Abstract
The procedures and methodologies employed to study microbial eukaryotic plankton have been thoroughly discussed. Two main schools exist—one insisting on classic microscopy methodologies and the other supporting modern high-throughput sequencing (DNA metabarcoding). However, few studies have attempted to combine both these approaches; most studies implement one method while ignoring the other. This work aims to contribute to this discussion and examine the advantages and disadvantages of each methodology by comparing marine plankton community results from microscopy and DNA metabarcoding. The results obtained by the two methodologies do not vary significantly for Bacillariophyta, although they do for Dinoflagellata and Ciliophora. The lower the taxonomic level, the higher the inconsistency between the two methodologies for all the studied groups. Considering the different characteristics of microscopy-based identification and DNA metabarcoding, this work underlines that each method should be chosen depending on the aims of the study. DNA metabarcoding provides a better estimate of the taxonomic richness of an ecosystem while microscopy provides more accurate quantitative results regarding abundance and biomass. In any case, the combined use of the two methods, if properly standardized, can provide much more reliable and accurate results for the study of marine microbial eukaryotes.
Highlights
The use of molecular ecology methodologies for the study of plankton is standard and considerable progress has occurred as a result of their use [1]
Studying planktonic eukaryotes using molecular ecology techniques has triggered a debate on the advantages and disadvantages of modern methods compared with classical methods and on the combination of such methodologies
The inclusion of the interaction in the model was significant based on a chi-square test at the 1% significance level (p < 0.001). This means that the methodology significantly explained the variance in a different way for each phylum; this was obvious when examining the relative abundance estimates from metabarcoding and the relative biomass from microscopy for each phylum (Figure 1, Dataset S1)
Summary
Published: 23 April 2021The use of molecular ecology methodologies for the study of plankton is standard and considerable progress has occurred as a result of their use [1]. The study of prokaryotic plankton using molecular methods has provided information that would have been impossible to obtain using microscopy or other analytical methods. Studying planktonic eukaryotes using molecular ecology techniques has triggered a debate on the advantages and disadvantages of modern methods compared with classical methods and on the combination of such methodologies. The groups most commonly determined and enumerated under the microscope are diatoms, dinoflagellates, ciliates, coccolithophorids, and flagellated cells [6,7]. How these groups correspond to taxonomic groups according to Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations
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