Effects of monensin residues on microbial community and the attenuation of antibiotic resistance genes during chicken manure composting

Abstract

Monensin is a polyether ionophore antibiotic widely used to prevent coccidiosis and inhibit Gram-positive bacteria. Composting is widely regarded as an effective strategy for reducing the abundance of antibiotic resistance genes (ARGs) in manure. However, the long half-life of monensin may impose selective pressure on ARG attenuation, while its potential ecological risk remains unclear. In this study, metagenomics was used to analyze the effect of monensin residues on microbial communities during chicken manure composting (1, 15, and 45 days). Results showed that monensin significantly changed the structure of microbial communities during composting. It suppressed functional groups within Firmicutes and Actinobacteria, particularly the genera Bacillus and Streptomyces . Simultaneously, it promoted tolerant taxa, including Proteobacteria and the genus Halomonas . The results of qPCR for six representative ARGs ( aadD , ant2-I , sul1 , sul2 , tetZ , and tetL ) revealed that monensin could reduce the attenuation of some ARGs. Furthermore, monensin increased the abundance of several mobile genetic elements (MGEs) during the middle composting phase, especially the integron intI1 and transposase tnpA . Co-occurrence network analysis suggested stronger associations among specific ARGs, MGEs, and tolerant bacteria under monensin exposure, indicating a potential increase risk of ARG dissemination. Monensin may suppress ARGs attenuation during manure composting by changing microbial communities and increasing the potential risk of ARG dissemination via MGEs. This study will provide a theoretical basis for the treatment of livestock waste and ecological risk assessment of monensin.