Salinity-driven shifts in estuarine viral community composition and diversity near the Shenzhen coast

Estuarine viral communities play a key role in microbial dynamics and ecosystem functioning. However, how viruses adapt to the highly dynamic estuarine environments remains largely underexplored. This study uses viromic sequencing to investigate the DNA viruses in estuarine water samples adjacent to the Shenzhen coast. Samples were divided into two major groups based on variations in quantified water parameters, corresponding to low-salinity and high-salinity waters. A total of 16,497 viral operational taxonomic units (vOTUs) were recovered, of which 85.59% were identified as novel viruses. β-diversity of viral communities supported the partition of samples based on salinity, and viral α-diversity differed significantly between low and high salinity. Taxonomically, Caudoviricetes dominated across all sites, with Myoviridae and Podoviridae more abundant in low salinity sites and Siphoviridae and Baculoviridae more abundant in high salinity sites. Gammaproteobacteria and Bacteroidota were the dominant host taxa, with distinct shifts in host abundance across the salinity gradient. Functional analysis revealed the abundant auxiliary metabolic genes involved in lipid, nucleotide, cofactor, and polysaccharide metabolisms. In particular, the alginate-degrading polysaccharide lyase family 6 was particularly abundant at high salinity sites. These results suggested that environmental factors, particularly salinity, shape the genomic diversity of estuarine viruses, which may further impact the biogeochemical processes in estuarine ecosystems.IMPORTANCEEstuaries are highly dynamic ecosystems with strong environmental fluctuations, particularly in salinity and nutrients. This study highlights how environmental factors shape viral diversity and function by examining viral populations across the salinity gradient, providing new insights into viral dynamics in these ecosystems. We identified novel viruses and viral-encoded auxiliary metabolic genes in estuarine samples, including the discovery of a previously unreported viral alginate lyase gene that was abundant at high salinity sites, which sheds light on the ecological role of viruses in nutrient cycling and ecosystem partition. In addition, the study provides valuable information on distinct viral populations and virus-host interactions across the salinity gradient, which are essential for predicting ecosystem responses to salinity changes. These findings provide important implications for a broader understanding of microbial and viral ecology in estuarine ecosystems.