Environmental DNA and metabarcoding analysis for characterization and identification of mammal and plant communities in a freshwater ecosystem

In a changing environment, the dynamics and distribution of species are important to study and improve the monitoring and protection of wildlife biodiversity. The use of eDNA has been shown to be a promising technique in community characterization. In this article, environmental DNA (eDNA) from water and sediment is used to observe the diversity of plants and mammals existing across a river stream in the French Alps. Firstly, the identification of taxa obtained by eDNA is compared with the taxa detected by traditional methods. The results show that both methods cover an important majority of the present species. But a complementary use of these two techniques seems to be the most interesting because of the specific detection of some taxa only by one of the two methods. Secondly, diversity indexes are calculated from the ASV obtained by the two types of matrices sampled for eDNA: water and sediment. No effect of the matrix is detected for the alphadiversity, but a community composition effect is detected on these samples. Thirdly, the abundance of the detected taxa is compared along an altitude gradient. It appears that altitude plays an important role in the distribution of species because of the change in environment observed in this study. To conclude, this study has given a perspective on the use of eDNA to assess diversity. This fast and non-invasive technique can be useful for detecting species, but important limitations need to be taken into account when using it.