Converting pig manure into biochar mitigates the antibiotic resistance of vegetable endophytes

Manure applications can facilitate the transmission of antibiotic resistance genes (ARGs) from the soil to the plant microbiome, with detrimental effects on human health through the food chain. Interventions to mitigate the spread of ARGs from animal waste to plants are essential for food safety. We previously demonstrated that converting composted manure into biochar can effectively mitigate the spread of ARGs into soil. However, it remains unclear whether compost-derived biochar can decrease the spread of ARGs in the vegetable endosphere. In this study, a pot experiment involving pakchoi (Brassica chinensis) was conducted to investigate the effects of compost-derived biochar on endophytic ARGs and the pakchoi microbiome. A total of 99 ARGs and 7 mobile genetic elements (MGEs) were identified in endophytes via high-throughput quantitative PCR. Compared with the compost amendment, the application of biochar produced from composted pig manure significantly decreased the diversity of ARGs and MGEs in vegetable endophytes. The abundance of ARGs, MGEs, and bacteria closely related to known pathogens in roots treated with biochar was much lower than that in roots treated with compost, but was similar to that in the control treatment. Fertilizer treatments influenced endophytic bacterial community assembly, while bacterial communities played an important role in shaping ARG profiles. Overall, the transmission of ARGs from animal waste to endophytic microbiomes in vegetables can be effectively mitigated using biochar derived from manure.