Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA

  title={Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA},
  author={Krista M. Ruppert and Richard J Kline and Md Saydur Rahman},
  journal={Global Ecology and Conservation},

Figures from this paper

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.

Combining Multiple Markers in Environmental DNA Metabarcoding to Assess Deep-Sea Benthic Biodiversity

Combining the three markers, annelids were found to be the most abundant (44.9%) and diverse [179 operational taxonomic units (OTUs)] metazoan group in the sediments of the Okinawa Trough.

Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review

Abstract Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms

High resolution species detection: accurate long read eDNA metabarcoding of North Sea fish using Oxford Nanopore sequencing

Long read nanopore sequencing of eDNA can be used to obtain accurate information on the fish and elasmobranch species composition in the North Sea and beyond and shows the applicability for long-read eDNA metabarcoding in field studies.

The current state of DNA barcoding of macroalgae in the Mediterranean Sea: presently lacking but urgently required

It is concluded that there are insufficient macroalgal genetic data from the Mediterranean and that this area would greatly benefit from studies involving DNA barcoding, enabling better cost-effective biodiversity monitoring through environmental DNA metabarcoding.

A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (Emys orbicularis, L. 1758)

A long DNA metabarcoding method based on the sequencing of short reads followed by de novo assembly, which can precisely identify the taxonomic groups of organisms associated with complex diets, such as omnivorous individuals is developed.


Environmental DNA (eDNA) studies have burgeoned over the last two decades and the application of eDNA has increased exponentially since 2010, albeit at a slower pace in the marine system. We provide

Influence of DNA extraction kits on freshwater fungal DNA metabarcoding

Background Environmental DNA (eDNA) metabarcoding is a common technique for efficient biodiversity monitoring, especially of microbes. Recently, the usefulness of aquatic eDNA in monitoring the

Influence of DNA extraction kits on the fungal DNA metabarcoding for freshwater environmental DNA

It may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals, according to results of this study.



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.

Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes

Two metabarcoding eDNA assays using the mtDNA 16S RNA gene with Illumina MiSeq platform to detect invertebrate fauna in the Laurentian Great Lakes and surrounding waterways are developed, with a focus for use on invasive bivalve and gastropod species monitoring.

Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus)

Evaluating whether eDNA metabarcoding has comparable sensitivity to targeted real‐time quantitative PCR (qPCR) for T. cristatus detection finds entire communities can be initially surveyed to best inform use of funding and time for species‐specific surveys.

New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

Large variation in the level of detection among the groups and between modern and ancient samples is found, and the in silico approach offered a reliable estimate of the suitability of a marker.

Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications

The data suggest that the presence of eRNA-only OTUs could be due to increased cellular activities of some rare taxa that were not identified in the eDNA datasets, unusually high numbers of rRNA transcripts in ciliates, and/or artefacts produced during the reverse transcriptase, PCR and sequencing steps.

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.

Using DNA meta barcoding to assess New Zealand's terrestrial biodiversity

It is argued that it is essential to integrate conventional monitoring methods with novel DNA methods, to validate methods, and to better use and interpret data to improve biodiversity assessment and conservation planning and land management decisions.

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.

Genetic monitoring of open ocean biodiversity: An evaluation of DNA metabarcoding for processing continuous plankton recorder samples

Overall, the metabarcoding data represent a substantial shift in perspective, making direct integration into current long‐term time‐series challenging.

Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment

The potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment is investigated, and the sensitivity and low cost of e DNA metabarcoding are advocated, urging this approach to be rapidly integrated into biomonitoring programs.