Comparison of Illumina MiSeq and microscopy methodologies for the analysis of diatom communities in five estuaries along the southern coast of the Korean Peninsula

Abstract

The study of microalgal communities is critical for understanding aquatic ecosystems. These communities are primarily composed of diatoms (Bacillariophyta), and two methods are commonly used to study them: microscopy and Illumina MiSeq. These two methods are distinct, and their differences are reflected in the results they yield. Thus, their suitability for analyzing diatom communities is often debated and evaluated. In this study, these two methods were used to analyze the diatom communities in the same water samples, and the results obtained were compared. The taxonomy of the species constituting the diatom communities was confirmed, and both methods showed that the species belonging to the Bacillariales and Naviculales orders (class Bacillariophyceae) are diverse. However, at the lower taxonomic levels (family, genus, and species), microscopy tended to show a bias toward detecting diatom species belonging to the Bacillariaceae and Naviculaceae families. The results obtained from the two methods differed in terms of the identification of each diatom present in the communities and the analysis of their structural characteristics. These results are consistent with the fact that diatoms belonging to the Nitzschia and Navicula genera are abundant in the communities, furthermore, only the Illumina MiSeq showed the abundance of the Melosira, Entomonis, and Amphiprora genera. Although the results obtained from microscopy tended to be biased, they were superior to those of Illumina MiSeq regarding species-level identification. Based on the results obtained via microscopy and Illumina MiSeq, it was revealed that neither method is perfect and that each has clear strengths and weaknesses. Therefore, for the effective and accurate analysis of diatom communities, it is desirable to combine the two methods.