Autumnal sedimentation of the Microcystis population was studied in Lake Nieuwe Meer (Amsterdam, The Netherlands). In summer, Microcystis formed a high percentage of the total phytoplankton in the water column, but a low percentage in sedimentation traps. The reverse was found during September and October, with a high percentage in the sedimentation traps, but a low percentage in the water column. The decrease in the numbers of Microcystis colonies coincided with a decrease in water temperature. In experiments with a strain of Microcystis, isolated from Lake Nieuwe Meer, the percentage of total colonies that were sinking increased in a few days to 100% after a shift from 20 degrees C to 15.3, 13.0 or 10.5 degrees C. The gas-vesicle volume in the cells remained constant during the incubations. Sinking of the colonies resulted from an increased glycogen content. Calculation of carbon (C) flows during the first 2 days of the incubation at reduced temperature showed that the glycogen accumulation was the result of a much lower rate of protein synthesis during the light period at the lower temperatures. Although the photosynthetic rate itself decreased at reduced temperature, it resulted in more fixed CO2 being stored as glucose. Because the respiratory rate also decreased (with an almost similar decrease to that of photosynthesis), glycogen accumulated at lower temperatures. It was calculated that after an incubation period of similar to 1 week at reduced temperature, the rate of photosynthesis had decreased by 10.1% of the value at 20 degrees C per 1 degrees C, while the rate of respiration had decreased only 1.8%. It is proposed that there is a feedback mechanism in which an increasing concentration of glycogen inhibits photosynthesis and stimulates respiration.