Status: Completed
Start date: 29 January 2017
Completion date: 30 June 2022
Project code: P01-I-004
Species/Threats: Multiple
Download project report (PDF, 2.94 MB)
The National eDNA Reference Centre (NRC) at the University of Canberra was established in 2022, building on its national leadership role fostered by the Centre. The project team wanted to use real-time sampling techniques of environmental DNA (eDNA) to build a tool that could find an invasive aquatic species.
The team used the Asian black-spined toad to develop a specific approach that can indicate whether an individual toad is from Indonesia or somewhere else in South-East Asia. This is important for detecting the toads and working out where captured specimens have come from, before they enter Australia.
The objectives of this project were:
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.
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.
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.
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.
The development of new eDNA detection methods are ongoing.
Bylemans J, Furlan E, Gleeson D, Hardy C and Duncan R (2018) Does size matter? An experimental evaluation of the relative abundance and decay rates of aquatic eDNA Environmental Science & Technology 52(11), 6408-6416. https://doi.org/10.1021/acs.est.8b01071
Bylemans J, Gleeson D, Hardy C, Duncan R and Furlan E (2019) A performance evaluation of targeted eDNA monitoring and eDNA metabarcoding for freshwater fishes Environmental DNA 1(4), 402-414. https://doi.org/10.1002/edn3.41
Bylemans J, Gleeson D, Hardy C and Furlan E (2018) Towards an ecoregion scale evaluation of eDNA metabarcoding primers: A case study for the freshwater fish biodiversity of the Murray-Darling Basin (Australia) Ecology and Evolution 8(17), 8697-8712. https://doi.org/10.1002/ece3.4387
Bylemans J, Gleeson D, Lintermans M, Hardy C, Beitzel M, Gilligan D and Furlan E (2018) Monitoring riverine fish communities through eDNA metabarcoding: determining optimal sampling strategies along an altitudinal and biodiversity gradient Metabarcoding and Metagenomics 2(30457). https://doi.org/10.3897/mbmg.2.30457
Furlan E, Davis J and 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. https://doi.org/10.1111/1755-0998.13170
Furlan E, Gleeson D, Wisniewski C, Yick J and Duncan R (2019) eDNA surveys to detect species at very low densities: A case study of European carp eradication in Tasmania Australia Journal of Applied Ecology 56(11), 2505-2517. https://doi.org/10.1111/1365-2664.13485
García-Díaz P (2019) A concise guide to developing and using quantitative models in conservation management Conservation Science and Practice 1(2), 11. https://doi.org/10.1111/csp2.11
Hinlo R, Lintermans M, Gleeson D, Broadhurst B and Furlan E (2018) Performance of eDNA assays to detect and quantify an elusive benthic fish in upland streams Biological Invasions 20(11), 3079-3093. https://researchprofiles.canberra.edu.au/en/publications/performance-of-edna-assays-to-detect-and-quantify-an-elusive-bent
Nichols S, Kefford B, Campbell C, Bylemans J, Chandler E, Bray J, Shackleton M, Robinson K, Carew M and E Furlan (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. https://doi.org/10.1111/fwb.13443
Rojahn J, Gleeson DM, Furlan E, and Haeusler E and Bylemans J (2021) Improving the detection of rare native fish species in environmental DNA metabarcoding surveys Aquatic Conservation: Marine and Freshwater Ecosystems 31, 990-997. https://doi.org/10.1002/aqc.3514
Rojahn J, Pearce L, Gleeson DM, Duncan, RP, Gilligan DM and Bylemans J. (2021) The value of quantitative environmental DNA analyses for the management of invasive and endangered native fish Freshwater Biology 66, 1619-1629. https://doi.org/10.1111/fwb.13779
Rojahn J, Trujillo-González A, Gleeson D et al (2024) Does mesocosm validation of environmental DNA methods translate to natural environment monitoring applications? A case study detecting a high-profile invader; the red eared slider turtle, Trachemys scripta elegans, in Australia Conservation Genetic Resources 16, 63-71. https://doi.org/10.1007/s12686-023-01333-3
Rourke ML, Fowler AM, and Hughes JM (2021) Environmental DNA (eDNA) as a tool for assessing fish biomass: A review of approaches and future considerations for resource surveys Environmental DNA 4, 9-33. https://doi.org/10.1002/edn3.185
Trujillo-Gonzalez A, Villacorta-Rath C, White NE, Furlan EM, Sykes M, Grossel G, Divi U, and Gleeson D (2021) Considerations for future environmental DNA accreditation and proficiency testing schemes Environmental DNA. https://doi.org/10.1002/edn3.243
