Post-Doctoral Research Visit F/M Numerical and metabolic simulation of microbial communities for CO₂ storage underground

The Inria center at the University of Bordeaux is one of the nine Inria centers in France and has about twenty research teams.. The Inria centre is a major and recognized player in the field of digital sciences. It is at the heart of a rich R&D and innovation ecosystem: highly innovative SMEs, large industrial groups, competitiveness clusters, research and higher education players, laboratories of excellence, technological research institute...

IFP Énergies nouvelles (IFPEN) is a major public-sector player in research, innovation and training in the fields of energy, transport and the environment. Organized into several centers, the main one of which is located in Rueil-Malmaison, IFPEN relies on research excellence to meet the major challenges of the energy transition. It operates within a rich ecosystem of industrial partners, start-ups, academic establishments, competitiveness clusters and public institutions, and plays a key role in developing sustainable solutions for industry and society.

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Within the framework of a partnership between Inria and IFP Énergies nouvelles (IFPEN) we develop numerical and metabolic models to study the influence of microorganisms that are naturally present in deep geological formations used for carbon capture storage (CCS). Our objective is to better understand the interactions between microbial communities, the lithic environment, and the CO₂ injected in deep carbon storage sites. These interactions produce biological phenomena that can influence, beneficially or detrimentally, the efficiency and reliability of carbon storage.

These interactions may include, for example, mineral bioalteration, production of metabolic gases (such as methane or hydrogen sulfide), or even biologically-induced carbonate precipitation (biocarbonatation) that contributes to the permanence of the storage by immobilizing CO₂ in mineral form and limiting the risk of leaks. Other effects, such as the formation of biofilms, may have contrasted impacts: in reservoirs, they may reduce injectivity, or increase corrosion in wells in the case of sulfate-reducing bacteria; whereas in geological cover formations, biofilms may reduce permeability and consequently reinforce the efficiency of the geological barrier. Understanding and modeling these mechanisms is thus essential for anticipating their long-term impact on the fitness of storage sites and for orienting risk management strategies.

To simulate these complex phenomena, we will couple two modeling tools developed at the IFPEN and Inria in a common framework. Inria provides its expertise in community-scale microbial metabolic modeling and codes that can simulate metabolic exchanges in complex microbial networks. With this approach we can anticipate the biological functions activated in a given environment, such as the conditions favorable for biofilm formation. IFPEN provides nonlinear dynamical models of biogéochemical reactions and codes that can predict their effects on the geological environment and the associated transformations. By integrating these complementary approaches we will construct a robust simulation workflow that can evaluate the influence of microbial processes on the performance of CO₂ storage sites.

The principal place of work will be the Inria center at the University of Bordeaux, in the offices of the Pleiade project-team https://team.inria.fr/pleiade/.

Travel between Bordeaux, Toulouse, and Reuil-Malmaison may be necessary from time to time, and expenses will be covered.

Assignments: Under the direction of David Sherman (Inria) and Arnaud Pujol (IFPEN), the recruited person will work on coupling two existing codes, one a logicial model developed by Inria to predict metabolic interactions within microbial communities, the other a nonlinear dynamical model developed by IFPEN to simulate biological and geochemical processes over time. Starting from collections of taxa identified by sampling or by literature search, and from nutritional constraints derived from the geological characteristics of each site, Inria's model will identify the biochemical functions that can be activated and potential inter-species interactions, in particuliar those that may produce biofilms. These results will be the entry point for IFPEN's numerical simulation of coupled biological-geological behavior, as well as sensitivity analysis. Forthermore, the combined workflow will make it possible to identify minimal microbial consortia, optimized for a given objective (reinforcement of geological barriers by biofilms, biocarbonatation, ...) thanks to the reasoning tools developped by Inria.

