Salinity-driven Shifts in DNA Virus Community Composition and Diversity in Estuarine Waters Adjacent to the Shenzhen Coast

Estuaries are sandwich zones between freshwater and marine waters. Estuarine viral communities play a key role in microbial dynamics and ecosystem functioning, yet the environmental factors influencing their composition and diversity remain underexplored. This study uses metagenomic sequencing to investigate the DNA viromes in riverine water samples adjacent to the Shenzhen coast. Alpha diversity was highest in G4 and strongly correlated with salinity (p < 0.001), while beta diversity showed a distinct clustering of viral communities between low and high-salinity sites. Significant positive correlations were found between water parameters and viral diversity (p < 0.044, r =0.3). A total of 16,497 viral operational taxonomic units (vOTUs) were identified, of which 85.59% and 11.56% were novel and known viruses, respectively. Taxonomically, Caudoviricetes dominated across all sites, with Myoviridae and Podoviridae more abundant in low salinity sites and Baculoviridae and Siphoviridae more abundant in high salinity sites. The bacterial phyla Proteobacteria (22.57%) and Bacteroidota (15.39%) were the dominant bacterial hosts, with distinct shifts in host abundance across the salinity gradient. Functional analysis revealed the abundance of viral auxiliary metabolic genes (AMGs) involved in lipid metabolism, nucleotide metabolism, cofactor metabolism, and polysaccharide metabolism. In particular, the alginate lyase gene was particularly abundant at high salinity sites. Phylogenetic analysis of the TerL gene revealed that many viral sequences were unclassified viruses, and the estuaries harbored considerable unexplored viruses. These results demonstrate that environmental factors influence the genomic diversity and ecological function of viruses in estuarine ecosystems and suggest a role for salinity in estuarine viruses' diversity and ecosystem function