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

By K. Deiner, Holly M. Bik, E. Mächler, M. Seymour, A. Lacoursière-Roussel, F. Altermatt, S. Creer, Iliana Bista, David M. Lodge, N. de Vere and 2 more. Molecular Ecology, 2017

1,687 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/49590eb6ee43faba30e6338e79f963c23eb086ca

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Citations in the corpus

Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation (2018, background): “For example, Deiner et al. (2016) found that eDNA recovered from rivers often derives from species in the catchment basin, including terrestrial organisms, reflecting the transport of eDNA from land to water.”
RESCRIPt: Reproducible sequence taxonomy reference database management (2020, background): “However, errors in public sequence databases are well documented [12,43,44] and can lead to misclassification errors in downstream results [12].”
From eDNA to citizen science: emerging tools for the early detection of invasive species (2020, methodology): “Although requiring bioinformatics expertise, HTS- based metabarcoding offers substantial capacity to survey entire communities with relatively little field sampling effort (Deiner et al. 2017).”
A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish (2020, background): “Environmental DNA (eDNA)-based species detection has revolutionised the manner in which biodiversity is surveyed and has proven to be a highly effective, efficient, economical and non-invasive approach to biomonitoring (Bohmann et al., 2014; Deiner et al., 2017; Taberlet et al., 2012).”
The need for robust qPCR‐based eDNA detection assays in environmental monitoring and species inventories (2020, methodology): “By far, the most frequently used sequence is the 650 bp COXI sequence (Elbrecht et al., 2019), as this has been embraced as a useful barcode for taxon identification using DNA sequencing techniques (Deiner et al., 2017; Hebert et al., 2003).”
Environmental DNA (eDNA) as a tool for assessing fish biomass: A review of approaches and future considerations for resource surveys (2021, background): “Second, and perhaps more importantly, a plethora of uncontrolled species- specific biotic and abiotic factors may affect eDNA concentrations, and in turn abundance and/or biomass estimates (Deiner et al., 2017; Hansen et al., 2018; Stewart, 2019; Yates et al., 2019).”
Taxonomic and geographical representation of freshwater environmental DNA research in aquatic conservation (2019, background): “…in palaeolimnology (Domaizon, Winegardner, Capo, Gauthier, & Gregory‐Eaves, 2017), in the use of eDNA metabarcoding in surveying plant and animal communities (Deiner et al., 2017), as well as in determining the environmental factors that affect the success of eDNA detection (Stoeckle et al., 2017).”
A practical guide to DNA metabarcoding for entomological ecologists (2020, methodology): “Detailed methodological procedures and bioinformatics processes have been discussed in previous reviews (Bik et al., 2012; Coissac et al., 2012; Deiner et al., 2017, section 4.3, boxes 2 and 3; also see Piper et al., 2019, fig.”
Reference databases, primer choice, and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters (2020, background): “These include non-invasiveness, better cost and time effectiveness, and increased taxonomic identification (Deiner et al., 2017).”
Assessing different components of diversity across a river network using eDNA (2019, methodology): “The emerging technique of environmental DNA (eDNA) metabarcod‐ ing is expected to become a complementary or even replacement method of classical morphological identification (Deiner et al., 2017; Hajibabaei, Shokralla, Zhou, Singer, & Baird, 2011; Lawson Handley, 2015).”
From environmental DNA sequences to ecological conclusions: How strong is the influence of methodological choices? (2019, background): “Our results thus corroborate other studies that demonstrated the robustness of beta diversity to bioinformatics analyses (Botnen, Davey, Halvorsen, & Kauserud, 2018; Deiner et al., 2017).”