Long-term field application of manure induces deep selection of antibiotic resistomes in leaf endophytes of Chinese cabbage.

Antibiotic resistomes in leaf endophytes of vegetables threaten human health through the food chain. However, little is known about the ability of long-term manure fertilization to impact the deep selection of antibiotic resistance genes (ARGs) in leaf endophytes of vegetables planted in different types of soils. Here, by high-throughput quantitative PCR, we characterized the ARGs of leaf endophytes of Chinese cabbage (Brassica pekinensis (Lour.) Rupr.) grown in long-term (14 year) manure-amended acidic, neutral and calcareous soils. In total, 87 ARGs and 4 mobile genetic elements (MGEs) were detected in all the samples. Manure fertilization significantly increased the ARG numbers and normalized abundance in leaf endophytes, especially in acidic soil. Moreover, in acidic soil, manure application also led to a higher increase in the normalized abundance of opportunist and specialist ARGs, and more opportunist and specialist ARGs posed a high risk according to their risk ranks. Random forest analysis revealed that Proteobacteria and MGEs were the major drivers affecting the normalized abundance of opportunist and specialist ARGs in both acidic and neutral soils, respectively. In calcareous soil, Cyanobacteria and Actinobacteria were the most important contributors. Collectively, this study expands our knowledge about the deep selection of plant resistomes under long-term manure application.