Metagenomic analyses reveal that mesophilic anaerobic digestion substantially reduces the abundance of antibiotic resistance genes and mobile genetic elements in dairy manures

Animal manure is considered one of the main reservoirs of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) that carry them. There is increasing concern regarding the dissemination of antibiotic resistance due to the application of manure as a soil amendment, and there is an urgent need to define alternatives to minimize this problem. Anaerobic digestion (AD) has shown the potential to reduce the levels of ARGs present in manure. However, little is known about the effect of AD on the entire set of MGEs, which play a crucial role in the dissemination of antibiotic resistance. In this study, we used a set of metagenomic and bioinformatics tools to evaluate the long-term effects of mesophilic anaerobic digestion on ARGs and MGEs in bovine dairy manure and the potential mechanisms driving these changes. The results indicated that the average ARG and MGE levels were significantly reduced by 53% and 74%, respectively, after AD. The results also suggested that microbial groups including Lactobacillales, Bacillales, Eubacteriales, Micrococcales, and Actinomycetales were main groups associated with ARGs and MGEs. The changes in ARG and MGE seemed to result from distinct microbial successions, such as the removal of aerobic species and the decline in facultative bacteria, which led to the establishment of typical microbial communities present in anaerobic digesters. The study also suggested that hydrolytic species are another important group that potentially harbors ARGs and MGEs. Overall, the results indicated that digested manure could have a reduced risk of dissemination of antibiotic resistance.