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Background  The bottom-up (food resources) and top-down (grazing pressure) controls, with other environmental parameters (water temperature, pH) are the main factors regulating the abundance and structure of microbial communities in aquatic ecosystems. It is still not definitively decided which of the two control mechanisms is more important. The significance of bottom-up versus top-down controls may alter with lake productivity and season. In oligo- and/or mesotrophic environments, the bottom-up control is mostly important in regulating bacterial abundances, while in eutrophic systems, the top-down control may be more significant.    Results  The abundance of bacteria, heterotrophic (HNF) and autotrophic (ANF) nanoflagellates and ciliates, as well as bacterial production (BP) and metabolically active cells of bacteria (CTC, NuCC, EST) were studied in eutrophic lakes (Mazurian Lake District, Poland) during spring. The studied lakes were characterized by high nanoflagellate (mean 17.36 ± 8.57 × 10 3  cells ml -1 ) and ciliate abundances (mean 59.9 ± 22.4 ind. ml -1 ) that were higher in the euphotic zone than in the bottom waters, with relatively low bacterial densities (4.76 ± 2.08 × 10 6  cells ml -1 ) that were lower in the euphotic zone compared to the profundal zone. Oligotrichida ( Rimostrombidium  spp.), Prostomatida ( Urotricha  spp.) and Scuticociliatida ( Histiobalantium bodamicum ) dominated in the euphotic zone, whereas oligotrichs  Tintinnidium  sp. and prostomatids  Urotricha  spp. were most numerous in the bottom waters. Among the staining methods used to examine bacterial cellular metabolic activity, the lowest percentage of active cells was recorded with the CTC (1.5–15.4%) and EST (2.7–14.2%) assay in contrast to the NuCC (28.8–97.3%) method.    Conclusions  In the euphotic zone, the bottom-up factors (TP and DOC concentrations) played a more important role than top-down control (grazing by protists) in regulating bacterial numbers and activity. None of the single analyzed factors controlled bacterial abundance in the bottom waters. The results of this study suggest that both control mechanisms, bottom-up and top-down, simultaneously regulated bacterial community and their activity in the profundal zone of the studied lakes during spring. In both lake water layers, food availability (algae, nanoflagellates) was probably the major factor determining ciliate abundance and their composition. In the bottom waters, both groups of protists appeared to be also influenced by oxygen, temperature, and total phosphorus.

Factors controlling bacteria and protists in selected Mazurian eutrophic lakes (North-Eastern Poland) during spring