Benthic Heterotrophic Protist Communities of the Southern Baltic Analyzed with the Help of Curated Metabarcoding Studies

SIMPLE SUMMARY: Unicellular eukaryotes (organisms with a nucleus), or protists, are an extremely diverse group of organisms and inhabit almost all environments. In the world’s oceans, they make up a large proportion of the overall diversity. Many heterotrophic protists feed on bacteria and, in this way, not only control bacterial abundance but also transport the bacterial-derived carbon to organisms at higher trophic levels in the food web. In recent years, many studies have focused on assessing the diversity of planktonic protists (organisms in the water column), but studies on seafloor dwelling (benthic) protists are much less frequent. So far, there are no extensive studies present that try to access the benthic protist communities in the Baltic Sea, one of Earth’s largest brackish water environments. Within our study, we try to make a first assessment of this diversity using the molecular technique of metabarcoding, which allows the simultaneous identification of many organisms from one sample via the barcoding of nucleic acids, such as DNA and RNA. To obtain an overview of how certain environmental factors such as salinity and water depth of the sediment may influence the community structure, we chose two regions of the southern Baltic. ABSTRACT: Heterotrophic protists are key components of marine ecosystems. They act as controllers of bacterial and microphytobenthos production and contribute significantly to the carbon flux to higher trophic levels. Still, metabarcoding studies on benthic protist communities are much less frequent than for planktonic organisms. Especially in the Baltic Sea, representing the largest brackish water environment on earth, so far, no extensive metabarcoding studies have been conducted to assess the diversity of benthic protists in this unique and diverse habitat. This study aims to give first insights into the diversity of benthic protist communities in two different regions of the Baltic Sea, Fehmarnbelt, and Oderbank. Using amplicon sequencing of the 18S rDNA V9 region of over 100 individual sediment samples, we were able to show significant differences in the community composition between the two regions and to give insights into the vertical distribution of protists within the sediment (0–20 cm). The results indicate that the differences in community composition in the different regions might be explained by several abiotic factors such as salinity and water depth, but are also influenced by methodological aspects such as differences between DNA and RNA results.