Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding

  title={Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding},
  author={Mieke van der Heyde and Michael Bunce and Grant W. Wardell-Johnson and Kristen Fernandes and Nicole E. White and Paul G. Nevill},
  journal={Molecular Ecology Resources},
  pages={732 - 745}
Biological surveys based on visual identification of the biota are challenging, expensive and time consuming, yet crucial for effective biomonitoring. DNA metabarcoding is a rapidly developing technology that can also facilitate biological surveys. This method involves the use of next generation sequencing technology to determine the community composition of a sample. However, it is uncertain as to what biological substrate should be the primary focus of metabarcoding surveys. This study aims… 

Environmental DNA metabarcoding of cow dung reveals taxonomic and functional diversity of invertebrate assemblages

This study investigates the potential of environmental DNA (eDNA) metabarcoding of cow dung samples for biomonitoring of dung‐associated invertebrates and discusses potential caveats of the method, as well as directions for future study and perspectives for implementation in research and monitoring.

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

Invertebrates for vertebrate biodiversity monitoring: Comparisons using three insect taxa as iDNA samplers

Carrion flies revealed the greatest total vertebrate species richness at the landscape level, despite the least amount of sampling effort and the fewest number of individuals captured for metabarcoding, followed by sandflies, which presented potential utility to further study related to host‐vector interactions.

Detection of Endangered Aquatic Plants in Rapid Streams Using Environmental DNA

Podostemaceae are a eudicot family of plants that grow on rapid streams and waterfalls. Two genera and six species of this family are distributed in Japan, all of which are threatened with

Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity

Simple Summary The innovative concept of environmental DNA has found its foot in aquatic ecosystems but remains an unexplored area of research concerning terrestrial ecosystems. When making

DNA metabarcoding captures subtle differences in forest beetle communities following disturbance

DNA metabarcoding is an emerging approach for monitoring biodiversity, but uncertainties remain about its capacity to detect subtle differences in invertebrate community composition comparable to

Molecular diet analysis in zebra and quagga mussels (Dreissena spp.) and an assessment of the utility of aquatic filter feeders as biological eDNA filters

An assay to monitor the eukaryotic diet of mussels and test their utility as biological eDNA filters to monitor planktonic communities is designed and it is shown that mussels could serve as an interesting complementary DNA source for biomonitoring.

Recommendations for tissue homogenisation and extraction in DNA metabarcoding of Malaise trap samples

With increased application of DNA metabarcoding in fast and high-resolution biodiversity assessment, various laboratory protocols have been optimised in recent years and their further evaluation is

Evaluating restoration trajectories using DNA metabarcoding of ground‐dwelling and airborne invertebrates and associated plant communities

Invertebrates are important for restoration processes as they are key drivers of many landscape‐scale ecosystem functions; including pollination, nutrient cycling and soil formation. However,

Pollen DNA metabarcoding identifies regional provenance and high plant diversity in Australian honey

The results show that pollen DNA metabarcoding is a powerful and robust method for detecting honey provenance and examining the diet of honeybees, and has the potential to be used as a novel monitoring tool for honeybee floral resources.



Environmental DNA metabarcoding studies are critically affected by substrate selection

It is demonstrated that single substrate eDNA metabarcoding likely underestimates the total eukaryotic diversity and future eDNA experimental design should consider incorporating multiple substrates or select substrate(s) best suited to the specific detection of target taxa.

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.

DNA from soil mirrors plant taxonomic and growth form diversity.

Whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes is tested and the universal applicability of DNA metabarcoding using soil samples from tropical environments is assessed.

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.

DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet

This method can be adapted to the analysis of dietary samples of various predator species in different ecosystems, for a number of conservation and ecological applications entailing large‐scale population level diet assessment through cost‐effective screening of multiple DNA metabarcodes, and the detection of fine dietary variation among samples or individuals and of rare food items.

DNA metabarcoding—a new approach to fauna monitoring in mine site restoration

Ecological restoration of landscapes is an integral part of the mining process. However, restoration is often constrained by a lack of consistent monitoring approaches. For example, the need for

Meta‐barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity

It is found that DNA from the soil surface reflects overall taxonomic richness and relative biomass of individual species, however, one species that was recently introduced was not detected and animal behaviour was shown to influence DNA deposition rates.

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding.

Compared with standard biodiversity data sets, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, less reliant on taxonomic expertise and auditable by third parties, which is essential for dispute resolution.

Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias

In silico PCR is a useful tool for predicting taxonomic bias in mixed template PCR and that researchers should be wary of potential bias when selecting metabarcoding markers, and results typically corresponded to insilico PCR predictions.