A new method for estimating environmental DNA sensitivity

Background

University of Canberra researcher, Dr. Elise Furlan, isolates eDNA from water samples by filtration.
University of Canberra researcher, Dr. Elise Furlan, isolates eDNA from water samples by filtration.

Invasive aquatic species are a major threat to native species and ecological communities, nationally and internationally. Early detection of such species while they are still rare is the key to preventing their establishment but can be problematic using conventional sampling. Traditional detection techniques are unable to identify species at all life stages and are often unable to detect incursions until the species has reached a reasonably high density, often after they have become established. This seriously limits the ability to successfully contain or eradicate the species.

Environmental DNA, or eDNA, relies on detecting trace amounts of DNA that animals release into their environment via shedding skin cells, faeces or urine. eDNA has the potential to overcome the limitations associated with traditional detection techniques, and provide a cost-effective, sensitive tool to assist in the early detection and ongoing monitoring of invasive aquatic species.

The Issue

Estimated eDNA concentration of the invasive Oriental weatherloach (Misgurnus anguillicaudatus) in three streams sampled during autumn and spring. Notice how the concentration can vary between sites and seasons.
Estimated eDNA concentration of the invasive Oriental weatherloach (Misgurnus anguillicaudatus) in three streams sampled during autumn and spring. Notice how the concentration can vary between sites and seasons.

The sensitivity of eDNA needs to be determined for each application, as it is likely to change depending on the particular field and laboratory methods used, the species targeted and environmental conditions. Previous detection models have not taken into account the sensitivity of each of these components and do not allow managers/researchers to determine the sensitivity of their particular eDNA survey.

The Research

The Invasive Animals CRC funded project, led by Dr Dianne Gleeson (University of Canberra, Institute for Applied Ecology) has been developing eDNA technologies for application in Australia. The research team has recently published a new method for estimating the concentration and dispersion of target DNA at survey sites to estimate the sensitivity of eDNA for each particular application. This method can be applied to eDNA surveys in any environment including freshwater, marine or terrestrial systems. It allows DNA concentration in the environment to be estimated, detection probabilities to be quantified, and to explore the sensitivity of alternative sampling regimes. The overall outcome is better informed management decisions.

Over the course of their five year project (2012-17) the project achieved the following impacts:

  • Completed eDNA field validations for three key invasive fish species (Perca fluviatilis, Misgurnus anguillicaudatus, and Cyprinus carpio).
  • Developed a standardised protocol that incorporates field sampling, laboratory methods, and data analysis and
    interpretation that is the most cost effective and efficient
    using available technologies.
  • Successfully implemented the direct application of eDNA for
    the management of an invasive species, redfin perch, with
    findings published in an international scientific journal.
  • Developed a multispecies detection method for whole fish
    community analysis within a water system.
  • Completed field-testing of the eDNA meta-barcoding high
    throughput detection system for multiple species within a
    community and submit results for publication.
The eDNA research team based at the University of Canberra, Australia
The eDNA research team based at the University of Canberra, Australia

Related articles

Bylemans, J., Furlan, E.M., Pearce, L., Daly, T., Gleeson, D.M.
(2016). Improving the containment of a freshwater invader
using Environmental DNA (eDNA) based monitoring. Biological
Invasions. 18: 3081.

Bylemans J., Furlan E.M., Hardy C.M., McGuffie P., Lintermans
M., Gleeson D.M. (2016) An environmental DNA (eDNA) based
method for monitoring spawning activity: a case study using the
endangered Macquarie perch (Macquaria australasica).

Furlan E, Gleeson D (2016) Improving reliability in environmental
DNA detection surveys through enhanced quality control. Marine
and Freshwater Research.

Furlan E, Gleeson D (2016) Environmental DNA detection
of redfin perch, Perca fluviatilis. Conservation Genetics
Resources. 8:115.

Furlan E, Gleeson D, Hardy C, Duncan R (2016) A framework
for estimating sensitivity of eDNA detection. Molecular Ecology
Resources. 16:641-654.

Hinlo R, Furlan E, Suitor L, Gleeson D.M. (2017). Environmental
DNA monitoring and management of invasive fish: comparison
of eDNA and fyke netting. Management of Biological Invasions
Management of Biological Invasions 8, (1) 89–10010.1111/1755-0998.12483