Manning et al. BMC Ecol Evo (2021) 21:27 BMC Ecology and Evolution https://doi.org/10.1186/s12862-021-01745-5 RESEARCH ARTICLE Open Access Diversity of dinofagellate assemblages in coastal temperate and ofshore tropical waters of Australia Tahnee Manning1* , Arjun Venkatesh Thilagaraj1, Dmitri Mouradov2 , Richard Piola3 , Clare Grandison3 , Matthew Gordon3 , Jef Shimeta1 and Aidyn Mouradov1 Abstract Background: Dinofagellates are a ubiquitous and ecologically important component of marine phytoplankton communities, with particularly notable species including those associated with harmful algal blooms (HABs) and those that bioluminesce. High-throughput sequencing ofers a novel approach compared to traditional microscopy for determining species assemblages and distributions of dinofagellates, which are poorly known especially in Aus- tralian waters. Results: We assessed the composition of dinofagellate assemblages in two Australian locations: coastal temper- ate Port Phillip Bay and ofshore tropical waters of Davies Reef (Great Barrier Reef). These locations difer in certain environmental parameters refecting latitude as well as possible anthropogenic infuences. Molecular taxonomic assessment revealed more species than traditional microscopy, and it showed statistically signifcant diferences in dinofagellate assemblages between locations. Bioluminescent species and known associates of HABs were present at both sites. Dinofagellates in both areas were mainly represented by the order Gymnodiniales (66%—82% of total sequence reads). In the warm waters of Davies Reef, Gymnodiniales were equally represented by the two superclades, Gymnodiniales sensu stricto (33%) and Gyrodinium (34%). In contrast, in cooler waters of Port Phillip Bay, Gymnod- iniales was mainly represented by Gyrodinium (82%). In both locations, bioluminescent dinofagellates represented up to 0.24% of the total sequence reads, with Protoperidinium the most abundant genus. HAB-related species, mainly represented by Gyrodinium, were more abundant in Port Phillip Bay (up to 47%) than at Davies Reef (28%), potentially refecting anthropogenic infuence from highly populated and industrial areas surrounding the bay. The entire assem- blage of dinofagellates, as well as the subsets of HAB and bioluminescent species, were strongly correlated with water quality parameters (R2 0.56–0.92). Signifcant predictors difered between the subsets: HAB assemblages were explained by salinity, temperature,= dissolved oxygen, and total dissolved solids; whereas, bioluminescent assemblages were explained only by salinity and dissolved oxygen, and had greater variability. Conclusion: High-throughput sequencing and genotyping revealed greater diversity of dinofagellate assemblages than previously known in both subtropical and temperate Australian waters. Signifcant correlations of assemblage structure with environmental variables suggest the potential for explaining the distribution and composition of both HAB species and bioluminescent species. Keywords: Bioluminescence, Dinofagellates, eDNA, Genotyping, Harmful algal bloom, High throughput sequencing *Correspondence: [email protected] 1 School of Science, RMIT University, Melbourne, VIC, Australia Full list of author information is available at the end of the article © The Author(s) 2021. 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The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/publi cdoma in/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Manning et al. BMC Ecol Evo (2021) 21:27 Page 2 of 14 Background about the importance of bioluminescence as a defence Dinofagellates are single-celled protists ubiquitously mechanism against predators. Changes in intensity of found in freshwater and marine environments where bioluminescence can be used as a sensitive indicator they occupy many ecological niches. Tey play signif- for the distribution of planktonic biomass in response cant roles from primary producers through to detritus to physical and chemical changes in surface waters [9], feeders. Dinofagellates belong to the class Dinophyceae, and may ofer the possibility of predicting HAB events which consists of 117 genera including about 4000 free- in known bloom forming localities [10]. living species, plus 500 species with parasitic or mutual- In recent years, omics