Size-specific effects of polyethylene microplastics (100–10,000 nm) on the soil resistome and pathogens revealed via metagenomics and machine learning

Microplastics (MPs) and antibiotic resistance genes (ARGs) are widespread, persistent environmental contaminants. However, the influence of MP particle size on ARGs dissemination and soil ecosystem health remains unclear. Herein, polyethylene MPs of three sizes (100, 1,000, and 10,000 nm) were incubated in ARG-contaminated soils for 45 days to evaluate their effects on soil physicochemical properties, microbial communities, ARGs, mobile genetic elements (MGEs), and pathogen abundance. MP exposure significantly increased soil water (up to 4.07-fold), total nitrogen (up to 50.34 %), and ammonium nitrogen (up to 38.54 %) contents. Conversely, soil organic carbon content decreased with increasing MP size. MPs markedly reduced the activities of key enzymes, including alkaline phosphatase (by 87.65 %), sucrase (by 10.96 %), and urease (by 54.17 %). Microbial α-diversity increased; however, the abundance of potentially pathogenic Pseudomonadota increased by up to 41.88 %, whereas that of beneficial Actinobacteria and Chloroflexi declined. MPs promoted the expression of 44 ARGs and 15 MGEs, with smaller MPs exhibiting stronger enrichment. They also increased the expression of virulence factors and the abundance of human- and plant-associated pathogens. Random forest modeling revealed that smaller MPs primarily drove these changes by altering soil physicochemical properties and microbial dynamics. Collectively, these findings demonstrate that MPs, especially smaller particles, simultaneously alter soil chemistry, suppress enzyme activities, reshape microbial communities, and enhance ARGs expression and pathogen proliferation, underscoring their significant ecological and human health risks in agricultural soils.