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On the basis of our collected material and historical information we assess phytoplankton dynamics in Kondopoga Bay, the Lake Onego in 1993-2011. The summer communities from continuously studied sampling stations contain 100 species belonging to eight divisions: Bacillariophyta, 40; Chlorophyta, 25; Cyanobacteria, 13; Chrysophyta, 12; Euglenophyta, 2; Dinophyta, 4; Cryptophyta, 3; and Xanthophyta, 1. Sample richness varied between 16 and 54 species, with a negative overall trend during the study period, but increases in Cyanobacteria and Dinophyta. Bioindication analysis shows that water acidification slowly rising from 1993 to 2011 with organic pollution (Index saprobity S) and the number of species with heterotrophic ability. In 1990s, the total abundance and biomass were on average 1.5 times higher than in 2000-2011, having similar fluctuation ranges (Pearson 0.74), with peaks in 1996 and 2006. At the same time, species richness decreased, showing a depletion of algal communities. Two critically impacted periods are revealed with the Shannon index in 1996 and 2007 and on the basis of the Aquatic Ecosystem State Index (WESI) calculation in 1995 and 2007, related to Kondopoga industrial wastewater influx enriched in nutrients and other contaminants. As a whole, the WESI was extremely high, reflecting a high self-purification capacity in respect to phosphate concentration in the bay. The canonical corresponded analysis (CCA) shows two different sets of taxa, those stimulated by temperature and nitric nitrogen (Anabaena scheremetievii Elenkin, Dolichospermum lemmermannii (Ricter) P.Wacklin, L.Hoffmann & J.Komárek, and Aulacoseira alpigena (Grunow) Krammer), and sensitive autotroph species inhabiting cool to temperate clear waters (Aulacoseira distans (Ehrenberg) Simonsen, Ankistrodesmus fusiformis Corda ex Korshikov, Mucidosphaerium pulchellum (H.C.Wood) C.Bock, Proschold & Krienitz). The comparative statistics with GRAPS program revealed two cores of species richness in years 1996 and 2011 that included most of species. The long-term dynamics of relative cell volume shows that phytoplankton communities were enriched with small-celled species, such as Cyanobacteria (Microcystis aeruginosa (Kützing) Kützing) and Cryptophyta (Cryptomonas sp. and Katablepharis ovalis Skuja) in the period between 1998 and 2006. Pearson correlation for Shannon index and relative cell biovolume is negative (-0.79), showing high stability of species rich communities under environmental impacts. Two periods of dinoflagellate blooms (1998, 2007) followed the peaks of total abundance and biomass (1996, 2006). Such correlation makes the Kondopoga Bay ecosystem comparable to those of large lakes in spite of a heavier anthropogenic impact from Kondopoga pulp and paper mill wastewater.