Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR

Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR

Environmental DNA (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...

Full description

Saved in:
Bibliographic Details
Published in:Molecular ecology resources Vol. 23; no. 2; pp. 396 - 409
Main Authors: Pont, Didier, Meulenbroek, Paul, Bammer, Vincenz, Dejean, Tony, Erős, Tibor, Jean, Pauline, Lenhardt, Mirjana, Nagel, Christoffer, Pekarik, Ladislav, Schabuss, Michael, Stoeckle, Bernhard C., Stoica, Elena, Zornig, Horst, Weigand, Alexander, Valentini, Alice
Format: Journal Article
Language:English
Published: England Wiley Subscription Services, Inc 01-02-2023
Subjects:
Abundance
Animals
Biodiversity
Biomass
Biomonitoring
Density
DNA - analysis
DNA - genetics
DNA barcoding
DNA Barcoding, Taxonomic - methods
DNA, Environmental - genetics
Ecosystem
Environmental DNA
Environmental Monitoring - methods
Fish
fish community
Fishes - genetics
metabarcoding
qPCR
quantitative monitoring
Rivers
Sampling
Species richness
Surveys
rivers
metabarcoding
quantitative monitoring
qPCR
environmental DNA
fish community
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Environmental DNA (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 quantitative (q)PCR 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 nonlinear 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 provide 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.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1755-098X
1755-0998
1755-0998
DOI:10.1111/1755-0998.13715