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Picoeukaryotes (protists < 2 µm) play an important role in marine ecosystems, although knowledge of their diversity and ecosystem functioning is limited. The White Sea is located in the sub-Arctic zone. However, its abiotic conditions are characterized by a number of features typical of the Arctic seas. In this study, the molecular diversity of picoeukaryotes in July 2014 in Kandalaksha Bay (the White Sea) was examined using conventional filter fractionation and Illumina sequencing. In < 2 µm size fraction 186 taxa were revealed that included some nanoplankton (2–20 µm) and even microplankton (>20 µm) taxa. Plankton assemblage was prevailed by autotrophs (>57% of all sequences). Putative picoeukaryotic autotrophs were mostly dominated by three genus: Micromonas sp., Bathycoccus sp. and Ostreococcus sp. (35% of all sequences). Putative heterotrophic picoeukaryote assemblage was more diverse and was presented by marine stramenopiles (MAST, Labyrinthulomycetes), Amoebozoa, Cercozoa and picozoa. Illumina sequencing revealed some new groups and genus of nano- and microplankton organisms which have been never detected in the White Sea. Our study revealed that diversity of picoeukaryotes in summer in the sub-Arctic White Sea corresponds to that of the other Arctic seas, such as the Beaufort and Norwegian Seas.