Phd Funded By The European Space Agency (Esa) On Microbial Biofilms

Universities and Institutes of France
October 01, 2022
Contact:N/A
Offerd Salary:Negotiation
Location:N/A
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Contract Type:Temporary
Working Time:Full time
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  • Organisation/Company: INRAE
  • Research Field: Biological sciences › Biology
  • Researcher Profile: First Stage Researcher (R1)
  • Application Deadline: 01/10/2022 23:00 - Europe/Athens
  • Location: France › Jouy en Josas
  • Type Of Contract: Temporary
  • Job Status: Full-time
  • Hours Per Week: 35
  • Offer Starting Date: 01/10/2022
  • Gene fitness in bacterial biofilms under altered (micro and hyper) gravity conditions

    Abstract

    Bacterial biofilms develop on nearly all surfaces posing a threat to the integrity of spacecraft and space station equipment1,2. Extensive effort toward understanding microbial responses to space environment highlighted the role of microgravity in promoting biofilm formation in many bacteria3,4. How microbial biofilm forms in space and how can we control them are important issues that require gaining basic knowledge about key genetic components responsible for adaptation to spaceflight conditions. This PhD project aims at identifying genes involved in the transition to a biofilm lifestyle under a range of simulated gravities relevant to ISS, Moon, Mars, Earth and hyper gravity condition. The project proposes to identify and functionally characterized key genes involved in biofilm formation and fitness under different gravity levels in two environmental bacterial species, the Gram- negative bacteria Pseudomonas fluorescens and the Gram-positive Bacillus subtilis, by a combination of CRISPR-interference screening, microfluidics, advance genetic and confocal microscopy approaches. The implementation of these approaches on biofilms under altered gravity will require to access to ESA-ground based facilities at the Instrumentation and Life Support laboratory (TEC-MMG) at ESTEC (Netherland).

    Objective

    This project aims at identifying genetic elements (i.e. genes, cis and trans- regulatory RNA elements) involved in the formation of biofilms under various microgravity conditions simulating the environments encountered on board the ISS, on the Moon, and on Mars (near 0g, 1/6g and 3/8g, respectively), as well as under conditions of hypergravity (20g). Genome wide screenings (CRISPRi) will be carried out in two bacteria species, B. subtilis and P. fluorescens, that have been already studied in the context of spaceflights (ref) to identify the genes whose repression affects the "fitness" of biofilms in different gravitational environments. The expression of gene candidates will be monitored during biofilm formation under altered gravity using fluorescent reporters. The objective is to identify potential targets for the development of bio-sensors to detect the formation of biofilms at an early stage in order to develop new strategies to mitigate their development on surfaces.

    Context

    The PhD thesis is part of a ESA-funded project which addresses this question of the role of gravity on the formation of biofilms. The thesis project will take place at INRAE, MICALIS, Jouy en Josas in the B3D team “Biofilms and Spatially Organized Communities”. Experimental parts of the study related to gravity-altered conditions will be also performed ESA ground-based facilities. The B3D team at INRAE has been working on microbial biofilms for more than a decade, investigating different aspects of their properties, from food security, surface colonization, virulence and antibiotic resistance5-7. More recently, the team started to explore the cellular and molecular basis of biofilm formation and surface colonization, with the aim of better understanding the molecular strategies that take place during biofilm development8-10. To do so, we are combining comparative genomic studies, temporal and spatial transcriptome profiling, coupled with high throughput monitoring and gene expression by 4D-CLSM using fluorescent transcriptional fusions, as well ad microfluidics. The detailed observation of biofilms, combined with extraction of quantitative parameters will benefit from the bio- imaging core facility of MICALIS that provides access to a variety of equipment to perform imaging work at the nanoscopic and microscopic scale (confocal, electronic microscopy and more recently Light Sheet microscopy).

    Methods

  • CRISPR interference (CRISPRi) coupled with NGS sequencing at genome- scale
  • Building sgRNA libraries (pool or arrayed)
  • Growing bacteria in flow cells using a microfluidic set up under ground (INRAE) and altered gravity conditions (ESA facilities)
  • Advanced fluorescent microscopy (3D and 4D-CLSM) and imaging analysis
  • Genetic studies and phenotyping
  • References

    1 Bijlani, S., Stephens, E., Singh, N. K., Venkateswaran, K. & Wang, C. C. C. Advances in space microbiology. iScience 24, 102395, doi:10.1016/j.isci.2021.102395 (2021).