For better knowledge of the proposed research subject:

1. Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. Belcour A, Frioux C, Aite M, Bretaudeau A, Hildebrand F, Siegel A. eLife, 2020, 9, ⟨10.7554/eLife.61968⟩
2. Community-scale models of microbiomes: articulating metabolic modelling and metagenome sequencing. Cerk K, Ugalde-Salas P, Ghassemi Nedjad C, Lecomte M, Muller C, Sherman DJ, Hildebrand F, Labarthe S, Frioux C. Microbial Biotechnology, 2024, ⟨10.1111/1751-7915.14396⟩
3. Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe.  Belcour A, Got J, Aite M, Delage L, Collén J, Frioux C, Leblanc C, Dittami SM, Blanquart S, Markov GV, Siegel A. Genome Research, 2023, 33, pp.972 – 987. ⟨10.1101/gr.277056.122⟩
4. Modeling acclimatization by hybrid systems: Condition changes alter biological system behavior models. Assar A, Montecino MA, Maass A, Sherman DJ. BioSystems, 2014, 121, pp.43-53. ⟨10.1016/j.biosystems.2014.05.007⟩
5. Interplay between microorganisms and geochemistry in geological carbon storage. Kirk MF, Altman SJ, Santillan EFU, Bennett PC. Int. J. Greenhouse Gas Control, 2016, 47, pp. 386-395. ⟨10.1016/j.ijggc.2016.01.041⟩
6. Underground gas storage as a promising natural methane bioreactor and reservoir? Molíková A, Vítězová M, Vítěz T, Buriánková I, Huber H, Dengler L, Hanišáková N, Onderka V, Urbanová I. Energy Storage, 2017, 47.⟨10.1016/j.est.2021.103631⟩
7. Life on the Rocks. Gorbushina AA. Microbiology, 2007, 9, pp. 1613-31. ⟨10.1111/j.1462-2920.2007.01301.x⟩
8. Enigmatic, ultrasmall, uncultivated Archaea. Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, Banfield JF. Proc Natl Acad Sci U S A. 2010 May 11;107(19):8806-11. ⟨10.1073/pnas.0914470107⟩
9. Bacterial Calcium Carbonate Precipitation in Cave Environments: A Function of Calcium Homeostasis. Banks ED, Taylor NM, Gulley J, Lubbers BR, Giarrizzo JG, Bullen HA, Hoehler TM, Barton HA. Geomicrobiology Journal, 27(5), 444–454. ⟨10.1080/01490450903485136⟩

Collaboration : The recruited person will be in contact with experts from the IFPEN in phenomenological modeling in geological environments, and with Inria project-teams concerned with modeling biological systems.

Main activities:

• Perform numerical simulations, analyze the results and identify microbial mechanisms of interest (biofilm formation, biocarbonatation, ...).
• Develop and couple simulation tools for modeling the behavior of microbial communities in the context of geological CO₂ storage
• Contribute to the scientific promotion of the project, through writing publications andreports, and participating in conferences

Additional activities:

• Present progress of ongoing work to colleagues and partners
• Discuss with scientific collaborators
• Review the scientific literature

Technical skills:

• Experience in software development and a willingness to adopt good software engineering practices.
• Experience in mathematical modeling and a willingness to improve models of biological and chemical systems.
• Optionally, knowledge of executing programs on high-performance computing or on Kubernetes platforms.

Languages:

• Ability to speak and write scientific English.

Relational skills:

• Ability to communicate with colleagues from the biological, chemical, and computer sciences
• Willingness to listen to and learn from these colleagues

• Subsidized meals
• Partial reimbursement of public transport costs
• Leave: 7 weeks of annual leave + 10 extra days off due to RTT (statutory reduction in working hours) + possibility of exceptional leave (sick children, moving home, etc.)
• Possibility of teleworking and flexible organization of working hours
• Professional equipment available (videoconferencing, loan of computer equipment, etc.)
• Social, cultural and sports events and activities
• Access to vocational training
• Social security coverage

The gross monthly salary will be 2788€ (before social security contributions and monthly witholding tax).