Temporal dynamics of the antibiotic resistome in pepper fruits: The trade-off between phytochemical defenses and heavy metal-induced co-selection.

Pepper fruits are globally consumed vegetables and spices that may serve as potential vectors for the dissemination of antibiotic resistance genes (ARGs) into the human food chain. This study investigated the associations of endogenous capsaicin and exogenous heavy metals with the resistome dynamics of peppers across successive harvest stages. Metagenomic analyses revealed temporal variations in the pepper resistome within the agroecosystem. High capsaicin levels during early harvest stages were negatively associated with ARG abundance, whereas the gradual decline of phytochemical defenses during later stages coincided with increased heavy metal accumulation and ARG enrichment. Analysis of large-scale field samples further supported the inverse relationship between capsaicin content and ARG abundance. RT-qPCR assays conducted under controlled laboratory conditions indicated that, unlike capsaicin, heavy metals (such as Cu and Cd) directly promoted the expression of metal resistance and efflux-related genes in a dose-dependent and synergistic manner. Exposure to 50 mg/L of Cu2+ increased the abundance of CopR by 11.63-fold, while 0.6 mg/L Cd2+ exposure increased the abundances of baeR and mdtB by 8.51- and 7.89-fold, respectively. Furthermore, heavy metal stress substantially enhanced horizontal gene transfer, with Cd exposure increasing conjugation frequencies by 2.57-fold. These findings demonstrate that the pepper microenvironment represents a dynamic ecological niche in which plant-derived chemical defenses and abiotic contaminants jointly influence ARG dissemination. This study provides new insights into the multifactorial mechanisms driving ARG migration in soil-pepper systems and offers a scientific basis for reducing antibiotic resistance risks in agricultural production.