Vertical distribution of heterotrophic nanoflagellates in the Baltic Proper

Heterotrophic nanoflagellates (HNF) are key players in marine microbial food webs, but their distribution remains poorly understood. We investigated abundance patterns of eleven HNF lineages in the Baltic Proper from May to September 2021 using Catalysed Reporter Deposition-Fluorescence In Situ Hybridisation (CARD-FISH). HNF were most abundant in surface waters, where they reached above 12,000 cells ml−1 in May. Median cell size varied between 3.3–4.1 μm. Cry1 cryptophytes, Marine Stramenopiles from MAST-2 lineage, and Kathablepharidacea dominated the HNF community in surface and suboxic/sulphidic waters below the halocline. Our results make an important contribution to the understanding of HNF ecology in the Baltic Sea.