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Microfluidics for understanding the physics of root-bacteria interactions and the development of green technologies (H/F)

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Date Limite Candidature : jeudi 23 septembre 2021

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General information

Reference : UMR7608-HARAUR0-004
Workplace : ORSAY
Date of publication : Thursday, September 2, 2021
Scientific Responsible name : Harold Auradou
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 November 2021
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

ROOTBACT is an interdisciplinary project at the interface of biological and biophysical systems. We propose to use microfluidics to study the hydrodynamic and chemotactic mechanisms involved in the colonization of plant roots by bacteria. We will focus on the nitrogen-fixing symbiosis of the legume alfalfa with the soil bacterium Sinorhizobium meliloti. We will develop a microfluidic chip for tracking interactions of bacteria with living roots in real-time, at the single cell and population level, and for defining physicochemical as well as biological parameters that influence bacterial dynamics in the root environment (the rhizosphere).
The specific objectives of ROOTBACT are twofold: 1) the physical characterization of chemotactic, aerotactic and rheotactic properties of the bacterium S. meliloti in microfluidic chips; 2) the design and development of microfluidic chips for tracking the interaction of S. meliloti with Medicago roots. These two tasks constitute the program of the PhD thesis that we propose in this project.
The student who will be recruited may have a background in physics or biology, but in all cases, we will be attentive to the student's interests and interdisciplinary skills that he/she may have acquired during his/her studies.

Work Context

The major strength of this project is the combination of the recognized expertise of the two partners in hydrodynamics of bacterial suspensions (including aerotaxis) at FAST and the biology of the legume-rhizobium symbiotic interaction at I2BC. This complementary expertise, gathered in a small geographical region, is the key to the success of this project.
→ FAST (CNRS, Université Paris-Saclay) has a strong experience in the hydrodynamics of bacterial suspensions in a confined environment. In recent years, H. Auradou has developed an experimental platform devoted to the characterization of active fluid under flow in porous media. C. Douarche is an expert in collective effects in swimming bacterial suspensions and in the motility of bacteria in heterogeneous environments. She also has developed advanced diagnostic tools to probe oxygen concentration in microfluidic devices. F. Moisy recently joined the group and brings his expertise in hydrodynamics and image processing.
→ I2BC (CNRS, CEA, Université Paris-Saclay) has expertise in plant- and insect-bacteria symbiotic interactions. P. Mergaert, E. Biondi and B. Alunni's research focuses on identifying and understanding the function of bacterial and host adaptations important in these symbioses, including studies on the bacterial motility and the production of antimicrobial peptides in symbiosis and in the bacterial competition. The team develops genetic, genomic, cell biology and imaging methodologies for these studies. The plant-bacteria interaction group at I2BC has all the competences needed to produce fine-tuned GMO bacteria for the purpose of the project and to study their symbiotic properties.
The two groups started a collaboration 3 years ago. During this period, they developed a protocol to monitor motility and aerotaxis in S. meliloti. An experimental setup allowing for simultaneous measurements of oxygen concentration and bacteria tracking where developed, yielding accurate determination of the aerotactic response of these bacteria. These preliminary results form a very encouraging basis for the experiences that we propose in this project.

Additional Information

The project is a recipient of the CNRS 80Prime call for proposals, which aims to raise new scientific and methodological questions on topics whose implementation requires the establishment of new collaborations between laboratories from at least two CNRS institutes.

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