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Environmental DNA: revolutionising how we investigate northern Australian aquatic life

  • Credit: Matt Mackintosh

  • Banner_eDNA sample collection©HRobson

  • FW turtle slider

  • Banner_Large tilapia in Ayr

  • eDNA filter post-filtering©H.Robson

  • Banner_eDNA PCR gel

TropWATER is leading this large-scale research programme which aims to develop rapid and cost-effective eDNA technology to identify and monitor all northern Australian aquatic species. This technology is revolutionising how we investigate life underwater and the TropWATER team are experts in using eDNA-based approaches for improving our understanding of freshwater biodiversity, and in practical monitoring and assessment applications. We are currently applying eDNA techniques to estimate the presence and distribution of aquatic invasive species (tilapia, climbing perch), rare and endangered species (sawfish, frogs, turtles), and to determine the potential effects of fish passage barriers on barramundi movements.

As the pace of development increases, there is a pressing need for more information on the health and biodiversity status of our aquatic environments. To acquire this knowledge, monitoring of species and populations is essential to obtain reliable distribution patterns in space and time. However, field sampling, especially in remote locations in northern Australia, is expensive and poses many resourcing, safety and logistical challenges. This has limited our knowledge of aquatic biodiversity in such areas.

Environmental DNA (eDNA) is an efficient, non-invasive and easy-to-standardise sampling approach, with field sampling that can easily be conducted by non-scientists. Coupled with sensitive, cost-efficient and ever-advancing DNA sequencing technology, it has transformed our way of doing environmental science. Whether using the multi-species (species-specific) or universal approach, eDNA techniques have a wide range of applications from biodiversity monitoring, early detection of invasive species, to animal diet assessment. These techniques can be used for a wide variety of taxonomic groups such as bacteria, viruses, fungi, plants, crustaceans, molluscs, invertebrates, fish, amphibians, birds and mammals.

DNA Metabarcoding is a very powerful approach, allowing the detection of many different species belonging to one, or multiple taxonomic groups, without any prior knowledge of species distribution in the study area. Thus, it has an enormous potential to boost data acquisition in biodiversity research. This game-changing approach will provide researchers, managers and citizen-scientists alike with a more reliable and cost-effective approach for environmental monitoring of aquatic resources, thereby avoiding the need for taxonomic expertise and correct identification of cryptic species. 

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What is environmental DNA (eDNA) and how does it work?

Environmental DNA (eDNA) is DNA that has been released by an organism into the environment, via faeces, hair, urine, skin or gametes. This DNA can be extracted directly from environmental samples such as soil, sediment, and water without having to catch the target organism. The use of eDNA technology allows positive identification of the presence of aquatic species at any life stage and from both sexes from the collection and analysis of DNA material in water samples from different environments (freshwater, marine). In other words, surveying an aquatic field site is as easy as collecting a water sample. 

What is DNA Metabarcoding?

The term “DNA barcoding” is used for species identification based on good quality DNA. The word “meta” is added when multiple species are identified from a single sample, e.g. DNA metabarcoding. DNA metabarcoding is a rapid method of biodiversity assessment that combines two powerful technologies: DNA-based identification and high-throughput DNA sequencing. DNA metabarcoding uses universal PCR primers to mass-amplify DNA barcodes from mass collections of organisms or from a single environmental sample containing degraded DNA–environmentalDNA (eDNA). The PCR product is sent to a next generation sequencer and the result is a wealth of DNA sequences which can be matched to sequences in a reference database to generate a list of species present.

Services provided by TropWATER

TropWATER provides state-of-the-art sequencing services and instrument availability to promote advances in genomics and molecular biology research. Located at James Cook University's Australian Tropical Science and Innovation Precinct (ATSIP), our lab services are available to investigators from institutions nationwide.

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