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A methodical approach for the assessment of pelagic biomass and the main carbon fluxes in remote and hardly accessible mountain lakes was elaborated and tested. Number and biomass of bacteria (BAC), autotrophic picoplankton (APP), heterotrophic nanoflagellates (HNF), ciliates (CIL), phytoplankton (PHY), zooplankton smaller than 40 μm (ZOOS) and zooplankton larger than 40 μm (ZOOL) were investigated regularly during two ice-free periods in 13 European mountain lakes (1st level approach – fixed samples elaborated in specialized laboratories). Carbon fluxes measured in 9 lakes included: primary production, exudation by PHY and BAC uptake of exudates, BAC production, elimination of BAC. These processes were measured in the field by specialized teams (2nd level approach). The ranges of values found in mountain lakes were evaluated and possible methodical and interpretative errors discussed. BAC were a significant component of pelagic biomass. The intercomparison between different partners showed differences in bacterial counts lower than 10%, whereas the mean cell volumes measured fluctuated by more than 40%. APP was never found in a significant quantity, except in one lake. HNF and CIL, though regularly found, were usually scarce and only occasionally significant in terms of biomass. The main components of pelagic biomass were BAC, PHY and ZOOL+ZOOS, except for acidified lakes, where zooplankton was very low. In oligotrophic mountain lakes, the percentage of extracellular production in the total primary production was considerable. Bacterial abundance and production often reached values quite comparable with the situation found in lowland mesotrophic lakes during winter.
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