Description of the thesis topic

The use of eDNAs is limited by our ability to understand the complexity of their life cycle in a hydrosystem. One innovative approach to characterising the spatio-temporal dynamics of eDNAs is modelling. Several teams have already begun to model the life cycle of eDNAs in a hydrosystem (Wilcox et al. 2016; Shogren et al. 2017; Carraro et al. 2023; Pont 2024). These models use several processes:
- an eDNA emission process: eDNAs are emitted by organisms as a function of parameters such as organism density and particle size distribution.
- a degradation process: eDNAs are degraded over time and at a rate that depends on parameters such as temperature.
- a displacement/sedimentation and remobilisation process: the eDNAs will be displaced or deposited according to hydraulic parameters, in particular the speed of the current.

From a model of this type, knowing all the parameters controlling the processes described above, we can then simulate the dynamics of eDNA in a hydrosystem and predict, for example, the average dispersion distance or the probability of detection of eDNA in a hydrosystem. An essential element is the modelling of current speeds, which requires both a hydrological model for the basin under study (to predict flows) and a hydraulic model (to predict current speeds).

Within the Aliquot project (PEPR-OneWater), as part of a thesis, we are going to use this type of modelling to: 1. understand the influence of the various transport model parameters (temperature, biomass, flow rate, etc.), 2. test and calibrate the model on the basis of eDNA injection experiments, 3. compare the diversity reconstructed by an eDNA transport model at catchment scale with field measurements, 4. test the influence of flow rate on the quality of the biodiversity signal carried by eDNAs.

Work Context

This position is in line with the objectives of the ALIQUOT project, winner in 2023 of the 1st call for projects under the OneWater - Water as a Common Good National Exploratory Research Programme. Launched in March 2022, this programme, funded by the France 2030 plan (€53m), aims to develop knowledge in the field of water in order to change the paradigm and rehabilitate water as a common good.

The ALIQUOT project aims to gain a better understanding of the dynamics of environmental DNAs in aquatic environments so that they can be used more effectively as sentinels of the diversity and functioning of socio-hydrosystems.

The Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA) is a dynamic, interdisciplinary research centre based in Lyon, dedicated to the study of complex interactions between ecosystems, living organisms and their environment. The laboratory takes a global approach to environmental sciences, combining ecology, molecular biology and modelling to gain a better understanding of ecological processes at the molecular and ecosystem levels.

The research topics covered by this post will be carried out in close collaboration with the INRAE RIVERLY research unit, also in Lyon, particularly with regard to hydraulic modelling.

The position is located in a sector covered by the protection of scientific and technical potential (PPST), and therefore requires, in accordance with the regulations, that your arrival be authorised by the competent authority of the MESR.

The position is located in a sector under the protection of scientific and technical potential (PPST), and therefore requires, in accordance with the regulations, that your arrival is authorized by the competent authority of the MESR.

Constraints and risks

Field work in aquatic environments

Travel to sampling sites, sometimes requiring assignments lasting several days with accommodation on site

Laboratory work in a 'clean' room (e.g. wearing gloves, masks, lab coat; walking forwards; frequent decontamination of the workstation, etc.)