Elimination of antibiotic resistance genes and adaptive response of Firmicutes during chicken manure composting

Abstract

Aerobic composting is an effective method for reducing the abundance of antibiotic resistance genes (ARGs), but its effectiveness is influenced by the complex conditions during the process. However, the impact of composting conditions on the fate of ARGs and the underlying mechanisms remains unclear. This study examined the profile of ARGs, their mobility potential, hosts, and the risk of antibiotic resistome under different chicken manure composting conditions. A total of 708 ARGs were identified, and composting reduced their relative abundance by 29.4%–82.4%. Composting amendments and aeration rates exhibited similar elimination efficiencies for ARGs at different levels. However, low initial moisture content (50%) caused a rebound in ARG abundance during the maturation phase. ARGs were mainly located on plasmids. After composting, the percentage of plasmid-born ARGs decreased from 46.3%–70.8% to 28.4%–49.0%. ARGs co-localized with mobile genetic elements displayed similar trends. The tolerance of Firmicutes to low moisture content played a key role in the rebound of ARGs and variations in their mobility potential. Composting reduced antibiotic resistance and ARG mobility in pathogens. Conversely, low moisture content hindered this attenuation effect in Firmicutes, which increased antibiotic resistome risk. This study provides comprehensive insights into the fate of ARGs and highlights the environmental risks of ARGs during composting.