Importance of ciliates as food for fish larvae in a shallow sea bay and a large shallow lake

•Sufficient protozoan food may enhance larval growth in the beginning of the exogenous feeding.•Ciliates represent essentially important food for fish larvae in both marine and lacustrine environments.•In the sea and in one lake ciliates formed respectively 36 and 63% of the total carbon biomass ingested by larval fish.•Consumption of ciliates is linked to their availability in the environment — if abundances are high proportionally more ciliates are consumed. We estimated the consumption of planktonic ciliates by fish larvae in the Väinameri Sea (a shallow semi-enclosed bay of the Baltic Sea) and Lake Võrtsjärv (a shallow and eutrophic lake). Our primary hypothesis was that planktonic ciliates constitute a substantial component of the diet of fish larvae in both environments. We also assumed that the contribution of ciliates to larval nutrition is bigger in lacustrine than in marine environment because ciliates are usually more abundant in lakes. The nutrition of field collected larval fish was determined by gut content analysis using epifluorescence microscopy. Our study revealed that ciliates occurred in the alimentary tracts of all fish species examined. We discovered that the consumption of ciliates by first-feeding fish larvae contributed approximately 40 and 60% of their total consumed carbon in the Väinameri and in Võrtsjärv, respectively. Ciliates represent essentially important food for fish larvae and sufficient protozoan food may enhance larval growth in the beginning of the exogenous feeding and shorten the most vulnerable period in larval stage before shifting to larger prey.