| Summary: | Eukaryotic plankton are important parts of the marine biome and play an important role in maintaining the stability of marine ecosystems. In order to characterize the eukaryotic plankton communities in the South Yellow Sea Cold Water Mass (CWM) and the South Yellow Sea nearshore waters (NW) in October 2019, Illumina high–throughput sequencing was performed using the 18S rDNA V9 region as the target gene. Environmental factors (depth, pH, salinity, temperature, Chl <i>a</i>, nitrate, nitrite, ammonium, silicate, phosphate) in two sea areas were measured, and their correlations with abundance and diversity of eukaryotic plankton were analyzed. A total of 807 species of plankton were identified, of which 663 species in 24 categories were from the CWM area, and 614 species in 26 categories were from NW. The total phytoplankton abundance in CWM waters was higher than that in NW. Dinophyta and Bacillariophyta were the most abundant phyla of phytoplankton in the two areas. Arthropoda and Cnidaria were the major zooplankton taxa. The dominant fungal population was mainly Basidiomycota. Both the CWM and NW have effects on dissolved inorganic nutrient concentrations and plankton abundance. Environmental factor correlation analysis showed that the concentration of dissolved inorganic nutrients within the CWM increased with water depth and the abundance of plankton gradually increased. Ammonium salts, nitrates, phosphates, silicates and water depth were important factors affecting phytoplankton growth. Phytoplankton abundance increased with increasing concentrations of inorganic nutrients. Bacillariophyta showed a strong positive correlation with silicates and depth. Depth and microscopic phytoplankton abundance were important factors influencing the structure of the zooplankton community.
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