The overlap of soil and vegetable microbes drives the transfer of antibiotic resistance genes from manure-amended soil to vegetables

Livestock manure, as a major source of antibiotic resistance genes (ARGs), could further transfer ARGs from soil to vegetables when it's used as fertilizer in field and then pose threat to human health. Meanwhile, manure inputs and vegetable planting also affect soil bacterial communities, but these effects on the transmission of ARGs from soil to vegetable is still lacking. Here, lettuce and endive were cultivated in manure-amended soils using pot experiment. The distribution of bacterial community, ARGs and intI1 gene were studied in manure-amended soil and vegetable roots and leaves at harvest. High-throughput sequencing analysis demonstrated that planting vegetables exerted significant effect on soil bacterial communities, which partly explained the decrease of certain ARGs and the intI1 gene in planted soil than in control soil. ARGs in vegetable and soil were interconnected. The bacterial community compositions among root endophyte, leaf endophyte, and phyllosphere were varied by Hierarchical clustering analysis. Higher abundance of shared bacterial taxa was found between root endophytes and soil microbes, which could lead to a relative higher detection frequency of ARGs in root endophyte. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes were dominant in the plant endophyte and phyllosphere microbes and had intensive correlations with ARGs. Taken together, our findings provided valuable insights into the role of bacterial community structure in the dissemination of ARGs from manure-amended soil to vegetables.