Morphological vs. DNA metabarcoding approaches for the evaluation of stream ecological status with benthic invertebrates: Testing different combinations of markers and strategies of data filtering.

Autor: Meyer A; Université de Lorraine, CNRS, LIEC, Metz, France., Boyer F; Université Grenoble Alpes, CNRS, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France., Valentini A; SPYGEN, Le Bourget du Lac, France., Bonin A; Université Grenoble Alpes, CNRS, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France.; SPYGEN, Le Bourget du Lac, France.; Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy., Ficetola GF; Université Grenoble Alpes, CNRS, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France.; Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy., Beisel JN; Université de Strasbourg, CNRS, ENGEES, LIVE UMR 7362, Strasbourg, France., Bouquerel J; Université de Lorraine, CNRS, LIEC, Metz, France., Wagner P; Université de Lorraine, CNRS, LIEC, Metz, France., Gaboriaud C; SPYGEN, Le Bourget du Lac, France., Leese F; University of Duisburg-Essen, Aquatic Ecosystem Research, Essen, Germany., Dejean T; SPYGEN, Le Bourget du Lac, France., Taberlet P; Université Grenoble Alpes, CNRS, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France.; UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway., Usseglio-Polatera P; Université de Lorraine, CNRS, LIEC, Metz, France.
Jazyk: angličtina
Zdroj: Molecular ecology [Mol Ecol] 2021 Jul; Vol. 30 (13), pp. 3203-3220. Date of Electronic Publication: 2020 Nov 23.
DOI: 10.1111/mec.15723
Abstrakt: Macroinvertebrate assemblages are the most common bioindicators used for stream biomonitoring, yet the standard approach exhibits several time-consuming steps, including the sorting and identification of organisms based on morphological criteria. In this study, we examined if DNA metabarcoding could be used as an efficient molecular-based alternative to the morphology-based monitoring of streams using macroinvertebrates. We compared results achieved with the standard morphological identification of organisms sampled in 18 sites located on 15 French wadeable streams to results obtained with the DNA metabarcoding identification of sorted bulk material of the same macroinvertebrate samples, using read numbers (expressed as relative frequencies) as a proxy for abundances. In particular, we evaluated how combining and filtering metabarcoding data obtained from three different markers (COI: BF1-BR2, 18S: Euka02 and 16S: Inse01) could improve the efficiency of bioassessment. In total, 140 taxa were identified based on morphological criteria, and 127 were identified based on DNA metabarcoding using the three markers, with an overlap of 99 taxa. The threshold values used for sequence filtering based on the "best identity" criterion and the number of reads had an effect on the assessment efficiency of data obtained with each marker. Compared to single marker results, combining data from different markers allowed us to improve the match between biotic index values obtained with the bulk DNA versus morphology-based approaches. Both approaches assigned the same ecological quality class to a majority (86%) of the site sampling events, highlighting both the efficiency of metabarcoding as a biomonitoring tool but also the need for further research to improve this efficiency.
(© 2020 John Wiley & Sons Ltd.)
Databáze: MEDLINE
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