Metabarcoding is a rapidly developing tool in marine zooplankton ecology, although most zooplankton surveys continue to rely on visual identification for monitoring purposes. We attempted to resolve some of the biases associated with metabarcoding by sequencing a 313-b.p. fragment of the COI gene in 34 “mock” samples from the North Sea which were pre-sorted to species level, with biomass and abundance estimates obtained for each species and taxonomic group. The samples were preserved either in 97% ethanol or dehydrated for 24 h in a drying oven at 65 °C (the routine way of preserving samples for dry weight measurements). The visual identification yielded a total of 59 unique holoplanktonic and 16 meroplanktonic species/taxa. Metabarcoding identified 86 holoplanktonic and 124 meroplanktonic species/taxa, which included all but 3 of the species identified visually as well as numerous species of hard-to-identify crustaceans, hydrozoan jellyfish, and larvae of benthic animals. On a sample-to-sample basis, typically 90–95% of visually registered species were recovered, but the number of false positives was also high. We demonstrate robust correlations of relative sequence abundances to relative biomass for most taxonomic groups and develop conversion factors for different taxa to account for sequencing biases. We then combine the adjusted sequencing data with a single bulk biomass measurement for the entire sample to produce a quantitative parameter akin to species biomass. When examined with multivariate statistics, this parameter, which we call BWSR (biomass-weighed sequence reads) showed very similar trends to species biomass and comparable patterns to species abundance, highlighting the potential of metabarcoding not only for biodiversity estimation and mapping of presence/absence of species but also for quantitative assessment of zooplankton communities.

Improving the conservation status and the management of Red List species requires knowledge on the biology and distribution of the organisms as well as an evaluation of the appropriateness of management measures. This study provides information on the trophic ecology and seasonal abundances of two Red List fish species from the Western Baltic Sea, snake blenny Lumpenus lampretaeformis (Walbaum, 1792), classified as “critically endangered” according to the German Red List, and eelpout, Zoarces viviparus (Linnaeus, 1758), classified as “near threatened” based on the HELCOM Red List. Beam trawl surveys were conducted to document abundances of both species in summer and winter in a marine protected area (MPA), where mobile bottom-contacting fishing gears will be excluded in the near future. The MPA is located in the German EEZ (exclusive economic zone) and aims to protect sandbank and reef habitats. Stomach content and stable isotope analyses (nitrogen and carbon) were performed to examine the diet of eelpout and snake blenny. To be able to position the two fish species in the food web, stable isotopes of macrozoobenthos, POM (particulate organic matter) and sand goby (Pomatoschistus minutus) were analysed as well. Eelpout and snake blenny were present in the study area in summer and winter, but reached higher abundances in summer. Diet composition overlapped strongly reflected by a similar trophic level, indicating potential food competition of the two species. Prey items were dominated by macrozoobenthos (Mollusca, Annelida, Arthropoda). Our study provides new information on the trophic position and seasonal abundance of the two fish species within an area soon to be placed under protection from mobile bottom-contact fishing. It therefore also provides a baseline to evaluate potential positive repercussions following the exclusion of mobile bottom-contacting fishing gears and might thus help to increase the understanding of fishing impacts on benthic ecosystems contributing to more effective conservation and management measures.