| Summary: | Anthropogenic activities strongly influence river habitat conditions and surrounding landscape patterns. A major challenge is to understand how these changes impact microbial community composition and structure. Here, a comprehensive analysis combining physicochemical characteristics in sediment with sequencing targeting the V4 region of the 16S rRNA gene was conducted to test the hypothesis that diverse habitat conditions induce dissimilarity of microbial community composition and structure in a regulated urban river. The results suggested that observed species richness and Shannon–Wiener diversity had a decreasing variation along the land use intensified gradient, while beta diversity also revealed significant separation of microbial community structure between headwaters and urban reaches. Total nitrogen (TN), total phosphorus (TP), oxidation–reduction potential (ORP) and total organic carbon (TOC) in sediment were the dominant factors in structuring bacterial and archaeal community assemblages. Further analysis in dominant fecal-associated bacteria indicated that elevated nutrient concentrations may significantly (<i>p</i> < 0.05) increase the relative abundance of <i>Clostridium</i> and <i>Acinetobacter</i> in sediment. The findings highlight the pivotal roles of alpha diversity and fecal-associated bacteria in understanding the dynamics of microbial communities in a regulated urban river ecosystem.
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