High molecular diversity of potentially harmful heterotrophic dinophytes in tropical shrimp aquaculture ponds reveals a new dinophyte Malayana penaeicida gen. et sp. nov. (Peridiniales, Dinophyceae)

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 frequent mass mortality outbreaks with unknown causes. Despite the significant impact, there is a notable lack of information on the occurrence and diversity of harmful dinophytes in this system. This study, therefore, aimed to assess the diversity of potentially harmful dinophytes in shrimp ponds by utilizing advanced microscopy and high-throughput short- and long-read amplicon sequencing for metabarcoding. The metabarcoding results of 18S rDNA V7-V9 region revealed diverse dinophyte communities in the shrimp ponds, with compositions differing among ponds over the shrimp rearing period. While a variety of core dinophytes was detected, considerably high prevalence of harmful heterotrophic dinophytes, including Pfiesteria piscicida, P. shumwayae, Luciella masanensis, and Gyrodinium jinhaense were observed. Notably, a relatively high cell abundance of a peridinialean dinophyte, with cell densities that reached 10⁶ cells L⁻¹, was observed. The cells exhibited distinct thecal morphologies, corroborated by the concatenated phylogenetic tree of 18S–ITS–28S rDNA obtained from long-read sequencing and the 18S and 28S sequences from single-cell isolation, which herein assigned to a new genus Malayana, as Malayana penaeicida gen. et sp. nov.