Heterotrophic protists Rotosphaerida, Thaumatomonadida and centrohelid heliozoans are among the less studied silicified protists in terms of their biogeography and ecology. These organisms inhabit fresh and brackish water, and leave behind siliceous structural elements after death that are species-specific and amenable to electron microscopic analysis.

This paper is the first to present data on species richness and taxonomic structure of silica-scaled heterotrophic protists – rotosphaerids, colourless free-living thaumatomonad flagellates and centrohelid heliozoans – in the large continuous water system of Siberia connecting Lake Baikal to the Kara Sea. In the study area, electron microscopy revealed 21 centrohelid heliozoan species from the genera Raphidiophrys (1), Acanthocystis (7), Choanocystis (3), Raineriophrys (2), Raphidocystis (6), and Pterocystis (2), seven rotosphaerid species from the genera Pinaciophora (3), Turriplaca (2), Rabdiophrys (1), and Pompholyxophrys (1), and one thaumatomonad flagellate species Thaumatomastix. Two species of rotosphaerids, Rabdiophrys cf. anulifera and Pinaciophora tridentata, and two species of centrohelid heliozoans, Acanthocystis cf. tubata and A. cf. cornuta, were found in the waters of Russia for the first time. The most widespread species in fresh water from Lake Baikal to the Lower Yenissei River were Pinaciophora fluviatilis and Raineriophrys cf. fortesca. These species disappeared from the protist assemblages of the Yenissei gulf of the Kara Sea due to higher salinity, with only three species, Acanthocystis cf. mylnikovi (at 3.12‰ salinity) and A. pectinata and Raphidocystis sp. 2 (at 8‰ salinity), found in the area. The sensitivity of silica-scaled heterotrophic protists to changes in habitat parameters suggests that these microeukaryotes could be new indicator organisms.