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

  title={Environmental DNA metabarcoding: Transforming how we survey animal and plant communities},
  author={Kristy Deiner and Holly M. Bik and Elvira M{\"a}chler and Mathew Seymour and Ana{\"i}s Lacoursi{\`e}re-Roussel and Florian Altermatt and Simon Creer and Iliana Bista and David M. Lodge and Natasha de Vere and Michael E. Pfrender and Louis Bernatchez},
  journal={Molecular Ecology},
  pages={5872 - 5895}
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… 

Comparison of environmental DNA and bulk‐sample metabarcoding using highly degenerate cytochrome c oxidase I primers

Compared metabarcoding results from bulk and eDNA samples taken from 19 streams spanning a wide gradient of farming intensities in New Zealand imply that bulk‐sample metabarcode resembles classical freshwater biomonitoring approaches better, as more indicator macroinvertebrate taxa are captured.

A review on the applications and recent advances in environmental DNA (eDNA) metagenomics

Although the application of eDNA is intensifying swiftly at a global scale, there are still some knowledge gaps, especially with methods and applications, and procedures require some refinements and validations to diminish the burden of false positives/negatives.

Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds

This research demonstrates that eDNA metabarcoding provides accurate qualitative and quantitative information on fish communities in small ponds, and results are consistent between different methods of DNA capture.

Validating environmental DNA metabarcoding for marine fishes in diverse ecosystems using a public aquarium

Environmental DNA metabarcoding has been widely touted as a powerful tool for monitoring biodiversity in marine ecosystems. However, this method still requires thorough validation and standardization

Environmental DNA metabarcoding for fish community analysis in backwater lakes: A comparison of capture methods

To detect fish communities in backwater lakes, the performance of eDNA metabarcoding with the use of 1 L surface water sampling is similar to that of capturing methods, and environmental factors that can cause PCR inhibition, should be considered in eDNA applications.

Fast processing of environmental DNA metabarcoding sequence data using convolutional neural networks

This work investigated whether convolutional neural networks (CNN) can optimize the processing of short eDNA sequences and found that the taxonomic assignments from the CNN were comparable to those of OBITools, with high correlation levels and a similar match to the regional fish fauna.

Application of Environmental DNA Metabarcoding for Predicting Anthropogenic Pollution in Rivers.

This study gives a novel approach to predicting the pollution status of rivers by eDNA data by observing that the relative abundance of indicative OTUs was significantly correlated with nutrient levels, and could be used to predict the nutrient status up to 79% accuracy on testing data sets.

Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness

In freshwater systems with fewer than 100 species, eDNA metabarcoding detected more species than conventional methods; however, more studies are needed in these environments to better evaluate relative performance.

Fine‐tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches

Accurate quantification of biodiversity can be demanding and expensive. Although environmental DNA (eDNA) metabarcoding can facilitate biodiversity assessments through non‐invasive, cost‐efficient

Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water

It is concluded that careful consideration on environmental sample type is needed when conducting eDNA surveys, especially for studies assessing community change.



Bioinformatic challenges for DNA metabarcoding of plants and animals

The bioinformatics tools available for DNA metabarcode of plants and animals are described, and others developed for DNA barcoding or microbial metabarcoding are revisited.

Towards next‐generation biodiversity assessment using DNA metabarcoding

The near‐term future of DNA metabarcoding has an enormous potential to boost data acquisition in biodiversity research as further developments associated with the impressive progress in DNA sequencing will eliminate the currently required DNA amplification step, and comprehensive taxonomic reference libraries can be built based on the well‐curated DNA extract collections maintained by standardized barcoding initiatives.

Environmental DNA metabarcoding of lake fish communities reflects long‐term data from established survey methods

It is demonstrated that eDNA metabarcoding can describe fish communities in large lakes, both qualitatively and quantitatively, and has great potential as a complementary tool to established monitoring methods.

Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

It is argued that the proposed DNA‐based approach has the potential to become the next‐generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.

Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers

The value of standard DNA barcodes for soil plant eDNA analysis in ecological investigations and biomonitoring programs is established and the collaborative development of DNA barcoding and metabarcoding is supported.

Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System

It is confirmed that eDNA metabarcoding is more efficient than a single traditional sampling campaign to detect species presence, especially in rivers, and gives a faithful description of local fish biodiversity in the study system, more specifically within a range of a few kilometers along the river in the authors' study conditions.

Next-generation freshwater bioassessment: eDNA metabarcoding with a conserved metazoan primer reveals species-rich and reservoir-specific communities

It is shown that eDNA can be used to assign each water sample to its reservoir of origin, and that e DNA outperforms conventional survey methods in single-sample richness comparisons, while revealing evidence for hundreds of unknown species that are undetected by conventional bioassessment methods.

Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding

An eDNA metabarcoding approach is used to target and amplify a hypervariable region of the mitochondrial 12S rRNA gene to characterize vertebrate communities at 10 oceanographic stations spanning 45 km within the Monterey Bay National Marine Sanctuary.

The ecology of environmental DNA and implications for conservation genetics

This work outlines a framework for understanding the ecology of eDNA, including the origin, state, transport, and fate of extraorganismal genetic material, and identifies frontiers of conservation-focused eDNA application where it sees the most potential for growth.

Tracking earthworm communities from soil DNA

It is shown that combining DNA metabarcoding and next‐generation sequencing facilitates the identification of earthworm species from soil samples, and the potential of environmental DNA as a tool to assess the diversity of other soil‐dwelling animal taxa is illustrated.