The respiration rates of a pelagic community and of its microbial fraction (< 1.2 μm) were measured at two depths in the oxic layer of a meromictic alpine lake (Cadagno, Switzerland) using the oxygen technique. The duration of the incubations were 12, 24 and 55 h. Bacterioplankton abundance (DAPI counts) and composition (whole cell hybridization using 11 group-specific rRNA-targeted oligonucleotide probes) were measured during the incubations. Respiration generally increased with time, especially in the microbial fraction, or remained similar. This result was not always consistent with changes in bacterial abundance and cell volume. The composition of the community also changed during the incubations. The abundance of β-Proteobacteria increased during the course of all the experiments. These results extend the previous conclusions drawn in marine environments to fresh waters and demonstrate that, in addition to changes in bacterial abundance, cell volume and biomass, changes in the taxonomic composition of the bacterial community can occur during discrete incubations of freshwater planktonic communities.