Mock community experiments can inform on the reliability of eDNA metabarcoding data: a case study on marine phytoplankton

Environmental DNA metabarcoding is increasingly implemented in biodiversity monitoring, including phytoplankton studies. Using 21 mock communities composed of seven unicellular diatom and dinoflagellate algae, assembled with different composition and abundance by controlling the number of cells, we...

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Bibliographic Details
Published in:Scientific reports 2023-11, Vol.13 (1), p.20164-20164, Article 20164
Main Authors: Marinchel, Nadia, Marchesini, Alexis, Nardi, Davide, Girardi, Matteo, Casabianca, Silvia, Vernesi, Cristiano, Penna, Antonella
Format: Article
Language:English
Subjects:
704/158
704/158/2452
704/158/853
704/829/826
Algae
Biodiversity
Copy number
DNA barcoding
Environmental DNA
Humanities and Social Sciences
multidisciplinary
Phytoplankton
Plankton
Science
Science (multidisciplinary)
Species richness
Statistical analysis
Taxa
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Summary:Environmental DNA metabarcoding is increasingly implemented in biodiversity monitoring, including phytoplankton studies. Using 21 mock communities composed of seven unicellular diatom and dinoflagellate algae, assembled with different composition and abundance by controlling the number of cells, we tested the accuracy of an eDNA metabarcoding protocol in reconstructing patterns of alpha and beta diversity. This approach allowed us to directly evaluate both qualitative and quantitative metabarcoding estimates. Our results showed non-negligible rates (17–25%) of false negatives (i.e., failure to detect a taxon in a community where it was included), for three taxa. This led to a statistically significant underestimation of metabarcoding-derived alpha diversity (Wilcoxon p  = 0.02), with the detected species richness being lower than expected (based on cell numbers) in 8/21 mock communities. Considering beta diversity, the correlation between metabarcoding-derived and expected community dissimilarities was significant but not strong (R 2  = 0.41), indicating suboptimal accuracy of metabarcoding results. Average biovolume and rDNA gene copy number were estimated for the seven taxa, highlighting a potential, though not exhaustive, role of the latter in explaining the recorded biases. Our findings highlight the importance of mock communities for assessing the reliability of phytoplankton eDNA metabarcoding studies and identifying their limitations.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-023-47462-5