The Pacific Ocean region remains one of the least explored eukaryotic microbial frontiers on Earth. Among its eukaryotic microbial inhabitants, toxicogenic dinoflagellates pose a significant but poorly characterised risk to small island human populations that rely heavily on marine food webs via subsistence fishing, as their toxins can bioaccumulate through food webs. Yet, the distribution, habitat associations, and community contexts of these organisms remain largely unknown across vast regions of the Pacific.
Here, we apply a custom designed high-throughput metabarcoding assay to investigate the epiphytic and benthic community composition of dinoflagellates across four small islands, including coral atolls in under-studied Pacific regions comprising the Coral and Arafura Seas (Australia) and Mangaia, Mitiaro, Penrhyn and Atiu islands of the Cook Islands. These regions are all characterised by documented cases of human Ciguatera Poisoning, a type of marine seafood-associated illness caused by epiphytic dinoflagellates of the genus Gambierdiscus.
Our results reveal pronounced regional differences in microbial community structure, highlighting strong habitat specificity and ecological context dependency of toxicogenic dinoflagellates. These findings underscore the limitations of generalized monitoring approaches and demonstrate the need for region-specific, ecology-informed molecular surveillance strategies. By integrating metabarcoding with microbial habitat analysis, this work contributes to a broader understanding of marine microbial diversity, interaction networks, and applied monitoring frameworks in remote marine ecosystems.