• Southern skink. Image - James Reardon

    Southern skink. Image - James Reardon

Synthesis publications on DNA metabarcoding: a window on the hidden world of New Zealand’s terrestrial biodiversity

Forensic science has revealed the potential to explore the diversity of life within any sample − not just from DNA in live cells, but from the skin, hair and bodily fluids of organisms inhabiting or moving through an environment.

This ability to extract and sequence DNA directly from environmental samples (environmental DNA, or eDNA) is transforming our understanding and measurement of biological diversity. It is no longer necessary to sight an organism or an individual to confirm its presence at a sampling location. ‘Metabarcoding’ of DNA thus provides a window into the world of microbial and microscopic diversity that would otherwise be largely hidden from view.

Current approaches for analysing biodiversity based on eDNA vary widely among laboratories, particularly among scientists focusing on different taxa. Comparing data collected by different researchers can be subject to biases, many of which remain poorly quantified. These biases are an impediment to scaling up the application of DNA metabarcoding and addressing national-scale questions.

Two fundamental issues must be overcome in order to harness the potential of eDNA. First, standardised procedures for identifying life from environmental DNA must be developed. Second, to achieve a nationally integrated picture of biodiversity that incorporates eDNA data, streamlined sharing of such data is critical.

To capitalise fully on this powerful new technology, the Metabarcoding for environmental monitoring (eDNA) team assessed the current strengths and weaknesses of DNA metabarcoding and developed a conceptual framework for validating eDNA data and integrating it with conventional methods. They also explored potential applications for national biodiversity assessment and for primary sectors. A nationally standardised framework for sharing, integration, validation, re-use and interpretation of the vast array of taxonomic data obtained from eDNA is a first for New Zealand.

Holdaway, R. J., J. R. Wood, I. A. Dickie, K. H. Orwin, P. J. Bellingham, S. J. Richardson, P. O. Lyver, P. Timoti, and T. R. Buckley. 2017. Using DNA metabarcoding to assess New Zealand's terrestrial biodiversity, New Zealand Journal of Ecology, 41: 251-62. https://doi.org/10.20417/nzjecol.41.28 Lear, G. I. , J. Dickie, S. Banks, H.L. Boyer, T.R. Buckley, R. Buckley, A. Cruickshank, K.M. Dopheide, S. Handley, J. Hermans, C.K. Kamke, R. Lee, S.E. MacDiarmid, D.A. Morales, R. Orlovich, J. Smissen, Wood, and R. Holdaway. 2017. Methods for the extraction, storage, amplifi cation and sequencing of DNA from environmental samples, New Zealand Journal of Ecology, 42(1):10-.

A virtual hub for sharing eDNA data

The Metabarcoding for environmental monitoring (eDNA) team has facilitated researchers from more than 20 research organisations and consortia, and stakeholders, to develop a ‘virtual data hub’ to share molecular genomic data across organisations, enable data visualisation, and detect biosecurity threats. International connections with the European Bioinformatics Institute, the eResearch 2020 consortium, the Biomes of Australian Soil Environments (BASE) project in Australia, and eResearch 2020 have provided significant in-kind support.

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