Symbiotic relationships profoundly influence the energy transfer efficiency of the deep‑sea “dark food chain” and the adaptability of life in extreme environments. Deep‑sea invertebrates form unique symbiotic consortia by establishing associations with various microorganisms, enabling them to cope with the survival pressures of these extreme habitats. In recent decades, research on symbiotic cellular microorganisms has revealed multiple important functions, expanding our understanding of deep‑sea symbiotic consortia. However, as critical acellular components of symbiotic systems, the ecological functions and interaction mechanisms of viruses remain poorly understood, which constrains a comprehensive understanding of deep‑sea symbiotic systems.

This study focuses on the interactions between symbiotic bacteriophages and their hosts—chemoautotrophic symbiotic bacteria—in deep‑sea hydrothermal vent ecosystems. By comprehensively employing bioinformatics and multi‑genomics approaches, we systematically elucidated the molecular interaction mechanisms between them.Our results show that symbiotic bacteriophages in deep‑sea hydrothermal vent environments specifically infect symbiotic Proteobacteria predominantly via lytic infection, revealing their host‑selection specificity patterns. Furthermore, we found that these bacteriophages play a key role in regulating the energy metabolism of chemoautotrophic symbiotic bacteria, and we elucidated the co‑evolutionary mechanisms between the two partners. These findings provide new scientific evidence for understanding virus–bacterium interaction mechanisms in deep‑sea hydrothermal ecosystems, and also lay an important foundation for deciphering the energy transfer dynamics of the “dark food chain” and the adaptive strategies of life in extreme environments.