1. As grazers on picoplankton and nanoplankton, planktonic ciliates form an important link in pelagic food webs. Ciliate communities may be controlled by predation by metazooplankton. In eutrophic systems, however, where the number of large crustaceans is often low, the mechanisms that regulate ciliate dynamics have rarely been described.
2. We conducted an enclosure experiment with natural and screened (145 μm) summer plankton communities to investigate the effect of the small-sized crustacean zooplankton on ciliate community structure and the microbial loop in a shallow eutrophic lake.
3. The removal of the larger fraction of crustaceans initiated a decrease in total ciliate abundance. At the community level, we observed a substantial increase in large-sized predacious ciliates (>100 μm) and a simultaneous decrease in the abundance of smaller ciliates (<20–40 μm) that were mostly bacterivores and bacterio-herbivores. The compositional shift in the ciliate community, however, did not cascade down to the level of bacteria and edible phytoplankton.