Know more

Work environment, missions and activities

Research Unit

The Laboratory of Environmental Biotechnology (LBE) is an INRAE unit located in Narbonne. The LBE's research aims to develop the concept of environmental biorefineries, which consists of valorizing residues, waste, organic effluents and biomasses into products of industrial interest (bioenergy, biomolecules, organic fertilizers ) while minimizing their environmental and health impact. The research focuses on the treatment and/or valorization of liquid effluents (particularly from the food industry), solid residues (agricultural residues, household waste and sludge from wastewater treatment plants) or specific biomasses such as microalgae or intermediate energy crops using microbial bioprocesses including the production of bioenergies (e.g., biogas and biohydrogen).

Scientific context
Anaerobic digestion is one of the few mature technologies available for the production of methane from waste. This process can be defined as a complex cascade of biochemical reactions catalyzed by different microorganisms and described in a reference model (ADM1). Currently, an important step in anaerobic digestion, the syntrophic organic acid oxidation (SOAO), is missing from the model, limiting its use. In this project, we propose to develop thermodynamically constrained metabolic models of SOAO and then to reduce these models for inclusion in ADM1. The improved reference model will be used to guide the development and implementation of new bioreactors for anaerobic digestion, handling higher loads and adapting to a broader spectrum of organic matter.

Project partners
This project lies at the interface between microbiology, bioprocess engineering and digital sciences. It will be carried out through collaboration between the LBE (INRAE, Nicolas Bernet & Elie Le Quéméner) and the Pléiade team (Inria-INRAE, Unité Biogeco, Simon Labarthe). It will also benefit from our collaboration with the Swedish University of Agricultural Sciences, where experiments on syntrophic microorganisms are being carried out, and from our collaboration with an industrial partner (SUEZ) for real data from monitoring industrial reactors.

Mission and activities
The PhD student will be in charge of developing several theoretical and modeling approaches around SOAO:
(i) build a theoretical framework that takes into account thermodynamic constraints for modeling SOAO
(ii) use this framework and the genomes of a syntrophic community to build a metabolic model that will be parameterized using experimental data supplied by our partners
(iii) use model reduction approaches to simplify this complex model
(iv) implement the reduced model in a new version of ADM1, which will be calibrated and validated.
 

Training and skills

Master's degree/Engineering degree

- Recommended training: 5 years' higher education (Master degree or equivalent) in process engineering or microbiology, with strong modeling skills.
- You read, write and speak scientific English.
- Skills required: autonomy, teamwork, rigor, good interpersonal skills, writing skills, supervision of internship students.
Experience: metabolic network modeling, bioprocess modeling, writing-up.

INRAE's life quality

By joining our teams, you benefit from (depending on the type of contract and its duration):

- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering.

• Contract: PhD position
• Duration: 3 years
• Beginning: 01/12/2023
• Deadline: 29/09/2023
• Contact : Elie.Le-Quemener@inrae.fr