Developing eDNA methods for tropical waters

In northern Australia, traditional techniques used to detect aquatic species can be difficult, labour-intensive and expensive due to factors such as remoteness, large scales, limited and variable site access, and hazards such as crocodiles. To support sustainable development in the region, we need to better understand, and keep track of, the health of our rivers, creeks and waterholes and the plants and animals that live in them. A method that allows managers and researchers to overcome many of these challenges would therefore be greatly beneficial.

What is environmental DNA (eDNA)?

eDNA is DNA that has been released by an animal into its aquatic environment, via faeces, hair, urine, skin, sperm or eggs. This DNA only lasts a short time in the environment before it is broken down. Water, sediment or soil samples taken from waterways contain this DNA and so will give information about which species are present in that environment without having to catch the target animal.

How does the project eDNA method work?

The eDNA method for this project uses genetic primers or probes that provide unique genetic identifiers for particular species, to amplify DNA codes from a water or sediment sample. DNA extracted from samples is matched against the primer or probe for that species. For example we can identify if a species of turtle at any life stage is present in a body of water by analysing the eDNA material in a water sample from that location. In other words, surveying an aquatic field site may be as easy as collecting a water sample.

Analysing environmental DNA (eDNA) is a relatively new technology which detects the presence of DNA from aquatic species in small water samples. The technique has a number of advantages over traditional monitoring, including:

  • Time and cost-efficiency.
  • Increased accuracy.
  • Ability to detect a wide range of species from a single water sample.
  • Targeted detection, e.g. of rare species or new pest species.
  • Greater safety when sampling in the field.

This project is developing eDNA technology and trial field programs for an array of northern Australian aquatic species of conservation and management significance. It aims to significantly improve the efficacy of field surveys and monitoring, hence providing a cost-effective tool to dramatically improve our knowledge of aquatic biodiversity in northern Australia. The information generated from this study can be used to inform planning processes, impact assessments and development decisions.

Project activities include:

  • Develop eDNA probes for up to 10 key aquatic species across different taxonomic groups.
  • Conduct field programs to test the probes and answer management questions relevant to the selected species.
  • Trial improved methods for field sampling and transporting eDNA samples, and understand how logistical and environmental factors affect detection probability.

The last point is critical for determining how eDNA monitoring could be rolled out in northern Australia and which species and situations it’s best suited for.

Planned outputs from this project include:

  • eDNA probes for key aquatic vertebrate species.
  • Protocols for eDNA field sampling.
  • Increased information on the distribution of key species.
  • Increased information on the distribution of pest species.
  • Comparisons of the effectiveness of eDNA to traditional sampling methods.
  • Public awareness about the application of eDNA probes, including public forums, technical reports, and online promotion.

This research applies across the Northern Hub region.

August 2021

The Northern Australia Environmental Resources Hub addressed key research questions to come up with practical, on-ground solutions to some of the north’s most complex environmental challenges. A transdisciplinary research approach has been at the heart of the hub. Integrating key research users – policy-makers and land managers including Traditional Owners and ranger groups – into the co-design of research projects has led to rapid uptake of research outcomes into land management practices and decision-making. The hub has produced this wrap-up video outlining these impacts from the perspectives of research users.

The project is led by Professors Damien Burrows and Dean Jerry from James Cook University (JCU). They are being assisted by other researchers at JCU, The University of Western Australia, Charles Darwin University, Griffith University and CSIRO.

This project is due for completion in June 2021.

Damien Burrows, James Cook University
[email protected]
(07) 4781 4262

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  • eDNA method is an exciting new method for monitoring aquatic environments. Photo: Michael Douglas.
  • Surveying for aquatic species may be as simple as collecting a water sample. Photo: Damien Burrows.
  • This project has developed an eDNA assay for the invasive cane toad Rhinella marina, photo NESP Northern Hub.
  • Surveying for aquatic species is as simple as collecting a water sample. Photo: Damien Burrows.
  • eDNA techniques are proving to have a wide range of applications in both marine and freshwater systems. Photo: Damien Burrows.