PhD defense : Martin Maliet-Garnier
08
JUL 2025
JUL 2025
Hello everyone,
I'm defending my PhD tuesday the 8th of july at 2pm in amphi Herpin in Esclangon, you are all welcome to join. The defense will be in french.
Here is the abstract :
Study of dense suspension of Pseudomonas aeruginosa
Motile bacteria self-organize in numerous collective phases, such as orientationally ordered phase or swarming state. These collective phases result from properties and activities at the single cell scale, such as growth rate, swimming speed and cell-cell interactions. Understanding how individual properties can trigger emergence of long range order is a crucial aspect of biological and physical studies on bacteria, and can lead to better understanding of the mechanisms of colonies and biofilms formation.
In this thesis we study the properties of bi-dimensionnal dense suspension of an elongated bacteria, Pseudomonas aeruginosa. We are able to obtain large and dense bacterial monolayers at the edge of 3D swarming colonies expanding on agar gels. We perform the detection of bacterial trajectories from high-speed movies through the use of DiSTNet2D, an innovative deep learning technique that computes segmentation and tracking altogether, taking advantage of temporal information. We show that dense monolayers of P. aeruginosa exhibit a dramatic slowdown of the dynamics of the system with increasing surface fraction in cells, despite no apparent changes in the static order, which we identify as being evidence of a glass transition occurring in the system.
We first study in detail the lack of spatial order in the system through the computation of order parameters and the observation of local structures. We show that the order of the system is independent of surface fraction. We then study the dynamics of th system by computing relaxation times on the position and the orientation of the cells, and show that both these times diverge when approaching a critical surface fraction, and stay linearly coupled together for more than three decades. We show that this ensemble slowdown of the dynamic is accompanied by fluctuations around the average behaviour, resulting in heterogeneities of displacements among cells, of growing intensity with surface fraction. Using mutants of various individual cell properties of the bacterium, we show that the motion properties of cells have no impact on neither the spatial order nor the glass transition in the system, but that the geometrical properties of cells play a strong role. The increasing of the aspect ratio of the cells results in an increase of both the orientational order and the crowding of the system, thus lowering the critical surface fraction at which the glass transition occurs.
After focusing our analysis on cases with only motility involved, we continue our research on a case when only the growth of cells is involved, by performing a preliminary study on growing microcolonies of non-motile strains of P. aeruginosa, taking advantage of the experimental setup and analysis pipeline. We show that the growth of cells in dense monolayers generates a pressure resulting in a net displacement of cells. When the density of cells is high enough, the pressure generated by the growth is enough to push cells out of the monolayer plane and the system becomes tri-dimensional in a process called verticalization. We conclude our study on the growth of cell monolayers by observing the growth of non-motile filamentous cells in an agar pad system. We show that the rigidity of the agar gel plays a strong role on the morphogenesis of the microcolonies, and that at high rigidity fractal patterns appear at the edge of the colonies.
