Phytoplankton are essential indicators of aquatic ecosystem health. Traditional phytoplankton detection methods using microscopy struggle to identify species with small particle sizes or unclear morphological characteristics. In contrast, molecular methods have high accuracy but struggle to simultaneously detect prokaryotic and eukaryotic organisms due to primer specificity. As algal blooms can be caused by both prokaryotes and eukaryotes, methods that can detect both are required. This study used both microscopic detection and high-throughput sequencing methods to analyze phytoplankton in seagoing waters in eastern coastal China. Two high-throughput sequencing primers targeting 16S rDNA for prokaryotes and 18S rDNA for eukaryotes were used, and the results were compared with those of microscopic analysis. Microscopy identified 230 phytoplankton species across 73 genera, mainly belonging to Bacillariophyta, Chlorophyta, Euglenophyta, Cyanophyta, Dinophyta, and Chrysophyta. Twenty-four species across 16 sampling stations exceeded 1 million cells/L. High-throughput sequencing yielded 8642 prokaryotic and 7375 eukaryotic operational taxonomic units, with 432 identified as phytoplankton. Chlorophyta and Bacillariophyta had the highest species richness, accounting for 34% and 17%, respectively. High-throughput sequencing detected more species than microscopic detection but relied on gene reference databases and provided only the relative abundance of species based on operational taxonomic unit counts.

Phytoplankton are an important part of aquatic ecosystems and substantially contribute to primary productivity. Under certain conditions, phytoplankton can grow or cluster in large numbers, resulting in enormous economic losses and serious threats to human life and health. In this study, complex causative species of algal blooms were examined and regulatory factors were determined in a reservoir formed by harbor construction. The reservoir is isolated from the harbor by sluice gates, forming a separate water region. Twelve species of phytoplankton, including normally and abnormally blooming species, were identified to be causing blooms in this continuous water. Different from the areas where simple algae caused blooms, multiple bloom-causative species, which were completely different, occurred at several stations. In this study area, whereas the abundance of algal cells was above 10 million cells/L, the total phosphorus concentration was higher than 0.2 mg/L. When the total phosphorus concentration was lower than 0.2 mg/L, there was no algal bloom. In waters with total algal cell abundance over 10 million, the N/P ratios were all <8. This study indicates that the occurrence of algal blooms in this water was influenced by the concentrations of total nitrogen and phosphorus, and total phosphorus plays a more important role.