| Abstract: | The explosive multiplication of phytoplankton caused by water eutrophication often occur in the intensive shrimp aquaculture. To comprehensively assess the diversity and community structure of phytoplankton in the waters of typical indoor industrial aquaculture system for Litopenaeus vannamei, a combination of high‐throughput sequencing and morphological identification methods were used in the present study. A total of 41 genera belong to nine phyla were detected by both methods. Chlorophyta, Cyanophyta and Bacillariophyta were found to be three dominant phyla. The high‐throughput sequencing revealed that green algae and cyanobacteria were the most dominant phytoplankton; however, diatoms were the first dominant phytoplankton by using the morphological identification. At the genus level, Picochlorum and Synechococcus were dominant, accounting for 20.94%–97.19% and 0.01%–52.81% of total phytoplankton, revealed by the high‐throughput sequencing. Therefore, more attention should be paid to their ecological impacts on the surrounding sea areas or potential toxicity to shrimp. Cyclotella was the most dominant genus revealed by the morphological identification. High‐throughput sequencing revealed a high diversity and small‐sized phytoplankton which were undetected by microscopy. Both methods provide similar information on the environmental drivers of phytoplankton community. NO3?, NH4+, DIP, DSi, DON and DOP concentrations were the main factors influencing the phytoplankton community structure and diversity. |
