Monitoring biodiversity of an alpine watershed using eDNA metabarcoding and ecological surveys: a collaborative work between students, scientists and citizens
Résumé
During the new master of Environmental Genomics program in Lyon, students conducted a two-year research project in collaboration with the scientific NGO ”Le CREA Mont Blanc”. In their first year, students collected environmental DNA (eDNA) from water and sediment in a river stream of the French Alps to determine the diversity of plants and mammals. They also visited the CREA observation sites, including camera traps and quadrats. Subsequently, DNA was extracted and amplified using primers targeting a chloroplastic gene for plants and 16S mitochondrial gene for mammals. In their second year, students developed an analysis pipeline to identify the taxa obtained by eDNA, in comparison with the ones detected by traditional methods: mammals were identified using camera trap images analyzed by artificial intelligence, scientists and participatory science (CREA’s Wild Mont-Blanc project), while plants identified by botanists (le CREA). Although the majority of the observed species were recovered by eDNA, some taxa were specifically detected by only one of the two methods. Additionally, the students found a significant effect of the matrix (water or sediment) on the community composition. Finally, they concluded that altitude plays a crucial role in species distribution. As both a pedagogical exercise and a means of communicating their findings, the students authored a scientific article aimed at contributing to the exploration of the impact of climate change on fragile Alpine biodiversity and sharing this knowledge with the public.