Nanoscale pesticide delivery suppresses pathogens and enriches beneficial microbiomes for safer crop protection

Nanocarrier-based pesticide delivery platforms substantially boost agrochemical utilization efficiency, yet their cascading ecological repercussions for rhizosphere and soil microbial ecology remain insufficiently understood. Here, a star polycation (SPc) nanocarrier was employed to construct a matrine nano-formulation (MT@SPc) with typical nano-pesticide characteristics. MT@SPc and commercial matrine formulation (MT SL) were employed as representative systems to further evaluate their impacts on rhizosphere and soil microbial ecosystems. Compared with MT SL, MT@SPc reshaped rhizosphere microbial communities by suppressing phytopathogens and promoting the enrichment of beneficial bacteria. Further validation using four representative bacterial isolates obtained from soil demonstrated that MT@SPc significantly inhibited the growth of the phytopathogen Pectobacterium carotovorum, whereas enriched beneficial bacteria exhibited lower susceptibility to MT@SPc. Multi-scale mechanistic analyses revealed that MT@SPc could interact with bacterial cell surfaces through physicochemical interactions, resulting in pronounced surface deformation and structural damage in P. carotovorum. Multi-omics analyses associated with physiological and biochemical assays further demonstrated that MT@SPc disrupted cell wall and membrane integrity, leading to ionic imbalance, metabolite leakage and oxidative stress. However, beneficial bacteria maintained higher stability, and their enrichment was associated with microbial community shifts following pathogen suppression. Overall, this study reveals that nano-pesticides drive rhizosphere community restructuring through differential microbial responses, providing mechanistic insights into nano-pesticide–microbiome interactions in complex ecological systems.