Structure of the river sediment microbiomes impacted by anthropogenic land uses, environmental and spatial variations

River sediments are impacted by anthropogenic land uses since they are the major sinks of pollutants. Sediment microbial communities play vital roles in the degradation of toxic compounds and the recycling of nutrients, sustaining healthy aquatic ecosystems. However, sediment microbiomes impacted by both anthropogenic and natural disturbances are not well documented. This study investigated the dynamics of sediment microbiomes in response to major anthropogenic land uses, environmental, and spatial factors across 25 locations along the Ganh Hao river in Vietnam, using high-throughput sequencing targeting the V3–V4 regions of the 16S rRNA gene. The sediment microbiomes were exclusively dominated by Proteobacteria (59–79%). Microbial taxa associated with shrimp farms, a major land use, were koll13, GCA004, Piscirickettsiaceae, Marinicellaceae, and Desulfobulbaceae. The resulting variation partitioning, based on CCA, indicated that spatial factors highly influenced the microbial profile and explained 41.8% of the microbial variation. However, the variation in sediment microbiomes was largely impacted by a combination of environmental factors (i.e., As, Pb and Cu concentrations, pH and EC) and the presence of shrimp farms which, together with spatial variation, explained 77.4% of the microbial variation. Overall, this study provides insights into the spatial structure of river sediment microbiomes and provides the biological signature of sediment microbiome in response to the major anthropogenic land use and seawater intrusion.