Viral-mediated top-down control shifts microbial profiles and greenhouse gas dynamics in paddy and maize soils

Soil viruses are abundant and active in terrestrial ecosystems, yet their contribution to microbial community assembly and biogeochemical functioning remains poorly resolved, particularly across contrasting agronomic regimes. Using deep viromics, CRISPR-based host prediction, and ecological network analyses in long-term paddy and maize fields, we show that viral regulation of bacterial communities is strongly management-dependent. In flooded paddy soils, viral diversity was significantly associated with bacterial diversity (R 2 = 0.858, p < 0.001). In aerobic maize soils, complex virus-host interaction networks ( β = -0.633, p < 0.01), emerged as the dominant structuring force after accounting for environmental factors. Gradient viral-addition microcosm experiments further verified the significance of phage. Viral pressure reshapes microbial function and greenhouse gases dynamics, with N 2 O and CH 4 emissions increasing 4 - and 1.4-fold, respectively, at high viral loads. Mechanistically, this was driven by the suppression of methane-oxidation genes ( pmoC ) and the concurrent enrichment of nitrous oxide-generating genes ( norB ). These findings demonstrate that soil viruses actively rewire microbial networks and metabolic potential in a context-specific manner, with direct implications for greenhouse gas fluxes from agroecosystems.