Original story by Laura Glitsos, ScienceNetwork Western Australia
THE WA Department of Fisheries is reporting positive outcomes from the incorporation of new DNA-based monitoring technology to protect and manage our aquatic ecosystems.
Dr Snow says applying real-time polymerase chain reaction can help identify microscopic forms of these pests in water samples so that we can detect their arrival at a very early stage. Image: Cory Doctorow
WA DoF supervising research scientist Dr Mike Snow says the application of methods such as real-time polymerase chain reaction (PCR) and DNA barcoding is changing the nature of monitoring and conservation.
DNA barcoding has already been incorporated for the rapid detection and identification of the Asian green mussel, a harmful marine pest which can have significant economic, environmental and even human health issues.
“One of the problems is that we often have to rely on expert taxonomists for identification of a particular species, which may sometimes not even be available in Australia as taxonomy is a traditional skill that is difficult to access these days,” Dr Snow says.
“And it can be particularly difficult to identify some pests like mussels or sea squirts from closely related species that are native to our waters.”
“But with DNA barcoding we can now rapidly identify and confirm these agents and we can take appropriate action, for example, we can turn a vessel around or clean a vessel in a much more efficient way.”
DNA barcoding uses a very short genetic sequence, or marker, from a standard part of the genome, in much the same way as a supermarket scanner distinguishes products using the black stripes of the Universal Product Code.
In addition, Dr Snow says applying real-time PCR can help identify microscopic forms of these pests in water samples so that we can detect their arrival at a very early stage and monitor for their spread.
It can also indicate the quantity of a specific pest in a sample.
This technology is based on amplifying a highly specific region of a pest organism’s DNA millions of times, with its positive amplification generating fluorescent light that can be detected by a laser in real-time.
“It is currently performed in a lab, but maybe one day will be able to be performed on site,” Dr Snow says.
He says that the application of these technologies has been so far very successful, and a scientific paper compiled by the DoF research team is in the process of publication.
Dr Snow says the next step will be building on the concept of “environmental DNA” or eDNA.
This method uses the latest ‘next generation sequencing’ technology to simultaneously identify the barcodes of up to millions of organisms in a sample.
It has shown great promise in identifying species based on the minute traces of DNA shed into the water column by all the animals living in it.
“It’s currently being explored for its practicality for detecting the range of pest or native fish species present in freshwater lakes, and it may be far more efficient than traditional trapping.”
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