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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.
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