Seasonal hydrological contrasts in water–sediment microbiome assembly and eutrophication indicators in a low-gradient urban river–lake network

Study region Kunshan, a low-gradient urban river-lake network in the central Taihu Basin (Yangtze River Delta), China. Study Focus Seasonal hydrological variability can reorganize microbial communities in connected river–lake systems, but responses may differ between water and sediment and alter the interpretation of water-quality indicators. We analyzed 94 surface-water and surficial-sediment samples collected in May and August 2024, representing pre-monsoon and summer-monsoon conditions, respectively. Bacterial community composition differed strongly by matrix and sampling period (NMDS stress = 0.0763; PERMANOVA R² = 0.665, p = 0.001), with matrix accounting for the largest share of variation. Water communities showed stronger seasonal displacement and lower evenness in August, whereas sediments maintained higher diversity. Indicator taxa also shifted by matrix and period, including Limnohabitans in May water, Cyanobium in August water, Nitrospira in May sediment, and Dechloromonas in August sediment. New Hydrological Insights for the Region Taxonomic turnover accompanied matrix-specific functional shifts and assembly changes. Water lost aerobic chemoheterotrophic potential in August, while sediment gained anaerobic chemoheterotrophic and nutrient-transformation capacity. Neutral models revealed contrasting effective immigration trajectories between water and sediment. August shifted to higher C:N, lower C:P, tightened coupling, and altered WQI/TLI links to stoichiometric gradients. These demonstrate asymmetric seasonal hydrological effects across the water–sediment interface and that C:N:P provides useful biogeochemical context to refine microbial and eutrophication indicator interpretation for regulated river-lake networks.