Real time eDNA tools to improve early detection and response approaches for high risk pest animals

Summary

Rapid detection and identification of high-risk invasive animals either at the point of entry or in the field are essential to prevent new incursions and to enable a rapid response for successful eradication. Detection and monitoring species using environmental DNA (eDNA) is recognised as a powerful tool, and has been shown to have greater sensitivity for less effort and for fewer negative affects compared to traditional survey methods. 

With eDNA now firmly established as a highly effective method for species detection, it is now able to be further refined for routine use in biosecurity applications.  

Status

Commenced

Objectives

  1. Develop rapid eDNA detection tools using real-time technology for in situ application 
  2. Develop new eDNA tests for at least two high-risk invasive species and apply these to field operations 
  3. Validate multi-species eDNA detection framework to enable all species to be detected from a sample or location 
  4. Develop eDNA capability within end-user organisations through targeted training and provide readily available eDNA services for ongoing surveillance 

Project Leader



Professor Dianne Gleeson
Project Team
  • A/Prof Dianne Gleeson – UC (co-project leader)
  • Dr Elise Furlan – UC  (co-project leader)
  • Prof Richard Duncan – UC 
  • Prof Arthur Georges – UC 
  • Prof Stephen Sarre – UC 
  • Dr Anthony Chariton – Macquarie University 
Project Partners
  • University of Canberra (UC)
  • New South Wales Department of Primary Industries (NSW DPI)

The project receives funding from the Australian Government Department of Agriculture, Water and the Environment

Outputs

February 2021 update:

Species specific DNA assays for red-eared slider turtles and Asian black spined toads are being collaboratively developed.

A technical framework has been created to test the proficiency of facilities in extracting and determining the presence or absence of eDNA in water samples.

August 2020 update:

A validated species-specific REST assay has been developed for application in Australia, and this is now being trialled in the field. The project is also working with Qld DAF and contacts in Indonesia to try and source Asian black-spined toad (ABST) tissue and eDNA samples.

Sensitivity limits for eDNA detection were tested in a large-scale carp eradication program in Tasmania, results indicate eDNA can detect low-density carp populations though the sensitivity of the surveys was low. eDNA surveys can be a useful tool for detecting remnant individuals following eradication programmes and a cost-efficient means of monitoring where positive detections are likely to be a rare occurrence.

February 2020 update:

Using the carp eradication programme in Tasmania as a model, detection limits for eDNA in field application have showed that 100 water samples from each lake was enough to detect the low-density carp populations in Lake Sorell and supported the species’ absence from Lake Crescent.

The sensitivity of these surveys overall was low, so further decline in carp density over time will mean more survey effort is required to ensure a high detection sensitivity.

Therefore, at present using eDNA to confidently detect an extremely low-density population still requires a substantial survey effort and financial investment.

This demonstrates that eDNA surveys can be a useful additional tool for not only detecting remnant individuals following eradication programmes and for cost-efficient means of monitoring potential incursions over longer time periods or broader spatial scales where positive detections are likely to be a rare occurrence.

The team has also undertaken joint field sampling with NSW DPI in urban Sydney settings, regions of the MDB, and within the Shoalhaven region in recent months to provide further tech transfer opportunities.

August 2019 update:

EcoDNA is the new name of the research team associated with this project, and its website was launched on 5 March 2019 (www.ecodna.org.au). The website will allow end-users to enquire about eDNA and eventually submit samples for analysis.

Real-time detection methods are being trialed using portable DNA sequencing tools. Whole genomes can be sequenced directly from water samples, however methods to improve species identification are underway. Work is currently underway on the eDNA metabarcoding abundance framework and models are being developed to predict competition between DNA sequences.

A proposed national reference laboratory will be developed over three years to perform research and extension to intergovernmental and cross-sectoral department business operations such as border surveillance using real-time tools. The ornamental fish trade will be examined as a
proof-of-concept.

Development of proposals for eDNA applications in an expanded list of biosecurity risks and established pests is being prepared in a report by the EcoDNA team.

February 2019 update:  

The development of new eDNA detection methods are ongoing. 

The research group launched www.ecoDNA.org.au to further enhance the outcomes of their research. 

Scientific publications:

  • Rojahn J, Pearce L, Gleeson DM, Duncan RP, Gilligan DM, Bylemans J. The value of quantitative environmental DNA analyses for the management of invasive and endangered native fish. (Submitted)
  • Furlan, E., Davis, J., Duncan, R. (2020).Identifying error and accurately interpreting environmental DNA metabarcoding results: A case study to detect vertebrates at arid zone waterholes. Molecular Ecology Resources, early online: https://doi.org/10.1111/1755-0998.13170
  • Nichols, S., Kefford, B., Campbell, C., Bylemans, J., Chandler, E., Bray, J., Shackleton, M., Robinson, K., Carew, M., Furlan E.(2019).Towards routine DNA metabarcoding of macroinvertebrates using bulk samples for freshwater bioassessment: effects of debris and storage conditions on the recovery of target taxa. Freshwater Biology, 65(4), 607-620.
  • Bylemans, J., Gleeson, D., Hardy, C., Duncan, R., Furlan, E. (2019). A performance evaluation of targeted eDNA monitoring and eDNA metabarcoding for freshwater fishes. Environmental DNA, 1(4), 402-414.
  • Furlan, E., Gleeson, D., Wisniewski, C., Yick, J., Duncan, R., (2019). eDNA surveys to detect species at very low densities: A case study of European carp eradication in Tasmania, AustraliaJournal of Applied Ecology, 56(11), 2505-2517.
  • Bylemans J, Furlan EM, Gleeson DM, Hardy CM, Duncan RP (2018) Does size matter? An experimental evaluation of the relative abundance and decay rates of aquatic eDNA. Environmental Science & Technology.
  • Bylemans J, Gleeson D, Lintermans M, Hardy C, Beitzel M, Gilligan D, Furlan E (2018) Monitoring riverine fish communities through eDNA metabarcoding: determining optimal sampling strategies along an altitudinal and biodiversity gradient. Metabarcoding and Metagenomics 2: e30457
  • Furlan E, Gleeson D, Wisniewski C, Yick J, Duncan R (2019) Applying eDNA surveys to confidently establish eradication success: A case study of European carp control in Tasmania, Australia. Journal of Applied Ecology
  • Hinlo MA, Lintermans M, Gleeson D, Broadhurst B, Furlan E (2018) Performance of eDNA assays to detect and quantify an elusive benthic fish in upland streams. Biological Invasions 20: 3079-3093

News articles:

20/02/20 – https://invasives.com.au/news-events/low-can-go-environmental-dna-edna-detection/