Composition and dynamics of particle-associated and free-living bacterial communities in the Weser estuary, Germany

We studied the spatio-temporal dynamics and community composition of the free-living and particle-associated bacterial community in the salinity gradient of the Weser estuary, Germany, between March and December 1999 and in May 2000. Bacterial numbers covaried with temperature and those of the particle-associated fraction with the turbidity, exhibiting highest proportions in the turbidity maximum between July and December. The analysis of the composition of the particle-associated bacterial community by fluorescence in situ hybridization (FISH) with group-specific oligonucleotide probes showed that Cytophaga/Flavobacteria (CF) comprised the highest proportions in the freshwater section (mean: 28 +/- 8.9% of DAPI cell counts) and decreased towards the marine section to 14.0 +/- 3.7%. alpha-, beta- and gamma-Proteobacteria constituted around 10% without pronounced variations among the various sections. The community analysis based on PCR-amplified fragments of the 16S rRNA gene, along with denaturing gradient gel electrophoresis (DGGE) and a cluster analysis of the banding patterns, exhibited pronounced differences along the salinity gradient and well-separated communities within the freshwater, brackish and marine sections. Seasonal differences within the separate communities and between the particle-associated and free-living bacterial communities were less pronounced. The sequence analysis of prominent bands revealed that the communities consisted of bacteria affiliated to Proteobacteria, CF and Actinobacteria. Clones of the CF cluster were rather distantly related to phylotypes from other aquatic environments, whereas clones related to Actinobacteria clustered closely together with phylotypes from other aquatic systems. Clones belonging to alpha- and beta-Proteobacteria also affiliated closely to phylotypes from other aquatic systems but more closely to isolated strains than the CF and Actinobacteria clones.