Unraveling the roles of shallow coastal habitats and salinity in shaping aquatic microeukaryotic communities using experimental and field approaches

Abstract Microeukaryotic communities in brackish coastal ecosystems are structured by complex interactions between environmental conditions and habitat heterogeneity. This study examines how moderate salinity levels (ranging from freshwater to salinity 6) and habitat type (water column, sediment, and biofilm) influence microeukaryotic diversity and community composition in shallow coastal waters of the Gulf of Finland, the Baltic Sea. Combining field surveys with controlled short-term aquarium experiments, we analyzed taxonomic responses using 18S rRNA gene amplicon sequencing. Alpha diversity differed significantly across habitats but showed only minor shifts across shallow coastal salinity gradients, with the water column showing the highest richness, followed by biofilm and sediment. However, no substantial shift in alpha diversity was observed across the natural salinity gradient. In contrast, short-term exposure to increased salinity significantly reduced alpha diversity in the water column, while sediment communities remained more stable, likely due to their buffering capacity and microhabitat complexity. Redundancy analysis revealed that habitat type had a stronger effect on beta diversity than salinity, explaining 15% of the variation in natural samples. In experimental aquaria, incubation time exerted the greatest influence. This highlights the strong influence of ecological succession, trophic interactions, and stochastic processes in controlled environments. Several less-documented taxa, such as Gregarinomorphea, Perkinsida, Filosa−Imbricatea, and Filosa−Thecofilosea, were abundant in both natural and experimental samples, highlighting underexplored diversity in Baltic Sea microeukaryotes. These results suggest that stochastic processes, habitat-specific factors, and temporal dynamics dominate over moderate salinity effects in shaping shallow coastal microeukaryotic communities.