Towards next‐generation biodiversity assessment using DNA metabarcoding

  title={Towards next‐generation biodiversity assessment using DNA metabarcoding},
  author={Pierre Taberlet and Eric Coissac and François Pompanon and Christian Brochmann and Eske Willerslev},
  journal={Molecular Ecology},
Virtually all empirical ecological studies require species identification during data collection. DNA metabarcoding refers to the automated identification of multiple species from a single bulk sample containing entire organisms or from a single environmental sample containing degraded DNA (soil, water, faeces, etc.). It can be implemented for both modern and ancient environmental samples. The availability of next‐generation sequencing platforms and the ecologists’ need for high‐throughput… 

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.

Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment

Analysis of taxonomic inferences of benthic macroinvertebrate samples of known taxonomic composition obtained using alternative metabarcoding protocols prove metabarcode valid for environmental status assessment and will contribute to accelerating the implementation of this technique to regular monitoring programs.

Next generation sequencing for characterizing biodiversity: promises and challenges

Several challenges should be taken up for coordinating actions at the interface between taxonomy, ecology, molecular biology and bioinformatics in order to develop methods and protocols compatible with both taxonomic and ecological studies.

Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions

The current state of genetic biodiversity monitoring of higher Eukaryotes using Oxford Nanopore Technology’s MinION portable sequencing platform is outlined, as well as areas of recent development are summarized.

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.

Increased performance of DNA metabarcoding of macroinvertebrates by taxonomic sorting

Sorting samples into basic taxonomic groups that require little taxonomic knowledge greatly improves the recovery of taxa with metabarcoding, and the effectiveness of molecular methods opens up the way for a paradigm shift in biomonitoring.

Strategies for sample labelling and library preparation in DNA metabarcoding studies

An overview of the three main workflows for sample‐specific labelling and library preparation in metabarcoding studies on Illumina sequencing platforms; one‐step PCR, two‐ step PCR, and tagged PCR is presented.

e-DNA meta-barcoding: from NGS raw data to taxonomic profiling.

A computational methodology suitable for the taxonomic characterization of 454 meta-barcode sequences is described in detail, and a dataset covering the V1-V3 region belonging to the bacterial 16S rRNA coding gene and produced in the Human Microbiome Project (HMP) from a palatine tonsils sample is analyzed.

Estimating intraspecific genetic diversity from community DNA metabarcoding data

A strategy to infer intraspecific genetic diversity from bulk invertebrate metabarcoding data and holds great promise for biomonitoring efforts that not only seek information about species diversity but also underlying genetic diversity.

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.



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.

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.

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.

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.

Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

The power of applying next-generation pyrosequencing to identify and enumerate eukaryote species assemblages in the context of assessing the impacts of human activity on ecosystems is illustrated.

ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

EcoPrimers, a software for identifying new barcode markers and their associated PCR primers, is presented, an efficient algorithm based on data mining, that allows the analysis of huge sets of sequences.

Using next‐generation sequencing for molecular reconstruction of past Arctic vegetation and climate

The suitability of the P6 loop for analysis of samples containing degraded ancient DNA from a mixture of species is demonstrated by high‐throughput parallel pyrosequencing of permafrost‐preserved DNA and reconstruction of two plant communities from the last glacial period.

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.

New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach

This work demonstrated that this new method for species identification using universal primers that amplify a very short but informative DNA fragment can be applied for diet analyses of a wide range of phytophagous species at large scales and is efficient for mammals, birds, insects and molluscs.

Biological identifications through DNA barcodes

It is established that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals and will provide a reliable, cost–effective and accessible solution to the current problem of species identification.