Graduate position: Standardisation of an environmental DNA method, to monitor the fish fauna of lentic systems.

Thesis proposal
Standardisation of an environmental DNA method, to monitor the fish fauna of lentic systems.

Contacts :
Tony Dejean (SPYGEN, Le Bourget du Lac) :

Isabelle Domaizon (INRA, Thonon les Bains) :

Maxime Logez (Irstea, Aix en Provence) :

Research labs
Mixed research unit RECOVER, Irstea, in a consortium mixing the French Agency for Biodiversity/Irstea/INRA and ONCFS, Aix en Provence, France.
Mixed research unit CARRTEL, INRA (National Institute in Agricultural Siences)-Université Savoie Mont Blanc, Thonon les bains, France.

Context :
Cifre PhD associating three public partners, AFB, Irtsea & INRA with a private partner SPYGEN (

National biomonitoring networks, especially for water surface ecosystem such as lakes, are necessary: i) to enhance our knowledge of system functioning, ii) to follow the temporal dynamic of communities, and their reaction to emerging stressors (global change, invasive species, etc.), and iii) to evaluate the ecological status of waterbodies during the managing plans of the Water Framework Directive (WFD). Until now, the monitoring of fish in lakes is realized with benthic and pelagic gillnets, following the standardised and normalized European protocol (CEN 2015). It pros and cons are to provide comparable data in time and space (among lakes) but it is time consuming, expensive to implement and it is lethal for the fish caught which are finally removed from the system.
The environmental DNA (eDNA) detect the species that occur in a system by amplifying and sequencing (metabarcoding) the DNA collected in an environmental sample (water, soil, etc). This technique is booming and has great advantages. Indeed it is a non-invasive technique (no removal of individuals) that can rapidly and consistently characterises the biodiversity (Valentini et al 2016 ; Pawlowski et al 2018). Nonetheless, some calibrations are still needed before fully exploiting the potential of this technique and before using it in routine in the national biomonitoring programs.
In this context, this thesis will aim to:

– Define and standardise a sampling protocol of eDNA to monitor the lentic systems, by analysing already collected data from European studies (in particular those realized by SPYGEN, e.g. Civade et al. 2016, Pont et al. 2018);

  • –  Compare the efficiency of the eDNA protocol with the traditional fish sampling methods (CEN);
  • –  Study the temporal variability of the eDNA signal to identify the best suited sampling period and to assess the ability of the eDNA to monitor the biological life cycle of some species;

– Evaluate the ability of the eDNA to quantify the fish species abundance through experimentations that will be realized in controlled conditions (Domaine du Paraclet – AFB).

The candidate must have a master degree in ecology (or its equivalent, e.g. engineer), have skill in water-system management and biostatistics. Knowledge of biomolecular tools and skills in bioinformatics would be appreciated. The candidate must also be interested by field work and by experimentations. English is necessary, French is optional.

The candidate will be located in Aix-en-Provence (France), but regular travels are planned to: SPYGEN office (Bourget du Lac), INRA of Thonon les bains and to the Paraclet (North of France, Boves – Somme).

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