We examined in situ abundance and activities of the major bacterial groups in the two most distinct compartments of experimentally divided Lake Grosse Fuchskuhle (Germany). The selected south-west (SW) and north-east basin (NE) differ substantially in their major chemical and biological parameters that potentially influence the dynamics and composition of microbial communities. Water from the basins were incubated in dialysis bags, which allowed for a relatively free exchange of nutrients, limiting solutes and low molecular organic matter but fully prevented exchange of organisms. To investigate the effect of top-down and bottom-up manipulations three size fractions of water samples were produced: (i) unfiltered, (ii) pre-filtered through 5.0 mu m pore size membranes to remove large particles, as well as grazers and (iii) pre-filtered through 0.8 mu m filters to remove all potential bacterivores. One set of dialysis bags was either incubated in acidic SW (rich in humic matter) or in almost neutral NE basin whereas a second set was transferred from the SW to the NE basin and vice versa. Our study revealed pronounced differences in growth rates among the major bacterial groups in relation to the treatments. Members of the Betaproteobacteria, in particular of the subgroup targeted by the BETA2-870 probe, were highly abundant in both basins, and most of them belonged to the Polynucleobacter necessesarius subcluster PnecC. Their specific growth rates surprisingly increased in all treatments when being transplanted into the acidic SW basin, indicating that pH and humic substances greatly affected growth of this particular group in the lake. In contrast, members of the Sphingobacteria/Flavobacteria group of the Bacteroidetes (both basins) as well as Actinobacteria (SW basin) were less abundant, especially in the presence of flagellates (