Phytoplankton community structure in a subtropical river revealed by <scp>DNA</scp> metabarcoding, with a focus on cell‐cyst coupling of <i>Unruhdinium</i> spp. (Dinophyceae)

The subtropical Jiulongjiang River serves as a crucial water supply, yet it has been plagued by frequent blooms of the dinoflagellate genus Unruhdinium. To investigate the diversity and spatiotemporal dynamics of Unruhdinium species, we conducted seasonal sampling in Xipi Reservoir and large-scale sampling across the Beixi Creek of Jiulongjiang River from 2020 to 2021. Our cyst germination experiments revealed the cyst-theca relationships of U. minimum and U. kevei, along with the identification of two undescribed species. Unruhdinium minimum resembles Peridiniopsis kulczynskii in terms of cell size and plate pattern and probably is a junior synonym. Utilizing DNA metabarcoding to target the large subunit ribosomal RNA gene (LSU rDNA D1-D2) in both water and sediment samples, we detected seven species of Unruhdinium, with U. minimum, U. kevei, and U. penardii var. robusta emerging as the most dominant. Notably, U. minimum exhibited a preference for warm waters, while U. penardii var. robusta thrived in colder conditions. In contrast, U. kevei was predominantly observed in the spring. The alleviation of eutrophication and elevated nitrogen/phosphorus ratios may account for the decline of Unruhdinium blooms in the Jiulongjiang River since 2011. Our results enhance the possibility of dinoflagellate dynamics in freshwater systems and inform future conservation efforts in the subtropical rivers.