Unveiling microalgal diversity in Slovenian transitional waters (Adriatic Sea)

This study presents the first comprehensive assessment of microalgal diversity in two Slovenian transitional waters (TWs): the shallow brackish lagoon of the Škocjanski Zatok Nature Reserve (SZNR) and the Rižana River estuary within the Port of Koper (PK) area. Between 2018 and 2021, water samples collected with a phytoplankton net were analyzed using light and scanning electron microscopy. In total, 240 species from 117 genera were identified in TW, dominated by diatoms and dinoflagellates, surpassing the diversity at a marine coastal station (91 species, 59 genera). Species richness was higher in PK (226) than in SZNR (154), mainly due to dinoflagellates and coccolithophores. Marine taxa predominated along the salinity gradient, with moderate contributions from brackish taxa and fewfreshwater forms, reflecting both natural and anthropogenic influences. Planktonic taxa dominated at all sites, while benthic forms were abundant in the lagoon, particularly in spring. Thirty-two taxa were recorded for the first time in Slovenian TW, mostly benthic or tychopelagic diatoms. The detection of Coolia monotis and five cyanobacterial genera with potentially harmful traits highlights the role of TW as an ecological interface. The taxonomic sufficiency analysis showed that the order level is sufficient to distinguish transitional from marine assemblages, beyond which ecological information is lost. Overall, this study highlights the importance of detailed taxonomic resolution for detecting microalgal diversity, including harmful and non-indigenous species to ensure robust ecological assessments under the WFD and MSFD directives.