A national framework for biodiversity assessment across natural and production ecosystems

  • Gavin Lear - students in the field (2)

    Gavin Lear - students in the field

  • Gavin Lear - students in the field

    Gavin Lear - students in the field

In a New Zealand first, researchers have developed a nationwide database to integrate and share eDNA data and other measures of biological diversity across landscapes.

eDNA, or environmental metabarcoding, is the analysis of DNA that has been extracted directly from environmental samples such as soil or freshwater. 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 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 other 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.

Research Partners

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.

Auckland University of Technology

Publications

Bulman, S., McDougal, R., Hill, K., Lear, G (2018) Opportunities and limitations for DNA metabarcoding in Australasian plant-pathogen biosecurity. Australasian Plant Pathology. Accepted

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., Weaver, L. (2018) Towards robust and repeatable sampling methods in eDNA-based studies. Molecular Ecology Resources. 10.1111/1755-0998.12907

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

Lear, G., Dickie, I., Banks, J., Boyer, S., Buckley, H.L., Buckley, T.R., Cruickshank, R., Dopheide, A., Handley, K.M., Hermans, S., Kamke, J., Lee, C.K., Macdiarmid, R., Morales, S.E., Orlovich, D.A., Smissen, R., Wood, J., Holdaway, R (2018) Methods for the Extraction, Storage, Amplification and Sequencing of DNA from Environmental Samples. New Zealand Journal of Ecology. 42(1) 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, Lewis G 2017. Following Rapoport’s Rule: the geographic range and genome size of bacterial taxa decline at warmer latitudes. Environmental Microbiology, 19(8), 3152-3162.  doi:10.1111/1462-2920.13797

Orwin, K.H., Dickie, I.A., Holdaway, R., Wood, J.R (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

Hermans, S. M., H. L. Buckley, B. S. Case, F. Curran-Cournane, M. Taylor, G. Lear.  2017. ‘Bacteria as Emerging Indicators of Soil Condition’, Applied and Environmental Microbiology, 83 (1): 1-13

Holdaway, R.J., Wood, J.R., Dickie, I.A., Orwin, K.H., Bellingham, P.J., Richardson, S.J., Lyver, P.O.B., Timoti, P. and Buckley, T.R., 2017. Using DNA metabarcoding to assess New Zealand’s terrestrial biodiversity. New Zealand Journal of Ecology 41(2): 251-262 DOI:10.20417/nzjecol.41.28

Study Area

The study was carried out within the boundaries of Ark in the Park, an eco-restoration project in the Cascades Kauri Park, northern Waitakere Ranges, Auckland. The project, a partnership between Forest and Bird, and Auckland Council, ultimately aims to help restore the the ecology of the area to its natural state by controlling non-native pests and predators.