Shrimp aquaculture plays a pivotal role in global seafood production, particularly in Southeast Asia, where it significantly contributes to the economy and food security. The sustainability of this industry, however, is threatened by disease outbreaks, including those caused by harmful dinoflagellates. Despite their significant impact, there remains a significant gap in research regarding the occurrence and diversity of these species in tropical shrimp ponds. This study, therefore, aimed to assess and compare the diversity of dinoflagellates between high-production healthy shrimp ponds and infectious pond with shrimp mortality by applying high-throughput sequencing (HTS) using an 18S rDNA metabarcoding approach. Our results showed a diverse range of dinoflagellate communities, with notable differences in composition between the healthy and infectious ponds. Out of the total ASVs detected, 110 (~11%) were linked to dinoflagellates, comprising 13 species from the Dinophyceae, two species from the Syndiniales, and one species from the Noctilucophyceae. In the healthy ponds, a variety of core dinoflagellates was detected, including Islandinium tricingulatum and Polykrikos schwartzii. However, in the infectious ponds, we detected a higher prevalence of harmful heterotrophic dinoflagellates, particularly Pfiesteria spp., Luciella spp., and Gyrodinium spp., which have been previously reported to cause farm organism infections and mortality. The detection of these species was linked to elevated shrimp mortality in the infectious pond, emphasizing their harmful effects on shrimp aquaculture. While harmful dinoflagellates such as Gonyaulax spinifera, Tripos furca, Margalefidinium fulvescens, and Noctiluca scintillans were identified, their precise impacts on the shrimp ponds remain to be further explored. This study demonstrated the effectiveness of molecular application in the early detection of these harmful species that often be missed by light microscopy. Our findings also highlight the crucial need for more comprehensive studies into this group of harmful dinoflagellates and their effects on aquaculture animals.
 

animal health, dinoflagellate, harmful algal bloom, heterotrophic, metabarcoding, parasitic