Data from:Linking Hydrodynamic Disturbances to Microeukaryote Biogeography: Ciliate Community Shifts Reveal Freshwater Plume and Seawater Intrusion Dynamics

Estuarine ecosystems are jointly regulated by freshwater plumes and seawater intrusion, yet their impacts mechanisms on community dynamics remain insufficiently understood. Here, we investigated the response of ciliate community to freshwater plume-seawater intrusion disturbance in a large subtropical estuary in China. Ciliate distribution exhibited clear turnover along environmental gradients in both community composition and abundance. In summer, community composition showed gradual horizontal and vertical shifts that corresponded with broad environmental gradients generated by strong freshwater plumes. In contrast, in winter, community variation was most pronounced between the inner and middle estuary, reflecting that the upstream compression of environmental gradients driven by strong seawater intrusion. These patterns were corroborated by our determinants analyses. Variation partitioning analysis revealed that physical factors explained a substantial proportion of community variation in both seasons, and structural equation modelling further demonstrated that physical factors exerted the strongest total effects on community structure. In addition, species abundances closely followed a log-normal distribution in both seasons, which is consistent with predictions of niche-based community theory. Niche differentiation along environmental gradients shaped by freshwater plumes and seawater intrusion may contribute to this pattern. Overall, our findings reveal a clear linkage between ciliate distribution and freshwater plume-seawater intrusion dynamics, suggesting that ciliate communities can sensitively reflect the spatial–temporal variability of these physical processes.