Postdoctoral Fellow In Microbial Ecology

Organisation/Company: La Rochelle Université
Research Field: Biological sciences » Biology, Environmental science » Ecology
Researcher Profile: Recognised Researcher (R2), Established Researcher (R3)
Positions: Postdoc Positions
Country: France
Application Deadline: 30 Nov 2024 - 18:00 (Europe/Paris)
Type of Contract: Temporary
Job Status: Full-time
Offer Starting Date: 3 Mar 2025
Is the job funded through the EU Research Framework Programme? Not funded by a EU programme
Is the Job related to staff position within a Research Infrastructure? Yes
Offer Description The research project for which the successful candidate will be selected will be part of Axis 1 'Zoonotic influenza and the microbial exposome' of the PSGAR (Programmes Scientifiques de Grande Ambition Régionale) of Nouvelle Aquitaine region 'Infectious diseases and health risks'. More specifically, it is associated with the EMERG project (Microbial Exposome and Health Risk: the benefits of One Health Management of zoonotic influenza-related issues) (2024-2028).
The exposome concept encompasses all the factors of exposure to the external environment, both specific and non-specific, to which an organism is subjected since its preconception and the consequences of these exposures at the level of the cells and organs at the origin of pathological processes. Although the exposome concept was established for human health and applied in particular to allergic diseases (such as asthma), the exposome concept can be extended to animals and plants. The study of the convergence/interaction between human and animal exposomes can thus be approached through the 'One Health' concept, including from an ecological point of view such as the recently proposed socio-eco-exposome. What's more, its study relates to the notion of biodiversity (biological, in particular microbial: viral, fungal, parasitic and bacterial), and to the dynamics of this biodiversity in relation to anthropisation, pollution and climate.
In this context, the EMERG project aims to characterize the microbial exposome in different biotopes in the Nouvelle Aquitaine region and to study its links with i) animal health (the link between avian influenza/porcine, with zoonotic potential, and the microbial exposome), human health (the link between the microbial exposome and the risk of emerging infections) and/or plant health (the link between the microbial exposome and the emergence of plant pathogens) ii) human development and pollution (the link between the microbial exposome and the environment in the context of avian influenza epizootics and the associated risk of pandemic emergence) and iii) climate (changes in migration corridors, invasive exotic species, etc.).
This is a cross-disciplinary project, at the interface of a number of disciplines (ecology, biology, microbiology, infectiology, physiology, environmental law, bioinformatics, modelling, veterinary science) and integrates research activities at all scales, combining fundamental and applied sciences.
Tasks:
The person recruited will be responsible for linking the occurrence of avian influenza events (primary introduction then secondary spread) and the microbial exposome.
Initially, the microbial exposome (bacteria, archaea, fungi and micro-eukaryotes) in coastal and terrestrial areas of New Aquitaine will be characterized (spatio-temporal monitoring and 3 types of sampling: water, sediment and air). Then, in a second phase, these exposomes, which are not a priori conducive to the development of avian influenza, will be compared with those of biotopes where avian influenza viruses are rife, in order to identify the elements specific to the context of these epizootics (abiotic or biotic environmental parameters, or possibly other pathogens and environmental descriptors).
The data obtained will be analyzed using biostatistical tools to determine the correlation between the various organisms making up the exposomes and the interaction networks existing in the microbial communities as a whole. These analyses will make it possible to establish indices that can be used as bioindicators of environments and/or conditions conducive to the development of avian influenza with zoonotic potential.
The person recruited will join the LIENSs laboratory (LIttoral Environnement et Sociétés). LIENSs is a trans-disciplinary research unit under the CNRS and La Rochelle University authorities, which integrates expertises in many scientific fields including environmental sciences (biology, ecology, ecophysiology, ecotoxicology, earth sciences, geophysics), humanities and social sciences (geography and history), and Engineering Sciences (chemistry and biotechnology). It takes strength from this high interdisciplinarity to address issues on the sustainable development of its main research object: the littoral zone.
The person recruited will work in the BIOFEEL (BIOdiversity and Functioning of Coastal Ecosystems) team, which studies the structure and functioning of coastal ecosystems, primarily using a trophic ecology approach. The team analyses biodiversity and its role at different scales, from individual to the ecosystem, and qualifies/quantifies the evolution of these ecosystems in response to environmental changes and societal issues.
Minimum Qualifications:
Applicants must hold a PhD in a field related to microbial ecology, molecular ecology or microbiology. They must have solid expertise in the analysis of environmental DNA data. Applicants must demonstrate that they can carry out independent research and lead a project within the EMERG research consortium. The person recruited will be required to realize frequent and lengthy stays to the various laboratories involved in the co-supervision of the post-doctoral project (Pau and Bordeaux).
Skills required:
In-depth knowledge of molecular biology and environmental microbiology. Proficiency in DNA/RNA extraction, PCR, meta-barcoding/metagenomics is essential. Additional experience with complex environmental samples with low DNA concentrations would be appreciated.
Bioinformatics expertise: sequence analysis (QIIME, DADA2, Mothur, or other DNA sequence data analysis platforms)
Expertise in biostatistics: statistical analysis, programming (R) and experience in network analysis (co-occurrence) is required
Interest in environmental research
Organisational skills, rigour, autonomy and method, respect for deadlines
Ability to communicate and work as part of a team
Ability to listen and take on board requests
Experience in promoting research: writing articles and giving talks
Ability to popularize and adapt to a varied audience
Additional Information Salary: From €2,700 gross salary per month (approx. 2,200 net) depending on experience
Recruitment open to anyone with a RQTH (Qualified Health and Disability certificate).
75% contribution to the cost of public transport to and from work
Sustainable mobility package for the use of a cycle/carpool for home-work journeys
Health insurance participation of €15/month
Collective catering on university campus
Teleworking possible for up to 2 days a week, depending on departmental needs and organization
Support for staff in their professional development and preparation for civil service entrance examinations
Sport, leisure and cultural activities for all employees
Selection Process To facilitate consideration of your application, it should include at least the following: (i) a covering letter, (ii) a detailed CV, (iii) a description of your technical and analytical skills and data modelling in ecology and co-occurrence network analysis, (iv) the contact details for at least two referees and (v) a copy of the highest diploma.
This application must be submitted using the dedicated application available by clicking here (RECH/LIENSs/24-002)
Interviews will take place mid December 2024.
The contract should start March 2025 (open to discussion).
Candidates will be asked to confirm receipt of their applications as soon as they have submitted them. If you do not receive confirmation of receipt by email, please re-submit your application.
Candidates will be informed of their selection for an interview as soon as possible; interviews will be conducted by videoconference. Approximately 3 candidates will be interviewed.

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