Study on the Diversity of Eukaryotic Phytoplankton in the Qingyuan Segment of the Beijiang River Based on DNA Metabarcoding with Different Primers
A comprehensive understanding of the phytoplankton diversity in the Qingyuan segment is a fundamental step in establishing a baseline for the aquatic ecological assessment of the Beijiang River Basin. The present study used a combination of morphological methods and two universal 18S rDNA primers to investigate the eukaryotic phytoplankton diversity at ten sampling sites in the Qingyuan segment of the Beijiang River Basin during the summer of 2025. A total of 259 eukaryotic phytoplankton species were detected in the 3NDF-euk-4v amplicons, while 268 species were detected in the 528F-706R amplicons. The two amplicons co-detected 165 species that were not identified by the morphological method. The results of Non-metric Multidimensional Scaling (NMDS) and Analysis of Similarities (ANOSIM) from the two universal primers and the morphological method both indicated that there were significant differences in the community structure of eukaryotic phytoplankton among the upper, middle and lower reaches of the Qingyuan segment of the Beijiang River Basin. The Mantel test comparing community matrices from the three methods indicated that the similarity between the 3NDF-euk-4v amplicons and the morphological results (r = 0.34, p < 0.01) was significantly higher than that between the 528F-706R amplicons and the morphological results (r = 0.31, p < 0.05). The relative abundances of Cryptophyta and Dinophyta obtained from the two amplicons were significantly higher than those from the morphological method (p < 0.01), whereas the relative abundance of Bacillariophyta was significantly lower (p < 0.05). Both primers successfully amplified most eukaryotic phytoplankton groups in the Qingyuan segment of the Beijiang River. Furthermore, the 3NDF-euk-4v primer exhibited greater discrimination and broader species coverage, and its resulting community structure was more similar to that obtained by the morphological method. Therefore, it is considered a more suitable universal primer for monitoring freshwater eukaryotic phytoplankton based on the 18S rDNA V4 region. The application of DNA metabarcoding for routine phytoplankton monitoring can be facilitated by standardizing operational procedures, combining multiple primers, and improving the DNA databases of native species.