Diatom DNA metabarcoding to assess the effect of natural radioactivity in mineral springs on ASV of benthic diatom communities

Baker, Lory-Anne; Beauger, Aude; Kolovi, Sofia; Voldoire, Olivier; Allain, Elisabeth; Breton, Vincent; Chardon, Patrick; Miallier, Didier; Bailly, Céline; Montavon, Gilles; Bouchez, Agnès; Rimet, Frédéric; Chardon, Cècile; Vasselon, Valentin; Éctor, Luc; Wetzel, Carlos E.; Biron, David G.

doi:10.1016/j.scitotenv.2023.162270

Cited by 5 publications

(1 citation statement)

References 79 publications

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“…In contrast, other investigations have shown that the morphological approach allows to identify a greater diversity [16,35,40,90,95,99] (Figure 3). Using the example of diatoms, it has been shown that most of the species identified by LM are not represented in a Some studies have shown that diversity detected by NGS is much higher than that found in LM.…”

Section: The 16s Rrna Gene As a Marker For Simultaneous Detection Of ...mentioning

confidence: 89%

Genetic Markers for Metabarcoding of Freshwater Microalgae: Review

Kezlya

Tseplik

Kulikovskiy

2023

Biology

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The metabarcoding methods for studying the diversity of freshwater microalgae and routine biomonitoring are actively used in modern research. A lot of experience has been accumulated already, and many methodological questions have been solved (such as the influence of the methods and time of sample conservation, DNA extraction and bioinformatical processing). The reproducibility of the method has been tested and confirmed. However, one of the main problems—choosing a genetic marker for the study—still lacks a clear answer. We analyzed 63 publications and found out that studies on eukaryotic freshwater microalgae use 12 markers (different nuclear regions 18S and ITS and plastids rbcL, 23S and 16S). Each marker has its peculiarities; they amplify differently and have various levels of efficiency (variability) in different groups of algae. The V4 and V9 18S and rbcL regions are used most often. We concentrated especially on the studies that compare the results of using different markers and microscopy. We summarize the data on the primers for each region and on how the choice of a marker affects the taxonomic composition of a community.

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