Environmental DNA metabarcoding: Transforming how we survey animal and plant communities |
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| Authors: | Kristy Deiner Holly M Bik Elvira Mächler Mathew Seymour Anaïs Lacoursière‐Roussel Florian Altermatt Simon Creer Iliana Bista David M Lodge Natasha de Vere Michael E Pfrender Louis Bernatchez |
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| Institution: | 1. Atkinson Center for a Sustainable Future, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA;2. Department of Nematology, University of California, Riverside, CA, USA;3. Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Dübendorf, Switzerland;4. Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland;5. Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK;6. IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, QC, Canada;7. Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK;8. Conservation and Research Department, National Botanic Garden of Wales, Llanarthne, Carmarthenshire, UK;9. Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK;10. Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, USA |
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| Abstract: | The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid sequencing 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 relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial 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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| Keywords: | bioinformatic pipeline biomonitoring citizen science conservation ecology eDNA invasive species macro‐organism species richness |
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