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Téranga Nature

L’ADN environnemental : une technique révolutionnaire pour traquer les espèces en danger

L’ADN environnemental : une technique révolutionnaire pour traquer les espèces en danger

Comment savoir si des dauphins roses peuplent encore l’Amazonie péruvienne sans les voir ? En analysant l’eau du fleuve pour retrouver les traces ADN que les mammifères marins y auraient laissées…

Les échantillons d’eau venaient du fin fond de l’Amazonie péruvienne, prélevés par des scientifiques traquant la présence de dauphins roses. Deux semaines plus tard, l’ADN environnemental, ou eADN, livrait son verdict: les traces des dauphins étaient bien là. Comme celles de plus de 650 autres espèces, dont des dizaines de mammifères: jaguars, daims, tamanoirs, singes, et 25 espèces différentes de chauve-souris.

“C’est assez époustouflant,” s’enthousiasme Kat Bruce, écologue spécialisée en études tropicales et fondatrice de la start-up NatureMetrics, qui avait réalisé le séquençage des échantillons pour le compte du WWF.

Cette nouvelle application de la recherche d’ADN pourrait selon ses promoteurs révolutionner l’étude de la biodiversité.

L’Union internationale de conservation de la nature (UICN), qui tient son congrès mondial jusqu’à samedi à Marseille, a d’ailleurs lancé un projet de 15 millions de dollars (12,6 millions d’euros) pour l’analyse de 30.000 échantillons qui seront prélevés dans certains des plus grands bassins fluviaux du monde, Amazone, Gange, deltas du Mékong ou du Niger…

Les espèces vivantes perdent en permanence des cellules, laissant dans leur sillage des traces génétiques

Alors que tous les spécialistes sonnent l’alarme sur l’effondrement en cours de la biodiversité, les promoteurs de cet “eBioAtlas” estiment qu’il permettra notamment d’éclairer quels programmes doivent être prioritaires dans un domaine aux financements toujours trop limités.

L’UICN prévoit ainsi d’utiliser ces données notamment pour son emblématique “Liste rouge” des animaux menacés.

“Nous espérons que l’eBioAtlas permettra de façon évolutive de boucher les trous dans la connaissance de cette extinction de masse,” explique Mike Morris, qui pilote le projet pour NatureMetrics.

“Cette technologie permet de manière simple et assez précise de dire où se trouvent les différentes espèces”, résume Paola Geremicca, de l’UICN.

Car les espèces vivantes perdent en permanence des cellules, laissant dans leur sillage des traces génétiques. Poils, peau, mucus, salive, tout finit dans les rivières. Mais surtout, “il y a beaucoup de caca”, explique le Dr Bruce.

Des déjections de poissons ou d’autres animaux, apportées par la pluie, ou laissées lorsqu’ils se baignent ou boivent. Leur ADN est alors détectable pendant plusieurs jours.

Cette recherche d’eADN a démarré il y a une dizaine d’années. Kat Bruce s’y est plongée à l’occasion de son doctorat, tout d’abord en cherchant à identifier les différentes espèces présentes dans des “soupes” d’insectes mixés.

Puis, au fil des expériences, il est apparu que la technique fonctionnait aussi pour repérer les empreintes dans l’analyse d’eau. Le séquençage des échantillons d’un ou deux litres dure deux jours et fournit en général autour de 30 millions de traces d’ADN. Il y en a tellement que ce sont les bases de données de référence qui font défaut pour identifier toutes les espèces.

Dans les échantillons d’Amazonie péruvienne, par exemple, seules 20% des traces de poissons ont ainsi pu être formellement identifiées jusqu’au niveau de l’espèce.

Quand les résultats des analyses sont transmises aux experts locaux ils sont souvent “abasourdis” en découvrant la quantité d’espèces inconnues, explique M. Morris.

Il faut alors se tourner vers des zoos ou des institutions locales à la recherche d’un spécimen qui puisse faire référence. Ou chercher à en trouver un dans la nature, avec des kits de prélèvements simplifiés.

Dans une étude publiée en 2018, des chercheurs ont retrouvé dans des échantillons prélevés dans les eaux-côtières de Nouvelle-Calédonie, territoire français du Pacifique Sud, l’ADN d’un nombre bien plus important d’espèces de requins que celles identifiées en 20 années d’observations visuelles.

“Même si les habitants ne voient pas de requins quand ils se baignent, ils sont toujours là,” relève David Mouillot de l’université de Montpellier, co-auteur de cette étude. Ce chercheur participe à un autre projet basé sur l’eADN, Vigilife, groupement public-privé qui vise à développer un “observatoire du vivant”.

Une des limites de la technique est aujourd’hui le monde végétal, les plantes étant plus difficiles à identifier précisément. Le eBioAtlas se concentrera d’ailleurs au début sur les vertébrés, avec l’ambition de créer une base de données en open-source, gratuite pour chercheurs et ONG et payante pour les entreprises. La technique semble en tout cas promise à un bel avenir.

Des chercheurs en Grande-Bretagne et au Danemark ont mené cette année des expériences en filtrant des échantillons d’air dans des enclos de zoos. Ils y ont retrouvé des traces e-ADN des animaux résidents… mais aussi d’autres espèces de la faune locale.

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