Microbial community and functional characteristics across the water-sediment continuum in typical rivers of the...

River ecosystems are facing increasing environmental pressures, and microbial communities play a key role in maintaining ecosystem stability. Although microbial research in lentic ecosystems has been relatively extensive, there is a lack of systematic comparative studies on the community structure and metabolic functions of fungi and bacteria across vertical gradients within the water-sediment continuum in flowing rivers, particularly those chronically exposed to salinity and nitrogen nutrients. This study investigated the microbial community structure, functional traits, and environmental responses across the water-sediment continuum of two Class V-polluted rivers, the Zhimai River and Xiaoqing River of the Yellow River Delta. Integrated analyses combining water quality assessment, high-throughput sequencing, and metabolomics revealed distinct microbial assembly mechanisms in the two rivers. In the Zhimai River, salinity-related factors, particularly sodium and potassium, influenced community composition, with Chytridiomycota (19.76%) and halophilic bacteria, such as Marivita (2.60%), exhibiting strong positive correlations. In contrast, nitrogenous nutrients, particularly ammonium nitrogen, played a key role as drivers in the Xiaoqing River. In this system, Absidia (23.08%), Hydrogenophaga, and Arenimonas were dominant and exhibited positive associations with nitrogen levels and perfluorooctanoic acid. These patterns indicate two response strategies, halophilic adaptation under salinity stress and nitrogen cycling under nutrient enrichment. The findings provide new insight into salinity- and nutrient-driven microbial processes in polluted river systems and offer a scientific basis for microbial remediation and ecological health assessment in the Yellow River Delta.