Evaluating a multigene environmental DNA approach for biodiversity assessment

  title={Evaluating a multigene environmental DNA approach for biodiversity assessment},
  author={Alexei J. Drummond and Richard D. Newcomb and Thomas R. Buckley and Dong Xie and Andrew Dopheide and Benjamin C. M. Potter and Joseph Heled and Howard Ross and Leah K. Tooman and Stefanie Grosser and Duckchul Park and Nicholas J. Demetras and Mark I. Stevens and James C. Russell and Sandra H. Anderson and Anna L. Carter and Nicola J. Nelson},
BackgroundThere is an increasing demand for rapid biodiversity assessment tools that have a broad taxonomic coverage. Here we evaluate a suite of environmental DNA (eDNA) markers coupled with next generation sequencing (NGS) that span the tree of life, comparing them with traditional biodiversity monitoring tools within ten 20×20 meter plots along a 700 meter elevational gradient.ResultsFrom six eDNA datasets (one from each of 16S, 18S, ITS, trnL and two from COI) we identified sequences from… 

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.

The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA.

A number of options and approaches that can be used when determining which primers and gene regions are most appropriate for either targeted species detection or metabarcoding macro-organisms from eDNA are discussed.

Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding

Test multiple sample substrates (soil, scat, plant material and bulk arthropods) to determine what organisms can be detected from each and where they overlap demonstrate the importance of selecting appropriate metabarcoding substrates when undertaking terrestrial surveys.

The ecologist's field guide to sequence‐based identification of biodiversity

The aim here is to succinctly describe the different technologies available within the omics toolbox and showcase the opportunities available to contemporary ecologists to advance the understanding of biodiversity and its potential roles in ecosystems.

The ecologist’s field guide to sequence-based identification of biodiversity

The aim here is to succinctly describe theerent technologies available within the omics toolbox and showcase the opportunities available to contemporary ecologists to advance the understanding of biodiversity and its potential roles in ecosystems.

Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes

This study uses a multigene approach, including the mitochondrial cytochrome-c-oxidase subunit I (COI) gene for analyzing species composition and the nuclear hypervariable region V8 of 18S rDNA for analyzing supraspecific biodiversity.

Environmental DNA reveals that rivers are conveyer belts of biodiversity information

It is shown for a subset of these families that eDNA samples overcome spatial autocorrelation biases associated with the classical community assessments by integrating biodiversity information over space, suggesting eDNA in river water also incorporates biodiversity information across terrestrial and aquatic biomes.

Spatial distribution of environmental DNA in a nearshore marine habitat

This study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments.

Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

This study employs eDNA metabarcoding to compare beta diversity patterns of complex pelagic marine communities in tropical coastal shelf habitats spanning the whole Caribbean Sea and detects highly diverse communities, which varied significantly among locations, and proved good descriptors of habitat type and environmental conditions.



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.

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

An overview of meiofaunal metagenetic analyses, ranging from sample preservation and DNA extraction to PCR, sequencing and the bioinformatic interrogation of multiple, independent samples using 454 Roche sequencing platforms, is provided.

Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost.

The taxonomic and ecological diversity of ancient fungal communities was assessed by combining next generation sequencing and metabarcoding of DNA preserved in permafrost by detecting 75 fungal OTUs from 21 orders representing three phyla, although rarefaction analyses suggested that the full diversity was not recovered.

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.

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.

Pyrosequencing enumerates and contrasts soil microbial diversity

This work is the most comprehensive examination to date of bacterial diversity in soil and suggests that agricultural management of soil may significantly influence the diversity of bacteria and archaea.

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity.

This study validates the effectiveness of high-throughput 454 sequencing technology for the survey of soil fungal diversity and identified the Agaricomycetes as the dominant fungal class.

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.

Distribution and Diversity of Soil Microfauna from East Antarctica: Assessing the Link between Biotic and Abiotic Factors

It was found that microfaunal composition and abundance were mostly correlated with the soil geochemical parameters; phosphorus, NO3 − and salinity, and likely to be the result of soil properties and historic landscape formation and alteration, rather than the geographic region they were sampled from.