Understanding Antarctic ecosystems using e-DNA

Dr Bruce Deagle with a test tube in his laboratory.
Dr Bruce Deagle is trialling methods to identify zooplankton and fish in seawater samples by amplifying environmental DNA. (Photo: Glenn Jacobson)
A scientist examines zooplankton specimens on a small silk sheet, collected by the continuous plankton recorder onboard the Aurora Australis.A crew member retrieves the continuous plankton recorder from the ocean off the back of the Aurora Australis.The Aurora Australis in the distance off the coast of Macquarie Island.

Can a small water sample tell you what sort of fish, krill, or even penguins and seals, are living in different parts of the Southern Ocean?

That’s what scientists from the Australian Antarctic Division are hoping to find out, using environmental DNA, or e-DNA.

Molecular ecologist, Dr Bruce Deagle, said e-DNA technology can identify hundreds of species in an environmental sample – such as water or soil – by sequencing DNA in the sample.

“Being able to characterise organisms in small water samples, by the traces of DNA they leave behind, could be a very useful technique for monitoring who or what is in the Southern Ocean,” Dr Deagle said.

“We can already monitor phytoplankton and bacteria using this method, but we want to see if we can identify larger zooplankton, like copepods and krill, as well as different fish species, and potentially even penguins and seals.

The approach relies on ‘barcodes’, which are segments of DNA unique to different species. These genetic markers are targeted in the sample, and then compared to a reference database to identify the organisms.

“e-DNA has been used in lakes and ponds, where the inhabitants don’t move much and the water doesn’t move in large volumes, but we don’t know yet whether it will be useful for open ocean samples,” Dr Deagle said.

To find out, Dr Deagle and his colleague Andrea Polanowski collected about 200 two-litre water samples during a voyage to Macquarie Island in March this year.

At the same time, they collected zooplankton samples using a Continuous Plankton Recorder (CPR) – a century-old technology.

The CPR is towed behind the ship, catching phytoplankton and zooplankton on a silk mesh that slowly winds through the instrument. The organisms captured on the silk can then be identified under the microscope.

“We’ll be able to compare the CPR zooplankton samples with our eDNA results to see how well they match,” Dr Deagle said.

“While we don’t have a direct comparison for fish, we’ll compare our eDNA results with our knowledge of what fish species should be there.

“We’ll also try to identify penguins and seals, just to see if we can detect free-floating DNA from these animals.”

Dr Deagle and his team are now experimenting with different sample processing methods to find one that is easy to use and provides consistent and comprehensive results.

If the technique works, it could open up new discussion in the Southern Ocean research community about whether it is a useful addition, or replacement, to existing ecosystem monitoring methods.