PhD : Molecular and cellular support of immune priming in the Pacific oyster (M/F)

Reference: PV-2024-1431/1


Duration in months :36

Start date:

Deadline for applications:15/04/2024



General areas of responsibility

- The project will take place in two Ifremer host units :

The "Host-Pathogen-Environment Interactions" Joint Research Unit is interested in describing the mechanisms governing interactions between these invertebrates, their pathogens and the environment, particularly during infectious episodes, and to characterise the adaptive responses of these animals and their pathogens to environmental pressures (IHPE « Interactions Hôtes-Pathogènes-Environnements »).

The ASIM unit (Amélioration et Santé des Invertébrés Marins - Improvement and Health of Marine Invertebrates) focuses its objectives on developing skills and acquiring knowledge in the field of the health of species of interest in marine aquaculture, with a particular focus on bivalve molluscs, interactions with associated pathogenic organisms.

Both units are well recognized for their pioneering work on mollusc-pathogen interactions, discovery of innate immune memory mechanisms in moluscs and integrated multi-omics approchaes. The candidate will ahve access to all the Montpellier University and Ifremer facilities (FACS, qPCR, scRNA-seq, metabolomics microscopy, bioinformatic thanks to the Ifremer Galaxy instance and DATAMOR cluster and animal experimentation platforms).




The increasing frequency and severity of diseases affecting farmed marine mollusks currently threaten the sustainability of this aquaculture sector, with few prophylactic or therapeutic solutions currently available. Recent advances have shown that the innate immune system of invertebrates can develop memory mechanisms allowing effective protection against pathogens. These properties have been called innate immune memory, immune priming or trained immunity. In the oyster Crassostrea (Magallana) gigas, the main mollusc cultivated in the world, we demonstrated the possibility of inducing an antiviral immune priming to protect these animals against a variant of the “Ostreid herpes virus-1” (OsHV-1 µVar), which currently impacts global production of this species. In this context, the objective of the thesis project is to unravel the molecular and cellular bases of immune priming in oysters using an innovative integrated multi-omics approach. This project will be developed as part of the PRIMOYSTER project ( which aims to develop biotechnological solutions based on antiviral IP mechanisms to protect oysters against OsHV-1 and support the sustainable development of oyster farming.


The thesis project will be organized around 4 complementary axes:

(1)        Identification of the molecular bases of antiviral priming

Parallel global transcriptomic and proteomic approaches will be performed on oysters treated with an immunostimulant according to the methodology implemented in the first year of the PRIMOYSTER project. This work will be possible thanks to the expertise and support of Ifremer's breeding infrastructures within the ASIM unit. The transcriptomic analyzes will be carried out by the RNAseq method, using methodologies and bioinformatics pipelines routinely used by the IHPE laboratory. The proteomic approach will be carried out using the nano LC-MS/MS method for quantitative analysis without a priori, already developed in the ASIM laboratory.

(2)        Identification of the cellular bases of antiviral priming

The recent application of scRNAseq technology to oyster immune cells (hemocytes) by the IHPE laboratory will help us to determine the impct of immune priming on the differentiation or activation of specific hemocyte populations and on cellular functions. In addition, a metabolomics approach will be performed using a targeted approach to identify modifications in main metabolic pathways (glycolysis, TCA, OxPHOS) known to be impacted by trained immunity.

(3)        Identification of the impact of antiviral priming on oyster fitness

We will also evaluate the impact of immune primng on oyster performance (measurements of larval development indices, growth capacities, reproductive success) across life stages and across generations. Moreover, as filter feeders, oysters inhabit a rich microbial environment that can have a deep impact on host health and fitness. To test potential correlation between IP and oyster microbiota dynamics, we will follow bacterial community diversity and composition in primed oysters using rDNA 16S gene barcoding. Data will be analyzed using methodology and bioinformatics pipelines already developed by the IHPE lab and the SEBIMER unit.

(4) Integration of data

The data obtained will be combined together and with the approaches carried out in parallel on the same samples by the partners of the ANR Primoyster consortium (notably epigenetics). It will allow us to find correlations between the multiomics data, identify biomarkers and to provide an integrated view of the key mechanisms leading to intra or transgenerational immune priming using newly developed bioinformatics tools (MOFA, multi-omics factorial analyses).


Key words


oyster, immunity, memory, priming, bioinformatics, omics approaches




Required Knowledge, skills, and characteristics


  • You will have a Master in biology /immunology and a lab experience in this field.
  • Knowledge in molecular molecular biology, global “omics” approaches and bioinformatics will also be needed and practical experience will be greatly appreciated.
  • Knowledge of animal experimentation on marine invertebrate models will also be highly appreciated.
  • As this project is part of a multidisciplinary network, you should be curious of other research fields and have good communications skills.



Specific working conditions


The project will be bi-located between the IHPE laboratory based at the University of Montpellier and the ASIM laboratory based at La Tremblade (France). This dual location will enable the candidate to cover all aspects of the project, from setting up experiments to multi-omics analysis, and to benefit from the complementary expertise of the two laboratories. The proposed timetable, which may be subject to change as the project develops, is for the first year to be spent at the La Tremblade site and the following years at the Montpellier site. All the material resources of the two units required for the development of this project (experimental infrastructures, bioinformatics and biological equipment) will be made available to the candidate. All the skills and the technical and financial environment necessary to support the candidate's training are available within these laboratories (immunity, virology, molecular biology, transcriptomics, epigenomics, metagenomics, proteomics) or within the collaborative network set up within the framework of PRIMOYSTER (2022-2026; 654k€).


Phd is a real opportunity to work on Ifremer's scientific and technological priority themes. It entitle 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.



The deadline for applications is April 15th, 2024. Nevertheless, we strongly urge you to let us know as soon as possible of your intention to apply, by contacting the subject supervisor and co-supervisor:


In paralell, please submit your application to the doctoral school : GAIA (Montpellier University, France)


Doctoral students' contracts will start as of October 1st, 2024, 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).




The Institute and the recruiting departement 

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.


How to apply for this position

Deadline for applications: 15/04/2024

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

Ifremer - French Research Institute for Exploitation of the Sea

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Location: France, Montpellier, La Tremblade
Categories: Bioinformatics, Biology, Cell Biology, Immunology, Molecular Biology, PhD,


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