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

Kristy Deiner,Anaïs Lacoursière‐Roussel,Louis Bernatchez,David M Lodge,Elvira Mächler,Natasha De Vere,Mathew Seymour,Iliana Bista,Simon Creer,Holly M Bik,Florian Altermatt,Michael E Pfrender

doi:10.1111/mec.14350

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.

Highlights

Anthropogenic influences are causing unprecedented changes to the rate of biodiversity loss and, ecosystem function (Cardinale et al, 2012)
Multispecies detection using DNA derived from environmental samples using high-throughput sequencing (“High-throughput sequencing (HTS)”; Box 1) is a fast and efficient method to survey species richness in natural communities (Creer et al, 2016)
To compliment these many recent reviews, here we concentrate on four aspects: a summary of environmental DNA (eDNA) metabarcoding studies on animals and plants to date, knowns and unknowns surrounding the spatial and temporal scale of eDNA information, guidelines and challenges for eDNA study design and emerging applications of eDNA metabarcoding in the basic and applied sciences

Summary

| INTRODUCTION

Anthropogenic influences are causing unprecedented changes to the rate of biodiversity loss and, ecosystem function (Cardinale et al, 2012). Environmental DNA metabarcoding can complement (and overcome the limitations of) conventional methods by targeting different species, sampling greater diversity and increasing the resolution of taxonomic identifications (Table 1). We expect the robustness of eDNA metabarcoding to reveal species richness estimates for animals and plants will be improved by coupling distribution or occupancy modelling with studies to determine the scale of inference in space and time for an eDNA sample (Figure 1). Overall, ascertaining abundance information using metabarcoding of eDNA for whole communities still lacks substantial evidence, but some studies in aquatic environments have shown positive relationships between the relative number of reads and relative or rank abundance estimated with conventional methods. Environmental DNA metabarcoding of different sample types has been highly successful in obtaining species richness estimates for animals in aquatic systems (Figure 1, Table 1). Finding ways to cut costs and speed up data generation (a goal common for any application of the tool), as well as creation of applications for exploration of data on smart phones and desktops alike, is needed to propel the use of eDNA applications in citizen science and education

| CONCLUSIONS

Findings

DATA ACCESSIBILITY