Metagenomics insights into gentamicin degradation and the dynamic of antibiotic resistance genes during co-composting of the gentamicin myelial residues with addition of various organic wastes

Increasing antibiotic mycelial residues (AMRs) and related antibiotic resistance genes (ARGs) pose a significant threat to ecosystems and public health. Composting is a crucial method for recycling AMRs. However, the variation in ARGs and gentamicin degradation in the composting process of gentamicin mycelial residues (GMRs) has received little at-tention on an actual industrial scale. This research investigated the metabolic pathways and functional genes on the gentamicin and ARGs removal during the co-composting of GMRs with addition of various organic wastes (rice chaff, mushroom residue, etc.) under various C/N ratios (15:1, 25:1, 35:1). The results showed that the removal effi-ciencies of gentamicin and the total ARGs were 98.23 % and 53.20 %, respectively, with the C/N ratio of 25:1. More-over, metagenomics and LS-MS/MS analysis demonstrated that the acetylation was the primary pathway for gentamicin biodegradation and the corresponding degrading genes were the categories of aac(3) and aac(6 '). How-ever, the relative abundance of aminoglycoside resistance genes (AMGs) were increased after 60 days composting. The partial least squares path modeling analysis demonstrated that the AMG abundance was directly influenced by the predominant mobile gene elements intI1 (p < 0.05) which was closely related to the bacterial community compo-sition. Therefore, the ecological environmental risks should be assessed in the future application of GMRs composting products.

Automated summary

Increasing AMRs and ARGs pose threats to ecosystems and public health. This research investigated the removal of gentamicin and ARGs during composting of GMRs with different organic wastes and C/N ratios. The results showed high removal efficiencies of gentamicin and total ARGs, but an increase in AMGs after 60 days of composting. The study also revealed the primary pathway for gentamicin degradation and the genetic factors influencing the abundance of AMGs.