    2 Landry, K. S., Morey, J. M., Bharat, B., Haney, N. M. & Panesar, S. S. Biofilms-Impacts on Human Health and Its Relevance to Space Travel. Microorganisms 8, doi:10.3390/microorganisms8070998 (2020).

    3 Kim, W. et al. Spaceflight promotes biofilm formation by Pseudomonas aeruginosa. PLoS One 8, e62437, doi:10.1371/journal.pone.0062437 (2013).

    4 McLean, R. J., Cassanto, J. M., Barnes, M. B. & Koo, J. H. Bacterial biofilm formation under microgravity conditions. FEMS Microbiol Lett 195, 115-119, doi:10.1111/j.1574-6968.2001.tb10507.x (2001).

    5 Bridier, A., Piard, J. C., Briandet, R. & Bouchez, T. Emergence of a Synergistic Diversity as a Response to Competition in Pseudomonas putida Biofilms. Microb Ecol 80, 47-59, doi:10.1007/s00248-019-01470-z (2020).

    6 Bridier, A. et al. Biofilms of a Bacillus subtilis hospital isolate protect Staphylococcus aureus from biocide action. PLoS One 7, e44506, doi:10.1371/journal.pone.0044506 (2012).

    7 Darsonval, M., Gregoire, M., Deschamps, J. & Briandet, R. Confocal Laser Microscopy Analysis of Listeria monocytogenes Biofilms and Spatially Organized Communities. Methods Mol Biol 2220, 123-136, doi:10.1007/978-1-0716-0982-810 (2021).

    8 Dergham, Y. et al. Comparison of the Genetic Features Involved in Bacillus subtilis Biofilm Formation Using Multi-Culturing Approaches. Microorganisms 9, doi:10.3390/microorganisms9030633 (2021).

    9 Sanchez-Vizuete, P. et al. Identification of ypqP as a New Bacillus subtilis biofilm determinant that mediates the protection of Staphylococcus aureus against antimicrobial agents in mixed-species communities. Appl Environ Microbiol 81, 109-118, doi:10.1128/AEM.02473-14 (2015).

    10 Noirot-Gros, M. F., Forrester, S., Malato, G., Larsen, P. E. & Noirot, P. CRISPR interference to interrogate genes that control biofilm formation in Pseudomonas fluorescens. Sci Rep 9, 15954, doi:10.1038/s41598-019-52400-5 (2019).

    Conditions

    Non-pathogenic bacteria will be manipulated in an environment dedicated to microbiology studies with access to all necessary equipment as well as access to a bio-imaging core facility at MICALIS. Access to the ESA ground-based European facilities will be granted thought dedicated continuously open calls.

    Collaborations:

    University of Napoli (Italia)

    Aristotle University of Thessaloniki (Greece)

    Expected valorisation

    Publication of results in international journals; scientific and technical reports to be delivered after each experiment carried out at ESA facilities; participation in meetings including an international conference.

    Fundings

    ESA and INRAE

    Competences

    - Strong foundations in microbiology and microbial genetics

    - Solid bases in molecular biology.

    - Knowledge of confocal microscopy not mandatory, but appreciated

    - Expertise in microfluidic manipulation not mandatory but also appreciated

    - Very good command of English

    - Open to mobility

    Benefits

    Publication of results in international journals; scientific and technical reports to be delivered after each experiment carried out at ESA facilities; participation in meetings including an international conference.

    Additional comments

    University of Napoli (Italia)

    Aristotle University of Thessaloniki (Greece)

    Web site for additional job details

    https: // www. micalis.fr/micaliseng/Poles-and-teams/Pole-Bacterial- Adaptation-...

    Offer Requirements
  • REQUIRED EDUCATION LEVEL
  • Biological sciences: Master Degree or equivalent

  • REQUIRED LANGUAGES
  • FRENCH: Basic

    Skills/Qualifications

    Competences

    - Strong foundations in microbiology and microbial genetics

    - Solid bases in molecular biology.

    - Knowledge of confocal microscopy not mandatory, but appreciated

    - Expertise in microfluidic manipulation not mandatory but also appreciated

    - Very good command of English

    - Open to mobility

    Contact Information
  • Organisation/Company: INRAE
  • Department: Micalis
  • Organisation Type: Public Research Institution
  • Website: https:// www. inrae.fr
  • E-Mail: romain.briandet@inrae.fr marie-francoise.noirot-gros@inrae.fr
  • Country: France
  • City: Jouy en Josas
  • Postal Code: 78350
  • Street: Domaine de Vilvert
  • Phone: +33 1 74 07 16 98
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