Ecology

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High diet overlap is assumed to cause competition between the three dominant pelagic planktivorous mesopredators in the Baltic Sea, sprat, herring, and stickleback11,24,25. Despite this assumption, stickleback populations have increased dramatically over the past decades, which raises the question of whether and how resources are partitioned26. While previous studies of fish diet overlap have mainly relied on microscopic identification of gut content, we implemented a DNA metabarcoding approach targeting two different gene regions, the 18S rRNA gene (18S) and the mitochondrial cytochrome c oxidase I gene (COI) to reveal the taxonomic diversity of prey, and a qPCR step to quantify rotifers that are at times abundant in the Baltic Sea. Our study highlights consistency between methods, with DNA metabarcoding resolving the plankton-fish link at the highest taxonomic resolution. Our results suggest a unique niche of stickleback that may enable high population growth in the open water, despite high competition between mesopredators, although this finding needs to be confirmed at larger scale. More than half of the DNA found in herring and sprat stomach contents was assigned to Pseudocalanus, supporting previous observations of high diet overlap between the two clupeids11,12. On the other hand, the diet of stickleback differed substantially from the two clupeids, with rotifers appearing as main prey DNA in spring. The high rotifer biomass in the environment and lack of competition from other predators indicate that this novel niche utilization may support the drastic increase of pelagic stickleback in the Baltic Sea.We find that copepods dominated the gut content of the two clupeids sprat and herring. Pseudocalanus and Temora occupied most of the sequence reads of the clupeid metabarcoding, two species that are often reported as preferred prey in previous studies11,12. Despite high contributions of these two copepods, Pseudocalanus was more than four times as abundant as Temora in clupeid gut contents. A strong preference for this copepod with marine origin can further confirm the increased competition between the clupeids, as Pseudocalanus has decreased due to decreased salinity12 and shares a similar vertical distribution as clupeid during daytime27. Our study using metabarcoding further reveals a large relative quantity (11%) of the ctenophore Mertensia in the gut samples of both clupeids. Similar, Clarke et al.28 reported an important contribution of gelatinous zooplankton to upper trophic levels in the Southern Ocean. Despite high abundances of ctenophores in the Baltic Sea and their assumed importance in marine food webs19, they are not reported as food for planktivorous fish. A possible explanation is the difficulty observing them microscopically, as their digestion rate is faster than crustaceans29, and no hard parts remain in the digestive system. Further, COI detected the presence of cladocerans, which was confirmed by the microscopic survey, but underrepresented with 18S that strongly amplify copepods20. Interestingly, more than twice annelid COI reads, including the benthic macroinvertebrates Bylgides and Marenzellaria, were associated to stickleback (15%) and herring (8%) than to sprat (4%), highlighting their ability to migrate vertically. These interactions suggest that together stickleback and herring contribute to benthic-pelagic coupling when oxygen is not restricting vertical migration in the southern Baltic Sea30.Sprat and herring share a similar feeding niche, which may explain previously observed declines in body mass and stomach fullness, and supports the theory of competition between the two species31. In contrast, stickleback revealed little diet overlap with the other mesopredators. The low relative abundances of Pseudocalanus (1–8%) in metabarcoding analyses indicates that the density-dependent competition may not limit the population growth of stickleback. The copepods that were shared in the diet of stickleback, sprat, and herring were Temora, Acartia, and Centropages have increased over the last decades, as opposed to Pseudocalanus32. Our results show that stickleback are able to feed on a broader spectrum of prey and highlight that stickleback utilizes the rotifer Synchaeta baltica as prey, which is an important component of the plankton community composition in the Baltic Sea18,20. Due to the difference of prey size, we can expect an overrepresentation of copepod to rotifer sequences compared with microscopic count data. High predation rate on S. baltica is supported by both the qPCR assay as well as microscopic counts, although only the eggshells were visible but not the soft-bodied rotifer. Despite the considerably lower carbon content per S. baltica (ca. 6 µg C ind−1) compared to copepods (ca. 20 µg C ind−1)33, the high number of rotifers likely act as a major food source for stickleback. 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