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Metabarcodes for the monitoring of freshwater benthic biodiversity through environmental DNA
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  • Gentile Francesco Ficetola,
  • Aurélie Bonin,
  • Frédéric Boyer,
  • Alice Valentini,
  • Albin Meyer,
  • Tony Dejean,
  • Coline Gaboriaud,
  • Philippe Usseglio-Polatera,
  • Pierre Taberlet
Gentile Francesco Ficetola
Università degli Studi di Milano
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Aurélie Bonin
Universite Grenoble Alpes
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Frédéric Boyer
Universite Grenoble Alpes
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Alice Valentini
SPYGEN
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Albin Meyer
Université de Lorraine Bibliothèque Ingénieurs Enim
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Tony Dejean
Spygen
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Coline Gaboriaud
SPYGEN
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Philippe Usseglio-Polatera
Université de Lorraine Bibliothèque Ingénieurs Enim
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Pierre Taberlet
Université Joseph Fourier
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Abstract

Environmental DNA and metabarcoding have great potential for the biomonitoring of freshwater environments. However, successful application of metabarcoding to biodiversity monitoring requires universal primers with high taxonomic coverage that amplify highly-variable, short metabarcodes with high taxonomic resolution. Moreover, reliable and extensive reference databases are essential to match the outcome of metabarcoding analyses with the available taxonomy and biomonitoring indices. Benthic invertebrates, particularly insects, are key taxa for freshwater biomonitoring. Nevertheless, so far, no formal comparison has assessed primers for metabarcoding of freshwater macrobenthos. Here we combined in vitro and in silico analyses to test the performance of metabarcoding primers amplifying regions in the 18S rDNA (Euka02 metabarcode), 16S rDNA (Inse01), and COI (BF1_BR2-COI) genes, and developed an extensive database of benthic invertebrates of France and Europe, with a special focus on three key insect orders (Ephemeroptera, Plecoptera and Trichoptera). In vitro analyses on 1514 individuals, belonging to 578 different taxonomic units showed very different amplification rates across primer combinations. The Euka02 marker showed the highest universality, while the Inse01 marker showed excellent performance for the amplification of insects. The BF1_BR2-COI metabarcode showed the highest resolution, while the resolution of Euka02 was often limited. By combining in vitro data with GenBank information, we developed a curated database including sequences representing 822 genera. The heterogeneous performance of the different metabarcodes highlights the complexity of the identification of the best markers, and advocates for the integration of multiple metabarcodes for a more comprehensive and accurate understanding of ecological impacts on freshwater biodiversity.

Peer review status:ACCEPTED

02 Apr 2020Submitted to Molecular Ecology
03 Apr 2020Submission Checks Completed
03 Apr 2020Assigned to Editor
07 Apr 2020Reviewer(s) Assigned
10 May 2020Review(s) Completed, Editorial Evaluation Pending
29 May 2020Editorial Decision: Revise Minor
01 Jul 2020Review(s) Completed, Editorial Evaluation Pending
01 Jul 20201st Revision Received
18 Jul 2020Editorial Decision: Revise Minor
16 Aug 2020Review(s) Completed, Editorial Evaluation Pending
16 Aug 20202nd Revision Received
27 Aug 2020Editorial Decision: Accept