Ifremer - French Research Institute for Exploitation of the Sea

PhD - Impacts of environmental contaminations on the microbiome of the pacific oysters (M/F)

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Reference: PV-2023-1284/1


Duration of contract:3 ans

Start date:

Deadline for applications:23/04/2023

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 Unit develops scientific knowledge on the transfer and biological effects of chemical contaminants in marine ecosystems. Our research work enriches the expertise in Public Policy Support and allows the assessment of chemical pressure on marine ecosystems.

The Unit's activity and production of scientific knowledge are oriented by: (i) the study of the spatio-temporal dynamics of legacy and emerging metallic and organic contaminants in sediments, seawater and marine organisms in the context of the land-sea continuum, and (ii) the study of the transfer of chemical contaminants and their biological effects at the level of individuals, populations and through marine food webs.

This work thus contributes to the characterization of the marine chemical exposome and its biological effects. The Unit contributes to the working groups of two Regional Sea Conventions, OSPAR (Atlantic) and Barcelona (Mediterranean), of ICES and is a member of the national reference laboratory for the monitoring of aquatic environments, Aquaref.

Unit website: https://ccem.ifremer.fr/


Any multicellular organism can be considered as a metaorganism consisting of a macroscopic host and its microbiota, i.e. a community of symbiotic bacteria, archaea, fungi and many other eukaryotic microbial species. The plasticity of the microbiota can contribute to the acclimatization capacities of the host and even to the adaptation of the population to environmental changes. Conversely, disturbances in host-microbiota interactions (dysbiosis) can lead to the development of various diseases. Many microbiota are often located at the interface between the external environment and host tissues (intestine, gills or mucus), which makes them particularly exposed to pollutants and pathogenic organisms. It is therefore essential to identify the factors that can maintain or alter their integrity.

The SymbioTox project is part of the Blue Chair in "Contaminants, Sea and Health" funded by Ifremer's exceptional scientific investment plan. Its objective is to study the impact of environmental stresses and contaminations on microbial communities (microbiota) associated with harmful bivalves and marine microalgae, as well as the consequences that these changes may have on human and ecosystem health. It is characterized by a strong transdisciplinarity thanks to the expertise of different units of the Atlantic Centre in chemical contamination (CCEM), microbiology and health (MASAE), physiology of mollusks (EMMA, ASIM) and toxic microalgae (PHYTOX).

This thesis project aims to (i) characterize the structure and role of prokaryotic and eukaryotic microbial communities associated with the pacific oyster Crassostrea gigas, and their alterations in response to anthropogenic contamination along the French coastline; (ii) study the role of the microbiome in the resistance of C. gigas to pathogens; and (iii) highlight the possible links between the microbiome and the metabolization of certain types of pollutants.

Key words

Microbiome; metabarcoding; Chemical exposome; Chemical pollutants; Crassostrea gigas.

Required Knowledge, skills, and characteristics

  • Master degree in ecology, molecular biology or microbiology.
  • Good knowledge of bioinformatics tools and R software.
  • Knowledge of molecular biology practices in the laboratory.
  • Ability to design an experimental plan.
  • Very good ability to combine laboratory work, field work and data processing.
  • Good organizational skills, rigor and initiative.
  • Ability to communicate and work in a team.
  • Proficiency in English / A good knowledge of French will be an asset.

Specific working conditions

  • Regular trips to the Ifremer sites of Bouin and La Tremblade.
  • Presentation of results and discussions in France and abroad.

PhD is a real opportunity to work on Ifremer's scientific and technological priority themes. It entitles the holder to a gross monthly salary of 2300 euros gross for a period of 3 years, which cannot be combined with other scholarships. 

How to apply for this position ?

Your application file must include:

  • a curriculum vitae
  • a covering letter
  • a reference letter
  • an academic transcript (Bachelor + Master 1 and first semester Master 2)

Your application must be compiled into 2 PDF files, up to 3 MB for each file:

In case of any problem in attaching your documents, please upload your CV on this page (this step is mandatory for your application to be considered) and send all the documents to the thesis supervisor: anthony.bertucci@ifremer.fr

The deadline for applications is April 23rd, 2023. Nevertheless, we strongly urge you to let us know as soon as possible of your intention to apply, by contacting the subject supervisor.

Doctoral students' contracts will start as of October 2nd, 2023, subject to the submission of administrative documents authorizing Ifremer to recruit the doctoral student (certificate of completion of the Master 2 or engineering degree + visa for foreign doctoral students outside the EU).

How to apply for this position

Deadline for applications: 23/04/2023

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

Détails de l'offre

PhD - Impacts of environmental contaminations on the microbiome of the pacific oysters (M/F)
44311 Cedex 03, Rue de l'Île d'Yeu Nantes, France
Date limite d'inscription
2023-04-23 23:59:59
Type de poste
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L'Ifremer contribue, par ses travaux et expertises, à la connaissance des océans et de leurs ressources, à la surveillance du milieu marin et du li...

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