Insights into the assembly mechanisms, co-occurrence patterns, and functional roles of bacterial community in an estuary system

Microbial drivers of biogeochemical cycles in estuaries remain understudied, particularly regarding biodiversity-function relationships. Using 16S rDNA sequencing, we analyzed taxonomic and functional profiles of bacterial communities in the water and sediment along the salinity gradient in Zhenhai Bay (South China). Significant differences in diversity, structure, composition, and function were observed between water and sediment habitats, indicating habitat influence. The terrestrial pollution sources detected in this study have a limited contribution to Zhenhai Bay, with unknown sources accounting for the majority of the total pollution, indicating the complexity of the estuarine environment in Zhenhai Bay. Additionally, most of the functional indicators of C, N, and S cycling were more enriched in the sediment, suggesting a more active biochemical cycle in the sediment than in the water. The spatial turnover of bacterial community composition in the water was much faster than the functional potential, and it showed higher functional redundancy in the water than in the sediment. Furthermore, except for the taxonomic community composition in the water, the functional community in the water and the taxonomic and functional community composition in the sediment were all dominated by stochastic processes. This indicated that strong environmental filtering of the taxonomic community in the water was due to hydrographic conditions or undetected environmental stressors. Overall, the results of this research provide a reasonable characterization of the taxonomy and function of microbial communities in an estuary and provide insights into how spatial changes in the taxonomic and functional community alter the nature and stability of microbial networks. IMPORTANCE: Understanding how bacteria drive essential processes like carbon and nutrient cycling is crucial for managing sensitive estuarine ecosystems. However, we lack clear knowledge of how the diversity of these microbes diversities relate to their actual functions in complex, real-world settings like Zhenhai Bay. This study provides a comprehensive picture of the identity and functional roles of bacterial communities across different habitats (water vs sediment) within a dynamic estuary. We found distinct patterns: sediment hosts more active nutrient cycling, water communities show greater functional flexibility, and pollution sources are surprisingly complex and largely unidentified. Critically, we show that the assembly of these communities is often governed by randomness, except in water, where environmental forces strongly filter which bacteria survive. These insights help predict how estuarine ecosystems might respond to pollution or change, improving management strategies to protect their health and the vital services they provide.