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The large and shallow lowland lakes constitute a distinctive type of lake ecosystem, because of their polymixis, frequent resuspension of bottom sediments and internal nutrient loading, high turbidity and usually high productivity and eutrophication rate. Lake Peipsi is one of the largest lake in Europe, its area is 3555 km2 and mean depth is 7.1 m. The study results for the vegetation seasons (May-October) obtained for the decade 1997-2008 allow to evaluate the long-term changes in the functioning of its ecosystem in terms of dynamics of phyto- and zooplankton and nutrient content in a lake. Lake Peipsi consists of three different parts: the northern, the largest and deepest one is eutrophic L. Peipsi s.s. (sensu stricto), the southernmost part is hypertrophic L. Pihkva, connected with L. Peipsi s.s. by the river-like L. Lammijarv. The decrease in nutrient loading to L. Peipsi observed in the early 1990s was brought about by social changes (collapse of Soviet type agriculture) rather than by the purification of point-pollution sources. In the northern part, Lake Peipsi s.s., the content of both nitrogen and phosphorus was stabilized, while the increase in phosphorus in the water of L. Pihkva was evident. The resistance of the three lake parts to external nutrient loading is different. It seems that the ecosystem of the southern lake part (L. Pihkva) is losing its resilience. The disturbance of the ecosystem is most likely caused by the fact that the slight trend of re-oligotrophication beginning in the early 1990s was reversed in the mid-1990s due to increasing P loading. The share of cyanobacteria in phytoplankton biomass increased from 20% to 60% in L. Peipsi s.s., and from 30% to 90% in the southern parts of the lake in the summer months. The lake was characterized by massive cyanobacterial blooms. Potentially toxic genera (Microcystis, Aphanizomenon, Anabaena, Gloeotrichia) dominated, and the quantity of microcystins in the lake was relatively large. The biomass of phytoplankton increased whereas that of all zooplankton groups - cladocerans, copepods and rotifers - decreased. The most essential decline affected rotifers: their abundance was about 60% lower in 2001-2008 than in the 1990s. The biomass of copepods decreased almost 50% and that of cladocerans 34%. In parallel with changes in plankton, the fish composition of L. Peipsi was characterized by sharp decline of planktivorous smelt (Osmerus eperlanus eperlanus m. spirinchus Pallas) and vendace (Coregonus albula (L). The most likely causes of the changes seem to be mainly the anthropogenic P input, decreasing N:P ratio, cyanobacterial toxins, and changes in ichthyocoenosis. Our data from last decade demonstrate a kind of disturbance in the ecosystem of the lake as compared to the second half of last century. The disturbance of the ecosystem is most likely caused by the fact that the slight trend of re-oligotrophication beginning in the early 1990s was reversed in the mid-199s due to increasing P loading from southern part of lake watershed.
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