Habitat determines the relationships among bacteria, resistance genes and mobile genetic elements in the soil–plant system.

The soil antibiotic resistome is considered to be primarily determined by bacterial community composition. However, the antibiotic resistance of plant microbiota and its association with the soil microbiome in soil–plant systems remain largely unknown. Here, we studied the connections between bacteria and resistance genes (RGs) (mainly antibiotic resistance genes, ARGs) and mobile genetic elements (MGEs) in different cropping systems (rice monoculture, and ryegrass–rice and vetch–rice rotation), growth periods (early, tillering and harvesting stages) and habitats (the soil, rhizoplane and phyllosphere) through high‐throughput qPCR and 16S rRNA sequencing. The results showed that habitat was the major factor affecting the distribution of bacteria, RGs and MGEs, whereas the cropping system had less of an effect. The relative abundances of ARGs, multidrug resistance genes, metal resistance genes and integrons were highest in the soil and lowest in the phyllosphere, as was the α‐diversity of the soil and plant microbiota. Most importantly, we found that bacteria had the strongest associations with RGs and MGEs in the rhizoplane rather than in the soil and phyllosphere, which might be due to the high network interactions among rhizoplane bacteria. These results suggest that the rhizoplane could be a hotspot for exchange of ARGs in the soil–plant system. Highlights: The distributions of bacteria, RGs and MGEs were primarily controlled by habitat.The strongest associations were found between rhizoplane bacteria and RGs and MGEs.Rhizoplane bacteria had the strongest network associations. [ABSTRACT FROM AUTHOR]