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PhD in evolutionary microbiology (M/F)

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Français - Anglais

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General information

Reference : UMR5175-STEBED-002
Date of publication : Monday, September 07, 2020
Scientific Responsible name : Stéphanie Bedhomme
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 January 2021
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

The genetic code being redundant, the majority of amino acids are coded by more than one codon. The frequency of use for all codons of a family of synonymous codons is not equal and these usage preferences vary greatly from one bacterial species to another. It has been shown that these preferences reflect a coadaptation with the translation machinery of the species. During horizontal transfer, a gene moves from one genomic environment to another and this can lead to a break in the coadaptation between the codon usage preferences of the gene and the transcription machinery, with consequences for the expression of the transferred gene and for the fitness of the recipient organism.
The aim of this thesis is to use experimental microbiology and in particular experimental evolutionary approaches to study the immediate and evolutionary consequences of horizontal transfers between genomes with different codon usage preferences. The project will focus more specifically on the horizontal transfer of antibiotic resistance genes and will consist in a part of phenotypic characterization of different bacterial species in which a collection of synonymous versions of a resistance gene will be introduced on a plasmid or in the chromosome. Part of the resulting collection will then be experimentally evolved in the presence and absence of antibiotics in order to study the post-transfer evolution of the transferred gene and the recipient genome.

Work Context

The PhD student will carry out his/her PhD work within the "Genetics and Evolutionary Ecology" team, in the "Evolutionary Ecology and Behavior" department at the Center for Functional and Evolutionary Ecology. This large team of about 30 people, including 12 researchers, is a scientifically rich and dynamic environment where research questions range from population genomics to community ecology and from phenotypic plasticity to speciation.

The doctoral work will be carried out in the context of the ERC HGTCODONUSE project which goal is to study the factors that determine the direction and frequency of horizontal transfers. In particular, through experimental and comparative approaches, we are interested in the impact of the difference in codon usage between the donor and recipient genomes of a transfer on the success of this transfer and the evolutionary mechanisms post-transfer.

During the three years of the PhD program, the PhD student will interact with:
- The thesis supervisor
- The post-doctoral student and the doctoral student working on the HGTCODONUSE project
- The staff of the GEMEX platform where the experimental approaches will be carried out.
- The doctoral students and all the staff of the GEE team.

The doctoral student will have a weekly meeting with the thesis director or members of the HGTCODONUSE project and will be strongly encouraged to attend the GEE team seminars and the ecology and evolution seminars in Montpellier.

Constraints and risks

The planned experimental work will take place in a laboratory of biosafety level L2 in compliance with the safety rules and good laboratory practices corresponding to this equipment.
The planned experimental work will require to come punctually on weekends, in particular for experimental evolution approaches.

Additional Information

Candidates should have an M2 or equivalent in molecular or evolutionary biology and possess both technical knowledge in molecular biology and a strong interest in evolutionary questions.

To apply, please provide a cover letter, a CV and the contact information of two people to be contacted for recommendation.

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