Antimicrobial Susceptibility in Nitrogen-fixing Bradyrhizobium spp. of Soybean Nodules in South Korea Determined by Species-level Intrinsic Antibiotic Resistances over Regional Environmental Properties

Abstract

Bradyrhizobium spp. are nitrogen-fixing, non-pathogenic symbionts that form nodules on soybean roots and stems. Antibiotic use in agricultural soils may facilitate the dissemination of antimicrobial resistance genes (ARGs), highlighting the need to evaluate antimicrobial resistance (AMR) in soil-associated bacteria. We analyzed indigenous Bradyrhizobium spp. isolated from 97 soybean plants collected across South Korea. Among 227 bacterial samples, 152 Bradyrhizobium isolates were tested for susceptibility to ten antibiotics using disk diffusion, and eight resistance genes were screened by PCR. Seven isolates were further subjected to whole-genome sequencing to identify ARGs and examine the genomic contexts of four representative ARGs. Bradyrhizobium spp. showed high levels of antibiotic resistance, with B. elkanii exhibiting higher resistance than other species. Resistance patterns were more strongly associated with species-level grouping than with regional factors. Genomic context analyses indicated that key resistance determinants were embedded within conserved chromosomal backbones flanked by housekeeping genes, suggesting primarily intrinsic and lineage-associated resistance rather than recent horizontal acquisition. These findings highlight the substantial AMR observed in soybean-nodulating Bradyrhizobium spp. in South Korea and support their role as stable chromosomal reservoirs of resistance in agricultural soils.