Home About Browse Search
Svenska


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

Bailet, Bonnie and Apotheloz-Perret-Gentil, Laure and Baricevic, Ana and Chonova, Teofana and Franc, Alain and Frigerio, Jean-Marc and Kelly, Martyn and Mora, Demetrio and Pfannkuchen, Martin and Proft, Sebastian and Ramon, Mathieu and Vasselon, Valentin and Zimmermann, Jonas and Kahlert, Maria (2020). Diatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for standardization. Science of the Total Environment. 745 , 140948
[Journal article]

[img] PDF
838kB

Abstract

Ecological 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. (C) 2020 The Authors. Published by Elsevier B.V.

Authors/Creators:Bailet, Bonnie and Apotheloz-Perret-Gentil, Laure and Baricevic, Ana and Chonova, Teofana and Franc, Alain and Frigerio, Jean-Marc and Kelly, Martyn and Mora, Demetrio and Pfannkuchen, Martin and Proft, Sebastian and Ramon, Mathieu and Vasselon, Valentin and Zimmermann, Jonas and Kahlert, Maria
Title:Diatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for standardization
Year of publishing :2020
Volume:745
Article number:140948
Number of Pages:17
Publisher:ELSEVIER
ISSN:0048-9697
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Ecology
Keywords:Bacillariophyta, Biomonitoring, Metabarcoding, Morphological identification, rbcL, 18S-V4
URN:NBN:urn:nbn:se:slu:epsilon-p-108636
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-108636
Additional ID:
Type of IDID
DOI10.1016/j.scitotenv.2020.140948
Web of Science (WoS)000579365600107
ID Code:18680
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Aquatic Sciences and Assessment
Deposited By: SLUpub Connector
Deposited On:16 Nov 2020 15:23
Metadata Last Modified:16 Nov 2020 15:31

Repository Staff Only: item control page

Downloads

Downloads per year (since September 2012)

View more statistics

Downloads
Hits