Metagenomics Insights into Gentamicin Degradation and the Dynamic of Antibiotic Resistance Genes During the Gentamicin Mycelial Residues Co-Composting

Increasing antibiotic mycelial residues (AMRs) and related antibiotic resistance genes (ARGs) have posed a significant threat to ecosystems and public health. Composting was one of the most important methods for recycling ARMs, the variation in ARGs and gentamicin degradation in the composting process of gentamicin mycelial residues (GMRs) has been much less studied on an actual industrial scale.In this study, the metabolic pathways and functional genes on the gentamicin and ARGs removal were investigated during the co-composting of GMRs under various C/N ratios (15:1, 25:1, 35:1). The results showed that the removal efficiency of gentamicin and the total ARGs were respectively 98.23% and 53.20% with the C/N ratio of 25:1. Furthermore, metagenomics and LS-MS/MS analysis suggested that the acetylation was the main pathway for gentamicin biodegradation and the corresponding degrading genes were the categories of aac(3) and aac(6’). However, the relative abundance of aminoglycoside resistance genes (AMGs) were increased after 60 days composting. The partial least squares path modeling analysis indicated that the AMGs abundance was directly influenced by the predominant mobile gene elements intI1 (p < 0.05) which was closely related to the bacterial community composition.The co-composting of GMRs was effective at removing gentamicin residues and the total ARGs. In addition, the relative abundance of AMGs may be further enhanced, creating ecological risks for the environment.