To compare the characteristics of protozoan community structure and water quality during the water storage and drawdown periods in the Three Gorges Reservoir area, the protozoan communities in 17 main stream and tributary sections from the reservoir tail to the dam were investigated in May and October 2017, respectively. A total of 55 species of protozoa were identified, belonging to 10 orders, 18 families, and 18 genera. In both periods, the dominant genus in both main streams and tributaries was Tintinnopsis, with a relative abundance of up to 87% during the water storage period. The average density and biomass of protozoa in the main stream were 40% higher during the water storage period compared to the drawdown period, and diversity was also significantly higher. In contrast, the average density and biomass of protozoa in the tributaries decreased by 14% during the water storage period compared to the drawdown period, with no significant change in diversity. The diversity of protozoa in the main stream was significantly higher than in the tributaries during the water storage period, but there was no significant difference during the drawdown period. Principal coordinate analysis (PCoA) showed a large difference in the community structure of protozoa between the water storage and drawdown periods, while the difference between the main stream and tributaries was small. Spearman correlation analysis indicated that the density and diversity of protozoa in the main stream were significantly positively correlated with conductivity, whereas the diversity of protozoa in the tributaries was significantly negatively correlated with pH. Redundancy analysis (RDA) showed that pH and conductivity were important factors affecting the community structure of protozoa in the Three Gorges Reservoir area. Based on the evaluation of the protozoan communities, the water quality in the tributaries was found to be more polluted than in the main stream, especially the tributaries near the Three Gorges Dam may be greatly affected.

Ecological succession is vital for forecasting ecosystem responses to environmental changes and their future states. Zooplankton, a primary natural food source in aquaculture, plays a crucial role in maintaining ecosystem function. Thus, understanding how zooplankton communities respond to environmental changes is essential for economic and ecological outcomes. In this study, we examined three types of aquaculture ponds (crab, crayfish, and fish ponds) with over 10 years of history and analyzed 27 environmental factors potentially influencing zooplankton dynamics throughout the year. Our results showed that Rotifera was the most abundant group in all three pond types, followed by Protista, Cladocera, and Copepoda. The dominant species across different seasons and ponds were Polyarthra vulgaris, Anuraeopsis fissa, and Trichocerca pusilla. The alpha diversity of zooplankton was influenced by various environmental factors across different pond types, with significant effects of antibiotics observed only in the fish ponds. The temporal and spatial distributions of zooplankton communities varied significantly. Deterministic processes, driven primarily by temperature and ammonia nitrogen, were identified as the primary mechanisms influencing zooplankton community assembly in freshwater aquaculture ponds. These findings inform management practices aimed at regulating key environmental drivers and optimizing zooplankton dynamics, with implications for maintaining ecosystem stability and productivity and, ultimately, supporting sustainable aquaculture.