Unveil the role of dissolved and sedimentary metal(loid)s on bacterial communities and metal resistance genes (MRGs) in an urban river of the Qinghai-Tibet Plateau

• Metal(loid)s and bacterial communities rather than MRGs had great seasonal changes. • WWTPs’ effluent reshaped metal(loid)s, bacterial communities, and MRGs in rivers. • Dissolved metal(loid)s showed no strong effects on bacterial communities and MRGs. • Hg and Cd in sediments broadly promoted the prevalence of corresponding resistomes. • Bacterial β diversity directly driven MRG abundance in both water and sediments. Though metal resistance genes (MRGs) are of global concern in aquatic ecosystems, the underlying factors responsible for MRGs dissemination, especially in urban rivers on the vulnerable Qinghai-Tibet Plateau, are rarely known. Here, we collected 64 samples including water and sediments during the wet and dry seasons and effluents from six wastewater treatment plants (WWTPs) during the dry season and measured 50 metal(loid)s, 60 bacterial phyla, and 259 MRGs. We observed the distinct difference of metal(loid)s, bacterial communities, and MRGs between water and sediments and the great seasonal changes in metal(loid)s and bacterial communities instead of MRGs. Thirty-one metal(loid)s were detectable in the water, with relatively low concentrations and no significant effects on the planktonic bacterial communities and MRGs. Interestingly, the WWTPs effluent partially promoted the prevalence of dissolved metal(loid)s, bacterial communities, and MRGs along the river. In the sediments, the average concentrations of 17 metal(loid)s exceeded their corresponding background levels in this region and strongly influenced the bacterial communities and the MRGs. Sedimentary Hg and Cd, mainly sourced from the intensive animal husbandry, were the major pollutants causing ecological risks and largely shaped their corresponding resistomes. Moreover, we found that bacterial communities predominantly determined the variation of MRGs in both water and sediments. Metagenome-assembled genomes further reveals the widespread co-occurrence of MRGs and antibiotic resistance genes (ARGs) in MRG hosts. Our study highlighted the concern of effluents discharged from WWTPs and emphasized the importance of controlling the anthropogenic inputs of sedimentary metal(loid)s in the plateau river ecosystems.