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By  Matt Marrison 19 June 2024 5 min read

Key points

  • Dr Cindy Bessey is a marine ecologist using environmental DNA (eDNA) to identify life – big and small – in the deep ocean.
  • A new project onboard RV Investigator is comparing eDNA techniques with traditional biodiversity survey methods.
  • eDNA techniques offer marine parks managers and industry a cost-effective and accessible tool to help manage the sustainable use and conservation of our marine environments.

When Dr Cindy Bessey looks at a drop of seawater, she sees a whole marine ecosystem waiting to be revealed. Using eDNA, she can identify the life that inhabits our marine environments by analysing the DNA that’s found in a sample of seawater.

It’s like scanning the items from a shopping basket at a self-service checkout except your supermarket is at the bottom of the ocean.

This emerging technology has diverse applications and benefits for marine ecosystem monitoring. Let’s get the drop on the science.

Dr Cindy Bessey with a giant pyrosome, a type of gelatinous zooplankton, collected during an ocean survey. Image: Rich Little.

The not so sea-cret life of a marine ecologist

Cindy is no stranger to the ocean. From the United States to Australia, she has studied marine ecosystems and life. Her research includes investigating threatened seagrass ecosystems and evaluating how commercial fish populations are responding to climate change.

Cindy’s current focus is tiny but in a big way! She’s working to advance eDNA collection techniques to provide a powerful tool for revealing life in the ocean. This includes life of all sizes, from tiny bacteria and invertebrates to the biggest fishes and marine mammals.

“All sorts of critters leave bits of DNA in the water column. We’ve been working on ways to collect that DNA and match it to known suspects,” Cindy says.

Her current project has Cindy taking to the high seas onboard our research vessel (RV) Investigator to put the new techniques to the test. This is part of a multi-voyage program called the South-East Australian Marine Ecosystem Survey, or SEA-MES for short.

Cindy and her colleagues are working in partnership with the National Environmental Science Program (NESP) Marine and Coastal Hub. The project will compare what they find using the new eDNA techniques with what is found by more conventional biodiversity survey methods.

Put simply, Cindy says they collect eDNA samples at the same time as trawl surveys using nets and visual surveys using towed camera systems. This process is called ‘paired sampling.’

“We can then directly compare the eDNA survey results with what was surveyed using the other techniques,” Cindy says.

Importantly, this allows the researchers to determine any differences in the results between the different survey methods.

The eDNA project is part of SEA-MES, a series of voyages using a variety of survey methods to study marine biodiversity off SE Australia. Image: Rich Little.

Innovative science helping us to sea life

The new eDNA techniques allow marine life to be revealed from all marine environments and levels of the ocean. If equipment is being deployed there, eDNA can be collected!

Sometimes this happens as part of an existing deployment such as when water is sampled using the CTD (conductivity, temperature and depth) instrument.

“We can collect water samples from discrete depths and sites using the CTD instrument and then analyse these samples for the DNA they contain,” Cindy says.

“Once we have the seawater samples, they are actively filtered over fine membranes to concentrate all the DNA. These samples can then be processed back in the lab to look for a whole range of organisms, from tiny plankton to fish.”

You can't hide from science, tiny batfish! eDNA provides a powerful tool for surveying rare, cryptic and hard to find species. Image: Rich Little.

However, the eDNA sampling equipment can also hitch a ride on other equipment, like a remora fish sucking onto the side of a shark. Conveniently, this also offers other benefits.

“Sometimes we let the movement of the ship do the filtering for us!” Cindy says.

Scanning the ocean darkly

The deep towed camera used to collect underwater imagery and sample eDNA at the same time in a process called 'paired sampling'. Image: Museums Victoria-Benjamin Healley.

Our marine engineers have designed a shiny new eDNA sampler to attach to the deep towed camera on RV Investigator. The sampler is opened once the camera is flying about one metre over the seafloor. It filters DNA from seawater as the camera is towed along.

The deep towed camera with its hitchhiking eDNA sampler can be deployed to depths of 4000 metres in search of life in the deepest, darkest depths of the ocean. The eDNA sampler itself has been built to withstand depths of 6000 metres.

The eDNA sampler is attached to the deep towed camera, which can be deployed to depths of 4000m. Image: Aaron Tyndall.

Importantly, the eDNA is collected at the same time the camera system is recording video and taking pictures.

“Collecting eDNA at the same time as video and photos allows us to directly compare the two survey techniques,” Cindy says.

“The paired nature of these methods gives us confidence that what we can detect by our forensic style eDNA methods is corroborated by our more conventional style of sampling methods.”

The deep towed camera shines a light on deep ocean life while also collecting eDNA for the analysis of other unseen species.

As a bonus, these innovative new eDNA techniques are likely to reveal much more than is seen on camera.

One drop to reveal them all

Our oceans are big, remote and deep. Studying the life in them, indeed just getting to your study areas, can present some huge challenges.

Furthermore, traditional survey techniques can give different results. Species may be rare or cryptic (difficult to find in the environment) and hard to catch or film. In an unhelpful situation for our marine researchers, some species will avoid sampling nets and cameras entirely!

This is where eDNA offers an exciting and powerful tool. We don’t need to sample or film a species to find out it’s there. We just need to collect a bit of the DNA it sheds into the ocean.

Cindy said this makes eDNA sampling very useful for establishing biodiversity baselines and subsequent monitoring.

“These new eDNA sampling techniques will improve the information available to marine park managers and industry, especially in offshore areas that are difficult or expensive to sample,” Cindy says.

“This offers huge benefits in terms of having access to the data needed to better understand and manage our oceans.”

Results of this project will complement a new eDNA species eDNA species mapping and monitoring partnership between Parks Australia and the Minderoo Foundation, which is also being supported by sea time on RV Investigator.

An eDNA sample from filtered water. Image: Bruce Deagle.

Like all science, collaboration is key to unlocking the greatest benefits. As the inspirational quote from Ryunosuke Satoro goes, “Individually we are a drop; together we are an ocean.”

And for every drop of seawater, eDNA gives us the potential to reveal the diversity of life in that ocean.

Our Dr Sahan Jayasinghe and Dr Cindy Bessey are part of a collaborative project team working to advance eDNA survey techniques. Image: Rich Little.


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