Putting the ‘CSI’ into CSIRO on World Water Day

Potentially applicable to coastal ecosystems around the world, the technique is based on a custom-made DNA microarray (gene chip), which contains DNA sequences from over 42,000 organisms found at the bottom of oceans and estuaries. A significant proportion of this genetic information was derived from samples taken around Sydney Harbour.

Using the chip, scientists can investigate how many and what type of organisms are present in sediments from these sites, providing valuable insight into the biodiversity and health of the ecosystem.

“What is so great about the chip is that we can now look for tens of thousands of different organisms whereas we used to be limited to about 30 to 40 species, which only revealed a tiny part of the whole picture,” says CSIRO aquatic ecologist Dr Anthony Chariton.

“The traditional approach involves using a microscope to identify and count every organism in a sample – a time-consuming process that required a highly skilled person to complete. The new technique is faster, cheaper, more accurate, more sensitive and can be used to assess biodiversity in all types of marine environments, from Port Phillip Bay to Darwin Harbour.”

In order to develop the chip, the interdisciplinary team obtained sequences from thousands of organisms such as crabs, marine snails and worms through to those that are invisible to the naked eye.

CSIRO molecular geneticist Dr Chris Hardy says that when samples from a particular site are applied to the chip, the DNA from organisms in the sample binds to gene targets on the chip. This results in a series of spots on the chip lighting up. Each organism corresponds to a different sequence of spots, so the more sequences that light up the more species are present in our sample.” 

The team compares samples from impacted sites (for example those affected by chemical contamination or drought) with samples from pre-impacted or unaffected sites to determine the number or type of species present. This provides valuable information about how these communities are changing in response to environmental pressures.

“Accurately assessing the health of our waterways is imperative if we hope to protect our ecosystems from human activity,” Dr Hardy says.

Using this new approach, scientists can quickly and accurately identify changes or declines in aquatic biodiversity and thereby improve the chances of effectively intervening and preventing further damage to our waterways.

This program has been assisted by the New South Wales Government through its Environmental Trust and the Australian Government Rural Industries Research and Development Corporation.