Alternative pathways of energy transfer guarantee the functionality and productivity in marine food webs that experience strong seasonality. Nevertheless, the complexity of zooplankton interactions is rarely considered in trophic studies because of the lack of detailed information about feeding interactions in nature. In this study, we used DNA metabarcoding to highlight the diversity of trophic niches in a wide range of micro- and mesozooplankton including ciliates, rotifers, cladocerans, copepods, and their prey, by sequencing 16- and 18S rRNA genes. Our study demonstrates that the zooplankton trophic niche partitioning goes beyond both phylogeny and size and reinforces the importance of diversity in resource use for stabilizing food web efficiency by allowing for several different pathways of energy transfer. We further highlight that small rarely studied zooplankton (rotifers and ciliates) fill an important role in the pathways of the Baltic Sea pelagic primary production, and the potential of ciliates, rotifers, and crustaceans in the utilization of filamentous and picocyanobacteria within the pelagic food web. The approach used in this study is a suitable entry point to ecosystem-wide food web modeling considering species-specific resource use of key consumers.

For information on sampling and analysis, see DOI: 10.1098/rspb.2021.0908