eDNA metabarcoding reveals biodiversity and depth stratification patterns of dinoflagellate assemblages within the epipelagic zone of the western Coral Sea

Abstract

Background Dinoflagellates play critical roles in the functioning of marine ecosystems but also may pose a hazard to human and ecosystem health by causing harmful algal blooms (HABs). The Coral Sea is a biodiversity hotspot, but its dinoflagellate assemblages in pelagic waters have not been studied by modern sequencing methods. We used metabarcoding of the 18 S rRNA V4 amplicon to assess the diversity and structure of dinoflagellate assemblages throughout the water column to a depth of 150 m at three stations in the Western Coral Sea. Additionally, at one station we compared metabarcoding with morphological methods to optimise identification and detection of dinoflagellates. Results Stratification of dinoflagellate assemblages was evident in depth-specific relative abundances of taxonomic groups; the greatest difference was between the 5–30 m assemblages and the 130–150 m assemblages. The relative abundance of Dinophyceae (photosynthetic and heterotrophic) decreased with increasing depth, whereas that of Syndiniales (parasitic) increased with increasing depth. The composition of major taxonomic groups was similar among stations. Taxonomic richness and diversity of amplicon sequence variants (ASVs) were similar among depths and stations; however, the abundance of dominant taxa was highest within 0–30 m, and the abundance of rare taxa was highest within 130–150 m, indicating adaptations to specific depth strata. The number of unclassified ASVs at the family and species levels was very high, particularly for Syndinian representatives. Conclusions Dinoflagellate assemblages in open water of the Coral Sea are highly diverse and taxonomically stratified by depth; patterns of relative abundance along the depth gradient reflect environmental factors and ecological processes. Metabarcoding detects more species richness than does traditional microscopical methods of sample analysis, yet the methods are complementary, with morphological analysis revealing additional richness. The large number of unclassified dinoflagellate-ASVs indicates a need for improved taxonomic reference databases and suggests presence of dinoflagellate-crypto and–morphospecies.

Diversity and biogeography of dinoflagellates in the Kuroshio region revealed by 18S rRNA metabarcoding

“…The vertical separation among surface and subsurface communities also appeared on the profiles of Shannon and Pielous's indices, proven by the Turkey Test (Supplementary Table 3). Similar vertical stratification of dinoflagellate and protist assemblages was observed in other ecosystems (Schnetzer et al, 2011;Cohen et al, 2021;Ollison et al, 2021;Carve et al, 2024). Carve et al (2024) also mentioned that the wind-induced vertical mixing could lead to highly similar assemblages in the mixed surface layer.…”

“…Similar vertical stratification of dinoflagellate and protist assemblages was observed in other ecosystems (Schnetzer et al, 2011;Cohen et al, 2021;Ollison et al, 2021;Carve et al, 2024). Carve et al (2024) also mentioned that the wind-induced vertical mixing could lead to highly similar assemblages in the mixed surface layer. Irradiance could be another factor because, at 100 m of KC stations, it was being approximately 1% relative to surface, suggesting possible existence of autotrophy at this depth.…”