DNA is everywhere—in water, soil, and even in the air. Today, scientists have at their disposal analytical methods capable of capturing and sequencing this environmental DNA (eDNA).
Thanks to major advances in PCR (Polymerase Chain Reaction) and sequencing technologies, the use of environmental DNA, or eDNA, has gained considerable momentum. The most recent breakthrough in this ever-evolving field: the collection and sequencing of DNA present in the atmosphere.
Environmental DNA: a reliable and non-invasive technique.
The principle of eDNA is based on the fact that all living organisms shed DNA fragments as they move through their environment—through urine, feces, hair, scales, secretions, and more. These genetic traces accumulate in the environment: in the ocean, rivers, lakes, soil, sediments, and, as demonstrated by two studies conducted in zoological parks, even in ambient air. Such traces provide valuable information for detecting the presence or passage of species—from microorganisms such as bacteria and viruses to elusive or rare species that are difficult, if not impossible, to monitor using conventional methods. Another key advantage of eDNA is its non-invasive nature. Only a small sample of the medium inhabited by the target species is required, without any direct intervention on the organisms themselves.
From simple traces to DNA barcoding.
Once collected, water or soil samples are sent to the laboratory for analysis. The protocol, consisting of no fewer than four steps, requires the utmost rigor on the part of scientists in order to avoid the risk of contamination.
The first step involves isolating DNA molecules using molecular biology techniques (such as precipitation and centrifugation), which are now well mastered and largely automated, thereby reducing costs. In a second step, this DNA is amplified through PCR to obtain sufficient quantities for sequencing.
DNA sequencing makes it possible to determine the sequence corresponding to a given species—that is, the specific fragment of nucleotides that characterizes and differentiates it from others. These sequences are then catalogued in international databases according to the concept of molecular barcoding, developed in 2003 by Canadian zoologist and ecologist Paul Hebert. Stored in the form of barcodes and integrated into computerized systems, DNA fragments can thus be easily compared and identified in record time.
A vast field of applications.
Within just a few years, environmental DNA (eDNA) has become a particularly valued tool for biodiversity studies. By analyzing environmental samples, researchers can identify and quantify organisms present in natural habitats, monitor rare or endangered species, or, conversely, track the emergence of invasive alien species that may disrupt ecosystems. Even more striking, the analysis of a single honey sample can reveal all the plant species visited by bees, while DNA trapped in just a few grams of sediment can provide insights into which species inhabited specific regions thousands of years ago.
Most recently, this technique has made a significant contribution to the fight against the Covid-19 pandemic. In this case, viral RNA was detected in wastewater, allowing researchers to quantify the presence of the virus and, consequently, to better anticipate the progression of the epidemic. In the future, this tool could also be used to identify the emergence of new variants at an early stage—pending further applications, equally fascinating, in many other fields.
Sources :
https://planet-vie.ens.fr/thematiques/ecologie/l-adn-environnemental-un-nouvel-outil-pour-espionner-les-especes-sauvages
https://www.ofb.gouv.fr/actualites/ladn-environnemental
https://www.notre-planete.info/actualites/4354-ADN-environnemental-biodiversite
https://www.lemonde.fr/sciences/article/2022/03/16/detecter-l-arn-environnemental-pour-suivre-l-epidemie-de-covid-19_6117759_1650684.html
https://www.encyclopedie-environnement.org/vivant/metabarcoding-codes-barres-adn-caracteriser-biodiversite/
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