Profiling of soil bio-composite pollution and driving factors in China

Soil biological contamination driven by antibiotic resistance poses escalating global health threats, yet national-scale assessments remain scarce. To bridge this knowledge gap, metagenomic analysis of 300 samples spanning five ecosystems (agricultural, bare land, forest, grassland, wetland) was employed to study the diversity, co-occurrence patterns, and driving factors of the soil resistome and pathogens across China. Our analyses revealed that antibiotic resistance genes (ARGs) were ubiquitously detected (23 types; 0.03-2.6 copies/cell), with multidrug (mexF, mexW), vancomycin (vanR/S), and bacitracin (bacA) resistance dominating. Eleven major mobile genetic element (MGE) types were identified, and co-occurrence network analysis confirmed robust ARG-MGE associations. Notably, 272 ARG-carrying pathogens (APs) were identified as a severe consequence mediated by bio-composite contamination, with widely distributed genera including Enterobacter, Klebsiella, Nocardia, Pseudomonas, exhibiting potential for multidrug and vancomycin resistance. AP richness peaked in agricultural soils and was lowest in bare lands. Random forest modeling and correlation analysis revealed mean annual precipitation (MAP; r = 0.19, P < 0.05) and grain production (GP; r = 0.18, P < 0.05) were weakly but significantly associated with ARG abundance, while soil pH, organic carbon and meat production governed AP richness. These findings demonstrate nationwide soil bio-composite pollution and underscore the need for prioritized interventions in high-risk ecosystems, though further mechanistic studies are required to validate the observed correlations.