Missions

Infectious disease is often the major selective agent in nature, and we cannot understand how natural populations evolve without understanding their pathogenic microbes. Beyond host immunity and abiotic factors, an important factor determining the ability of pathogens to invade and proliferate in a host is the resident microbiota. However, we are only beginning to glimpse its diverse 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 of how pathogens interact with other pathogens and how pathogen-pathogen interactions are affected by host microbiota, host genetics, and the abiotic environment. In the PATHOCOM project (https://figshare.com/articles/preprint/PATHOCOM_proposal/13174337), we aim to set 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 modeling. In this context, this postdoctoral project is part of the third step of the PATHOCOM project, which aims to test, among others, the effect of the genetics of A. thaliana on pairwise interactions between 6 bacterial pathogenic strains (3 strains of the bacterial pathogen Pseudomonas syringae and 3 strains of the bacterial pathogen Xanthomonas campestris). To achieve these goals, the recruited post-doc will (i) set up large GWAS in in vitro conditions and field conditions, and (ii) functionally validate several QTLs using last-generation tools of plant genome editing (e.g. CRISPR/Cas9). The recruited post-doc will work with a panel of 200 Illumina whole-genome sequenced A. thaliana accessions from the southwest of France, including 50 accessions that have also been sequenced with the PacBio technology. The recruited post-doc will benefit from tools allowing high-throughput phenotyping (pipetting robots, barcoded bacterial strains, high-throughput imaging of vegetative growth…). This 24-month postdoctoral project (with an extension of 12 months) 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, Tübingen, Germany) and Joy Bergelson (New York University, USA).

Activities

The postdoc will be in charge of setting up GWA mapping experiments to test the effect of 200 natural accessions of A. thaliana on 6 pairs of pathogenic strains under in vitro conditions and field conditions. While GWAS in in vitro conditions will be conducted in France (Toulouse), GWAS in field conditions will be conducted in the USA (3-4 stays of 6 weeks each). The post-doc will also be in charge of functionally validating several QTLs using last-generation tools of plant genome editing. To achieve these goals, the postdoc will work with another postdoc on the same project during the same period, but with complementary skills. In addition, the post-doc will be able to rely on a collective of several people working on tasks close to those mentioned for this profile (e.g. engineer, assistant engineer, and technician).

Skills

Applicants should have excellent skills in molecular biology to functionally validate candidate genes underlying plant QTLs affecting pathogen-pathogen interactions. In particular, applicants must master the latest generation of plant genome editing tools. Skills in quantitative genetics, experimental designs, and statistical analysis will be a plus. Fluent English is required.

Work Context

The LIPME 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:
https://en.lipme.fr/ecogen-1

Constraints and risks

The postdoc will be located at the LIPME. He/she will have to spend 3-4 stays of 6 weeks each in the lab of Joy Bergelson to set up GWAS. The laboratory is governed by internal regulations.