Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment

Rivera, Sinziana F.; Vasselon, Valentin; Jacquet, Stéphan; Bouchez, Agnès; Ariztegui, Daniel; Rimet, Frédéric

doi:10.1007/s10750-017-3381-2

Cited by 81 publications

(75 citation statements)

References 61 publications

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“…However, in this case, we directly applied the ecological profile of the OTUs, without taxonomic assignment, avoiding the problem associated with incomplete DNA reference databases, which can easily inject bias (Apothéloz-Perret-Gentil et al, 2017;Groendahl et al, 2017;Rivera, Vasselon, Jacquet, et al, 2018b;Zimmermann, Glöckner, Jahn, Enke, & Gemeinholzer, 2015). Even though the number of species included in the DNA reference libraries is constantly increasing (Rivera, Vasselon, Jacquet, et al, 2018b), the proportion of OTUs that can be assigned to the species level remains far from satisfying. Published reports have described a wide range of classification coverage, including 35.7% , -Perret-Gentil et al, 2017), 23% (Rivera, Vasselon, Jacquet, et al, 2018b), and as low as 10% for marine samples (Rivera, Vasselon, Ballorain, et al, 2018a).…”

Section: Performances Of the Otu-based Indices Depend On The Sst Chmentioning

confidence: 99%

“…Even though the number of species included in the DNA reference libraries is constantly increasing (Rivera, Vasselon, Jacquet, et al, 2018b), the proportion of OTUs that can be assigned to the species level remains far from satisfying. Published reports have described a wide range of classification coverage, including 35.7% , -Perret-Gentil et al, 2017), 23% (Rivera, Vasselon, Jacquet, et al, 2018b), and as low as 10% for marine samples (Rivera, Vasselon, Ballorain, et al, 2018a). Our approach is similar to those of Apothéloz-Perret-Gentil et al (2017) One technical drawback of the index described in this investigation is that when new samplings are carried out in Mayotte, the OTUs generated from these new data may differ from those obtained from the datasets used our index development.…”

Section: Performances Of the Otu-based Indices Depend On The Sst Chmentioning

confidence: 99%

“…To generate complete reference libraries, these unclassified OTUs must be resolved (Groendahl, Kahlert, & Fink, 2017;. As such, the quality index calculation will only be based on the ecological values from a portion of the species or genera while others go unidentified, among which may be dominant, relevant species (Rivera, Vasselon, Jacquet, et al, 2018b). As such, the quality index calculation will only be based on the ecological values from a portion of the species or genera while others go unidentified, among which may be dominant, relevant species (Rivera, Vasselon, Jacquet, et al, 2018b).…”

Section: Introductionmentioning

confidence: 99%

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The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)

Tapolczai

Vasselon

Bouchez

et al. 2018

Ecology and Evolution

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Extensive studies on the taxonomic resolution required for bioassessment purposes have determined that resolution above species level (genus, family) is sufficient for their use as indicators of relevant environmental pressures. The high‐throughput sequencing (HTS) and meta‐barcoding methods now used for bioassessment traditionally employ an arbitrary sequence similarity threshold (SST) around 95% or 97% to cluster sequences into operational taxonomic units, which is considered descriptive of species‐level resolution. In this study, we analyzed the effect of the SST on the resulting diatom‐based ecological quality index, which is based on OTU abundance distribution along a defined environmental gradient, ideally avoiding taxonomic assignments that could result in high rates of unclassified OTUs and biased final values. A total of 90 biofilm samples were collected in 2014 and 2015 from 51 stream sites on Mayotte Island in parallel with measures of relevant physical and chemical parameters. HTS sequencing was performed on the biofilms using the rbcL region as the genetic marker and diatom‐specific primers. Hierarchical clustering was used to group sequences into OTUs using 20 experimental SST levels (80%–99%). An OTU‐based quality index (IdxOTU) was developed based on a weighted average equation using the abundance profiles of the OTUs. The developed IdxOTU revealed significant correlations between the IdxOTU values and the reference pressure gradient, which reached maximal performance using an SST of 90% (well above species level delimitation). We observed an interesting and important trade‐off with the power to discriminate between sampling sites and index stability that will greatly inform future applications of the index. Taken together, the results from this study detail a thoroughly optimized and validated approach to generating robust, reproducible, and complete indexes that will greatly facilitate effective and efficient environmental monitoring.

