Urban habitat types modulate soil contamination and bacterial functional traits through antibiotic resistance genes...

Urban soils are important reservoirs for contaminants, including metal(loid)s and antibiotic resistance genes (ARGs), posing threats to ecosystem function and public health. However, the variation in these contaminants across urban habitat types remains poorly understood. This study integrated shotgun metagenomics, 16S rRNA sequencing, quantitative PCR, and multivariate modeling to investigate the co-distribution of ARGs, metal(loid)s, and bacterial functional traits across six urban habitat types: afforestation areas, croplands, orchards, parks, ruderals, and semi-natural remnants. Our findings revealed habitat-specific contamination patterns, with croplands and orchards showing the highest ARG risks and strong co-selection signals mediated by mobile genetic elements (MGEs) and biocide/metal resistance genes (BMRGs). In contrast, ruderals and remnants exhibited significantly lower ARG abundances (<1.2 × 10⁴ copies/g) and metal(loid) concentrations (Cd < 0.05 mg/kg and Pb < 10 mg/kg), as well as nearly 50 % fewer plasmid-associated ARGs, indicating reduced horizontal gene transfer potential. Integrative modeling identified functional genes and BMRGs as the most consistent drivers of MGE dynamics, while MGEs showed limited direct influence on ARGs, suggesting that mobility alone may not explain the spread of resistance in urban soils. Metagenomic analyses linked ARG profiles to disruptions in bacterial functions essential for nutrient cycling and ecosystem services, indicating that resistance risks in urban soils are closely tied to declines in functional capacity. A substantial overlap in ARGs between orchard soils and fruits underscored the potential for soil-to-human transmission. These results provide a cross-habitat framework that links contaminant profiles, resistance mobilization, and functional consequences in urban soils.