Metagenomic profiling of rhizosphere and phyllosphere bacterial communities in response to alkyl glycoside-stabilized selenium nanoparticles in a paddy ecosystem under antibiotic resistance gene mitigation

This study investigates the effects of alkyl glycoside-stabilized selenium nanoparticles (AG-SeNPs) on the abundance and distribution of antibiotic resistance genes (ARGs) in a rice paddy ecosystem, encompassing rhizosphere soil, phyllosphere, and rice grains. A pot experiment was conducted with six treatments, including control (no Se fertilizer), biofertilizer, sodium selenite, and three concentrations of AG-SeNPs (15, 30, and 60 g ha-1). Full-length 16S rRNA gene amplicon sequencing was performed on the PacBio Sequel II platform to characterize bacterial community composition at the species level. Functional predictions (PICRUSt2), co-occurrence network analysis, null model analysis, redundancy analysis (RDA), random forest modeling, and structural equation modeling (SEM) were employed to elucidate the mechanisms underlying ARG attenuation. Results indicate that foliar application of 30 g ha-1 AG-SeNPs significantly reduced ARG abundance across all compartments, reshaped microbial communities, and enhanced deterministic filtering in the phyllosphere. Key ARGs (tetPA, tetGF) were associated with taxa such as Mariniphaga anaerophila and Sediminibacter magnilacihabitans. The study provides insights into the microbially mediated, environmentally driven pathways through which nano-selenium mitigates antibiotic resistance in agricultural systems.