Ciliates are a protozoan group of abundant and morphologically diverse species with a body length between 0.01 and 2 mm. The majority of species are bacterivorous, but ciliates also feed on filamentous cyanobacteria, flagellates and unicellular algae. Some species are omnivorous, others are predatory feeding on protozoans, and occasionally on rotifers and zooplankton. In streams and rivers, ciliates display a distinct depth distribution in the streambed sediments, being highly resistant to hydrological disturbances1. Ciliates together with species of testate amoebae are excellent bioindicators serving as an important tool in evaluating the biological water quality using the saprobic index of aquatic systems. Ciliates are effectively grazing on bacteria due to their small size and high doubling rate, distinctly reducing microbial biomass. They serve as food source for meiobenthic organisms such as early stages of microturbellarians and, consequently, link to meio- and macrobenthic invertebrates in aquatic food-webs2. These protozoans tolerate a wide range of temperatures and most species have a cosmopolitan distribution. Ciliated protozoans are best studied and identified alive, because morphological and behavioural characteristics play a critical role in species identification.