Comparing morphotypes and phylospecies concepts in assessing coccolithophore diversity across a mesoscale meander system

Utilizing genetic methods to investigate marine microeukaryote assemblages in their natural habitat has uncovered unexpected diversity across various taxonomic levels. Nonetheless, there has been limited comparison between the phylogenetic species concept and the traditional morphological taxonomy, which remains the cornerstone of contemporary ecological, physiological, and paleontological microeukaryote research. This is particularly the case within the coccolithophores (Haptophyta), which are characterized by their intricate morphology. However, many questions remain unanswered regarding inter- and intra-specific variability as well as cryptic speciation, which can only be elucidated using molecular tools. In this context, we examined coccolithophore populations using these two taxonomic approaches across a mesoscale meander system in the southern Indian Ocean. High-throughput sequencing using metabarcoding of the 18S V4 gene region, improved for haptophytes, revealed 86 amplicon sequence variants (ASVs) across nine families of coccolithophores, which was a substantial improvement over the coccolithophore resolution identified with broad eukaryote 18S V9 genetic markers. With scanning electron microscopy (SEM) we characterized 112 coccolithophore morphotypes, 71 of which were heterococcolithophores. Broad scale trends in community diversity and structure were revealed by both 18S and SEM analysis. Metabarcoding lacked high-level taxonomic resolution for many clades, particularly in the Syracosphaerales, however was able to reveal potential cryptic speciation/genetic variability for other clades, for example within the Helicosphaeraceae and Calcidiscaceae. We conclude that while improvements in reference libraries and genetic markers have made metabarcoding a reasonable substitute for labour-intensive SEM analysis, caveats remain, in that it does not allow for the characterization of life cycle dynamics and high-level taxonomic resolution remains limited.