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Diatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for standardization

hal.structure.identifierSwedish University of Agricultural Sciences = Sveriges lantbruksuniversitet [SLU]
dc.contributor.authorBAILET, Bonnie
hal.structure.identifierUniversité de Genève = University of Geneva [UNIGE]
dc.contributor.authorAPOTHÉLOZ-PERRET-GENTIL, Laure
hal.structure.identifierInstitut Ruđer Bošković [IRB]
dc.contributor.authorBARIČEVIĆ, Ana
hal.structure.identifierCentre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques [CARRTEL]
dc.contributor.authorCHONOVA, Teofana
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
dc.contributor.authorFRANC, Alain
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorFRIGERIO, Jean-Marc
hal.structure.identifierUniversity of Nottingham, UK [UON]
dc.contributor.authorKELLY, Martyn
hal.structure.identifierFreie Universität Berlin
dc.contributor.authorMORA, Demetrio
hal.structure.identifierInstitut Ruđer Bošković [IRB]
dc.contributor.authorPFANNKUCHEN, Martin
hal.structure.identifierFreie Universität Berlin
dc.contributor.authorPROFT, Sebastian
hal.structure.identifierFera Science Ltd
dc.contributor.authorRAMON, Mathieu
hal.structure.identifierCentre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques [CARRTEL]
dc.contributor.authorVASSELON, Valentin
hal.structure.identifierFreie Universität Berlin
dc.contributor.authorZIMMERMANN, Jonas
hal.structure.identifierSwedish University of Agricultural Sciences = Sveriges lantbruksuniversitet [SLU]
dc.contributor.authorKAHLERT, Maria
dc.date.issued2020-11
dc.identifier.issn0048-9697
dc.description.abstractEnEcological assessment of lakes and rivers using benthic diatom assemblages currently requires considerable taxonomic expertise to identify species using light microscopy. This traditional approach is also time-consuming. Diatom metabarcoding is a promising alternative and there is increasing interest in using this approach for routine assessment. However, until now, analysis protocols for diatom metabarcoding have been developed and optimised by research groups working in isolation. The diversity of existing bioinformatics methods highlights the need for an assessment of the performance and comparability of results of different methods. The aim of this study was to test the correspondence of outputs from six bioinformatics pipelines currently in use for diatom metabarcoding in different European countries. Raw sequence data from 29 biofilm samples were treated by each of the bioinformatics pipelines, five of them using the same curated reference database. The outputs of the pipelines were compared in terms of sequence unit assemblages, taxonomic assignment, biotic index score and ecological assessment outcomes. The three last components were also compared to outputs from traditional light microscopy, which is currently accepted for ecological assessment of phytobenthos, as required by the Water Framework Directive. We also tested the performance of the pipelines on the two DNA markers (rbcL and 185-V4) that are currently used by the working groups participating in this study. The sequence unit assemblages produced by different pipelines showed significant differences in terms of assigned and unassigned read numbers and sequence unit numbers. When comparing the taxonomic assignments at genus and species level, correspondence of the taxonomic assemblages between pipelines was weak. Most discrepancies were linked to differential detection or quantification of taxa, despite the use of the same reference database. Subsequent calculation of biotic index scores also showed significant differences between approaches, which were reflected in the final ecological assessment. Use of the rbcL marker always resulted in better correlation among molecular datasets and also in results closer to these generated using traditional microscopy. This study shows that decisions made in pipeline design have implications for the dataset's structure and the taxonomic assemblage, which in turn may affect biotic index calculation and ecological assessment. There is a need to define best-practice bioinformatics parameters in order to ensure the best representation of diatom assemblages. Only the use of similar parameters will ensure the compatibility of data from different working groups. The future of diatom metabarcoding for ecological assessment may also lie in the development of new metrics using, for example, presence/absence instead of relative abundance data.
dc.language.isoen
dc.publisherElsevier
dc.subject.enBacillariophyta
dc.subject.enBiomonitoring
dc.subject.enMetabarcoding
dc.subject.enMorphological identification
dc.subject.enrbcL
dc.subject.en18S-V4
dc.title.enDiatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for standardization
dc.typeArticle de revue
dc.identifier.doi10.1016/j.scitotenv.2020.140948
dc.subject.halSciences de l'environnement
bordeaux.journalScience of the Total Environment
bordeaux.page140948
bordeaux.volume745
bordeaux.peerReviewedoui
hal.identifierhal-03152486
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03152486v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Science%20of%20the%20Total%20Environment&rft.date=2020-11&rft.volume=745&rft.spage=140948&rft.epage=140948&rft.eissn=0048-9697&rft.issn=0048-9697&rft.au=BAILET,%20Bonnie&APOTH%C3%89LOZ-PERRET-GENTIL,%20Laure&BARI%C4%8CEVI%C4%86,%20Ana&CHONOVA,%20Teofana&FRANC,%20Alain&rft.genre=article


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