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Environmental DNA metabarcoding: Transforming how we survey animal and plant communities


Deiner, Kristy; Bik, Holly M; Mächler, Elvira; Seymour, Mathew; Lacoursière-Roussel, Anaïs; Altermatt, Florian; Creer, Simon; Bista, Iliana; Lodge, David M; de Vere, Natasha; Pfrender, Michael E; Bernatchez, Louis (2017). Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Molecular Ecology, 26(21):5872-5895.

Abstract

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing (“HTS”) platforms now enable the rapid sequenc- ing of DNA from diverse kinds of environmental samples (termed “environmental DNA” or “eDNA”). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called “eDNA metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate rela- tive abundance. We highlight eDNA applications in freshwater, marine and terres- trial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.

Abstract

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing (“HTS”) platforms now enable the rapid sequenc- ing of DNA from diverse kinds of environmental samples (termed “environmental DNA” or “eDNA”). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called “eDNA metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate rela- tive abundance. We highlight eDNA applications in freshwater, marine and terres- trial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Evolutionary Biology and Environmental Studies
Dewey Decimal Classification:570 Life sciences; biology
590 Animals (Zoology)
Uncontrolled Keywords:bioinformatic pipeline, biomonitoring, citizen science, conservation, ecology, eDNA, invasive species, macro-organism, species richness
Language:English
Date:November 2017
Deposited On:05 Jan 2018 20:20
Last Modified:19 Aug 2018 12:25
Publisher:Wiley-Blackwell Publishing, Inc.
ISSN:0962-1083
OA Status:Hybrid
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1111/mec.14350
PubMed ID:28921802
Project Information:
  • : FunderSNSF
  • : Grant IDPP00P3_150698
  • : Project TitleBridging biodiversity and ecosystem functioning in dendritic networks: a meta-ecosystem perspective

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