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Pierre Jorcin slides on a pair of gloves, attaches a plastic tube to a filter, plunges it into the water, presses the start button on a small pump and then slowly begins walking through the river stream. Thirty minutes later, he has gathered three litres of water and filtered thousands of particles. The entire procedure seems simple, banal even. But Jorcin’s gesture is part of a microscopic revolution. In the process, the scientist has collected fragments of environmental DNA, also known as eDNA.
“Every living organism leaves traces of DNA behind, whether in water, soil or in the air. And those traces hold out for some time before eventually degrading,” Jorcin explains. “By collecting them, we can identify and catalogue the organisms we find like bacteria, mammals, amphibians, fish, etc.”
The samples Jorcin collects are then transported a few kilometres away to the University of Savoie Mont Blanc in Chambéry, an Alpine town in southeast France. That is where the offices of Spygen are based, a French pioneer in environmental DNA and the only company in the country that markets eDNA kits. Spygen sells the kits to NGOs, universities and private stakeholders, and then collects the samples to decode them.
Dozens and dozens of samples are processed in the small premises of the company, which analyses the trapped eDNA to try and identify what species it belongs to. “We extract the DNA from the filters and then run it through the sequencing machines,” says Jorcin, who is a project manager at the company. After sequencing, a long succession of four letters emerges – A, T, C, G – representing the genetic code of all species. “Then it’s up to us to find which species the code belongs to by looking through reference databases,” he explains.
Spygen didn’t end up at the foot of the Alps by accident. While the practice of sampling and sequencing eDNA was first tested by a US microbiologist in the 90s, this small revolution truly began about 60 kilometres south of Chambéry. Researchers from the Alpine ecology lab in Grenoble in 2008 found that the method could be used to detect bullfrogs, an invasive species, in places it had not yet been seen.
A year later, scientist and Spygen co-founder Alice Valentini came up with the idea of using eDNA in her study on Himalayan brown bears, an endangered species. “To get a better understanding of the bear’s low reproductive capacity, Valentini tested the eDNA of food in its feces, which allowed her to get a precise rundown of its diet. It was a completely new method," says Benjamin Allegrini, president of the company. "That’s when we understood the full scope of eDNA. Not only can we detect what organisms or species exist in different environments, but we can also understand how they interact with one another,” he says, beaming.
A passionate birdwatcher since he was a child, Allegrini kicked off his career, binoculars in hand, as an ornithologist and went on to study bats. “Then I discovered how much we could learn from DNA," he recounts. Once he had earned a degree in molecular biology, he decided to devote himself entirely to Spygen from 2018 onwards.
“The more we know about our environment, the more we’ll be able to protect it,” says Allegrini, who recently published a book on eDNA. “That’s why it’s important to develop new technologies like eDNA, which can revolutionise how we see the world.”
The number of scientific papers on environmental DNA has skyrocketed since Spygen was founded in 2011, with each publication confirming the effectiveness of the method a little more.
It is now a widely used approach, and is even part of France’s new national strategy to protect biodiversity, which was published late last year. The country plans to “regularly and extensively” document its national biodiversity with a census creating during a “large-scale campaign to collect and analyse environmental DNA”.
- Author: Cyrielle CABOT, France 24
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