Carbon starvation facilitates low pH-dependent viral lysogeny and auxiliary metabolic potentials in paddy soils

Soil organic carbon turnover is regulated by microbes, yet the contribution of soil viruses under contrasting pH remains unclear. Here we recovered viral communities from twelve Chinese paddy fields spanning a broad pH gradient (5.6–8.2) and validated our findings using a global virome dataset, by combining size fractionation and tangential flow filtration to enrich viral particles. Soil pH strongly shaped viral community composition, lysogeny, and carbon-related auxiliary metabolic genes. Moderately acidic soils exhibited higher lysogeny and enrichment of auxiliary metabolic genes linked to carbon fixation and degradation. Path analysis indicated that viral-host cooperation enhanced adaptation under carbon limitation and revealed that pH drives viral functional traits both directly and indirectly through host community structuring. Together, these findings uncover a key role of soil viruses in regulating host adaptation and carbon cycling under contrasting pH, emphasizing their overlooked contribution to agricultural carbon dynamics under environmental change. Soil viruses influence carbon cycling across pH gradients, with acidic soils showing greater lysogeny and carbon related genes, as revealed by viral communities recovered through size fractionation and tangential flow filtration from twelve paddy fields.