Temporal Dynamics of Virus-Bacteria Interactions Regulate Carbon Cycling in Straw- Amended Paddy Soils

Straw retention is a key practice for advancing agricultural sustainability and achieving resource cycling, yet the biological mechanisms governing its decomposition and carbon turnover remain poorly understood, particularly the underappreciated role of soil viral communities. Using time-series metagenomics in a straw-amended paddy soil, we demonstrate that viral dynamics lagged behind bacterial responses and correlated with total carbon and nitrogen pools, whereas bacterial communities were shaped by available nutrients; virus-bacteria interactions strengthened the functional coupling between bacterial diversity and ecosystem multifunctionality. We observed a clear temporal succession in virus-bacteria interactions: an initial phase of cooperation was followed by a sharp transition to lytic dominance aligned with increased viral richness that marked activation of the viral shunt, and a new equilibrium was established in the freezing stage. Viral regulation of decomposition was evidenced by their life-history shift to lytic dominance, preferential targeting of bacterial decomposers, and concurrent enrichment of auxiliary metabolic genes (AMGs) for cellulose degradation and nitrogen cycling. Accordingly, virus-bacteria interactions are central regulators of carbon turnover in straw-amended soils, where the viral shunt alleviates stoichiometric constraints and AMGs enhance metabolic potential, and this combination of top-down and metabolic reprogramming positions the viral community as a key determinant of carbon cycling, offering a novel biological strategy to optimize resource use and strengthen the sustainability of straw-based agricultural systems.