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Cited by 13Environmental DNA in Biodiversity StudiesInvertebrate Taxonomy and EcologyMicrobial Community Ecology and Physiology

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Enhancing metabarcoding of freshwater biotic communities: A new online tool for primer selection and exploring data from 14 primer pairs

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Tournayre, Orianne, Tian, Haolun, Lougheed, David R., Windle, Matthew J. S., Lambert, Sheldon, Carter, Jennipher, Sun, Zhengxin, Ridal, Jeff, Wang, Yuxiang, Cumming, Brian F., Arnott, Shelley E., Lougheed, Stephen C.·2024·Environmental DNA
DOI 10.1002/edn3.590

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Abstract

Freshwater ecosystems are complex, diverse, and face multiple imminent threats that have led to changes in both structure and function. It is urgent that we develop and standardize monitoring tools that allow for rapid and comprehensive assessment of freshwater communities to understand their changing dynamics and inform conservation. Environmental DNA surveys offer a means to inventory and monitor aquatic diversity, yet most studies focus on one or a few taxonomic groups because of technical challenges. In this study, we (1) create an eDNA metabarcoding dataset (natural water bodies) with 14 validated primer pairs; (2) create a free online, user‐friendly tool for primer selection that can be used for any metabarcoding data (SNIPe); and (3) using SNIPe, explore our dataset to derive subsets of informative, cost‐effective primer pairs that maximize detection of freshwater diversity. We first evaluated the completeness of public reference sequence databases and the efficiency of 14 primer pairs in silico, in vitro on five mock communities (mix of DNA from tissues of select taxa), in vivo on water samples from aquarium samples with known taxonomic composition, and finally in vivo on water samples from freshwater systems in Eastern Canada. Results from analyses using SNIPe revealed that 13 or 14 primer pairs are necessary to recover 100% of the species in water samples (natural systems), but that four primer pairs are sufficient to recover almost 75% of taxa with little overlap. Our work highlights the power of eDNA metabarcoding for reconstructing freshwater communities, including prey, parasite, pathogen, invasive, and declining species. It also emphasizes the importance of marker choice on species resolution, and primer characteristics and filtering parameters on detection success and accuracy of biodiversity estimates. Together, these results highlight the usefulness of eDNA for freshwater monitoring and should prompt more studies of tools to survey all communities.

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Metadata

Authors
Tournayre, O., Tian, H., Lougheed, D. R., Windle, M. J. S., Lambert, S., Carter, J., Sun, Z., Ridal, J., Wang, Y., Cumming, B. F., Arnott, S. E., & Lougheed, S. C.
Affiliations
  • York University (CA)
  • Queen's University (CA)
  • McGill University (CA)
  • St. Lawrence River Institute of Environmental Sciences (CA)
  • Parks Canada (CA)
  • Brockville Aquatarium Brockville Ontario Canada
Corresponding author
Tournayre, Orianne
ORCID
Venue
Environmental DNA
Publisher
Wiley
Published
2024-07
Volume
6
Issue
4
ISSN
2637-4943 (ISSN-L)
DOI
10.1002/edn3.590
OpenAlex
W4400926086
Cited by
13
References
5
Citations by year
2026: 3 · 2025: 7 · 2024: 3
FWCI
3.55
Type
journal article
Language
en
Open access
Licence
Locations
  • Environmental DNA (publishedVersion, cc-by-nc)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Queen's University
  • Natural Sciences and Engineering Research Council of Canada
  • Social Sciences and Humanities Research Council of Canada
Topics
  • Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Invertebrate Taxonomy and Ecology
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords
eDNA metabarcoding, primer selection, snipe, mock communities, biodiversity monitoring, aquatic biodiversity, species detection, freshwater conservation

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