Shift in the microbial community composition of surface water and sediment along an urban river

•Microbial community in the urban river exhibited spatial variations due to the joint influence of chemical variables•The microbial OTUs richness decreased in the urban area•TP, NO3- and metals (Zn, Fe) were the most determining factors impacting the surface water microbial compositions•Higher abundance of genes associated with xenobiotic metabolism were observed in the urban surface water and sediments [Display omitted] Urban rivers represent a unique ecosystem in which pollution occurs regularly, leading to significantly altered of chemical and biological characteristics of the surface water and sediments. However, the impact of urbanization on the diversity and structure of the river microbial community has not been well documented. As a major tributary of the Yangtze River, the Jialing River flows through many cities. Here, a comprehensive analysis of the spatial microbial distribution in the surface water and sediments in the Nanchong section of Jialing River and its two urban branches was conducted using 16S rRNA gene-based Illumina MiSeq sequencing. The results revealed distinct differences in surface water bacterial composition along the river with a differential distribution of Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes and Acidobacteria (P