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

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.--

Early detection and spatial monitoring of an emerging biological invasion by population genetics and environmental DNA metabarcoding

“…eDNA may be a relatively cheap solution (Deiner et al, 2017;Ficetola, Miaud, Pompanon, & Taberlet, 2008) to detect new invaders at an early stage when eradication is still possible (Jerde, Mahon, Chadderton, & Lodge, 2011). eDNA may be a relatively cheap solution (Deiner et al, 2017;Ficetola, Miaud, Pompanon, & Taberlet, 2008) to detect new invaders at an early stage when eradication is still possible (Jerde, Mahon, Chadderton, & Lodge, 2011).…”

“…Recently, eDNA methods have been developed to target some of the most harmful aquatic invaders such as in crayfish (Tréguier et al, 2014), molluscs (Clusa, Miralles, Basanta, Escot, & Garcia-Vazquez, 2017), mosquitoes (Schneider et al, 2016), fishes (Nevers et al, 2018), pathogenic fungi (Schmidt, Kéry, Ursenbacher, Hyman, & Collins, 2013), amphibians (Dejean et al, 2012), and plants (Gantz, Renshaw, Erickson, Lodge, & Egan, 2018). In parallel, the multispecies approach offered by eDNA metabarcoding may transform the monitoring of aquatic biodiversity (Deiner et al, 2017;Pont et al, 2018;Valentini et al, 2016), but its utility for the detection of emerging cryptic aliens faces several challenges. First, the taxonomic resolution of metabarcoding may not discriminate closely related taxa, given the aim to cover broad taxonomic groups using short conserved markers.…”

Hybridization and extensive mitochondrial introgression among fire salamanders in peninsular Italy

“…Derived from the shared history of individual characters of organisms, this expectation forms the basis for the extensive use of single markers (notably mitochondrial DNA) to draw inferences about the evolutionary history of populations and species 1 , as well as to assess their identity and geographic distribution using barcoding approaches 2,3 . In practice, however, discordant patterns of variation among characters and among markers are not uncommon (e.g.…”

Using Environmental DNA to Improve Species Distribution Models for Freshwater Invaders

“…Another method to assess limitations of primer detections is assessing detectability of the species "in time" after its removal from the controlled environment. When working on multiple species assessment using a metabarcoding approach, it is recommended, to sequence the control samples, compare the sequencing control outputs with the actual samples, and if none of the last achieve high quality sequence reads by appropriate clean up steps; removal of singletons, chimeras, as well as including a record of removed sequences (Deiner et al, 2017a). Bias due to universal primer preferential amplifications of species can alter the relative abundance of individual species eDNA (Deiner et al, 2017a).…”

“…When working on multiple species assessment using a metabarcoding approach, it is recommended, to sequence the control samples, compare the sequencing control outputs with the actual samples, and if none of the last achieve high quality sequence reads by appropriate clean up steps; removal of singletons, chimeras, as well as including a record of removed sequences (Deiner et al, 2017a). Bias due to universal primer preferential amplifications of species can alter the relative abundance of individual species eDNA (Deiner et al, 2017a). A PCR-free method, namely sequence capturing offers promising solutions in order to avoid amplification bias (Shokralla et al, 2016).…”