The southern Yellow Sea (SYS) shows extensive spatial variations in water masses, particularly YS Warm Current Water (YSWCW) and YS Coastal Current Water (YSCCW) in cold and YS Bottom Cold Water (YSBCW) and Changjiang Diluted Water (CDW) in warm seasons. These hydrographic processes result in significant spatial changes in nutrients, stratification, and turbidity, which may highly regulate phytoplankton distribution in the SYS. Here, we provide high spatial resolution datasets of phytoplankton in the SYS in all seasons during 2011–2012. Diatoms thrived in eutrophic CDW and YSCCW regions. Notably, benthic/meroplanktonic diatoms, including Paralia sulcata and Rhaphoneis spp., were dominant near the Changjiang Estuary and Subei Shoal. However, cryptophytes and haptophytes were dominant in oligotrophic offshore regions controlled by YSWCW and YSBCW. Phytoplankton abundance and chlorophyll a were considerably lower in the YSWCW and YSBCW than in other regions, and the community composition varied significantly among regions. Algal blooms were observed off the SYS coast in spring and near the Changjiang Estuary in summer, which were characterized by abundant nutrients, low turbidity, and a relatively stable water column. Canonical correspondence analysis demonstrated that stratification in cold and nutrients in warm seasons were most important variables correlated with phytoplankton community. Variation partitioning analysis confirmed that spatial changes in phytoplankton community composition were largely structured by nutrients rather than by physical factors in all seasons except winter. Our findings highlight the significance of water column stability and nutrients associated with water mass variation in shaping spatial changes of phytoplankton community in the SYS.
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