PhD on Roles and impacts of iron-oxidizing bacteria in the dynamics of the deep critical zone: France

Description of the PhD project

This PhD project is part of the IRONSTONE interdisciplinary research program funded by the French National Research Agency (ANR) over the period 2021-2025. Recent subsurface work has revealed the importance and potentially global significance of subsurface microbial biomass. However, the biogeochemical processes regulated by the activity of microorganisms in these environments and the impact of these processes on the quality of the water resource, the alteration of rocks or the exchange of greenhouse gases between the subsurface and the atmosphere remain poorly constrained to date. With this in mind, the IRONSTONE project explores, from the microscopic to the critical zone scale, how spatial heterogeneities and temporal variation of environmental conditions in fractured aquifers affect microbial dynamics, the kinetics of microbial-catalyzed reactions, especially those mobilizing iron, and associated elemental fluxes.

This PhD project will experimentally and quantitatively characterize the metabolic activity of Fe-oxidizing bacteria (FeOB) and the resulting biogeochemical fluxes (Fe, C, N, S) in a fractured aquifer. These FeOB use the oxidation of ferrous iron dissolved in water to obtain the energy necessary for their metabolism and growth. They are autotrophic and can excrete organic carbon (in the form of very large mineral-organic assemblages) in significant quantities when they are in iron-rich microaerobic environments. Thus, FeOB development in the subsurface is highly dependent on groundwater circulations and associated redox gradients and chemical disequilibria. Specifically, the spatial and temporal distribution of FeOB is controlled by the potential for mixing between oxygen-rich groundwater and deep anoxic iron-rich fluids. These mixing zones constitute intermittent hotspots of microbiological activity whose impact on biogeochemical fluxes remains to be determined. Similarly, the degradation pathways and fate of organic matter produced by FeOB in these hotspots remain major unknowns. To achieve these objectives, the PhD student will implement cultural approaches (using FeOB isolates and enriched microbial consortia collected in fractured aquifers), isotope labeling, environmental genomics techniques, geochemical and mineralogical monitoring involving high-resolution microimaging approaches as well as thermodynamic modelling. The generated knowledge will be used to feed reactive transport models that will be tested in the field within the IRONSTONE project. They will also allow to establish microbial indicators of reaction processes in the critical zone. Finally, this thesis project will allow to better constrain the relationships between hydrological circulations, deep microbial dynamics and biogeochemical functioning of the critical zone.

In summary, the objectives of the PhD project will be to:

  1. Characterize the reactional rates involving Fe, C, N (and related elements) by populations of iron-oxidizing bacteria in relation to changing environmental conditions;
  2. Determine microbial processes and rates of biomass production and Fe transformation under suboxic and anoxic conditions following subsurface blooms of iron-oxidizing bacteria;
  3. Identify microbial markers (key genes for metabolic pathways and adaptation to microaerobic conditions) responsive to environmental changes such as redox conditions, with the aim to support field studies.

Working environment

This PhD project will be conducted between the UMR 6553 Ecobio (University of Rennes) and the Geomicrobiology team of the Institut de physique du globe de Paris (UMR 7154 – Université Paris Cité). It will be directed by Bénédicte Ménez (50%, HDR, IPGP) and co-supervised by Alexis Dufresne (50%, Ecobio). The PhD student will thus benefit from a strong national dynamic and from privileged collaborations with students and researchers of the Geosciences Rennes and the Institute of Physics of Rennes laboratories, which are partners of the IRONSTONE project. The PhD student will benefit from an interdisciplinary working environment (microbial ecology, geochemistry, mineralogy, geomicrobiology, hydrology), regular national workshops organized in the framework of IRONSTONE as well as the support of advanced technical platforms in the partner laboratories of Rennes and Paris.

Constraints and risks

This PhD project will involve some field missions in Brittany (hydrological observatory site of Ploemeur-Guidel,, for the sampling of microbial consortia as well as the implementation of controlled laboratory experiments at Ecobio and their characterization at Ecobio and IPGP.

Additional information

Candidates should have a Master’s degree and/or an engineering degree with multidisciplinary knowledge in microbiology, microbial ecology and Earth sciences (notions of geochemistry and mineralogy). An interest in bioinformatics and in the use of modeling software, notably thermodynamic modeling, is desirable. Practical laboratory experience (microbial cultures, molecular biology) will be an asset. Good oral and written communication skills in English are also required.

Applications should include a CV and a cover letter, as well as the contact information of at least two references in the academic field and/or university. They should be mailed in response to the corresponding offer and sent jointly to Bénédicte Ménez ( and Alexis Dufresne (

Applications will be considered until the position is filled. The starting date of the PhD is the beginning of September 2023 at the latest.

  • Workplace: Ecobio Rennes UMR 6553 & Geomicrobiology team, Institut de physique du globe de Paris UMR 7154 – Université Paris Cité – FRANCE
  • Scientific supervisors: Bénédicte Ménez – Alexis Dufresne
  • Type of contract: PhD contract
  • Contract duration: 36 months
  • Start date: September 2023 at the latest
  • Working hours: full time
  • Gross monthly salary: the salary will evolve each year in accordance with the revalorization of the doctoral contracts (from 2044 € gross monthly the first year to 2300 € gross monthly the third year)
  • Funds: ANR IRONSTONE project
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