A revolutionary ecological technique to save nature

Until very recently, researchers responsible for monitoring polar bear populations in the Arctic faced a difficult task: they had to spend hours in a helicopter to spot an individual, then immobilize and chip it, or survey hostile terrain in search of rare animals. . hairs or excrement… But the situation has changed: today they only have to find traces of ursids in the snow and take samples. It will contain fragments of animal DNA. ” When you put your hand on an object, you leave part of your cells there, and therefore part of your DNA. It’s the same as breathing or sweating, which releases cells into the air. And this is true for all organisms in nature, all of which leave DNA traces behind them. “, describes Claude Miaud, director of research at the Center for Functional and Evolutionary Ecology. These “traces” can remain on the ground, in water and even in the air for several days or even weeks.

We target the “genetic barcode” left by the animal

In the late 2000s, researchers, including Claude Miaud, wondered whether it would be possible to recover this “ecological” DNA, or eDNA, to track its owner and thus infer its presence in the environment. To do this, they used a barcoding technique, a process that targets a specific region of DNA unique to each species. A type of genetic barcode (barcode) to determine who owns a DNA molecule found in nature.

” Our first publication in 2008 showed that we could track the development of the invasive bullfrog by detecting its presence in a pond from a simple water sample. Claude Miaud notes. At about fifty sites in southwestern France, the team thus found the elusive batrachian in 38 ponds by analyzing only a few deciliters of water, which naturalists sent to the area for several days failed to find. 7 sites.

” This first approach, which focused on a single species, quickly evolved into metabarcoding: you could search for the barcodes of all amphibians in existence, even if it meant taking water. Techniques have since improved, allowing both vertebrates and invertebrates to be studied in a wide variety of environments: rivers, oceans, soils, ambient air, and more. Last year, the international alliance Vigilife launched a large-scale operation called Sentinel Rivers, which aims to compile the most comprehensive inventory possible of the biodiversity of several large rivers, for example through eDNA, to detect fish and large mammals. molluscs and even bacteria. After taking dozens of samples along 600 kilometers of the Guyanese Maroni River, the program plans to tackle the Douro in Portugal, the Magdalena in Colombia or the Zambezi in Mozambique.

The technique makes it possible to identify more and more species

” In addition to these inventories, we are seeing an increasing number of studies using eDNA in a very original way, for example to gain information about the ecology of a species. Claude Miau observes. Among hundreds of years of scientific publications, some use eDNA as a tool to study a species’ life cycle, diet, and even genetics. Using seawater containing DNA left behind by whale sharks, the researchers were able to identify genetic variations between individuals, going so far as to estimate the number of reproductive females in a group. eDNA applications are developing rapidly.

to reconstruct the past

eDNA not only revolutionizes the work of naturalists, but is also useful for paleontologists: thus, it allowed us to determine the history of various occupations over 250,000 years by Denisovan Man, then Neanderthal and Homo Sapiens, in the Denisova Cave in Russia. . In 2014, another team traced back the last six thousand years of grazing history of the site, thanks to tracks left by cattle trapped in the sediments of a lake in the Alps.

What is this new DNA technique in the air for?

1. Monitoring the state of biodiversity

Taking inventory of biodiversity is simple: experts look for the DNA of organisms that come to drink or bathe in the river, or install drinking vessels in nature. Some researchers are even more imaginative: in 2020, an international team is betting on leeches to identify the large mammals of the island of Borneo. Biologists analyzed the DNA in the stomachs of 557 bloodsucking worms and traced their victims. Even better: they compared the results to leech sampling sites—areas more or less exploited by humans—and were able to determine the impact of deforestation on faunal diversity.

2. Find extinct species

In 2020, researchers analyzed the water of Brazilian ponds and rivers, targeting 30 genetic barcodes corresponding to endangered or threatened frog species. The result: they identified two species that were believed to be locally extinct, but above all else Megaelosia bocainensis, a frog that had not been seen since 1968, so much so that it was thought to be extinct. eDNA proved he was still alive somewhere.

3. Study pollinator behavior

Complex interactions between plants and the organisms that pollinate them form the basis of terrestrial ecosystems. To study these pollination networks—to learn who feeds on what—scientists now rely on eDNA: the massive sequencing of pollen carried by insects that reveals all the plants visited by foragers. In 2019, two Danish researchers did the opposite: they started from DNA traces found in flowers to trace back to their winged hosts. A third possibility: analyze the honey, which contains the genetic material of the bees that produce it, but also the genetic material of the forage plants, even the small insects that produce the honeydew, a substance consumed by the bees in time.

4. Track the migration

The pollen carried by an insect contains valuable information about its travels. In 2018, Spanish and Polish researchers wanted to learn more about the incredible migration of the Painted Lady butterfly, which travels several thousand kilometers every year. They collected 47 Lepidoptera and identified 157 plants they encountered along the way using eDNA. The presence of plants endemic to certain regions of Africa has made it possible to track their journey more precisely. Fish can also be tracked: by taking a few liters of water at different levels of the water flow, it is possible to determine the progress of salmon, eels and other migratory fish.

5. Track pathogens

Viruses, fungi, parasites… These pathogenic organisms can also betray their DNA. Hence the idea of ​​using the technique to observe their distribution in an environment. A 2019 study in Norway looked at “crayfish plague,” a fungus that has been known to be fatal to European crayfish. Until then, the classic monitoring method consisted of placing cages with crabs in different locations and regularly monitoring their health status. eDNA from simple water samples detected the presence of the parasite two and a half weeks earlier than traditional methods… and without touching a single crab.

6. Spot pollution

Many terrestrial and aquatic organisms—small invertebrates or single-celled organisms—are very good indicators of the presence (or absence) of various pollutants: oil, heavy metals, and even uranium. By detecting them through eDNA, the health status of the natural environment can be determined. Useful for monitoring the progress of pollution projects for industrial sites (abandoned mines, etc.) or for understanding the impact of oil drilling on the ocean. To further speed up diagnosis, European researchers are working on developing artificial intelligence that can automatically assess environmental quality when confronted with DNA sequences found in soil or water samples.

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