Soil‐borne legacy facilitates the dissemination of antibiotic resistance genes in soil–plant continua

Antimicrobial resistance (AMR) disseminates throughout the soil–plant continuum via complex microbial interactions. Plants shape root- and leaf-associated microbiomes that sustain plant health; however, soil-borne legacies—enriched with antibiotic-producing microbes and resistance genes—govern AMR dynamics across agroecosystems. Using 16S rRNA gene sequencing, shotgun metagenomics, and high-throughput quantitative PCR, we profiled antibiotic resistance genes (ARGs), mobile genetic elements, and virulence factor genes across bulk soil, rhizosphere, phyllosphere, and root endosphere within soil–tomato and soil–strawberry continua. Recurrent bacterial wilt amplified the resistome, particularly polypeptide resistance genes, thereby establishing the rhizosphere as a major hotspot of ARG accumulation. Multidrug-resistant Ralstonia solanacearum (R. solanacearum) strains acted as major ARG reservoirs, harboring resistance determinants on both chromosomes and megaplasmids. Collectively, these findings demonstrate that pathogen-driven restructuring of the plant microbiome accelerates ARG dissemination, establishing soil-borne diseases as critical amplifiers of AMR across agricultural ecosystems.