Post doc in Microbiology in Roscoff, Bretagne – Deadline 15 November 2021

The Institute and the recruiting department

A pioneer in ocean science, IFREMER’s cutting-edge research is grounded in sustainable development and open science. Our vision is to advance science, expertise and innovation to:

– Protect and restore the ocean

– Sustainably use marine resources to benefit society

– Create and share ocean data, information & knowledge.

With more than 1,500 personnel spread along the French coastline in more than 20 sites, the Institute explores the 3 great oceans: the Indian, Atlantic and Pacific oceans. A leader in ocean science, IFREMER is managing the French Oceanographic Fleet and its dedicated scientists create ground-breaking technology to push the boundaries of ocean exploration and knowledge, from the abyss to the atmosphere-ocean interface.

Well-established in the international scientific community, our scientists, engineers and technicians are committed to advance knowledge about our planet’s last unexplored frontiers. They provide the science we need for informed decision-making and public policy and they transfer this knowledge and technology to businesses to fulfill public and private needs. Core to our mission is also to strengthen public awareness about the importance of understanding the ocean and its resources, and empowering future generations of leaders through education and outreach national campaigns.

Founded in 1984, IFREMER is a French public organization and its budget approximates 240 million euros. It is operating under the joint authority of the French Ministry for Higher Education, Research and Innovation, the french Ministry of the Sea, the French Ministry for the Ecological and Solidary Transition, and the French Ministry of Agriculture and Food.

General areas of responsibility

The Roscoff marine station (SBR) constitutes an ideal scientific and logistical environment for the research project of Le Roux team (Génomique des Vibrios) thanks to the presence of technological platforms (bioinformatics, imaging, crystallography, aquariums) and basic research projects developed in the departments (ecology, biology of marine microorganisms). Conversely, the team roots its scientific questions and experimental models in the needs of applied research that Ifremer must conduct (pathogenic oyster bacteria).

The position is part of the ERC advanced DYNAMIC project, which aims to understand the role of phages in the eco-evolutionary dynamics of pathogenic hollow oyster vibrios. Under the supervision of the scientific leader of the project, he/she will work in close collaboration with a technician to perform experimental work and a bioinformatician for the in silico analyses.

General areas of responsibility

He/she will be in charged of a specific aim of the DYNAMIC project, which is to understand the eco-evolutionary processes underlying interactions between bacteria and phages in nature. The first part of this work (18 months) will be based on a sampling already performed in 2021. How the abundance of the V. crassostreae species (an oyster pathogen) and epidemic clones vary with time? Does phages dynamic correlate with host dynamic and at which genetic level? Does the infection network of phage-vibrio reveal adaptation with time? The second part of the work (18 months) will be divided in few additional samplings to highlight putative local adaptation of phages and vibrios and a metagenomic analysis of the virome during the time serie sampling 2021.

Principal activities

  • He/she will quantify the crassostreae species and specific epidemic clones by qPCR (or digital PCR) along a time serie sampling already performed in 2021 (35 dates, 4 seawater fractions and oysters samples)
  • Perform infection matrix of all phages versus all vibrios to highlight modularity or nestedness of the infection network.
  • Will be involved in sampling of a French Atlantic coastal zone site (July 22, 23)
  • Will perform time shift and local adaptation analysis
  • Will be involved in a metagenomic analysis of the seawater virome
  • Participation in the team’s duties (for example culture and media preparation)

He/she will be co-supervised by CEFE – CNRS Montpellier) for the statistic analysis and Institut Pasteur for the metagenomic analysis.

Collaborative work environment

  • Internal collaborative relationship: Project team, (8 persons), from the LBI2M unit in Roscoff (100 persons) and from the station (350 persons) various meetings and seminars will promote interaction. Regular exchanges will take place with colleagues from the PFOM unit of Ifremer Plouzané/Argenton.
  • External collaborative relationship: He/she will work in close collaboration with CEFE (Montpellier).

Required Knowledge, skills, and characteristics

  • PhD in microbiology

Required knowledge, skills and characteristics

Knowledge, skills and abilities

  • microbiology, environmental microbiology
  • a good knowledge in ecology and evolution
  • rigor and organization for works producing a large data set
  • ability and willingness to perform several experiments in parallel
  • a strong expertise in statistical analysis and management of biological (incl. multivariate) data

Human qualities

  • a high degree of enthusiasm for the advertised project
  • curiosity, adaptability and communicative skills
  • a fondness for support of and interaction with other group members

Specific working conditions

  • Field sampling (July 2022 and 23)
  • Lab work at the SBR (DNA extraction, qPCR and or digital PCR; isolation, storage of phages and vibrios ; cross infection assays ; statistic analysis)
  • Short stays at Montpellier

How to apply for this position

Deadline for applications: 15/11/2021

All applications are processed exclusively via our website. Interested candidates can apply by clicking the “Apply” button. 

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