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

Keck, Francois and Vasselon, Valentin and Rimet, Frédéric and Bouchez, Agnes and Kahlert, Maria (2018). Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units' ecological profiles. Molecular Ecology Resources. 18 :6 , 1299-1309
[Journal article]

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Official URL: https://doi.org/10.1111/1755-0998.12919

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.

Authors/Creators:Keck, Francois and Vasselon, Valentin and Rimet, Frédéric and Bouchez, Agnes and Kahlert, Maria
Title:Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units' ecological profiles
Series/Journal:Molecular Ecology Resources (1755-0998)
Year of publishing :2018
Volume:18
Number:6
Page range:1299-1309
Number of Pages:11
Publisher:Wiley
ISSN:1755-0998
Language:English
Publication Type:Journal article
Refereed:Yes
Article category:Scientific peer reviewed
Version:Accepted version
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 105 Earth and Related Environmental Sciences > Other Earth and Related Environmental Sciences
Keywords:biomonitoring, diatoms, environmental DNA, metabarcoding, phylogenetic signal
URN:NBN:urn:nbn:se:slu:epsilon-e-5143
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-5143
Additional ID:
Type of IDID
DOI10.1111/1755-0998.12919
Web of Science (WoS)000449535600010
ID Code:15787
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Aquatic Sciences and Assessment
Deposited By: SLUpub Connector
Deposited On:24 Jan 2019 08:15
Metadata Last Modified:23 Jul 2020 09:22

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