Salinity-Driven Dynamics of the Ulva-Associated Virome and Their Implications for Holobiont Adaptation

Abstract Background The role of viruses in mediating microbial community adaptation to environmental stress remains a critical frontier in host-microbe interactions. While the structure and function of bacterial communities associated with the green alga Ulva are known to respond to salinity, the involvement of the algal virome in this process is entirely unexplored. Results Using metagenomic sequencing of 89 Ulva samples along a salinity gradient (5–35 PSU), we demonstrate that salinity is the dominant factor shaping the viral community, explaining 73% of the taxonomic and 34% of the functional variation. Viral richness and diversity declined significantly with increasing salinity. The response of viruses to salinity was highly host-specific, with those infecting Rhodobacteraceae exhibiting the strongest correlations. Crucially, we identified a suite of phage-encoded auxiliary metabolic genes (AMGs) that were both differentially abundant and enriched under high-salinity stress. These AMGs are functionally predicted to facilitate bacterial osmoadaptation through synergistic mechanisms including cell wall modification ( glmS , glf ), osmolyte synthesis ( preT ), epigenetic regulation via folate-dependent DNA methylation ( DNMT1 , DHFR ), and antioxidant defense ( dfrB , mec ). Conclusions Our findings reveal that phages are not passive followers of their bacterial hosts but active contributors to holobiont resilience by deploying a targeted genetic toolkit for salinity adaptation. This study provides a mechanistic model for viral-mediated environmental adaptation in a key marine holobiont, fundamentally advancing our understanding of tripartite "host-bacteria-phage" interactions in a changing ocean.