Mots-Clés

Microbiology ecology evolution bacterial traits adaptation (meta-)genomics bacterial metabolisms phylogenomics bioinformatics pan-genome

Description

18-month postdoctoral position in bacterial genomics and ecology at INRAE (French National Institute for Agriculture, Food, and Environment)

Where: Paris-Saclay Food and Bioproduct Engineering research unit (UMR0782 SayFood), Bd Gaspard Monge, 91120 Palaiseau, France

Starting date: July 1st 2022

Deadline for applications: Applications will be reviewed as received and the position will remain open until filled.

Project title: Ecogenomics of the genus Halomonas and identification of the genetic determinants involved in environmental adaptation (from salt marsh to fermented food).

Background: At global scale, salinity is one of the most important driver of bacterial community assembly. Halotolerant and halophilic bacteria have colonized diverse natural environments (seawater, lakes, salt marsh, sediments, soil, leaves of salt-secreting desert tree) as well as fermented foods, in which salt acts as preserving agent. In particular, these halotolerant and halophilic bacteria are frequently found in cheese, sometimes in high abundances. Therefore, the introduction of fermented foods by mankind has created a new ecological niche for halotolerant and halophilic microorganisms.

Model system: Among these microorganisms, bacteria belonging to the genus Halomonas have been isolated and/or detected in diverse natural environment as well as at the surface of various cheeses. Recent analyses performed in our research group on a large dataset (MetaPDOCheese, funded by France Génomique) indicated that Halomonas was highly prevalent in numerous cheeses and that some members of this genus could be keystone species of this ecosystem. Thus, Halomonas appears to be a relevant candidate to study the genetic determinants involved in environmental adaptation. However, to date, we currently have a limited and fragmentary knowledge of the ecology, genetic diversity and metabolic potential of this genus, especially in the cheese ecosystem.

Objectives: The project aims to characterize the ecology and metabolic potentials of the members of the genus Halomonas as well as to understand the processes of domestication of these bacteria in the fermented food environment. To do so, this project will focus on the

(i) Global distribution, abundance and diversity of Halomonas across ecosystems (seawater, lakes, salt marsh, sediments, soil, fermented food);

(ii) Genetic diversity and metabolic potential present in the hundreds of available Halomonas genomes;

(iii) Identification of the genetic traits involved in the adaptation to the cheese ecosystem.

Mandatory requirement: PhD degree in bioinformatics, microbiology, genomics or microbial ecology.

Key words: Microbiology, ecology, evolution, bacterial traits, adaptation, (meta-)genomics, bacterial metabolisms, phylogenomics, bioinformatics, pan-genome.

Required: Knowledge in bacterial metabolism, comparative genomics and phylogenomics. Ability to work on HPC systems and to handle large datasets, following FAIR principles. Excellent skills in verbal and written communication. Motivation, creativity, curiosity, team-work, and good inter-personal relationship with colleagues.

Preferred: Experience with Anvi’o, Snakemake, R.

Gross salary: From 2,442 to 2,630 euros per month, depending on experience.

How to apply: By email to Vincent Hervé (vincent.herve@inrae.fr) with a motivation letter explaining why you are interested by this position and how you think you are qualified, your CV and names and e-mail addresses of two or three referees who can write letters of reference on your behalf.