Spatial shifts in size structure, phylogenetic diversity, community composition and abundance of small eukaryotic plankton in a coastal upwelling area of the northern South China Sea

Abstract Summer upwelling off Hainan Island (northern South China Sea) is influenced by fresher coastal water masses. To assess the ecological effects of this complicated oceanography, a cruise was conducted in August 2016. We investigated the spatial patterns of phytoplankton size structure, diversity and quantity of small eukaryotes (0.2–20 μm) across the upwelling system. In the inner-shelf waters, nanophytoplankton contributed a higher proportion to phytoplankton biomass than microphytoplankton and picophytoplankton. High-throughput sequencing of 18S rRNA genes and community analysis indicated that the horizontal variation in community structure of small eukaryotes was larger than the vertical. The relative sequence proportions of dinoflagellates, diatoms, ciliates and Micromonas in the surface layer gradually decreased from the inner shelf to the slope, whereas the Rhizaria, Bathycoccus and Ostreococcus exhibited an opposite trend. The spatial patterns of taxon-specific rDNA copy numbers were similar to the patterns based on the relative proportions. Redundancy analysis revealed that turbidity, salinity and ${\mathrm{NO}}_3^{-}$ were the most important environmental variables in structuring the community of small eukaryotes. The cell abundance of photosynthetic picoeukaryotes was significantly correlated with the rDNA abundance of Mamiellophyceae and the cell abundance of nanoeukaryotes was significantly correlated with the rDNA abundance of dinoflagellates plus diatoms.