In hypersaline water bodies, the microphytobenthos plays a very important ecosystem role and demonstrates variability along with a salinity change. Due to anthropogenic activity, the sharp salinity increase in Bay Sivash occurred after 2014. To assess the changes in the microalgae community during the bay ecosystem transformation, the study was conducted four times in 2018 and 2019. At every sampling period, the samples were taken in a salinity gradient (from 7 to 10 sites). A total of 40 species of microalgae were identified during all research, including Cyanobacteria (Cyanophyceae, 2 species), Ochrophyta (Bacillariophyceae, 35 species), Haptophyta (Prymnesiophyceae, 2 species), and Miozoa (Dinophyceae, 1 species). According to the calculated similarity indices of Jaccard and Czekanowski–Sørensen–Dice, the species composition significantly differed during sampling periods. A total of 15 species were recorded at salinities of 80–90 psu, and 10 species at higher salinities, which contribute 64% of all species found in this study. The microalgae abundance was two times more in the floating green algae mat than on the bottom. There was no significant correlation between the number of species and salinity in all sampling periods. In November 2018, a significant positive correlation between the number of species in the sample and total suspended solids (TSS) and dissolved organic matter (DOM) was revealed. A significant correlation between the cell length in different species and salinity and DOM concentration was noted. Before the onset of the salinity increase, 61 species of microalgae were found in Eastern Sivash, of which only 12 have now been recorded, 31% of the currently found species. The characteristics of the total microphytobenthos abundance also significantly changed during all studies. Many characteristics have changed in the bay: the concentration of total suspended matter and dissolved organic matter, the temperature regime, composition of zoobenthos and plankton, and oxygen concentration. Due to this, it is unlikely that only the salinity increase caused the microphytobenthos changes in the lagoon.
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