General areas of responsibility
The Sète Environmental Resources Laboratory (LERLR) and the Animal and Systems Adaptation and Adaptability Laboratory (L3AS) from Ifremer are part of the MARine Biodiversity, Exploitation and Conservation (MARBEC) Joint Research Unit (https://umr-marbec.fr/en/), whose supervisory authorities are the French National Research Institute for Sustainable Development (IRD), Ifremer, the University of Montpellier and the National center for Scientific Research (CNRS). MARBEC is one of the largest laboratories working on marine biodiversity and its uses in France with around 230 agents, including 80 researchers, assistant professors and professors. The unit is located in Sète, Montpellier and Palavas-les-Flots, as well as in the Indian Ocean, Asia, Africa and South America. MARBEC studies the marine biodiversity of lagoon, coastal and offshore ecosystems, mainly Mediterranean and tropical. Among the many current research projects, MARBEC particularly carryies out research projects on the distribution of habitats and their functional roles in the face of global change using complementary innovative tools.
Summary
Mediterranean lagoons are now subjected to multiple local and global anthropic pressures. This results in the modification of the ecosystem structure, functioning and provided services. Understanding the future response of lagoon biological communities is therefore of major interest for defining effective conservation actions to preserve or restore these ecosystems. Metabarcoding is nowadays used as an integrative tool to characterize biodiversity from environmental DNA (eDNA). This tool, commonly used in the marine environment, has not been developed yet for macrophytes even though they play an essential role in the formation of habitats for many species. This thesis project aims to develop methods based on eDNA to assess the diversity of macrophytes and their microbiome, a potential indicator of the host health status. More specifically, the project will focus on (i) evaluating the effectiveness of molecular tools to identify macrophytes, (ii) characterizing the microbiome associated with the macrophytes health status, and (iii) optimizing in situ sampling strategy and eDNA capture tools for macrophyte holobionts in marine environments. Based on experimental and in situ approaches, the development of these methods may allow to anticipate regime shifts of these ecosystems and help implement preventive management measures.
Key words
Macrophyte holobiont, environmental DNA, metabarcoding, bioinformatics, biomonitoring, Mediterranean lagoons
Required Knowledge, skills, and characteristics
- Master degree in research.
- You will have a strong background in molecular biology (DNA extraction, PCR, Sanger and high throughput sequencing) and data analyses (bioinformatics, R).
- You will be aware of laboratory precautions.
- Good knowledge in phylogeny, and/or marine/aquatic ecology would be advantageous.
- Highly motivated by the thesis research project, rigorous, dedicated and autonomous.
- Proficient in English.
- Ability and attraction for reading, analyzing and synthesizing scientific publications and results, writing and oral presentations.
- Ability to discuss and interact with internal or external collaborators to Ifremer and MARBEC.
Specific working conditions
Modalités d’exercices :
- Full time
- Ship boarding for the day
- Possibility of working outside working days depending on sampling missions
- Laboratory work
- Data analyses
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.
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 three subject supervisors: Angélique Gobet (angelique.gobet@ifremer.fr), Vincent Ouisse (vincent.ouisse@ifremer.fr) et Yannick Gueguen (yannick.gueguen@ifremer.fr).
In parallel, please submit your application to the doctoral school : ED 584 GAIA (Univ. Montpellier)
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 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.
Deadline for applications: 15/04/2024
All applications are processed exclusively via their website. Interested candidates can apply by clicking the “Apply” button.
For more information about the opportunity click here.