Exploring potential ecological risks of antibiotic–resistance genes in soil–plant systems caused by manure application

Residual antibiotics and antibiotic resistance genes (ARGs) in manure have attracted increasing attention for their potential to contaminate agricultural soils and enter the food chain. Previous studies have primarily focused on their fate in soil and water environment, while the specific transmission pathways and the ecological risks associated with ARGs in various soil–plant systems remain poorly understood. In this study, we investigated the migration behavior and transmission mechanisms of ARGs in three representative cropland soils (black, fluvo–aquic, and red soils) using pakchoi as a model plant. The results demonstrate that ARGs in pakchoi are influenced not only by the presence of manure and chlortetracycline (CTC) but also by soil type. The presence of CTC in soil promoted the proliferation of Acinetobacter and increased the possibility of transmitting pathogenic bacteria (Klebsiella, Rhodococcus, Corynebacterium_1 and Pseudarthrobacter) to pakchoi. Moreover, the levels of intI1 were the highest in CTC–manure treatments for black and red soils (1.70 and 1.65 times higher compared with that for fluvo–aquic soil, respectively), indicating an elevated risk of antibiotic resistance spreading and horizontal gene transfer in pakchoi. Furthermore, the introduction of CTC and manure into soil altered the composition of potential host bacteria, primarily Chryseobacterium and Exiguobacterium, which harbor ARGs such as mdtB, oleC, katG and bcrA in pakchoi. PICRUSt function prediction analysis revealed that the variations of ARGs were primarily influenced by metabolism–related functional microorganisms. These findings provide valuable insights into the transmission routes and potential ecological risks associated with ARGs in diverse soil–plant systems.