Seasonal patterns of the bacterioplankton community composition in a large mesotrophic lake

The composition of the bacterioplankton community in mesotrophic Lake Constance was studied from April 1996 to December 1997 by fluorescence in situ hybridization (FISH) with group specific oligonucleotide probes and denaturing gradient gel electrophoresis (DGGE). Between 10 and 59% of the DAPI-stained cells were detected as Bacteria with means of 38 +/- 12, 27 +/- 10 and 23 +/- 6% at 3, 20, and 50 m depth, respectively. In the euphotic zone at 3 m depth, beta-Proteobacteria always constituted highest proportions of the bacterial community detected by FISH and constituted 6 to 23% of the DAPI-stained cells with a mean of 12%. Proportions of bacteria belonging to the Cytophaga/Flavobacteria (CF) cluster and the alpha-Proteobacteria at this depth were 5.4 +/- 2.5 and 4.1 +/- 3.5%, respectively. Proportions of beta-Proteobacteiia decreased at 20 and 50 m, whereas that of alpha-Proteobacteria remained constant and that of the CF-cluster increased to 7.4%, such that they comprised similar proportions as beta-Proteobacteria at 50 m depth. gamma-Proteobacteria were always of minor importance and constituted only 2.2 +/- 1.3% of the DAPI cell counts. Cumulative proportions of all detected bacterial groups constituted 75% of the Bacteria counts at 3 m, 84% at 20 m and 99% at 50 m. The DGGE analysis of the bacterioplankton community showed seasonal and vertical variations of the banding patterns even though several bands occurred throughout the study period and at all depths. A cluster analysis revealed distinct bacterial clusters of the phytoplankton spring bloom and the later period and of epilimnetic and hypolimnetic waters. The sequence analysis of the excised bands indicated that all groups which were detected by FISH were represented in the patterns. Sequence similarities of the retrieved sequences to known isolates were <90 to 96.1%, and to other phylotypes as close as 99%. Phylotypes of beta-Proteobacteria and Actinobacteria of the typical banding patterns affiliated closely with recently described clusters of typical freshwater bacteria. In addition, we identified phylotypes of the Holophaga/Acidobacterium and Nitrospira phylum during the stratified period in samples from 50 m and during mixing from all 3 depths.