Deciphering particle-scale microbial divergence with anaerobic enrichment during thermophilic succession:...

Composting, also referred to as aerobic fermentation, is a key method for recycling organic waste. The composting pile is characterized by substantial heterogeneity, which may influence microbial populations; however, the effects of this spatial heterogeneity on microbial communities have not been sufficiently investigated. In this study, we compared the microbiomes of particle-associated and composite samples collected during the thermophilic phase-the most active period for organic matter degradation. Our findings reveal marked microbial divergence between particle-associated and composite samples. Notably, anaerobic groups such as Clostridia and Deltaproteobacteria were enriched in particle samples, whereas Bacilli dominated the composite samples. In both sample types, the microbial community underwent continuous succession throughout the thermophilic stage. Specifically, composite samples shifted from early Bacilli dominance to a gradual increase in Actinobacteria in later stages, while particle samples showed a progressive rise in Clostridia, peaking at Day 6. This pattern underscores that composting is driven by both aerobic and anaerobic microbial populations. Based on bioinformatic screening, we selected three thermophilic bacterial isolates that were prevalent in both particle and composite samples and evaluated their capacity to accelerate composting. Inoculation with these isolates led to a rapid temperature rise (peaking at 74.1 °C) and a prolonged thermophilic phase. Overall, this study demonstrates that the spatial heterogeneity of composting piles creates distinct microenvironments that foster both aerobic and anaerobic microbial populations, with divergent successional trajectories between particle-associated and composite samples, and further shows that bioinformatics-driven selection of thermophilic isolates can effectively accelerate the composting process.