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PhD metagenomics of wheat

This offer is available in the following languages:
Français - Anglais

Date Limite Candidature : mercredi 17 août 2022

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General information

Reference : UMR5557-YVAMOE0-002
Date of publication : Wednesday, July 27, 2022
Scientific Responsible name : Yvan MOENNE-LOCCOZ
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 26 September 2022
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

The soils in which cereals are grown can have a microbial community capable of inhibiting phytopathogens and/or inducing ISR responses in the plant, thus limiting root diseases. These soils are said to be disease suppressive. In other, non-suppressive soils, the microbial community does not have these capacities and root diseases can be significant. Nevertheless, the ecology of the rhizospheric microbial community will also depend on the genotype (lineage) of the plant, which will modulate the resistance capacities.
The suppressiveness capacities of soils to diseases are poorly understood still, and the plant traits capable of modulating the suppressiveness of soils to diseases are very little studied. In this context, the project aims to test the following hypotheses:
The capacities of soils to suppress diseases are linked to the diversity of the microbial community, and soil management techniques improving the organic status of the soil are likely to increase the suppressiveness of soils to diseases.
Soil suppressiveness to disease is also highly dependent on plant line, and comparison of lines should help identify plant genetic traits associated with better soil suppressiveness to disease.
The project will be largely based on metagenomic approaches, which may be supplemented by metabarcoding, qPCR, or the analysis of plant-microorganism interaction mechanisms. It will include the following parts:
1. Comparison, on agronomic trials (barley or wheat), of soil organic matter management techniques with regard to their consequences on the microbial ecology of the rhizosphere and the health of the plant.
2. Comparison of the rhizospheric microbial ecology of a large number of wheat lines (more than 200 lines) grown in the same natural soil, in order to allow an association genetic analysis of the genetic traits of wheat involved in suppressiveness of soil to diseases, i.e. via their impact on the microbial functioning of the rhizosphere.
3. Comparison of a large number of wheat lines (more than 200 lines) grown in the presence of a synthetic microbial community, in order to allow association genetic analysis of wheat genetic traits involved in soil suppressiveness to diseases.

Work Context

The PhD project will be directed by Yvan Moënne-Loccoz and co-directed by Daniel Muller, in the Rhizosphere team of the UMR CNRS Microbial Ecology. This team is interested in the ecology of phytobeneficial microorganisms.
The thesis project is part of collaborations with several French, Swiss and German teams, and the recruited person will be required to collaborate with these teams (in French and in English).

Constraints and risks

For joint experiments carried out in Clermont-Ferrand, missions of several days/weeks will probably be necessary on the Clermont site of Crouël.

Additional Information

Required profile :
Skills in microbial ecology.
Skills and interest in omics approaches, in particular metagenomics. This will notably require strong skills with R software, or the ability to acquire the skills needed to master R.
Basic skills in statistics.
Ability to work in a team, and in collaboration with other research teams.
Good command of French and English.

Applications will include a CV, a cover letter with an explanation of the techniques mastered and a justification of suitability for the position, and the full contact details of two referees.

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