Kareniaceae in focus: A molecular survey of harmful algal dinoflagellates in the South China Sea.

In recent years, species of the family Kareniaceae have been forming algal blooms worldwide, leading to significant fish mortality. The biodiversity of this group of dinoflagellates has been underestimated, primarily due to their highly similar morphologies. In this study, using high-throughput sequencing (HTS) targeted the large subunit ribosomal DNA (LSU rDNA) of dinoflagellates, 21 Kareniaceae species were identified from the South China Sea (SCS), including nine species newly recorded in Chinese coastal waters. Additionally, species-specific real-time fluorescent quantitative PCR (qPCR) assays targeting the internal transcribed spacer (ITS) for three Karenia species (Karenia longicanalis, K. papilionacea, and K. selliformis) isolated from the SCS were established. Karenia longicanalis and K. papilionacea were identified as the most prevalent Karenia species in summer in the Zhujiang Estuary via qPCR. Further qPCR analysis during a Karenia spp. bloom in the Beibu Gulf on August 3, 2023, revealed K. selliformis as the most abundant species, followed by K. longicanalis, K. mikimotoi, and K. papilionacea. Both HTS and qPCR methods successfully detected the targeted Karenia species in field samples; however, qPCR assays identified them at more stations than HTS. The integration of qPCR assays with HTS provides a comprehensive and precise assessment of the diversity of Kareniaceae species and harmful dinoflagellates. This multi-method approach enhances our understanding and management of harmful algal blooms, thereby contributing to the improved protection of marine ecosystems.