Publié le 22 mar 2017
Par Cecile Marechal

PHD POSITION AVAILABLE  in Metagenomic analysis of lignin degradation by termite gut microbiota

Context: This PhD will be realized in the framework of the European Project ZELCOR “Zero Waste Ligno-Cellulosic Biorefineries by Integrated Lignin Valorisation” founded by the Bio-Based Industries Joint Undertaking (BBI). This project will be realized in collaboration with 18 EU laboratories and industries, including researchers from INRA (Marseille, Versailles, Reims, Toulouse - France), University of Warwick (UK), Wageningen University and Research center (Netherlands) and, Aalto University (Finland).

The PhD will work in a rich collaborative network with the different partners.

Lab Host: Laboratoire de Systèmes Biologiques et des Procédés (LISBP), situated at the INSA Toulouse, France (website:

Scientific context: Lignin is the major aromatic component of plant cell walls constituting 10-30 % of the lignocellulosic biomass. Lignin represents also a barrier that limits the access to lignocellulosic polysaccharides useful for the production of biofuels and other value-added chemicals. With the urgent need of the development of second generation biorefinery, the study of lignin degradation and the identification of novel organisms and catalysts for lignin breakdown are of current concern.
Despite the lignin’s recalcitrance, microbial communities found in the digestive system of different organisms (ruminants, termites, insects…) participate to lignin bioconversion. Termites represent one the most efficient organisms able to transform highly lignified biomass; the microbial communities found in termite gut facilitate the assimilation of such lignocellulosic biomass by producing the enzymatic machinery needed for biomass deconstruction. Moreover, such microbial communities display high diversity and metabolic versatility that can be exploited to develop processes for lignin bioconversion. In this project we are thus interested on characterizing the functional diversity of microbial consortia issued from termite gut involved on lignin transformation.

PhD objectives: The objective of this PhD is to understand how microbial communities contribute to lignin transformation and how substrate structure and culture conditions impact the functional diversity of such microbial consortia. A second objective is to correlate the information on microbial communities, substrate composition and enzyme activities with information related to process performances.
To elucidate the mechanism used by microbial consortia for lignin transformation, we propose to select microbial consortia displaying a high lignin-degrading activity from natural termite gut microbiomes. The effects of substrate properties on enzymatic activities and functional diversity of microbial consortia will be undertaken by an integrated approach combining new high-throughput
sequencing technologies with the macro-kinetic analysis of bioreactors.

The PhD work will consist in:
1) The macro-kinetic analysis of bioreactors using lignin-residues as substrates for microbial consortia (in
collaboration with IRD).
2) The detailed physico-chemical characterization of the lignin residues (in collaboration with INRAVersailles,
Reims and Wageningen University) and its metabolites.
3) The functional analysis of microbial consortia using metagenomic approaches (metagenomics,
metatranscriptomics, metaproteomics and enzymatic kinetics) during lignin transformation (collaboration
with Warwick University and INRA-GeT platform).

• Master’s degree in microbiology, molecular microbial ecology, biochemical engineering, or biotechnology.
• Experience in basic molecular biology methods (DNA/RNA extraction-purification, PCR, qPCR, sequencing).
• A background in bioinformatics and biostatistics. Knowledge on NGS data analysis and on microbial ecology.
• Experience in implementing and operating bioreactor.
• Knowledge on analytical chemistry would be appreciated (HPLC/GC).
• Good writing and communication skills.
• Creative, out-of-the-box thinker.
• Excellent interpersonal skills to work effectively and closely with team members and different partners.
• A good knowledge of spoken and written English is a highly valuable asset.
• A good knowledge of spoken French is also appreciated. If needed, training can be provided.

Applications should include a CV, a brief description of research interests and past research experience, copies of exam-certificates and grades, a summary of Master’s thesis and a cover letter motivating why you are interested in the position. The candidates are encouraged to provide letters from at least two reference persons. The evaluation of candidates will begin on 15 May 2017 and will continue until the position is filled.

Application deadline: 15 May, 2017
Salary: 1500€ net/month

Guillermina Hernandez-Raquet (INRA Research director)
Phone: +335 61 55 99 77 / +336 20 61 81 11.