In order to explore the composition of epiphytic algae and its related environmental factors, 12 sampling sites in the natural reaches and the backwater reaches (including perennial backwater sections and fluctuating backwater sections) were investigated among tributaries of the Caotang River, the Meixi River, and the Daxi River in the Fengjie district of the Chongqing section of the Three Gorges Reservoir under different hydrological regimes (i.e., storage and non-storage periods). Results showed that 103 species of epilithic algae belonging to 45 genera and 4 families are found in the 3 tributaries. This included 67 species belonging to 34 genus in the natural sections and 82 species (64 species in perennial backwater sections and 41 species in fluctuating backwater sections) belonging to 34 genera in the backwater sections. During the storage period, the dominant species in the natural sections were Melosira varians, Cocconeis placentula, Diatoma vulgure, Gyrosigma scalproides, and Oscillatoria tenuis, while the dominant species in the backwater sections were M. varians, Cymbella affinis,D. vulgure, Eucapsis alpina, and M. granulata. During the non-storage period, the dominant species in the natural sections were M. varians, C. affinis, and C. placentula, whereas the dominant species in the backwater sections were O. princeps, O. rupicola,O. formosa, Synedra acus, Ulothrix sp., Merismopedia elegans, and O. tenuis. These results suggested that the compositions of dominant species showed significant differences during the non-storage period, while little difference was found during the storage period. In addition, the dominant species did not show a significant change in the natural sections, but a marked difference was observed in the backwater sections. Similar dominant species were observed in both perennial and fluctuating backwater sections during the non-storage period, but significantly different dominant species were found during the storage period. Redundancy analysis suggested that the composition of epilithic algae was influenced by different environmental factors, such as temperature, electrical conductivity, pH, total nitrogen, and total phosphorus. Indeed, changes in the cell densities of dominant algae at the different sites were mainly affected by temperature and the concentrations of nitrogen and phosphorus. These results suggest that the different hydrological regimes had an important role not only on the reservoir water environment, but also the dynamics of epilithic algal communities.
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