Duration of contract:3 ans
Deadline for applications:02/05/2021
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 for the Ecological and Solidary Transition, and the French Ministry of Agriculture and Food.
General areas of responsibility
The IHPE is developing integrative research on the interactions between animals, their pathogens and their environments. It brings together staff from four institutions: the CNRS, Ifremer, the University of Montpellier and the University of Perpignan. The laboratory benefits from numerous equipment, access to state-of-the-art platforms and in particular high-throughput sequencing and bioinformatic analysis resources.
The TReV team studies pathogen virulence and host resistance in order to understand the dynamics of pathogen transmission in various aquatic pathosystems. The team is made up of 9 researchers with complementary skills (in marine microbiology, cell biology, pathophysiology of molluscs, ecology and evolution) which allows us to conduct interdisciplinary and integrative research projects.
Vibrios are responsible for major crises in aquaculture. Our laboratory has shown that the vibrios of the Splendidus clade, which are opportunistic pathogenic bacteria for the oyster Crassostrea gigas, have cytopathic activities towards the oyster's immune cells, the hemocytes. In addition, some of the virulence factors are also involved in the ability of some of these vibrios to resist predation by marine amoebae. During a sampling campaign aimed at studying the diversity of amoebae in coastal marine environments, we demonstrated that vibrios of the Splendidus clade were found associated with amoebae in oyster farming areas. The objective of the thesis is to study the interactions between vibrios of the Splendidus clade and marine amoebae in order to determine the role of these interactions in the emergence of pathogenic bacteria. This interdisciplinary project will combine approaches in functional biology, ecology and evolution. The results of this work will allow a better understanding of the role of predator / prey interactions in the mechanisms of emergence of pathogenic vibrios in the marine environment.
Emergence of pathogens, Host-pathogen interactions, vibrios, marine amoebae.
Required Knowledge, skills, and characteristics
Specific working conditions
The doctoral project is structured around three main complementary goals:
1- Studying associations between vibrios and amoeba in the marine environment, and their evolutionary history.
Methods: qPCR, Genome sequencing, Bioinformatics analyzes: Genome annotations, Comparative genomics, Molecular phylogeny.
2- Studying the relative weight of vibrio-amoeba interactions on the selection of virulence and the emergence of pathogenic bacteria.
Methods: Functional screening by transposon bank (INseq) and experimental evolution studies.
3- Studyng the cellular and molecular mechanisms of interactions between pathogenic vibrios and marine amoebae.
Methods: Functional microbiology, cell biology, fluorescence microscopy and electron microscopy.
The project will benefit from the infrastructures of the IHPE laboratory (culture rooms, microscopy, installations for experimental pathology in an aquatic environment, high-throughput sequencing facility and bioinformatics resources) as well as collections of marine vibrios and marine amoebae from the coastal marine environment, but also the resources available within Ifremer (Palavas experimental platform, Sebimer bioinformatics service, production of Ifremer standardized oysters for research).
The work will be carried out in collaboration with various national and international partners including Vincent Delafont (EBI, Poitiers), Mark Mandel (University of Wisconsin-Madison, USA), Frédérique Le Roux (Equipe GV, Roscoff), Guillaume Martin, Oliver Kaltz and Emmanuel Fronhofer (ISEM, Montpellier).
This 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 1900 euros for a period of 3 years, which cannot be combined with other scholarships.
How to apply for this position ?
Your application file must include :
Your application must be compiled into 2 PDF files, up to 1.5 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 : firstname.lastname@example.org and email@example.com
The deadline for applications is 2nd of May 2021. 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 1st, 2021, 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: 02/05/2021
All applications are processed exclusively via our website. Interested candidates can apply by clicking the “Apply” button.Continue reading
|Title||PhD : Studying the role of vibrios interactions with marine amoebae in the emergence of pathogens (M/F)|
|Employer||Ifremer - French Research Institute for Exploitation of the Sea|
|Job location||155 Rue Jean Jacques Rousseau, 92138 Issy-les-Moulineaux|
|Published||March 1, 2021|
|Application deadline||May 2, 2021|
|Job types||PhD  |
|Fields||Ecology,   Bioinformatics,   Molecular Biology,   Microbiology,   Cell Biology,   Evolutionary Biology,   Marine Biology,   Computational Biology  |