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Evaluating biodiversity using environmental DNA (eDNA)

In the study of biodiversity, evaluating the distribution or the presence of organisms in a given site is an important approach. But what if the species studied are not easily accessible or the site holds a large diversity of species? This is when environmental DNA proves to be helpful to researchers.

Krobia itanyi, un poisson de la famille des cichlidae fréquemment rencontré dans les cours d’eau de Guyane (Crédits photo : I. Rogister).

Krobia itanyi, un poisson de la famille des cichlidae fréquemment rencontré dans les cours d’eau de Guyane (Crédits photo : I. Rogister)

In French Guiana, freshwater ecosystems (creeks, rivers and marshes) offers a great diversity of fish. Nevertheless, turbidity, depth and current make scientific observations difficult. Traditional sampling is then carried out using nets or toxic agents. However, not only do these methods select particular species but they destructive. Their use is therefore questioned by researchers and the need to develop alternative methods becomes urgent.

Environmental DNA (eDNA) is an emerging method and is a non-invasive alternative to traditional methods. It implies the detection and amplification of genetic traces present in the sample taken. The analysis of the sequences obtained subsequently allows the identification of the organisms present in the study site. In full swing, this method may, however, show some weaknesses.

Hyphessobrycon roseus, un tétra (characidae) connu uniquement du bassin du Maroni  (Crédits photo : Y. Brosse).

Hyphessobrycon roseus, un tétra (characidae) connu uniquement du bassin du Maroni
(Crédits photo : Y. Brosse).

Through their study, researchers from the laboratory Evolution et Diversité Biologique (EDB) in Toulouse and members of LabEx CEBA, wanted to test the efficiency of this method to describe the diversity of freshwater fish and to obtain a picture of fish assemblages in French Guiana freswater ecosystems. The efficiency of this method was mainly studied in the temperate waters of the planet and the results provided a realistic overview of the fish assemblages in these sites. The interest was therefore to verify the efficiency of environmental DNA in French Guiana.

They sampled a total of 39 sites in French Guiana and compared diversity and assemblages composition using traditional capture methods and metabarcoding method. The results show that traditional methods provide a more complete but spatially limited inventory of fish assemblages while the metabarcoding method gives a more partial but spatially extensive inventory. These observations lead to the conclusion that metabarcoding could be used for rapid and large scale biodiversity assessments. On the other hand, at a local scale, the two methods prove to be complementary and allow an understanding of realistic fish biodiversity.


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