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Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR
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  • Didier Pont,
  • Paul Meulenbroek,
  • Vincenz Bammer,
  • Tony Dejean,
  • Tibor Eros,
  • Pauline Jean,
  • Mirjana Lenhardt,
  • Christoffer Nagel,
  • Ladislav Pekarik,
  • Michael Schabuss,
  • Bernhard Stoeckle,
  • Elena Stoica,
  • Horst Zornig,
  • Alexander M. Weigand,
  • Alice Valentini
Didier Pont
University of Natural Resources and Life Sciences Vienna

Corresponding Author:didier.pont@boku.ac.at

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Paul Meulenbroek
University of Natural Resources and Life Sciences Vienna
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Vincenz Bammer
Bundesamt für Wasserwirtschaft
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Tony Dejean
Spygen
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Tibor Eros
Hungarian Academy of Sciences Centre for Ecological Research Balaton Limnological Research Institute
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Pauline Jean
SPYGEN
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Mirjana Lenhardt
University of Belgrade
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Christoffer Nagel
Technical University of Munich
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Ladislav Pekarik
Institut of Zoology, Slovak Academy of Sciences
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Michael Schabuss
PRO FISCH OG Ecological Consultants
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Bernhard Stoeckle
Technical University of Munich
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Elena Stoica
National Institute for Marine Research and Development Grigore Antipa
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Horst Zornig
PRO FISCH OG Ecological Consultants
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Alexander M. Weigand
Luxembourg National Museum of Natural History
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Alice Valentini
SPYGEN
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Abstract

eDNA metabarcoding is an effective method for studying fish communities but allows only an estimation of relative species abundance (density / biomass). Here, we combine metabarcoding with an estimation of the total abundance of eDNA amplified by our universal marker (teleo) using a qPCR approach to infer the absolute abundance of fish species. We carried out a 2850 km eDNA survey within the Danube catchment using a spatial integrative sampling protocol coupled with traditional electrofishing for fish biomass and density estimation. Total fish eDNA concentrations and total fish abundance were highly correlated. The correlation between eDNA concentrations per taxon and absolute specific abundance was of comparable strength when all sites were pooled and remained significant when the sites were considered separately. Furthermore, a non-linear mixed model showed that species richness was underestimated when the amount of teleo-DNA extracted from a sample was below a threshold of 0.65.106 copies of eDNA. This result, combined with the decrease in teleo-DNA concentration by several orders of magnitude with river size, highlights the need to increase sampling effort in large rivers. Our results show a comprehensive description of longitudinal changes in fish communities and underline our combined metabarcoding/qPCR approach for biomonitoring and bioassessment surveys when a rough estimate of absolute species abundance is sufficient.
12 Jan 2022Submitted to Molecular Ecology Resources
19 Jan 2022Submission Checks Completed
19 Jan 2022Assigned to Editor
24 Jan 2022Reviewer(s) Assigned
18 May 2022Review(s) Completed, Editorial Evaluation Pending
23 Jun 2022Editorial Decision: Revise Minor
21 Jul 2022Review(s) Completed, Editorial Evaluation Pending
21 Jul 20221st Revision Received
15 Sep 2022Editorial Decision: Accept
07 Oct 2022Published in Molecular Ecology Resources. 10.1111/1755-0998.13715