Could e-DNA enhance ecosystem monitoring?

Scientist 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.

Environmental DNA or e-DNA could be the next ‘disruptive innovation’ when it comes to monitoring changes in Southern Ocean ecosystems.

Australian Antarctic Division molecular ecologist, Dr Bruce Deagle, said the technology allows scientists to identify hundreds of species in an environmental sample – such as water or soil – by sequencing DNA in the sample.

The approach relies on ‘barcodes’, which are segments of DNA unique to different species. These genetic markers are amplified from the total DNA extracted from the sample, and their sequences are then compared to a reference database to identify the organisms.

“If we can collect a small volume of water and characterise what’s in it, this technique could be very useful for monitoring changes in the occurrence of organisms 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.

“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.”

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 and catches 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’d expect to see a good fish community, but if we only get a handful of eDNA results, then that may suggest the method is not very useful.

“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.

“We need to ensure that our processing method captures all the eDNA in the sample and not just a subset of what’s there,” he said.

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.

“DNA could be a good tool for monitoring but we have to decide if we want the data in that form – if it’s going to be useful,” Dr Deagle said.

“Use of the technology could disrupt old, long-term ecosystem monitoring datasets, but at his stage, our focus is on showing what’s possible.”

Wendy Pyper
Australian Antarctic Division
*Australian Antarctic Science Project 4313