Impact of seasonal shifts in virus-prokaryote interactions on carbon cycling in straw-amended paddy soils

Straw retention is a key practice for sustainable agriculture, yet the biological mechanisms ​governing​ its decomposition and carbon cycling remain poorly understood, particularly the role of soil viral communities. Through metagenomic analysis across three distinct environmental stages in straw-amended paddy soils, we found that viral community composition and richness exhibited distinct temporal patterns compared to their prokaryotic hosts. While prokaryotic communities were primarily shaped by available nutrients, viral dynamics showed stronger correlations with total carbon and nitrogen pools. Statistical partitioning confirmed that straw retention had a significant, independent influence on viral communities. Importantly, our results indicate that virus-prokaryote interactions, characterized by co-occurrence networks and metabolic profiling, significantly modulated the relationship between prokaryotic diversity and soil multifunctionality. We observed distinct stage-specific shifts in these interactions: an early phase characterized by cooperative associations was followed by an increased prevalence of lytic indicators, aligning with the enrichment of auxiliary metabolic genes (AMGs) for cellulose degradation and nitrogen cycling. These findings suggest that virus-prokaryote interactions are key modulators of carbon turnover in straw-amended soils, where the potential activation of the viral shunt and AMG-mediated metabolic potential enhance decomposition potential. Our study highlights the importance of integrating viral-driven host turnover and metabolic enhancement into models of resource cycling in sustainable agriculture. • Straw retention induces an asynchronous response between viral and bacterial communities • Viral richness strengthens the link between bacterial diversity and soil multifunctionality • Viral lifestyle shifts to lytic dominance reshape the virus-bacteria interaction networks • Viral auxiliary metabolic genes for decomposition are enriched under straw retention