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Unicellular organisms cover the majority of the eukaryotic “tree of life” and usually show fast reproduction rates, large species diversity, especially in the water bodies, and pronounced physiological adaptability to different types of stress. These organisms not just depend on physical and chemical features of the environment, but play key roles in the formation of this environment. Protists can form sustainable populations in the habitats where the multicellular organisms experience physiological stress and therefore become extinct. Rather recently, the new brackish-water biodiversity pattern was discovered for microbial planktonic species in the Baltic Sea, namely the protistan species-maximum concept for critical salinity zone (Telesh, Schubert, Skarlato, 2011). It was found that the unexpectedly high species richness of phyto- and zooplankton communities in the Baltic waters (more than 4000 taxa in total) was dominated by protists (up to 85% of all plankton species). These paradoxical results challenge the Remane’s Artenminimum (species-minimum) concept, which argues that taxonomic diversity is the lowest in brackish waters with salinity 5 to 8 psu, in the so-called horohalinicum. We infer that pronounced adaptability of protists allow these small-sized fast evolvers developing considerable species richness and filling in the biodiversity gap in large brackish water bodies. Our most recent hypothesis assumes that in stressful environmental conditions cells of free-living protists display remarkable mechanisms of adaptation which differ from those of large multicellular organisms (Telesh, Schubert, Skarlato, 2013). Studies of cell metabolism (presumably mixotrophy), stress proteins, ion channels and cell cycle in the model species of free-living unicellular eukaryotes (dinoflagellates, amoebae, and ciliates) alter traditional views on biodiversity in certain habitats, such as large estuaries, lagoons and brackish-water seas, and shed more light on the fast and effective adaptations of protists. This new knowledge underpins novel biodiversity concepts and stimulates cyto-physiological and ecological paradigm shifts. Grants: RFBR 13-04-00703, BMBF 01DJ12107, RAS Program “Biodiversity”.