Postdoc in Microbial Genomics of Extremophiles

The position (24 months) is open in the “Extremophiles” group led by Prof. Gaël Erauso in the Environmental Microbiology & Biotechnology team at the Mediterranean Institute of Oceanography (MIO) at Aix-Marseille University

Context & objectives

Extremophiles are fascinating prokaryotes able to cope with very challenging life conditions such as high temperatures or very low or high pH values that no other life form survives. Such harsh conditions are typical in hydrothermal systems such as shallow (or deep) vents (SHV) driven by magmatic (volcanic) activity. Most known extremophilic bacteria and archaea species described (among which only a tiny fraction is used for biotechnological applications) have been isolated from such hydrothermal systems. Recent metagenomic studies reveal that these natural environments constitute large reservoirs of untapped extremophile diversity. As most of this diversity remains uncultured and poorly characterized, culturing is a priority but is particularly challenging for hyperthermophiles given their growth conditions (high temperatures, low pH, and anoxia). The development of innovative methods is needed not only to address fundamental issues related to life at the limits or linked to astrobiology science but also to fully exploit the biotechnological potentials of these extremophiles. This evidence was a strong incentive guiding our research dedicated to studying extremophiles for academic and applied purposes. 

The postdoc position is proposed in the framework of two research projects, « X-TREMOPHILES » funded by the French scientific research agency CNRS, and « HYPERTHERMOBIOGAZ, » funded by the Norwegian Research Council. 

X-TREMOPHILES is a multidisciplinary project to study the unknown or poorly characterized thermophiles: their diversity and function in SHV ecosystems. Sampling campaigns were conducted in 2017 and recently in spring 2022 on the SHVs of the Aeolian volcanic islands in Italy (other campaigns are scheduled) for microbiology and geochemistry. The study of the microbial diversity of these sites, assessed by sequencing rRNA 16S gene amplicons, revealed an unprecedented richness and abundance of bacteria and uncultivated archaea representing new candidate phyla whose distribution is strongly correlated with physico-chemical parameters, defining several niches or habitats within these ecosystems. First metagenomic data tend to confirm the richness and novelty of this diversity. Thermodynamic modeling of the main microbial metabolisms in situ shows that redox reactions of sulfur compounds represent the primary energy source in these ecosystems and reveal the coupling between the geochemical cycles of Fe, N, and S. These aspects will also be addressed in the analysis of metagenomic data. Cultures targeting diverse metabolic types have been done, and others are underway aiming at enriching, if not isolating, some of the most interesting extremophilic microorganisms (in terms of novelty and interest for biotech applications) to study them in vivo by combining cultural and genomic methods (in collaboration with project partners).

HYPERTHERMOBIOGAZ project is a collaboration between our group and a Norwegian company (Hyperthermics®) commercializing a biogas plant process to convert large volumes of industrial organic wastes (e.g., agriculture, paper pulp, or aquaculture) in biogas (mix of dihydrogen and methane), a renewable source of energy, whereby hyperthermophilic bacteria are used to increase the efficiency and yield of the overall process compared to conventional mesophilic digestions. Our current project involves developing new methods to enrich and cultivate novel hyperthermophiles performant under industrial conditions and validate their utilization for the process and commercial use. Metabarcoding and meta/genomics will be essential at crucial steps of the project: 1) to describe the diversity and metabolic potential of the samples at different stages of the enrichment/isolation procedure, 2) to complete functional characterization of the novel isolates (or consortia).  

  • The postdoc, as a specialist in the bioinformatic analyses of the metagenomic data, will be involved in both projects, being at the interphase between microbial ecology and biotechnological applications of extremophiles; as such, he(she) will have many interactions with other researchers participating in one or other projects. The successful candidate will join the “Extremophiles” group, located at the Mediterranean Institute of Oceanography (MIO) on the Aix-Marseille University campus of Luminy, nearby the beautiful Calanques of Marseille.
Your tasks
  • Use and develop bioinformatic tools to analyze amplicons and shotgun metagenomic sequences.
  • Statistical analyses of microbial diversity from field sampling and lab experiments (bioreactor consortia)
  • Reconstruct and annotate metagenomics-assembled genomes (MAGs) 
  • Analyze the metabolic potential of the cultivated consortia or isolated strains (MAGs or strain genomes)
  • Coordinate with project partners to achieve the project’s goals. 
  • Publication of results in scientific journals and presentation at conferences
  • Maintain strict confidentiality of results deemed sensitive by the P.I. of the projects (especially for HYPERTHERMOBIOGAS).
  • Support/help training of students with bioinformatic tools (co-supervises Master student’s work related to the research projects
Your profile
  • Ph.D. in a relevant area (Microbiology, Bioinformatics, Genomics)
  • Experience in metabarcoding and metagenomics data generation and analyses (assembly, binning, annotation, comparative genomics)
  • Strong statistics (using R) and bioinformatic skills; programming skills are highly recommended (Unix, Python…)
  • Knowledge of microbial metabolism and ecology would be appreciated
  • Keen interest in extremophile research: microbial evolution and biotechnological applications would be an asset.
  • Excellent communication and organizational skills; demonstrated ability for teamwork and multidisciplinary collaboration.
  • Good communication skills in English (fluency in French or English is necessary), including scientific writing. 

Our offer

We offer an exciting position in an international and dynamic team of researchers and an attractive scientific working environment, including excellent equipment and technical support. We foster flat hierarchies and active participation. Your career development is encouraged by qualification and training opportunities. 

This is a full-time position of 2 years (possibility to extend for one year) and a tentative start date of 15.03.2023 (or shortly after that). Salary is paid according to experience, following the French salary scheme for the public sector for postdoctoral research. 

Are you interested?

We look forward to receiving your application with the usual documents (letter of motivation indicating research interests and experience, CV, certificates/references, and publication list)

starting date : as soon as possible. Application and inquiries can be addressed to Prof. Gaël Erauso:


This project is funded by the French National research Agency « ANR ». It is an interdisciplinary and international long-terme collaboration between researchers at the Mediterranean Institute of Oceanography, Geoscience Environnement Toulouse, Institut du Globe de Paris, Medis, Entropie, The Stony Brook University.