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Portail > Offres > Offre UMR2594-FABROU-004 - Post-doc en génomique écologique (H/F)

Post-doc in ecological genomics (M/W)

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

Date Limite Candidature : samedi 27 août 2022

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General information

Reference : UMR2594-FABROU-004
Date of publication : Saturday, August 6, 2022
Type of Contract : FTC Scientist
Contract Period : 36 months
Expected date of employment : 14 November 2022
Proportion of work : Full time
Remuneration : between 2757 and 3915 € gross monthly depending on experience
Desired level of education : PhD
Experience required : 1 to 4 years


Infectious disease is often the major selective agent in nature, and we cannot understand how populations evolve without understanding their pathogenic microbes. Beyond host immunity, an important factor determining the ability of pathogens to invade and proliferate in a host is the resident microbiota, but we are only beginning to glimpse its multifarious impacts. We know even less about interactions among pathogenic microbes themselves. Any effort to explain how pathogen communities, or pathobiota, develop within a host requires knowledge about the extent to which pathogens engage in competition, commensalism and cooperation, both with other pathogens and the rest of the microbiota. In the PATHOCOM project (https://figshare.com/articles/preprint/PATHOCOM_proposal/13174337), we aim at setting up a program that integrates large-scale field observations of microbiota/pathobiota in the plant Arabidopsis thaliana with ultra-high-throughput experimental tests of host-dependent interactions among microbes, allowing predicting stable pathogen-pathogen-microbiota interactions by modelling. In this context, the postdoctoral project corresponds to the second step of the PATHOCOM project and aims at characterizing the spectrum of in planta interactions (competition, commensalism, cooperation…) among 600 bacterial strains (150 strains from each of the bacterial pathogens Pantoea agglomerans, Pseudomonas syringae and Xanthomonas campestris + 150 strains of the bacteria Sphingomonas sp. as a proxy for the non-pathogenic background microbiota). To establish this matrix of pairwise interactions, the recruited person will benefit from tools allowing high-throughput phenotyping (pipetting robots, barcoded bacterial strains, barcoded plant lines, high-throughput imaging of vegetative growth…). This 36-month postdoctoral project is funded by the ERC (European Research Council) and will be carried out as part of an interdisciplinary and collaborative project with the research groups of Detlef Weigel (Max Planck Institute, Tubingen, Germany) and Joy Bergelson (New-York University, USA).


The post-doc will be in charge of characterizing in planta the spectrum of pairwise interactions among 600 bacterial strains isolated from natural populations of Arabidopsis thaliana (450 pathogenic strains + 150 non-pathogenic strains, 200 strains isolated from France, Germany and USA). The post-doc will also be in charge of characterizing in planta the evolution of complex mixtures of bacteria (from 150 to 500 strains) that will be free to collapse to their endpoints. The post-doc will interact with three other post-docs with strong skills in microbiology (located in Tübingen and New-York), who will perform a similar characterization of the spectrum of pairwise interactions among the 600 bacterial strains. In addition, the post-doc will be assisted in his / her activities by two engineer assistants.


Applicants should have strong skills in ecology and molecular biology. Complementary to the skills in microbiology of the three other post-docs working in Tübingen and New York, the candidate should also have skills in plant development, in order to assess the impact of co-infections on the vegetative growth of Arabidopsis thaliana plants. Skills in handling large datasets and statistical analyses are not required but will need to be developed in the first year. Fluent English is required.

Work Context

The LIPM offers an excellent scientific environment of teams working on plant-microbe or plant-plant interactions (https://en.lipme.fr/). As a member of the LabEx (Laboratory of Excellence) TULIP (https://www.labex-tulip.fr/labex-tulip_eng/) and of the FR AIB Research Federation (http://www.fraib.fr/), the LIPME also benefits from key interactions with other relevant plant and ecology labs, local facilities and platforms (including in imaging and high-throughput phenotyping).
For more information about the ECOGEN team:

Constraints and risks

The postdoctoral fellow will be located at the LIPME, but will have to spend every year short stays (2-3 weeks) in the research groups of Detlef Weigel and Joy Bergelson. The laboratory is governed by internal regulations.

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