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Article

Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches

1
Diatom Lab, Institute of Environment, Natural Resources and Biodiversity, University of León, 24007 León, Spain
2
Department of Biodiversity and Environmental Management, Faculty of Biological and Environmental Sciences, University of León, 24007 León, Spain
3
Department of Molecular Biology, Faculty of Biological and Environmental Sciences, University of León, 24007 León, Spain
*
Author to whom correspondence should be addressed.
Academic Editor: Terry J. Gentry
Water 2021, 13(10), 1351; https://doi.org/10.3390/w13101351
Received: 18 March 2021 / Revised: 7 May 2021 / Accepted: 11 May 2021 / Published: 13 May 2021
(This article belongs to the Special Issue Advances in Mountain and Mediterranean Wetlands Conservation)
Benthic diatoms have traditionally been used as bioindicators of aquatic ecosystems. Because diatom-based monitoring of water quality is required by European legislation, molecular-based methods had emerged as useful alternatives to classical methods based on morphological identification using light microscopy. The aim of this study was to test the reliability of DNA metabarcoding combined with High-Throughput Sequencing (HTS) techniques in the bioassessment of the trophic status of 22 Mediterranean shallow ponds in NW Spain. For each pond, the Trophic Diatom Index (TDI) was calculated from inventories obtained by identification using light microscopy (LM) followed by high-throughput sequencing (HTS) at the molecular level. Ponds were subsequently classified into five water quality classes. The results showed a good correspondence between both methods, especially after applying a correction factor that depended on the biovolume of the cells. This correspondence led to the assignment to the same quality class in 59% of the ponds. The determination and quantification of valves or DNA sequences was one of the main pitfalls, which mainly included those related to the variability in the relative abundances of some species. Accordingly, ponds with similar relative abundances for the dominant species were assigned to the same quality class. Moreover, other difficulties leading the discrepancies were the misidentification of some species due to the presence of semi-cryptic taxa, the incompleteness of the reference database and the bioinformatic protocol. Thus, the validation of DNA-based methods for the identification of freshwater diatoms represents an important goal, as an alternative to using traditional methods in Mediterranean shallow ponds. View Full-Text
Keywords: benthic diatoms; DNA barcoding; ecological assessment; shallow pond benthic diatoms; DNA barcoding; ecological assessment; shallow pond
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MDPI and ACS Style

Borrego-Ramos, M.; Bécares, E.; García, P.; Nistal, A.; Blanco, S. Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches. Water 2021, 13, 1351. https://doi.org/10.3390/w13101351

AMA Style

Borrego-Ramos M, Bécares E, García P, Nistal A, Blanco S. Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches. Water. 2021; 13(10):1351. https://doi.org/10.3390/w13101351

Chicago/Turabian Style

Borrego-Ramos, María, Eloy Bécares, Pedro García, Alejandro Nistal, and Saúl Blanco. 2021. "Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches" Water 13, no. 10: 1351. https://doi.org/10.3390/w13101351

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