Capturing marine biodiversity with power of genetics

Australian Antarctic Division

Scientists at the Australian Antarctic Division are studying small drops of the enormous Southern Ocean to find out which animals live within it – using new genetic methods.

The ocean – encircling an entire continent and joining the world’s oceans – supports a polar food web that is globally unique and teeming with life.

Ongoing monitoring of Southern Ocean biodiversity will be crucial for scientists to assess the impact of a rapidly changing climate on the marine ecosystem.

“It’s hugely important to actually monitor how things are changing,” said AAD genetics researcher Dr Leonie Suter. “It’s a pretty big deal.”

How best to capture that information has been the subject of a two-year research project, detailed in the journal of Molecular Ecology.

Old versus new

The Continuous Plankton Recorder (CPR) has been capturing snapshots of the ocean for the last century.

It’s a device dropped into the water and towed behind a ship at a constant speed on a narrow path, for 450 nautical miles at a time.

It works by trapping plankton between fine sheets of silk, the contents of which is examined back in the laboratory by taxonomists who microscopically identify, log and analyse whole organisms.

CPR surveys have been run by the Australian Antarctic Program across vast swathes of the Southern Ocean since 1991, involving ships from several nations.

A staggering amount of data has been amassed – around 47,000 samples analysed from more than 1000 CPR tows for a total of approximately 240,000 nautical miles.

Now a new method harnessing the power of genetic sequencing, called ‘environmental DNA metabarcoding’, promises to extend our information about biodiversity.

Biochemical barcodes

If DNA is like a biochemical barcode unique to every species, eDNA metabarcoding records the traces of those organisms left in their surroundings.

“Environmental DNA is pretty much the DNA that is shed by any organism into the environment,” said Dr Leonie Suter.

“So in the marine environment, imagine a fish shedding a scale or doing a poo, or spawning, or dying and slowly decaying.”

“With genetic methods, we can extract this DNA from quite small water samples and from that determine what actually lives in the environment.”

Unlike conventional methods, analysing eDNA doesn’t require an entire organism to establish a snapshot of what’s in the water.

The team analysed water samples taken from the Southern Ocean between Tasmania and Macquarie Island.

Two litres of life signs

For comparable results, where 1500 litres of seawater was filtered through the Continuous Plankton Recorder over five nautical miles, the eDNA method relied on just two litres taken at a single location, piped cleanly and directly from the ocean onto the Aurora Australis research vessel.

“All you’re really doing is turning a tap and in your lab collecting two litres of water that you can filter on site. This filter is then used for genetic analysis,” said Dr Suter.

“So you don’t need to even go on the deck of the ship or anything, you’re in a quite safe environment. You turn your tap and collect your sample to find out what lives in the ocean, which is quite amazing.”

Dr Suter said this eDNA metabarcoding method is a relatively new concept in the Southern Ocean.

“The open ocean is quite different to other environments. The water body is just so big,” she said.

“It all dilutes quite quickly, there are currents and other factors that spread the eDNA out quite quickly. So we weren’t sure how well this would work.”

How the two methods compare

When eDNA and CPR samples were both processed genetically, eDNA detected about two thirds of the species that were detected with CPR.

“This is quite amazing considering the difference in sampled water volume. Both methods detected similar species that contributed to community differentiation across different environments,” said Dr Suter.

When eDNA metabarcoding was compared to morphological analyses (whole organisms) of CPR samples, eDNA detected up to 1.5 times more species.

“The overlap of species detected with the two methods was small, suggesting that eDNA is more of a complementary method to traditional CPRs.”

Because the open ocean is prone to quickly degrading the quality of minute eDNA samples, multiple eDNA samples at different times of the day should be collected to establish a more complete picture.

Dr Suter said more refining of sampling and processing could lead to an unprecedented biodiversity monitoring capacity in the open ocean for future research.

A huge achievement

“It’s personally a really big achievement for me because I’ve got three little kids at home,” said Dr Suter, also the lead author.

“I started working on this when my twins were four months old. So it’s been pretty big for me to achieve this work. And obviously it’s not just my work. It’s a big team effort.”

“I’m really proud that we managed to get it out.”

Looking to the future

In addition, the team is now developing targeted Antarctic krill markers to test how abundant the species is in the Southern Ocean and inform the future management of the krill fishery.

The AAD’s new icebreaker RSV Nuyina will also be equipped for ongoing monitoring of eDNA.

“Whenever the ship goes out we hope to be collecting water samples to analyse and start creating a long-term monitoring program,” said Dr Suter.

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