The  holobiont approach aims to assess the health of host organisms in the  context of their associated microbiomes. Studies have demonstrated a  clear association between shifts in the composition of microbiomes in  response to changes in the surrounding environment and disturbances in  host physiology or fitness. Interactions within microbiomes are  important for their hosts. However, those are still rarely investigated  and remain poorly understood, particularly regarding the mechanisms  leading to adverse outcomes for hosts organisms.
In this context,  the Ifremer Blue Chair in “Contaminants, SEA and Health” investigates  how marine invertebrates (bivalve molluscs) and toxic microalgae are  affected by the chemical exposome and the consequences for ecosystem  functions and human health (one health concept), with a particular focus  on the microbiome associated with these species. This highly  collaborative programme benefits from the interactions between research  units at the Ifremer Atlantic centre in Nantes. The expertise of these  units is in the evaluation of the quality of marine waters and the  contaminants that affect them, the land-sea continuum and the cumulative  impacts of human activities, and the management of aquaculture and  fisheries resources.
Main missions
In recent years,  Ifremer produced different sets of metagenomic data to study microbiomes  associated with microalgal communities or marine bivalves. The main  objective of this postdoctoral position in to better comprehend  microbiome functions and interactions between partners (within  microbiome and with the host organism) in aquatic organisms.
Within  the Blue Chair programme, coordinated by Anthony Bertucci, the postdoctoral fellow will use and develop innovative  bioinformatic methods to complement the existing taxonomic information  by a more functional approach of the microbiome and its modifications.  He/She will collaborate with the Ifremer bioinformatics service  (SeBiMER) in Brest, as well as researchers and  PhD students from the CCEM (Chemical Contamination of Marine  Ecosystems), PHYTOX (Physiology and Toxins of microalgae) and MASAE  (Microbiology, Food, Health and Environment) units. In addition to the  prediction of metabolic pathways, this project should identify metabolic  and co-occurrence networks that might rule the assembly and maintenance  of microbial communities based on metagenomic and metabarcoding data  previously obtained by the research units of the Atlantic Centre from  either microalgal communities, marine bivalves, sea-food products or  synthetic microbiomes. This should help to identify factors and/or  underlying mechanisms that could explain microbial assemblies and  community changes and the occurrence of adverse outcomes in response to  environmental parameters such as temperature, pCO2 or chemical  pollution. Microbial metabolic networks that will BE identified could  later BE investigated by the development, in collaboration with research  units, of other meta-omics approaches such as metatranscriptomics or  metabolomics in bivalves exposed to environmental stressors, during  harmful algal blooms or in the improvement of food conservation  processes.
Missions will include the collection and processing of  metabarcoding and WGS data, the re-examination of pre-existing data,  and the development of multi-omic analyses in microalgae, bivalves or  food products. All the results will BE valorised in international  conference, publication and outreach events.
Collaborative work environment
Researchers,  engineers, lab technicians and PhD students from CCEM, PHYTOX and MASAE  units in Nantes and SEBIMER in Brest. Opportunities to participate in  national and international conferences and workshops.
- Full-time position
- Temporary contract of 24 months
Profile
PhD in microbial ecology, molecular biology, bioinformatics, computational biology.
- Experience in metabarcoding, metagenomics or metatranscriptomics.
- Experience with multivariate statistical analyses will be an asset.
- Ability to work in a team, interest for collaborative projects.
- Good knowledge and hands-on experience in DNA/RNA extraction.
- Experience with Next Generation Sequencing techniques and dedicated bioinformatic tools.
- High degree of autonomy and critical thinking.
- High motivation for lab work.
- Excellent scientific writing and results presentation skills.
This call is open to highly motivated applicants of any nationality who already have a research experience (PhD or postdoctoral contracts) outside mainland France (i.e. a research experience in French overseas is eligible). Thesis accreditation must have been obtained less than three years before the starting date of the future post-doctoral contract. Candidates must not have been previously employed as doctoral or post-doctoral researcher in an Ifremer research unit nor in a joint research unit involving Ifremer. (These joint research units are the following: MARBEC, LEMAR, LOPS, AMURE, BEEP, LEEISA, IHPE, ENTROPIE, EIO, GEO-OCEAN, DECOD).
The Institute
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.
More information about this opportunity can be found here.