Long-term application of swine manure and sewage sludge differently impacts antibiotic resistance genes in soil and phyllosphere

Field application of organic fertilizers may promote the spread of antibiotic resistance genes (ARGs) in farmland ecosystems, which represents a major threat to public health. However, impacts of multi-year organic fertilization on the spread of soil and phyllosphere ARGs and the possible transmission pathways remain elusive. Here, we investigated the patterns of ARGs and structures of bacterial and fungal communities in soil and wheat crop phyllosphere, under long-term fertilization of swine manure or sewage sludge using high-throughput quantitative PCR and amplicon sequencing. It was found that application of swine manure and sewage sludge had more influence on the prevalence of ARGs in phyllosphere than in soil. SourceTracker analysis revealed that a few bacterial taxa from swine manure and sewage sludge could survive in soil, but hardly in phyllosphere. Mantel test and variation partitioning analysis further revealed that shift in the microbial community compositions was an important factor affecting soil ARGs, while horizontal gene transfer mediated by mobile genetic elements might contribute to the spread of phyllosphere ARGs. Overall, these results demonstrated that long-term application of swine manure and sewage sludge differently impacts the ARGs in soil and phyllosphere, which have implications for sustainable agricultural management