Characteristics of benthic toxic dinoflagellate communities within three coastal regions of the Great Barrier Reef, Australia

Benthic dinoflagellates are fundamental to marine ecosystems, contributing to marine food webs, species interactions, and community diversity. They are also known to produce a range of biotoxins that are harmful to humans and wildlife. This study provides one of the most comprehensive regional surveys of benthic dinoflagellates across Australia's Queensland coast, characterising their diversity, distribution, and ecological associations in three contrasting regions: Townsville, Gladstone, and Hervey Bay. Using high-throughput sequencing of the 18S rRNA gene (V8–V9 region), 44 toxic or potentially toxic taxa were detected, spanning both epiphytic and planktonic genera, including Gambierdiscus , Amphidinium , Ostreopsis , Coolia , Prorocentrum , Karenia , and Alexandrium . Benthic toxic dinoflagellate (BTD) assemblages showed strong spatial structuring driven by region, habitat type, and macroalgal host identity. Several taxa exhibited pronounced host specificity, for instance, Ostreopsis siamensis and Coolia tropicalis were associated exclusively with Sargassum , while Amphidinium klebsii occurred only on Lobophora . Riverine influence and benthic habitat type further shaped community composition, with some toxigenic taxa confined to estuarine environments. Co-occurrence analyses revealed both positive and negative associations among taxa, suggesting that interspecies interactions, alongside environmental filtering, contribute to local community dynamics. These findings underscore the ecological complexity of BTD assemblages and highlight the importance of integrating molecular tools with habitat-based monitoring to assess spatial risk and support early-warning systems for harmful algal bloom (HAB) events in tropical and subtropical marine ecosystems. • DNA metabarcoding reveals high benthic dinoflagellate diversity across Queensland's coast. • Region, habitat and macroalgal host influence dinoflagellate spatial assemblages. • Interspecies interactions, alongside environmental filtering, contribute to local community dynamics. • Findings inform targeted monitoring and risk assessment for harmful algal blooms.