Evaluation and sensitivity analysis of diatom DNA metabarcoding for WFD bioassessment of Mediterranean rivers

Pérez-Burillo, Javier; Trobajo, Rosa; Vasselon, Valentin; Rimet, Frédéric; Bouchez, Agnès; Mann, David G.

doi:10.1016/j.scitotenv.2020.138445

Cited by 51 publications

(35 citation statements)

References 33 publications

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“…For instance, Fistulifera saprophila, which was actually present in the samples, was not detected by LM in any pond. Our results are in agreement with this point, regarding other studies [10,11]. On the contrary, some other species were not recorded by HTS, probably because of the lack of some taxa in the reference library or because they were not detected by molecular methods; some dead diatom valves can be retained in the collected biofilm growing on the stems, so they could only be detected by LM.…”

Section: Discussionsupporting

confidence: 92%

“…The comparison of morphological and molecular-based inventories demonstrated a similarity of 20.1% in terms of species number. In fact, the results are comparable with the 15.7% found in [16] and other studies in rivers, ranging from 13 to 26.7% [9,11,15,38].…”

Section: Discussionsupporting

confidence: 90%

“…With respect to the ecological classification according to TDI scores, 59% of ponds were assigned to the same quality class in both methods, with only one class of difference for the others, hence with similar results to studies performed in rivers (57% in [15]; 69.8% in [11]; 64% in [16]). Similarly, the comparison between transformed (applying CF) and untransformed data showed an improvement in the assignment to quality classes derived from morphological data, as also reported by the same authors.…”

Section: Discussionsupporting

confidence: 66%

“…In recent times, many studies have shown the advantages of DNA barcoding combined with High-Throughput Sequencing (HTS) methods, compared to conventional approaches [3][4][5][6][7], and thus DNA-based monitoring has been postulated as a promising tool in recent years for the assessment of aquatic ecosystems [8][9][10][11][12]. The development of high-throughput techniques have made this process quicker and easier, and now there are studies available evaluating its application in the biomonitoring of rivers [8][9][10][11][13][14][15] and large lakes [16].…”

Section: Introductionmentioning

confidence: 99%

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

Borrego-Ramos

Bécares

Garcı́a

et al. 2021

Water

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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.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionsupporting

confidence: 90%

Section: Discussionsupporting

confidence: 66%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Borrego-Ramos

Bécares

Garcı́a

et al. 2021

Water

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“…Following advances in the field of molecular ecology, high-throughput sequencing (HTS) techniques, especially DNA metabarcoding, seem to be a promising tool for future monitoring and assessment protocols, providing reliable, high quantity and quality standardized data with lower cost and time compared to common taxonomic methods [108][109][110][111][112]. These techniques use gene markers to identify taxa-specific sequences in the cell's DNA, i.e., a barcode [109,111]. These sequences are stored in a database and are assigned to a diatom species.…”

Section: Molecular-based Diatom Indicesmentioning

confidence: 99%

Benthic Diatoms in River Biomonitoring—Present and Future Perspectives within the Water Framework Directive

Μασούρας

Karaouzas

Dimitriou

et al. 2021

Water

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The European Water Framework Directive 2000/60/EC (WFD) has been implemented over the past 20 years, using physicochemical, biological and hydromorphological elements to assess the ecological status of surface waters. Benthic diatoms (i.e., phytobenthos) are one of the most common biological quality elements (BQEs) used in surface water monitoring and are particularly successful in detecting eutrophication, organic pollution and acidification. Herein, we reviewed their implementation in river biomonitoring for the purposes of the WFD, highlighting their advantages and disadvantages over other BQEs, and we discuss recent advances that could be applied in future biomonitoring. Until now, phytobenthos have been intercalibrated by the vast majority (26 out of 28) of EU Member States (MS) in 54% of the total water bodies assessed and was the most commonly used BQE after benthic invertebrates (85% of water bodies), followed by fish (53%), macrophytes (27%) and phytoplankton (4%). To meet the WFD demands, numerous taxonomy-based quality indices have been developed among MS, presenting, however, uncertainties possibly related to species biogeography. Recent development of different types of quality indices (trait-based, DNA sequencing and predictive modeling) could provide more accurate results in biomonitoring, but should be validated and intercalibrated among MS before their wide application in water quality assessments.

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Present and Future Perspectives for Bioassessment of Running Water Using Diatoms

Almeida,

Feio

2024

Diatom Photosynthesis

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Evaluation and sensitivity analysis of diatom DNA metabarcoding for WFD bioassessment of Mediterranean rivers

Cited by 51 publications

References 33 publications

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

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

Benthic Diatoms in River Biomonitoring—Present and Future Perspectives within the Water Framework Directive

Present and Future Perspectives for Bioassessment of Running Water Using Diatoms

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