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PhD offer (M/W) between Toulouse and Rennes: Microfluidic study of bacterial communications in porous media

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Français - Anglais

Date Limite Candidature : jeudi 24 juin 2021

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General information

Reference : UMR5502-YOHDAV-009
Workplace : TOULOUSE
Date of publication : Thursday, June 3, 2021
Scientific Responsible name : Yohan Davit, Tanguy le Borgne
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 October 2021
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

We are studying couplings between fluid flow and mechanisms controlling the development of microorganisms in porous media. More specifically, this project aims at exploring how communications between bacteria, in particular quorum-sensing (QS), are influenced by flow in porous media. Bacteria communicate via signalling molecules, called autoinducers, that are produced by bacterial cells, transported by the flow, diffuse through the different phases and may interact with the solid surface or react. Recent studies [Kim et al., 2016] suggest that the heterogeneities in the flow yield a spatially distributed QS response. Furthermore, the Rennes team has recently demonstrated the chaotic nature of flow in porous media [Heyman et al. 2020] and the team in Toulouse has developed novel experimental and numerical approaches for studying these problems [Smith et al. 2017]. This opens opportunities to answering various fundamental questions for communications in complex porous structures i.e.: What is the network of communications in porous media? Are there long-distance interactions and what is their role? Are there strong retroactions between the porous structure, flow and QS ? In particular, how does the chaotic nature of the flow affect the patterns of communications?

The PhD student will use novel experimental and simulation tools developed by the two groups in order to study bacterial communications in porous media. The core of the work is experimental and based on microfluidics. We are currently developing different types of microfluidic systems, along with bacterial mutants allowing us to visualize QS by fluorescence microscopy. The successful candidate will work in a safety level 2 biology laboratory, manipulate microorganisms such as Pseudomonas aeruginosa PAO1 or Staphylococcus aureus, and participate actively to discussions within the team and with biologists.

We are looking for an extremely motivated student who will be fully involved in a multidisciplinary project at the interface between physics, fluid mechanics and microbiology. The relevant background includes experimental fluid mechanics, microfluidics, biophysics, bioengineering, microbiology or microbial ecology. Whatever the background is we are looking for somebody who has already experience in growing bacterial cells, will be leading microfluidic experiments with biofilms and will be able to fully grasp complex concepts of fluid mechanics.

[Heyman et al. 2020] Stretching and folding sustain microscale chemical gradients in porous media. PNAS
[Dehkharghani et al. 2019] Bacterial scattering in microfluidic crystal flows reveals giant active Taylor–Aris dispersion. PNAS.
[Smith et al. 2017] Cell morphology drives spatial patterning in microbial communities. PNAS
[Kim et al. 2016] Local and Global Consequences of Flow on Bacterial Quorum Sensing. Nat. Microb.

Work Context

The specificity of this position is that it will be divided in 2 sites. The successful candidate will be localized in Toulouse for the first half of the PhD (Institut de Mécanique de Fluides de Tououse) and in Rennes (Géosciences Rennes) for the second half.

The research project is based on two large European projects funded by the European Research Council (ERC StG BEBOP in Toulouse PI Y. Davit & CoG ReactiveFronts in Rennes PI T. le Borgne). BEBOP aims at developing new generations of biotechnologies, such as self-repairing construction materials or self-cleaning bioreactors, that rely on the use of bacteria to control the properties of porous structures. ReactiveFronts focuses on the dynamics of biogeochemical reactions induced by fluid mixing in subsurface environments, to explore hot spots of chemical reactions and microbiological activity the environment.

The team in Toulouse includes 2 other PhD students and 2 postdocs working on biofilms. The team in Rennes includes 3 PhD students and 4 postdocs.

Constraints and risks

- Work in a level 2 biological safety lab with constraining protocols
- Manipulate pathogenic bacteria
- Work with light sources including lasers

Additional Information

For more info about research activities @ Toulouse, http://yohan-davit.com
For more info about research activities @ Rennes, https://reactivefronts-erc.univ-rennes1.fr/

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