Description du poste et Missions
Closure date for receipt of applications: 15/05/2025
Who are we?
This project is proposed by the “Marine Resources in French Polynesia” unit. This unit conducts research dedicated to developments in aquaculture and the adaptation of species of economic interest to global changes. In this context, we have experimental infrastructures that allow integrated studies from the field to the laboratory and from populations to the finest mechanistic aspects. As part of international partnerships with New Zealand (Cawthron Institute) we are developing new aquaculture protocols aimed at improving the robustness of species with regard to climate change and diseases. These developments are carried out on temperate and tropical bivalve species. The idea is to develop non-lethal stress treatments at the larval level that influence the developmental trajectory of our species of interest to improve their robustness during subsequent exposures (at juvenile or adult stages) to the same stresses.
What is the subject of the thesis ?
During this PhD project, you will develop protocols for influencing the developmental trajectory on biparental families of two species of tropical bivalves (the rock oyster, Saccostrea echinata and the pearl oyster, Pinctada margaritifera) and two species of temperate bivalves (the green mussel, Perna canaliculus and the Pacific oyster, Magallana gigas). By working on species with very different thermal regimes, we will increase the potential for application of these methods in a broader perspective at the global level. You will use different treatments at the larval level with exposures to abiotic stresses (sub-lethal temperatures) and biotic stresses (non-pathogenic bacteria) and you will test at later life stages the tolerances to the same stresses or to different stresses (e.g.: do larvae stressed by temperature resist better to a disease?). Results already published on certain bivalve species by our groups (Fallet M et al, microbiome, 2022) or preliminary results obtained by our consortium on pearl oyster (robustness increase by thermal shaping) are guarantees of success of this project.
A second part of this project will be devoted to understanding the molecular mechanisms underlying the acquisition of robustness. For this, a combination of experimental and omic approaches will be developed. The subgroups having undergone differential robustness to diseases or thermal stresses as well as their controls, will be subjected to sublethal thermal stresses or exposures to pathogens and they will be sampled regularly after exposure (0, 6h, 12h 24h, 48h post-exposure). These samples will then be subjected to comparative molecular approaches to characterize the mechanisms of robustness acquisition. To characterize these mechanisms, we will develop RNA-seq approaches (de Lorgeril et al, nature communications, 2018). We will also characterize the allele frequency at the genome level of the different families and conditions (stressed larvae vs. controls) in order to assess the absence of selection during larval stress (Fallet et al., microbiome, 2022). The epigenotype of the different families and conditions will be characterized in order to identify the epigenetic modifications underlying the observed phenotypic changes. Genotypes and epigenotypes will be characterized by whole genome sequencing by Enzyme-Methyl-Whole-Genome-Sequencing (Valdivieso et al., STOTEN, 2025), and the (epi)genotype will be extracted by approaches mastered by our consortium (Gawra et al. Science Advances, 2023). Additionally, we will develop a targeted comparative metabolomics approach to assess potential trade-offs between growth and robustness (Duperret et al., submitted) and an integrative omics approach will be developed to integrate the data (Duperret et al., submitted).
What will your mission be?
You will develop all of this work in collaboration between three laboratories (the SECOPOL UMR in French Polynesia, the IHPE UMR in Montpellier and the Cawthron Institute in Nelson, New Zealand). The work on the Pacific oyster and the green mussel will be carried out at the Cawthron Institute facilities and that on the pearl oyster and the rock oyster will be carried out at the Ifremer facilities in Vairao (Tahiti). The omics analyses will be carried out at the IHPE laboratory in Montpellier. During the thesis, you will spend 18 months in French Polynesia, 12 months in mainland France (Montpellier) and 6 months in New Zealand.
What will your activities be?
You will develop experimental approaches to larval stress and verify the robustness acquired at later life stages.
You will participate and develop comparative omics approaches and the characterization of underlying molecular mechanisms. You will manipulate various omic datasets (epi)genomics, transcriptomics, and metabolomics), analyse them, apply appropriate statistical approaches, and integrate the different omics layers (integrative omics).
How are your activities organised?
• Full-time: 100%
• Travel between French Polynesia, mainland France, and New Zealand
Key words
Aquaculture; climate change; thermal tolerance limits; adaptation solutions; integrative omics, developmental plasticity
Profil recherché
Who are you?
- Master degree in molecular biology, genomics or physiolgy
You have the following skills, knowledge and experience:
- Animal experimentation
- NGS analysis (transcriptomics and/or genomics and/or epigenomics) on non model species
- Bash, R, Python Programming
- metabolomics
You have the following qualities:
• Organizational skills, thoroughness, initiative, and dynamism.
• Ability to communicate and work in a team.
• Proficiency with IT and statistics tools.
• Driving license B preferred.
Informations utiles
- Localisation: Polynésie française, France - pas de déplacement
- Contrat: CDD - 3 ans
- Salaire: 2300,00 EUR par mois
- Niveau de qualification: Ingénieur/Cadre/Bac +5
- Expérience: 1 an
- Modalités de travail: Temps complet
- Fonction: Ingénierie - Chimie/Pharmacie/Bio.
- Secteur: Secteur Energie/Environnement, Service public autres
- Télétravail: Partiel
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)
Your application must be compiled into 2 PDF files, up to 2 Mo for each file.
The deadline for applications is May 15th, 2025. Nevertheless, we strongly urge you to let us know as soon as possible of your intention to apply, by contacting the subject supervisor: Guillaume MITTA
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?
- Contact: Guillaume Mitta, email : Guillaume MITTA
- Deadline application submission 15th of may 2025
- Auditions: end of May
- Decision : early june
Qui sommes nous ?
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