Using laboratory microcosms, we studied direct and indirect interactions among different components of bi- and tritrophic communities. Filamentous cyanobacteria (Phormidium sp.) and autotrophic flagellates (Chlorogonium elongatum) were primary producers. The second trophic level was represented by ciliates Furgasonia blochmanni and Pseudomicrothorax dubius grazing on the filamentous cyanobacteria and two filter feeders, Euplotes octocarinatus and Stylonychia pustulata, feeding on the autotrophic flagellates. An oligochaete, Chaetogaster sp., was used as the top predator. An experiment was carried out for all combinations of two factors: (1) the identity of the cyanobacteria consumer (Furgasonia or Pseudomicrothorax) and (2) the presence or absence of the top predator. Significant effects of the treatments on both the abundance of cyanobacteria and filter feeding ciliates and predator-induced defense in Phormidium and Euplotes were observed in a 36-day experiment. The experiment showed that the substitution of one species (Furgasonia) for another (Pseudomicrothorax) seemingly playing the same ecological role may lead to significant changes in the whole community.