technologies, such as genom- ist symbiotic lifestyles representing essential symbionts ics, transcriptomics, proteomics, and metabolomics, of reef-building corals [1]. Living under diverse environ- have been extensively applied to study marine dinofag- mental conditions, dinofagellates have developed high ellates, uncovering essential molecular pathways, such as complexity in behaviour, nutritional modes (photoauto- in toxin biosynthesis, symbiosis, lipid biosynthesis, and trophic, heterotrophic, and mixotrophic) and broad mor- HAB formations [11, 12]. Application of molecular tech- phological diversity, ranging from 5 µm to 2 mm. niques to the taxonomy of dinofagellates such as high- Dinofagellate species are known to be a major compo- throughput sequencing (HTS) genotyping has led not nent of harmful algal blooms (HABs) with a set of physi- only to advanced methods for identifcation of these spe- cal and chemical efects causing a signifcant hazard to cies but also provides a new tool for understanding their ecosystems, fsheries, and animal and human health [2]. evolutionary complexity and diversity as well as their Physical efects can lead to depletion of oxygen in the roles in marine ecological networks [13–18]. water and an increase in viscosity due to the excretion of Regions targeted for assessment of dinofagellate diver- mucilage. Chemical consequences include the secretion sity include lcf [19], the nuclear ribosomal internal tran- of toxins, that can trigger cell necrosis, afect cell wall scribed spacer region (ITS2) [15, 17, 20], cytochrome c penetrability, and suppress the digestive system of other oxidase 1 (COI) [21], heat shock protein (HSP90) [22], marine organisms as well as potentially humans via either 28S rRNA and 18S rRNA [13, 23–30]. 18S rRNA and 28S direct exposure or consumption, for example, afected rRNA have proven highly popular for assessing the diver- shellfsh [3]. HABs are naturally occurring global phe- sity of many marine microorganisms [13, 24–26, 28–31]. nomena but can be triggered by anthropogenic activities, Recently, the DinoREF dinofagellate database, has been including shipping, eutrophication, and global warming. developed based on V4 regions of 18S rRNA sequences Tere are HAB forming species that also exhibit bio- [32]. Originally, this database was used to assess the luminescence such as Noctiluca scintillans, although diversity and seasonal changes of dinofagellates in the not all bioluminescent dinofagellates are considered Gulf of Naples [27]. HABs. Sixty-eight dinofagellate species have evolved Te east Australian coastline ranges from the tropi- bioluminescence, the function of which is still not cal waters of the Great Barrier Reef and Coral Sea to the entirely clear [4]. Bioluminescence is a result of the temperate waters of the Tasman Sea, with water move- biochemical process of interaction between a lucif- ment driven north to south via the East Australian Cur- erase protein and its substrate, a luciferin, in the pres- rent. Because of climate change, many marine species ence of a luciferin-binding protein [5]. One of the most are shifting to higher latitudes [12, 33]. Tis has led to widely accepted hypotheses proposes that lumines- changes in the diversity of marine populations in these cence increases the survival of dinofagellates, acting locations, and has triggered extensive study linking as a ‘‘burglar alarm’’ [6]. Te role of bioluminescence changes in planktonic communities to changes in physi- as a defence against zooplankton grazers was shown by cal, biological and chemical oceanographic conditions [3, increased bioluminescence of Lingulodinium polyedra 13–17, 34–37]. in response to amides produced by their copepod graz- Davies Reef (DR) is part of the Great Barrier Reef system ers [7]. As a result of bioluminescence, dinofagellates within the sub-tropic zone in the Coral Sea, approximately can successfully persist within marine phytoplankton 70 km from shore [38, 39] (Fig. 1). In contrast, Port Phillip communities dominated by the similarly sized competi- Bay (PPB) is located 2000 km south within the temperate tors, diatoms and green algae. However, the existence zone, bordered by Melbourne, the capital city of Victoria, of non-bioluminescent N. scintillans blooms in the that accommodates 4.96 million people (Fig.