Although lakes play a major role in the storage of organic carbon, processes involved are not yet very well characterized, especially for oligotrophic lakes. Whether a lake functions as a net source or sink for carbon depends on relative rates of primary production, inputs of terrestrial organic matter and respiration. The microbial community will affect the efficiency of carbon cycling and thereby potential carbon storage. Because the organic matter fluxes are smaller in oligotrophic lakes they have been studied less intensively with respect to their carbon cycling compared to eutrophic lakes. Whether they play an appreciable role in freshwater carbon cycling relies on unraveling primary and secondary production. Here we present the results from such a study in oligotrophic Lake Lucerne, Switzerland. Based on in situ carbon isotopic labelling experiments using dark, glucose-labelled and transparent, DIC-labelled bottles positioned at different depths in the water column, we conclude that even though the photic zone was very deep, integrated primary productivity was consistently low. The carbon processing efficiency of the heterotrophic producers was such that photosynthesized organic matter was fully consumed, even during times of maximum productivity. This implies that the heterotrophic producers were well adapted to rapidly respond to a temporary increase in primary productivity, which is in line with calculated bacterial growth efficiencies in the surface water layer. Highest glucose-based productivity, as a measure of the heterotrophic potential, was observed in the deepest parts of the water column. Chemoautotrophy was shown at 60 m water depth and is of relatively minor importance for overall fluxes. Mixotrophy was recognized as a strategy to keep up production when light conditions become less favorable for autotrophic growth. A mesocosm experiment earlier in the year indicated lower primary production, which agrees well with the timing of this experiment preceding the annual spring bloom. During the low-productivity season the coupling between phytoplankton and bacterial production was much weaker and potentially more organic matter could escape recycling at that time, although quantitatively fluxes remained very low.
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