Harmful algal blooms in the benthic system (BHAB) are a major environmental problem that has increased worldwide in the context of global climate change. While systematic cell-based BHAB monitoring for risk assessment and early warning systems have been recommended, implementation of a standardized sampling method is challenging owing to the benthic nature of these harmful microalgal taxa. This study investigated the molecular diversity of benthic harmful dinoflagellates in tropical reefs of Perhentian Islands, Malaysia, using artificial substrate (AS) and sampling natural substrates (NS), combined with environmental DNA (eDNA) analysis and high-throughput amplicon sequencing targeting the small subunit (SSU) and large subunit (LSU) rDNA markers. Our results revealed that the AS method effectively captured a representative subset of the benthic dinoflagellate community, with significant taxonomic overlap between AS and NS. Both markers enabled high-resolution detection of BHAB taxa, particularly of Gambierdiscus and Ostreopsis, which are challenging to identify by light microscopy. The LSU rDNA marker provided finer taxonomic resolution, capturing a broader range of dinoflagellate species. The molecular approach consistently aligned with cell quantification data, supporting AS and DNA metabarcoding as robust methods for BHAB monitoring. The findings highlight the potential of these methods for early detection, especially areas susceptible for ciguatera and BHAB-related poisoning, offering a systematic approach for routine cell-based monitoring.
The dinoflagellate Tripos furca, known for its frequent and massive blooms in coastal waters, has been associated with significant fish mortality in aquaculture areas. In mid-May 2022, a notable bloom event, characterized by intense red discoloration, was observed along the Penang Strait in the northern Malacca Strait. Our field survey identified a high-density bloom of T. furca. To investigate the mechanisms driving the bloom dynamics of this species, monthly sampling was undertaken until the bloom subsided, covering 19 stations across the Penang Strait. Our results showed that the abundances of T. furca changed over time and space, a bloom peak of 8.2 × 105 cells l-1 was observed in late June, triggered by elevated sea surface temperatures and phosphate availability, while nitrogen was consistently abundant. The bloom's persistence was associated with the influence of the 2020-2022 La Niña and Indian Ocean Dipole, which caused warmer sea temperatures. Metabarcoding of the V7-V9 18S rDNA region revealed high intraspecific genetic diversity within the T. furca bloom subpopulations, suggesting both clonal reproduction and possible sexual processes. The bloom termination was linked to a seasonal shift in temperatures and changes in nutrient regimes that caused a transition of phytoplankton compositions to Noctiluca- and diatom-dominated populations contributed to the bloom's decline. Early detection of the bloom has successfully prevented severe losses to the aquaculture farms in the area, emphasizing the importance of early intervention. This study also enhances our understanding of T. furca bloom dynamics and provides insights into managing harmful algal blooms in tropical coastal regions.