Viruses are a key regulator of the microbial carbon cycle in the deep-sea biosphere.

The marine biosphere profoundly influences atmospheric chemistry and climate through its carbon cycle. Viruses, the most abundant and diverse entities in marine ecosystems, significantly shape global carbon dynamics by infecting microbes and altering their metabolism. Both DNA and RNA viruses drive these processes in surface oceans, yet their roles in the deep sea-a sunlight-independent ecosystem that stores vast carbon reserves-remain largely unexplored. Here we show that viruses regulate the microbial carbon cycle in the deep-sea biosphere, based on viromic analysis of 66 global sediment samples spanning 1900 to 24,000 years. We identified 324,772 DNA viruses and 61,066 RNA viruses, revealing high diversity and long-term persistence. These viruses co-participate in host carbon metabolism via synergistic genes that encode carbohydrate-active enzymes, with DNA viruses primarily aiding synthesis and RNA viruses supporting decomposition. Integrated virome and microbiome data indicate that viral genes form novel metabolic branches, compensating for host deficiencies and enhancing pathway efficiency in processes like fructose-mannose and pyruvate metabolism. Our findings position deep-sea viruses as key regulators of marine microbial carbon cycling, with implications for global biogeochemical models and climate resilience. This work offers the first holistic perspective on DNA and RNA viruses in deep-sea carbon dynamics, illuminating their ecological significance across geological timescales.