene exchange analyses indicate the potential of viruses to facilitate host adaptation to metal stress. These findings provide insights into the ecological roles of viruses in the polymetallic nodule province, establishing a vital pre-mining baseline of microbial ecosystem for future environmental impact assessments.
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