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Research article - Peer-reviewed, 2018

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

Keck, Francois; Vasselon, Valentin; Rimet, Frederic; Bouchez, Agnes; Kahlert, Maria

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.

Keywords

biomonitoring; diatoms; environmental DNA; metabarcoding; phylogenetic signal

Published in

Molecular Ecology Resources
2018, volume: 18, number: 6, pages: 1299-1309

Authors' information

Keck, Francois
Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment
Vasselon, Valentiin
National Institute of Agricultural Research (INRA)
Rimet, Frédéric
National Institute of Agricultural Research (INRA)
Bouchez, Agnes
National Institute of Agricultural Research (INRA)
Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment

UKÄ Subject classification

Other Earth and Related Environmental Sciences

Publication Identifiers

DOI: https://doi.org/10.1111/1755-0998.12919

URI (permanent link to this page)

https://res.slu.se/id/publ/96324