The neurotoxin domoic acids (DAs), primarily produced by the toxic pennate diatom genus Pseudo-nitzschia, is the causative agent of the Amnesic shellfish Poisoning (ASP). Although the (sub)tropical coastal waters of the South China Sea (SCS) provide optimal conditions for the growth and proliferation of these diatoms, the contamination status of DA toxins have often been overlooked, with only low levels in detected in the coastal waters of China. However, harmful algal blooms dominated by Pseudo-nitzschia have been repeatedly recorded in the SCS. To specifically address the presence of DA-toxins and potential toxigenic algal species in high risk areas of DA contamination in China, a comprehensive investigation was conducted in the subtropical Pearl River Estuary (PRE) waters of the SCS across four representative seasons from 2020 to 2021. This study yielded several significant findings, revealing phenomena that, although previously undiscovered, have indeed existed in the coastal waters of China. Results from high-performance liquid chromatography with tandem mass spectrometry (HPLC-MS/MS) indicated that DA components were widespread in the phytoplankton, zooplankton, shellfish, snails and crustaceans sampled from the field environment, with no DA components detected in sediments. A high abundance of Pseudo-nitzschia species and DA levels in the marine organisms were observed, showing a highly consistent spatial and temporal distribution. The summer showed maxima of DAs, containing known toxic species and a broader range of Pseudo-nitzschia genotypes, while other seasons showed minimal DA levels but still included known Pseudo-nitzschia genotypes. High-throughput sequencing of 18S–5.8S rDNA internal transcribed spacer region 1 (ITS1) further revealed the biodiversity of Pseudo-nitzschia species in the PRE area. This research not only differentiated DA components among various biological vectors but also provided a detailed understanding of DA dynamics and the seasonal multi-species assemblages of causative Pseudo-nitzschia taxa identified through taxonomically enhanced high-throughput rDNA sequencing and morphological identification. Furthermore, environmental factors were analyzed to elucidate DA dynamics and the seasonal fluctuations of Pseudo-nitzschia assemblages in the SCS area. These assemblages were found to be driven by seasonal temperature changes, and the presence of DA positively correlated with the abundance of Pseudo-nitzschia.

domoic acids, pseudo-nitzschia species, high-throughput sequencing, phytoplankton, diagnostic pigments, Pearl River Estuary