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eDNA’s monster potential

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eDNA’s monster potential

Environmental DNA is an exciting and increasingly accessible tool to help scientists monitor and protect the world’s ecosystems – revealing the past, measuring the present and helping to predict what might happen in the future.

When one of the world’s top scientists goes hunting for one of the world’s most mysterious monsters, it’s a marriage made in media heaven.

Otago Professor Neil Gemmell’s search for Scotland’s Loch Ness monster has created a perfect storm of popular science stories that have captured the global imagination.

For media everywhere, proving or disproving the monster myth is an irresistible tale. For Gemmell, it’s been an irresistible opportunity to introduce cutting-edge science to the world.

His Loch Ness project showcases the use of DNA found in an environment (eDNA) to identify everything that lives in that area — its biodiversity.

Techniques tested and refined by his laboratory at the Department of Anatomy could revolutionise how we monitor our environment and expand our understanding and knowledge of our world.

The science involves using the detritus of life to reveal the past, measure the present and predict the future. It works because life is messy, says Gemmell. Everything leaves behind genetic fingerprints.

“Whenever a creature moves through its environment, it leaves behind tiny fragments of DNA from skin, scales, feathers, fur, faeces and urine. This eDNA can be captured, sequenced and then used to identify that creature by comparing the sequence obtained to large databases of known genetic sequences from hundreds of thousands of different organisms."

“If an exact match can’t be found we can generally figure out where on the tree of life that sequence fits.”

So if there really is — or was — a Loch Ness monster, Gemmell’s team should find evidence of it.

The technology has been around a while, but since DNA sequencing costs have plummeted, it has become increasingly practical to discover secrets hidden in water, soil and air.

Measuring biodiversity helps us to assess the health of ecosystems, but traditional monitoring methods can be slow, labour-intensive, invasive and probably inadequate, so improved methods are needed.

Gemmell’s lab has been at the forefront of developing how best to use eDNA technology as an alternative, with particularly rigorous testing by PhD student Gert-Jan Jeunen.

eDNA has been trialled in a number of ecosystems, but using it in large bodies of water has been relatively limited because of their dynamic nature.

Jeunen compared eDNA monitoring with traditional methods to see how it fared in getting results over time and distance — which are important considerations in aquatic environments such as oceans.

First, he had to find the best way to extract eDNA from water samples. Different researchers were already using a variety of methods to do this, so Jeunen compared them to find the one that gave the highest DNA yields and the most consistent results.

Using the most efficient protocol, he went on to test what eDNA could discover and how far eDNA is transported by water movement. togetherwith Gemmell and his other supervisors, Dr Michael Knapp (Anatomy), Associate Professor Miles Lamare (Marine Sciences) and Professor Hamish Spencer (Zoology), Jeunen explored how time, tides and seasons affected eDNA.

Working at the well-studied mouth of Otago Harbour meant eDNA results could be compared with prior knowledge of species diversity. Analyses showed that eDNA gave a very accurate picture, which should lead to quicker, cheaper and more reliable monitoring.

“In some ways it seemed like science fiction: being able to measure the biodiversity of a whole area from a bottle of water,” says Jeunen.

It opened up new possibilities for investigating hard-to-reach places such as oceans, subterranean caves and deep lakes — like Loch Ness.

The search of Loch Ness has always been about much more than monsters, says Gemmell.

“It’s about cutting-edge science that can make a real difference in how we monitor and protect the world’s increasingly fragile ecosystems. Whether it’s as small as a marine worm or as large as a blue whale, as old as a woolly mammoth or a species new to science, it can now be studied without even being seen.”

DNA lasts longer when frozen, which makes it ideal for learning about the past. Tests from ice cores taken from glaciers and permafrost have yielded eDNA for plants, insects and even woolly mammoths from the Ice Age — giving us a clearer picture of life on Earth hundreds of thousands of years ago.

eDNA has also been used to track rare dolphins in the wild and to follow polar bears across the ice by using DNA left in their footprints.

It’s also a powerful tool for early detection of invasive species that threaten to drive out natives in sensitive areas — hopefully allowing measures to be put in place to stop them before they become well established.

Biological controls over pests are another part of Gemmell’s wider research, with gene-editing a potentially powerful weapon for conservationists aiming for a predator-free New Zealand by 2050.

The future could see using eDNA becoming part of daily life for individuals as well as scientists, says Gemmell.

“In a few years we may be able to use eDNA monitoring tools for personal use, such as being able to test the water for E. coli abundance before going swimming, or test the sea before surfing to see if there are any sharks in the area — although false negatives may be a problem.”

It’s not a far cry from what is already being done using eDNA to monitor coastal fish such as snapper. “We can target species of fish that are commercially and recreationally important and see what is happening to the local population in an area over time.”

The technology is getting to the point where it could be likened to being able to take a photograph of someone who has left the room.

“We can monitor things that have been problematic to measure in the past, such as migrating whales that may be present in an area for only a few days a year. eDNA can give us genetic data that can tell us what species, maybe how many there were, maybe even which individuals were present on a given day in a given year.

“It’s an incredibly powerful tool for monitoring trends in populations that are recovering from past exploitation or predation such as southern right whales and Maui dolphins. It’s also useful in monitoring things like great white sharks — it’s nice to know if they are frequenting your surfing beach.”

Gemmell forecasts recreational tools for keen fishermen like himself. “You could be able to find out what’s in the water, how many trout there are in a stream and what they are eating. So if you know what is there and you don’t catch anything you’ll have no excuses — you’ll have no one to blame but yourself.”

It seems unlikely that the ultimate big one — the Loch Ness monster — will get away from Gemmell and his colleagues fishing for answers as to what really lies in the depths in Scotland. Once the number crunching is done, he and his team will have some answers.

And the world will be better informed about both an age-old myth and some very real 21st century science that could change the future.

NIGEL ZEGA


Professor Neil Gemmell: “Whether it’s as small as a marine worm or as large as a blue whale, as old as a woolly mammoth or a species new to science, it can now be studied without even being seen.”
Photo: Alan Dove