Phages Shape the Transformation of Organic Matter During Composting

Microorganisms drive the biotransformation of dissolved organic matter (DOM) during organic wastes composting, yet the role of phages with different lifestyles (i.e., temperate and virulent) in this process remains poorly understood. Here, bulk metagenomic sequencing combined with electrospray ionisation (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to investigate the dynamics of temperate and virulent phage communities, microbial functional traits represented by the growth yield (Y)–resource acquisition (A)–stress tolerance (S) life-history strategies (Y-A-S) framework, and molecular changes in DOM composition, as well as their potential linkages during the composting of a rice chaff and chicken manure mixture. Our results revealed that the ratio of temperate/virulent phage, microbial Y/A strategy, and microbial-/plant-derived DOM components exhibited highly consistent dynamic patterns, all peaking during mid-composting stage when temperatures are elevated and remaining low at the initial and final stages. Random forest analysis further identified the ratio of temperate/virulent phages and the microbial Y/A strategy as key predictors of the variance in microbial Y/A trade-offs and microbial−/plant-derived DOM components, accounting for 10% and 13% of the explained variance, respectively. Together, our results demonstrate that an increased prevalence of temperate phages promoted the microbial Y-strategy and the accumulation of microbial-derived DOM components, while a greater dominance of virulent phages favoured the A-strategy and plant-derived DOM enrichment. These findings offer new insights into the ecological role of phages in mediating material transformation during organic waste composting.