Functional Thermophilic Inoculants in Composting: Performance Benefits and Biosafety Trade-Offs

Microbial inoculation is widely used to improve composting performance, yet its effectiveness hinges on inoculum composition, substrate characteristics, and composting technology, which remain poorly understood. This study compared single versus mixed inoculants across different substrates and assessed their interactions with biochar amendment and nanomembrane covering, focusing on organic matter transformation, inorganic nutrient dynamics, and biological pollution control. Mixed inoculation significantly improved heating performance in cattle manure compost compared to single strains (p < 0.05) and sustained thermophilic conditions in sludge-sawdust compost, but showed limited impact in chicken manure-sludge compost. It reduced humic acid (HA) accumulation in chicken manure-sludge compost (14.29% to −39.28%) while increasing HA content in sludge-sawdust compost (3.55–5.41 g/kg, p < 0.05). Inorganic nitrogen retention was enhanced; specifically NO3−-N concentrations rose by 175.1–222.6% in the chicken manure-sludge and by 6.7–17.9% in the sludge-sawdust compost. Microbial community analysis indicated enrichment of inoculant strains during the thermophilic phase, supporting nitrogen conservation and humification. However, inoculation increased potential pathogenic bacteria by over 51.2% across all composts and enriched predicted antibiotic resistance genes (ARGs) by 9.9–22.96% in chicken manure-sludge compost, while reducing the membrane covering’s inhibitory effect on predicted ARGs (rebound by 29.5%). Moreover, we found that the predicted ARG profiles, derived from 16S-based PICRUSt2 functional inference, covaried strongly with microbial community structure, with environmental factors such as organic carbon shaping predicted ARG dynamics mainly through indirect effects on microbial communities. These findings highlight that while mixed inoculation boosts composting efficiency, it also raises biosafety concerns. Thus, a comprehensive evaluation integrating organic, inorganic, and biological perspectives is essential before promoting thermophilic inoculants.