Water-mass structuring and vertical segregation of protist communities in the Korea Strait during late spring

The Korea Strait is a dynamic boundary system where Kuroshio-derived offshore waters interact with land-derived coastal inputs, generating pronounced environmental gradients during spring. Here, we investigated the spatial, vertical, and interannual structuring of protist communities during the late spring periods of 2024 and 2025 by integrating hydrographic, 18S rRNA gene amplicon sequencing, and microscopy-based morphological analyses. Compared to coastal waters, offshore waters were characterized by higher temperatures and salinities but exhibited lower nutrient concentrations. Coastal waters supported elevated phytoplankton biomass and were enriched with nutrient-responsive taxa, while taxonomic richness was consistently greater in offshore waters, particularly in the surface and Deep Chlorophyll Maximum (DCM) layers, where oligotrophic specialists, such as pelagophytes and marine stramenopiles (MASTs) lineages, prevailed. Strong vertical segregation further differentiated water-column assemblages from sediment assemblages, which were taxonomically richer and dominated by resident benthic rhizarians, parasitic Syndiniales, and cyst-forming dinoflagellates that function as seed reservoirs for future pelagic diversity. Interannual phosphate limitation in 2025 modulated taxonomic composition by slightly increasing the relative abundances of small-sized taxa, such as cryptophytes and picochlorophytes, yet coastal-offshore water-mass-influenced dynamics remained the primary driver of spatial structure. Collectively, our findings demonstrate that during the late spring transition, the Korea Strait is a functionally heterogeneous boundary system in which physical forcing, stratification, and benthic-pelagic linkages jointly regulate protist community organization, underscoring the importance of integrating molecular and morphological approaches in resolving microbial ecosystem dynamics.