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Section: Performances Of the Otu-based Indices Depend On The Sst Chmentioning

confidence: 99%

Section: Performances Of the Otu-based Indices Depend On The Sst Chmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)

Tapolczai

Vasselon

Bouchez

et al. 2018

Ecology and Evolution

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“…Therefore, metabarcoding has been promoted as an attractive alternative to traditional identification using microscopy for biomonitoring (Baird & Hajibabaei, ). Recent studies have shown that molecular inventories of diatom communities can be used to calculate various biotic indices (Kermarrec et al., ; Rivera et al., ; Vasselon, Rimet, Tapolczai, & Bouchez, ; Visco et al., ).…”

Section: Introductionmentioning

confidence: 99%

Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles

Keck

Vasselon

Rimet

et al. 2018

Molecular Ecology Resources

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DNA metabarcoding has been introduced as a revolutionary way to identify organisms and monitor ecosystems. However, the potential of this approach for biomonitoring remains partially unfulfilled because a significant part of the sampled DNA cannot be affiliated to species due to incomplete reference libraries. Thus, biotic indices, which are based on the estimated abundances of species in a community and their ecological profiles, can be inaccurate. We propose to compute biotic indices using phylogenetic imputation of operational taxonomic units (OTUs') ecological profiles (OTU-PITI approach). First, OTUs sequences are inserted within a reference phylogeny. Second, OTUs' ecological profiles are estimated on the basis of their phylogenetic relationships with reference species whose ecology is known. Based on these ecological profiles, biotic indices can be computed using all available OTUs. Using freshwater diatoms as a case study, we show that short DNA barcodes can be placed accurately within a phylogeny and their ecological preferences estimated with a satisfactory level of precision. In the light of these results, we tested the approach with a data set of 139 environmental samples of benthic river diatoms for which the same biotic index (specific sensitivity index) was calculated using (a) traditional microscopy, (b) OTUs with taxonomic assignment approach, (c) OTUs with phylogenetic estimation of ecological profiles (OTU-PITI) and (d) OTU with taxonomic assignment completed by the phylogenetic approach (OTU-PITI) for unclassified OTUs. Using traditional microscopy as a reference, we found that the combination of the OTUs' taxonomic assignment completed by the phylogenetic method performed satisfactorily and substantially better than the other methods tested.

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“…This concept was expanded to enviromental samples, in "DNA-metabarcoding" (Pompanon et al 2011), where species are identified in natural samples using their DNA. Several studies have demonstrated that this approach may be applicable to river diatoms (Kermarrec et al 2013b;Zimmermann et al 2015;Visco et al 2015;Rivera et al 2017). However, these studies also showed that a potential limitation of metabarcoding was an insufficient coverage of existing taxa of the reference barcoding library.…”

Section: Introductionmentioning

confidence: 99%

The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes

Rimet¹,

Abarca²,

Bouchez³

et al. 2018

Fottea

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Diatoms are used routinely to assess pollution level in rivers and lakes. Current methods are based on identification by light microscopy, which is laborious. An alternative is to identify species based on short DNA fragments and High-Throughput Sequencing (HTS). However a potential limitation is the incomplete coverage of species in reference barcode libraries. Usually these libraries are compiled by isolating cells, before culturing and sequencing them, which is tedious and often unsuccessful. Here we propose the use of rbcL sequences from environmental samples analysed by HTS. We set several criteria to ensure good sequence quality and correspondence with the target species observed in microscopy: the sequence needed to be abundant in the sample, and with no insertions nor deletions or stop codon, phylogenetic neighbour taxa had to correspond to neighbour taxonomic taxa expected from morphological observations. Four species from tropical rivers are given as examples, including one that is new to science.

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Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment

Cited by 81 publications

References 61 publications

The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)

The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)

Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles

The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes

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