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 for predicting stable pathogen-pathogen-microbiota interactions by modeling. In this context, the engineer position is part of the third step of the PATHOCOM project, which aims to test the effect of abiotic factors on pairwise interactions between 18 bacterial pathogenic strains (9 strains of P. syringae and 9 strains of X. campestris), in in vitro and field conditions. To achieve these goals, the recruited engineer will benefit from tools allowing high-throughput phenotyping (pipetting robots, barcoded bacterial strains, barcoded plant lines, high-throughput imaging of vegetative growth…). This 30-month engineer position 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).

Activités

The engineer will be in charge of testing the effect of 4 abiotic factors (climate, physicochemical properties of the soil) on 153 pairs of pathogenic bacterial strains (Pseudomonas syringae and Xanthomonas campestris) in in vitro conditions and field conditions. To achieve his/her tasks, the engineer will be able to rely on a team of colleagues from the host group (three postdocs, another engineer, and one technician) working on projects closely related to those assigned to this position. The engineer will have to ensure technological monitoring to identify the latest methodologies that will make it possible to speed up the different steps of the experiments (seed sowing, inoculation of bacterial solutions, high-throughput phenotyping, DNA extraction, preparation of libraries for high-throughput sequencing, data analysis, etc.). The engineer will also be responsible for organizing plant infections in in vitro conditions using pipetting robots.

Compétences

Applicants should have excellent skills in (i) microbiology, molecular biology, and bacterial genetics, (ii) in vitro culture (microbes and plants), (iii) setting up experiments in field conditions, (iv) manipulation of pipetting robots, and (v) high-throughput phenotyping. Skills in handling and processing large datasets will be a real asset. Fluent English is required.

Contexte de travail

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

Contraintes et risques

The research engineer will be located at the LIPME. He/she may have to spend four weeks every year in the lab of Joy Bergelson to set up field experiments. The laboratory is governed by internal regulations.