eDNA (AnaEE France)

Analyse et Expérimentation sur les Ecosystèmes

Responsable de la plateforme : Stephen MULERO
Responsable scientifique : Frédéric BOYER

The AnaEE technical platform has been set up to allow ecologists to perform large-scale analysis of environmental DNA via a metabarcoding approach. DNA metabarcoding refers to high throughput DNA-based identification of multiple species from environmental DNA. The main applications of this technique consist in diet analysis from feces, in biodiversity inventory from soil samples, and in palaeo-environment reconstruction using lake sediments and permafrost samples.

Submit a project :

 

If you have a preliminary question before submitting a project, please contact us at the following address :

• stephen.mulero univ-grenoble-alpes.fr

If you would like to submit a project, please use the submission form on the following page :

• AnaEE France : submit a project

 

The personnel involved in the eDNA platform is qualified to assist researchers in the following steps of the analysis of environmental samples :

• conception of the experimental design
  (e.g. how many samples should be taken ?
  how many sequence reads are required ?
  how many positive and negative controls should be done ?
  how to produce the reference database ?)

• wet lab analysis  
  (i.e., DNA extraction from the environmental sample and PCR-based amplification of selected regions)

• standard bioinformatic analysis of sequencing output
  (using a collection of program developed within the eDNA platform, and specifically dedicated to DNA metabarcoding : the OBITools)

• advice on the interpretation of results, especially on methodological limits

Note that next generation sequencing is performed using the Illumina technology and outsourced outside of the eDNA platform.

The eDNA platform has experience working on various environmental matrices : soil, lake sediments, permafrost, and feces. It also has experience with the identification of various groups of organisms within these matrices, including plants, vertebrates, arthropods, earthworms, fungi, bacteria.

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Examples of paper published using data produced in the eDNA platform

Optimizing environmental DNA sampling effort for fish inventories in tropical streams and rivers. Cantera, I ; Cilleros, K ; Valentini, A ; Cerdan, A ; Dejean, T ; Iribar, A ; Taberlet, P ; Vigouroux, R ; Brosse, S ; 2019 - SCIENTIFIC REPORTS 9 pp -

Conditionally autoregressive models improve occupancy analyses of autocorrelated data : An example with environmental DNA. Chen, WT ; Ficetola, GF ; 2019 - MOLECULAR ECOLOGY RESOURCES 19 pp 163-175 -

Environmental DNA provides information on sediment sources : A study in catchments affected by Fukushima radioactive fallout. Evrard, O ; Laceby, JP ; Ficetola, GF ; Gielly, L ; Huon, S ; Lefevre, I ; Onda, Y ; Poulenard, J ; 2019 - SCIENCE OF THE TOTAL ENVIRONMENT 665 pp 873-881 -

Unlocking biodiversity and conservation studies in high-diversity environments using environmental DNA (eDNA) : A test with Guianese freshwater fishes. Cilleros, K ; Valentini, A ; Allard, L ; Dejean, T ; Etienne, R ; Grenouillet, G ; Iribar, A ; Taberlet, P ; Vigouroux, R ; Brosse, S ; 2019 - MOLECULAR ECOLOGY RESOURCES 19 pp 27-46 -

DNA from lake sediments reveals long-term ecosystem changes after a biological invasion. Ficetola, GF ; Poulenard, J ; Sabatier, P ; Messager, E ; Gielly, L ; Leloup, A ; Etienne, D ; Bakke, J ; Malet, E ; Fanget, B ; Storen, E ; Reyss, JL ; Taberlet, P ; Arnaud, F ; 2018 - SCIENCE ADVANCES 4 pp -

Comparing three types of dietary samples for prey DNA decay in an insect generalist predator. Kamenova, S ; Mayer, R ; Rubbmark, OR ; Coissac, E ; Plantegenest, M ; Traugott, M ; 2018 - MOLECULAR ECOLOGY RESOURCES 18 pp 966-973 -

Diet shifts by adult flightless dung beetles Circellium bacchus, revealed using DNA metabarcoding, reflect complex life histories. Kerley, GIH ; Landman, M ; Ficetola, GF ; Boyer, F ; Bonin, A ; Rioux, D ; Taberlet, P ; Coissac, E ; 2018 - OECOLOGIA 188 pp 107-115 -10.1007/s00442-018-4203-6

Ancient environmental DNA reveals shifts in dominant mutualisms during the late Quaternary. Zobel, M ; Davison, J ; Edwards, ME ; Brochmann, C ; Coissac, E ; Taberlet, P ; Willerslev, E ; Moora, M ; 2018 - NATURE COMMUNICATIONS 9 pp - 10.1038/s41467-017-02421-3