Bridging ecological processes to elevated antibiotic resistance risk in tomato microbiome under fungicide stress

From a "One Health" perspective, antibiotic resistance genes (ARGs) harbored by the plant microbiome pose a significant threat to public health, yet their ecological mechanisms under fungicide stress remain largely unexplored. Here, a comprehensive framework integrating selection, dispersal, antagonistic interactions, and horizontal gene transfer (HGT) is established to elucidate the ecological risks and assembly mechanisms of the tomato resistome under fungicide stress, using multi-omics and several validation experiments. The indirect/direct ecological risks of ARGs in aboveground tomato tissues increase by 1.69-93.81-fold and 1.29-123.49-fold under fungicide exposure, respectively, compared to the control. Dispersal and selection emerge as the dominant ecological processes shaping the resistome under fungicide stress, driven by antibiotic-resistant bacteria (ARB) with streamlined and multifunctional metabolic traits, respectively. A fluorescently labeled ARB migration model and an indigenous ARB-based conjugation model demonstrate that fungicides promote the upward dispersal of native ESKAPE pathogens and intensify HGT among them, facilitating the emergence of multidrug-resistant bacteria. Validation experiments confirm that fungicides induce metabolic reprogramming of flavonoid biosynthesis in roots, which enhances HGT by modulating various physiological phenotypes. These findings underscore the ecological risks posed by fungicides in promoting ARG dissemination within the plant microbiome through multiple ecological mechanisms.