Les missions du poste
Closure date for receipt of applications : 19/05/2025
Who are we?
Within the MASAE unit (Microbiology, Food, Health, Environment), the Laboratory of Health, Environment, and Microbiology (LSEM) develops research activities related to pathogenic microorganisms for humans (mainly viruses and bacteria) in the land-sea continuum and shellfish, to understand the mechanisms of transfer, persistence, or emergence within the coastal environment. Our research, at the interface of human health and the microbiological quality of the coastal environment, is based on our activities as the National Reference Laboratory for the microbiology of shellfish and the monitoring of the sanitary quality of shellfish production areas (LSEM coordinates REMI, the network for microbiological monitoring of shellfish production areas). The virology team is notably involved in the Obepine+ wastewater epidemiology platform and coordinates the European project PREVIR, aimed at developing a tool to predict viral contamination of coastal watersheds
What is the subject of the thesis ?
Shellfish contamination with human pathogens poses significant public health and economic challenges, especially due to foodborne outbreaks linked to consumption. Shellfish, particularly oysters, become contaminated through filter-feeding in coastal waters affected by human sewage, retaining viral particles like norovirus (NoV) and potentially sapovirus (SAV). While NoV is a leading cause of viral gastroenteritis, SAV has been less frequently studied in shellfish, leaving open questions about its prevalence and impact.
This project aims to investigate prevalence, diversity, and persistence of SAV in coastal environments and oysters. For this, we plan to sample oysters, estuarine water, and wastewater, to quantify SAV genome by digital RT-PCR. Targeted metaganomics will BE used to identify viral genotypes in positive samples. In addition, live oysters will BE artificially contaminated with these viruses to study their accumulation and localization in oyster tissues. The project will also assess the persistence of infectious SAV in seawater and oysters through controlled experiments using human cell cultures, providing crucial insights into its role in shellfish contamination and the broader implications for public health.
What will your mission BE?
A PhD is a training program for and through research. Under the supervision of the thesis director and co-supervisor, your mission will BE to design, implement, and critically analyze the results of experiments to address the questions posed within the framework of this thesis. You will train for research careers through experimental practice, literature review, analysis and presentation of your results, and writing publications. You will BE integrated into the team and participate in the life of the LSEM laboratory and the MASAE unit. Externally, you will BE required to participate in remote meetings with project collaborators (Japanese team)
What will your activities BE?
- Bibliography
- Setting up molecular biology techniques for the detection and sequencing of SAV
- Conducting experiments in various disciplines : molecular biology, human cell culture, virology...
- Analysis of samples collected in previous projects
- Sampling in coastal areas
- Data analysis (biostatistics, bioinformatics)
- Writing thesis manuscript (in French or English)
- Writing scientific papers (in English)
- Participate to congress or conferences (French and/or English)
- Specific professional training by the Ecole Doctorale or Ifremer
How are your activities organised?
- 100 % rate of activity
- Occasional remote working possible
- Position is based in Nantes, France
- Occasional travelling for sampling on the coastline
- Occasional travelling to congresses or conferences
Key words
Sapovirus - norovirus - shellfish quality - food safety
Le profil recherché
Who are you?
Master 2 (or equivalent) in virology, microbiology or host-pathogens interactions, clinical microbiology, food microbiology
You have the following skills, knowledge and experience :
- Strong knowledge in microbiology, especially virology
- Previous experience in a research laboratory
- Know-how in the culture of mammalian cells and virology (viral production, titers...)
- Know-how in molecular biology (nucleic acids extractions, PCR, sequencing)
- Some know-how in bioinformatics or statistics would BE appreciated
- Redactional and bibliography skills
- English skills (written and oral)
You have the following qualities :
- Curiosity, enthusiasm, thirst for knowledge
- Scientific rigor
- Organized mindset
- Teamwork
- Autonomous, initiative
Bienvenue chez Ifremer
Join Ifremer, an ally of planetary well-being, to gain a better understanding of and better protection for the ocean.
From the abyss to the surface, from the coast to the open SEA, Ifremer is the French research institute that is wholly dedicated to the Ocean. Its teams carry out research, innovate and produce expert reports to protect the ocean, exploit its resources in a responsible manner and shares marine data.
Ifremer contributes its scientific expertise to throw light on public policies and develops solutions drawn from the ocean to meet the challenges of the ecological transition. Ifremer is the operator of France's oceanographic fleet with its shipbuilding subsidiary Genavir, and imagines, designs and deploys leading edge technological means to solve the ocean's mysteries.
Join our teams, made up of 1500 scientists and research support staff, present all along the coastal areas of France and French overseas territories.
www.ifremer.fr
Infos complémentaires
What are your benefits?
- 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.
- We have a teleworking agreement and our staff have 12 comp time days and supra statutory leave.
- We allocate a significant budget to developing skills, through individual or collective training actions.
- We have a CSR policy inspired by the purposes of the institute (sustainable mobility allowance, etc.)
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)
The deadline for applications is June 6th, 2025. Nevertheless, we strongly urge you to let us know as soon as possible of your intention to apply, by contacting the subject supervisor : Soizick Le Guyader and Marion Desdouits.
In parallel, please submit your application to the doctoral school : VAAME
Doctoral students' contracts will start as of October 6th, 2025, 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).
What are the next steps?
Applications will BE evaluated by the thesis director and co-supervisor. Candidates whose profiles best match the subject will BE contacted by email in June and invited to a remote audition, which will BE attended by the thesis supervisors and representatives from the VAAME doctoral school. The selected candidate will BE notified in the days following this audition, at the end of June / beginning of July.
