There is debate about whether results from mesocosm studies should be extrapolated to natural ecosystems. Critics argue that the abiotic and biotic characteristics of mesocosms do not represent the in situ conditions of the habitats in which they are designed to mimic. We addressed this idea by deploying mesocosms in two lakes of varying trophic status (mesotrophic and eutrophic). Water chemistry was relatively similar between the mesocosms and the respective lakes. In contrast, biological variables including most phytoplankton, nanoflagellates, ciliates, and zooplankton were lower in the mesocosms than they were in the respective lakes. There was also a shift in zooplankton composition such that mesocosm assemblages diverged from pelagic to littoral communities. While our results show that freshwater planktonic organisms can vary considerably between mesocosms and in situ habitats, we also suggest that factors such as isolation from lake sediments, the lack of predators, and the temporal scale at which mesocosms are filled and sampled should be considered when designing and interpreting mesocosm studies. Nevertheless, mesocosms are an important tool for developing and testing general ecological hypotheses that cannot be achieved using other approaches alone.

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.

The ciliate–metazooplankton trophic coupling is well documented from both laboratory and field experiments. The knowledge about these relationships during winter ice-covered periods is very scarce. The abundance and composition of planktonic ciliates, rotifers and crustaceans were studied during the ice-covered and ice-free periods in the Łuczański Canal (Masurian Lakeland, Poland). We hypothesised that in winter, rotifers play a major role in the top-down control of ciliates and that ciliate–metazooplankton relationships differ not only between the ice-covered and ice-free periods, but also between ice-covered months. Our study showed that ciliates formed a significant part of zooplankton biomass during the winter ice-covered period when crustaceans occurred in very low abundances. Despite cold water temperature and the presence of ice cover, time was probably a cue that initiates zooplankton development. The ciliate, rotifer and crustacean numbers and biomass, as well as chlorophyll a concentrations, were lower in February than in ice-free periods. In the winter month with ice cover, bottom-up control by resources was more important than top-down control by zooplankton grazing in regulating ciliates. In the spring month with ice cover, crustaceans and rotifers may include ciliates as an important part of their diets. In April, the studied groups of organisms were not related to each other in contrast to the summer, when zooplankton communities were closely related to each other. In autumn, rotifers may play an important role in controlling ciliates. The abundance, composition and ciliate–metazoan relationships can vary considerably not only across seasons, but also across ice-covered months.