Ecological drivers and functional roles of phage communities in the Yangtze River's freshwater ecosystems

The Yangtze River, China's largest and most significant freshwater system, is facing increasing pollution pressures due to rapid urbanization. While bacterial-mediated antibiotic resistance has been extensively studied, the functional roles and ecological risks of phage communities remain poorly understood. Here, we conducted a comprehensive virome analysis across four habitats (free-living setting, particle-associated setting, sediment, and bank soil) using 204 samples from the Yangtze River. We identified 18,865 viral operational taxonomic units (vOTUs) and observed significant correlations between viral communities and metagenome-assembled genomes (MAGs) across all habitats. Notably, the virus-to-host ratio (VHR) decreased significantly with increased elevation. Functional annotation revealed 1367 viruses contigs carrying genes associated with six functional categories, each showing distinct habitat-specific patterns. Carbohydrate-degrading enzymes (CAZy) were abundant in free-living setting water. Among phage-borne ARGs, vancomycin resistance was predominated, especially in sediment and bulk soil, while mercury resistance were most prevalent in sediments. Chitinase genes constituted the most abundant group among phage-encoded genes for plastic degradation. We identified 84 high-confidence virus-host pairs, predominantly infecting Proteobacteria. Random forest modeling identified elevation as the dominant driver of viral community abundance across habitats. Higher elevations were correlated with increased pH and reduced NH₄⁺-N concentrations, suggesting nutrient limitation may weaken virus-host interactions. This study provides the first systematic assessment of viral diversity and functional potential in the Yangtze River, offering novel insights into phage ecology in freshwater.