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

Abstract

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.

Trait‐based diatom functional diversity as an appropriate tool for understanding the effects of environmental changes in soda pans

“…Nowadays, a new generation method, DNA metabarcoding, has established the conditions for the identification of operational taxonomic units (OTU) in many hundreds of samples simultaneously (Taberlet, Bonin, Zinger, & Coissac, 2018). This method seems likely to broaden our knowledge of biodiversity and with phylogenetic estimation of OTU ecological profiles it will move closer to functional biomonitoring (Keck, Vasselon, Rimet, Bouchez, & Kahlert, 2018).…”

“…However, functional diversity metrics (He et al, 2015) have rarely been used recently, even though they promise to improve our knowledge of community and ecosystem responses to environmental changes at different scales (Péru & Dolédec, 2010). Furthermore, functional diversity can be a good indicator of ecosystem stability (Schneider et al, 2017) and can be strongly correlated with DNAbased phylogenetic diversity (Li et al, 2019) through ecological traits as phylogenetic signals (Keck, Rimet, Franc, & Bouchez, 2016;Keck et al, 2018;Winter, Devictor, & Schweiger, 2013). Consequently, functional diversity can play an effective role in conservation management using phylogenetic tools (Webb, Ackerly, McPeek, & Donoghue, 2002).…”

Comparison of morphological, DNA barcoding, and metabarcoding characterizations of freshwater nematode communities

“…Our results showed that the different methods will not discover the same diversity, as the molecular methods recovered fewer annotated species than obtained by morphological analysis, although more OTUs were generated by metabarcoding than by barcoding. Despite reports of the high accuracy of molecular methods (Cowart et al, ) and their ability to recover a higher diversity, as demonstrated in the metabarcoding of diatoms (Keck et al, ; Rimet, Vasselon, A.‐Keszte, & Bouchez, ; Zimmermann, Glöckner, Jahn, Enke, & Gemeinholzer, ), in many studies a larger number of species or taxa was identified with traditional microscopy. Examples of the superiority of microscopy in species identification include a study of estuarine plankton, in which 56 taxa were revealed by microscopy but only 37 by metabarcoding (Abad et al, ); a study of copepods, in which 54 species were identified morphologically versus.…”

“…Metabarcoding has facilitated studies of small multicellular organisms, either whole communities or specific groups, with marine eukaryotes being a frequent focus (Brannock & Halanych, ; Dell'Anno, Carugati, Corinaldesi, Riccioni, & Danovaro, ; Haenel, Holovachov, Jondelius, Sundberg, & Bourlat, ). It can also be used in combination with morphological analyses, as demonstrated in studies of estuarine plankton (Abad et al, ; Harvey, Johnson, Fisher, Peterson, & Vrijenhoek, ; Leasi et al, ) and nematodes (Holovachov, ; Macheriotou et al, ) in marine habitats but also diatoms and other small organisms in freshwater habitats (Keck, Vasselon, Rimet, Bouchez, & Kahlert, ; Rimet, Vasselon, A.‐Keszte, & Bouchez, ). For nematodes in soil and marine habitats, however, combined microscopy and metabarcoding investigations have been carried out only at the family level (Darby, Todd, & Herman, ; Griffiths, Groot, Laros, Stone, & Geisen, ; Holovachov, Haenel, Bourlat, & Jondelius, ; Treonis et al, ), and direct comparisons of the performances of morphological identification, barcoding, and metabarcoding at the species level are still scarce (Leasi et al, ).…”

Phylogenetic placement of environmental sequences using taxonomically reliable databases helps to rigorously assess dinophyte biodiversity in Bavarian lakes (Germany)

“…Due to a huge number of reads, and the diversity of organisms captured by HTS of environmental DNA, initial OTU annotation using reference databases usually allows for confident taxonomic classifications only up to coarser taxonomic ranks (such as phylum, class, or order: Quast et al, 2013). This method has been recently used in barcoding and biomonitoring projects of protists (Elferink et al, 2017;Keck, Vasselon, Rimet, Bouchez, & Kahlert, 2018;Medinger et al, 2010;Vergin et al, 2013). family, genus, or species), is the phylogenetic placement of reads in reference trees, which also offers the advantage of estimating statistical support values for annotations, regardless of the read's length (Dunthorn et al, 2014).…”