A national framework for biodiversity assessment across natural and production ecosystems

  • Botanical survey, Nethorn. Image - Andrea Byrom

    Botanical survey, Nethorn. Image - Andrea Byrom

In a New Zealand first, researchers have developed a nationwide database to integrate and share eDNA data to allow biological diversity across our diverse landscapes to be assessed and compared.

The analysis of eDNA requires the extraction and identification of DNA directly from environmental samples such as soil or freshwater.

Environmental DNA, or eDNA, refers to the DNA that is shed or excreted from biological organisms, for example as skin, hair, faeces or urine. It provides a window into the world of biological diversity that is otherwise largely hidden from view.

This powerful new technology is transforming how biological diversity is measured. It is being used by a BioHeritage research team led by Dr Gavin Lear, University of Auckland, to develop a nationwide database – or virtual hub – that integrates eDNA data with existing monitoring programmes.

New Zealand needs state-of-the-art molecular tools, such as eDNA metabarcoding, to detect biosecurity incursions and to assess the state of biodiversity and ecosystem function.

Creating a national database for eDNA information allows these data to be kept in consistent format for use by researchers all over the country, maximising opportunities for biodiversity and biosecurity monitoring.

It has the potential to unite currently disparate data generated across different populations and organisations, plus bring together diverse users including citizen scientists, regional councils, the Department of Conservation, iwi and private landowners.

Ultimately, the virtual hub provides robust information that can be used to detect biosecurity threats, assess conservation performance and enable data visualisation.

To date, more than 20 research organisations and consortia are feeding into and using the virtual hub and more are being encouraged to do so. The research team is also collaborating with Australia’s Biomes of Australian Soil Environments (BASE), in line with a strategic intent to partner with relevant international groups in high-impact areas.

In addition to the virtual hub, the research team is exploring potential real-world applications for national biodiversity assessment for primary sectors.

This project is helping the BioHeritage Challenge achieve its goal of creating a bioheritage scorecard for Aotearoa New Zealand, through national monitoring and reporting frameworks.

BioHeritage’s role is to break down barriers between organisations and individual scientists by coordinating and focusing the research of top scientists from 18 Challenge Parties.

This project is being driven by Challenge Party the University of Auckland, which is drawing together best national teams from across Crown Research Institutes, universities and other institutions and stakeholders.

University of Auckland

Dickie, I.A., Boyer, S., Buckley, H.L., Duncan, R.P., Gardner, P., Hogg, I.D., Holdaway, R.J., Lear, G., Makiola, A., Morales, S.E., Powell, J.R., and L. Weaver. 2018. Towards robust and repeatable sampling methods in eDNA-based studies.  Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.12907

Hermans, S. M., H. L. Buckley, B. S. Case, F. Curran-Cournane, M. Taylor, and G. Lear. 2017. Bacteria as emerging indicators of soil condition, Applied and Environmental Microbiology, 83(1): 1-13. https://doi.org/10.1128/AEM.02826-16

Hermans, S. M., Buckley, H. L., and G. Lear. 2018. Optimal extraction methods for the simultaneous analysis of DNA from diverse organisms and sample types, Molecular Ecology Resources, 18(3) 557-569. https://doi.org/10.1111/1755-0998.12762

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

Laroche, O., Wood, S.A., Tremblay, L.A., Ellis, J.I., Lear, G., and X. Pochon. 2018. A cross-taxa study using environmental DNA/RNA metabarcoding to measure biological impacts of offshore oil and gas drilling and production operations, Marine Pollution Bulletin, 127: 97-107.  https://doi.org/10.1016/j.marpolbul.2017.11.042

Laroche, O., Wood, S.A., Tremblay, L.A., Lear, G., Ellis, J.I., and X. Pochon. 2017. Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA to assess offshore oil production impacts on benthic communities, PeerJ 5: e3347.  https://doi.org/10.7717/peerj.3347

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, amplification and sequencing of DNA from environmental samples, New Zealand Journal of Ecology, 42(1): 10-+.  https://doi.org/10.20417/nzjecol.42.9

Lear, G., Lau, K., Perchec, A., Buckley, H., Case, B., Neale, M., Flerer, N., Leff, J., Handley, K., and G. Lewis. 2017. Following Rapoport’s Rule: the geographic range and genome size of bacterial taxa decline at warmer latitudes, Environmental Microbiology, 19(8), 3152-3162.  https://doi.org/10.1111/1462-2920.13797

Orwin, K.H., Dickie, I.A., Holdaway, R., and J.R. Wood. 2018. A comparison of the ability of PLFA and 16S rRNA gene metabarcoding to resolve soil community change and predict ecosystem functions, Soil Biology and Biochemistry, 117: 27-35.  https://doi.org/10.1016/j.soilbio.2017.10.036

Sub-projects

A national framework for biodiversity assessment across natural and production ecosystems

We are trying to determine the best DNA extraction method to identify a wide range of organisms present…

eDNA hub

Scientists are encouraged to contribute their environmental DNA (eDNA) datasets to Aotearoa’s first national biodiversity database where researchers…

Investigating local patterns in microbial communities: characterising and quantifying the links between soil and freshwater

By collecting both soil and stream samples within a single catchment, we want to determine whether there is…

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