Fertilization Strategies Regulate Soil Viral Diversity and Functional Potentials in Nutrient Cycling

Soil viruses are increasingly recognized as key regulators of microbial communities and biogeochemical cycles, yet their responses to long-term fertilization strategies remain poorly characterized. We conducted a four-year pot experiment in subtropical China to evaluate how chemical fertilizer (CF), biochar (BC), and organic fertilizer (OF) application influenced soil viromes compared with an unfertilized control (CK) treatment. Metagenomic analyses recovered 1581 viral contigs with distinct community structures across treatments. Lytic viruses dominated overall, with higher proportions in BC and OF treatments, positively correlated with soil fertility indicators. Diversity indices indicated that BC and OF treatments significantly enhanced viral richness and evenness relative to CK and CF treatments, reflecting broader microbial host niches. Virus–host link predictions revealed expanded networks under BC and OF treatments, particularly with Pseudomonadota, Cyanobacteriota, and Acidobacteriota, suggesting amendment-specific viral regulation. Functional annotation showed that OF and BC application enriched viral KEGG categories related to metabolism, transport, and signal transduction. Moreover, BC and OF application promoted nitrate reduction, nitrogen fixation, and phosphorus mobilization. Together, these findings highlight organic amendments as critical drivers of soil viral diversity and functional potential, linking viromes dynamics to sustainable nutrient cycling in agroecosystems.