Microbial community competition rather than high-temperature predominates ARGs elimination in swine manure composting

Aerobic composting is commonly used in pig manure treatment, however, antibiotic resistance genes (ARGs) and their unclear transformation during composting process make the treated manure land using risky. The effects of enhanced thermophilic phase strategy (external heating (HTC) and thermophiles inoculation (MC)) on ARGs removal and the underlying mechanisms were investigated during swine manure composting. HTC increased the total relative abundance (RA) of ARGs by 32.38%, and MC decreased by 21.50% compared to CK by the end of the composting. Mantel test indicated that it was not temperature (P > 0.05), but environmental parameters (pH, Electric Conductivity (EC), etc.) and metabolic products (nitrogen forms) significantly affected the ARGs profile. Partial least-squares path modeling (PLS-PM) suggested that microbial community structure (bacterial abundance and diversities) was the main factor for ARGs evolution. Co-occurrence analysis revealed that HTC could promote the propagation of ARG hosts in later stage of the composting because the strong selection of thermophiles resulted in ecological niches vacancy, and MC enhanced the competition between hosts and nonhosts for ecological niches by increasing thermophiles diversities. These results suggested that competitive inhibition to potential ARGs hosts could be a helpful strategy in ARGs threaten elimination during composting.