A national framework for biological heritage assessment across natural and production landscapes

  • Botanical survey, Nethorn. Image - Andrea Byrom

    Botanical survey, Nethorn. Image - Andrea Byrom

  • Broom (Cytisus scoparius) flowers. Image - John Hunt

    Broom (Cytisus scoparius) flowers. Image - John Hunt

  • Glenfern. Image - Andrea Byrom

    Glenfern. Image - Andrea Byrom

Project 1.3

Leader: Dr Gavin Lear The University of Auckland

Mission Statement

To reverse the decline in New Zealand’s biological heritage we require tools to detect incursions, and changes in biodiversity and ecosystem function in order to implement effective mitigation strategies and assess conservation performance. The integration of nationally-consistent eDNA methodologies with existing monitoring programmes will deliver a step change in biodiversity assessment.


A first step in managing New Zealand’s Biological Heritage is to understand “what is out there”.

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, and provides unprecedented taxonomic breadth at a scale not practically achievable through conventional identification of individual organisms.

Two fundamental issues must be overcome in order to harness the potential of eDNA. First, standardised procedures for identification of 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 achieve this the project will develop a New Zealand-wide framework and platform for biological heritage measurement and monitoring using environmental DNA (eDNA) data.

Existing biodiversity assessment initiatives have not explicitly incorporated biosecurity and bioprotection information, and also, they typically exclude the vast majority of New Zealand’s biological heritage such as fungi, microbes, and invertebrates. This is despite the importance of these taxa for ecosystem function and biosecurity.

Developing an eDNA framework and platform to measure and monitor biological heritage will allow surveillance of common, endangered, invasive, and elusive species and underpin environmental reporting. The methods will be extended across New Zealand to provide accessible, robust, and complete information on biological heritage at different temporal and spatial scales. Methodologies developed here will also contribute to other projects within New Zealand’s Biological Heritage National Science Challenge (NSC), and vice versa.

The team’s research lays a solid foundation for the use of eDNA techniques both for biodiversity monitoring and assessment of biosecurity risks. The research has exciting potential to not only unite currently-disparate data generated across different taxa and organisations, but also to bring together diverse users including citizen scientists. Integration of nationally-consistent eDNA methodologies and existing monitoring programmes will deliver a step change in biodiversity assessment.

  1. Standardise eDNA data collection and bioinformatics processes across research groups.
  2. Establish national eDNA informatics platform for the measurement and monitoring of biological heritage across landscapes and for the detection of incursions.
  3. Use eDNA data to address questions on ecological function, biosecurity and biodiversity conservation at the New Zealand-wide scale.
  1. How does biological heritage scale spatially and temporally, and how does this scaling affect our ability to provide robust biodiversity information?
  2. How is biological heritage changing over time, and how will it respond in the future?
  3. How well do measures of diversity and function derived from eDNA correlate with traditional measures?
  4. How correlated are the community attributes of freshwater systems and the terrestrial catchments they drain?
  5. How widespread are invasive pests and diseases and how can eDNA contribute to early detection of new organisms?
  6. How do we best extract ecosystem function information from eDNA data?

A nationally-standardised framework for sharing, integration, validation, re-use and interpretation of the vast array of taxonomic data obtained from eDNA, a first for New Zealand. Coupled with rapid developments in sequencing technology and bioinformatics, the research is providing the groundwork for the next transformational change: a corresponding shift in focus from method development to realworld applications that provide rich information for a range of purposes, including conservation planning and land management decisions.

  • MfE will be using eDNA to complement existing State of the Environmental reporting
  • Regional councils will be using eDNA metrics to complement existing terrestrial and freshwater environmental monitoring and reporting
  • DOC will be using eDNA in their Tier 1 monitoring framework as well as for detection of threatened species
  • MPI and other biosecurity stakeholders will be using eDNA to detect and monitor threats both pre- and post-border
  • Primary production stakeholders will be using eDNA to monitor ecosystem functioning across productive landscapes
  • At least one iwi will be using eDNA to complement existing Maori specific environmental indicators.

The Project Leader will be Dr Gavin Lear (University of Auckland), and the team will include representatives from all institutions engaged in eDNA data collection and analysis. This includes both CRIs and universities. This team has all the expertise required for delivering on the goals of the Project and Challenge Mission, including molecular bioinformatics, data analysis, molecular biology, ecology, and environmental monitoring and reporting.

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

Wu, J,. Anderson, B.J,. Buckley, H.L., Lewis, G., Lear, G. 2016 Aspect has a greater impact on soil bacterial community structure than elevation. FEMS Microbiology Ecology 93(3). DOI:10.1093/femsec/fiw253


Identifying the biases associated with DNA extraction methods for eDNA research

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…


Holdaway, R.J., J.R.Wood, I.A. Dickie, K.H. Orwin, S.J. Richardson, P.O.’B. Lyver, and T.R.Buckley. 2016. Using DNA metabarcoding to assess New Zealand’s terrestrial biodiversity. New Zealand Journal of Ecology, in review.
This manuscript describes the current state of the field of metabarcoding technologies and outlines their future application across New Zealand.

What's New?

Our writing team.
The challenges of working with eDNA

12 December 2017 - Whats new

New paper leading the way in coordinating New Zealand’s scientific community to begin harmonising methods for the extraction,…

Co-designing the commons protocols.
Aotearoa New Zealand Data Commons Project

3 November 2017 - Whats new

Data integration and reuse at scale can create significant value for all parties but it only works if…

Kōkako. Image - Grant Capill
Ark in the Park facilitating eDNA research

22 August 2017 - Whats new

Ark in the Park, an eco-restoration project in the Waitakere Ranges, is providing researchers with the perfect laboratory…

DNA lab. Image - Tom Fraser
eDNA update

13 April 2017 - Whats new

Environmental DNA will be one of several exciting disruptive technologies discussed at the Crazy and Ambitious Conference.…