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Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles
Author(s) -
Keck François,
Vasselon Valentin,
Rimet Frédéric,
Bouchez Agnès,
Kahlert Maria
Publication year - 2018
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12919
Subject(s) - operational taxonomic unit , biology , phylogenetic tree , ecology , phylogenetics , community , biotic index , environmental dna , benthic zone , ecosystem , biodiversity , 16s ribosomal rna , genetics , bacteria , gene
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 ( OTU s’) ecological profiles ( OTU ‐ PITI approach). First, OTU s sequences are inserted within a reference phylogeny. Second, OTU s’ 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 OTU s. 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) OTU s with taxonomic assignment approach, (c) OTU s with phylogenetic estimation of ecological profiles ( OTU ‐ PITI ) and (d) OTU with taxonomic assignment completed by the phylogenetic approach ( OTU ‐ PITI ) for unclassified OTU s. Using traditional microscopy as a reference, we found that the combination of the OTU s’ taxonomic assignment completed by the phylogenetic method performed satisfactorily and substantially better than the other methods tested.