Structure and dynamics of bacterial biofilms: from single cells to collective phenomena – FILMOTIL

Experiences aim at characterizing biofilms at different levels: we study the trajectories of individual bacteria by fluorescence microscopy techniques and quantitatively analyze their swimming and trapping in biofilm using fine techniques of image analysis. Similarly, the diffusivity of cellular aggregates and the local and global structures are studied by similar techniques during the different stages of biofilm development. These observations are correlated with environmental parameters of the cellular environment (nutrients, temperature, oxygen level, ...).
Experiences are coupled to the theory, and different theoretical approaches are tested. We want to identify the minimum set of parameters required to reproduce in silico the growth of a biofilm and predict the structure of the self-assembly. A close link between experiment and theory is developed to extract experimentally all required parameters for the theoretical model.

Mechanisms of bacterial motility and chemotaxis are now fairly well known at the single cell level, however the behavior of an entire population of cells still poses some fundamental questions. The study of a cell population of Escherichia coli in an oxygen gradient shows that bacteria are capable of exhibiting collective behavior and self-assemble to form regular patterns. Similarly, when observing the morphogenesis of a bacterial biofilm of Bacillus subtilis that forms a floating pellicle on the top of liquids, we detect certain types of self-assemblies of cells very early during the development of the biofilm. And we suspect the existence of collective effects in the volume of the growth medium, long before the beginning of the pellicle formation. These assemblies can play a particularly important role in conditioning the development of biofilm and its structure as well as its mechanical properties.

Indeed, a study of the evolution of the macroscopic structure of a biofilm of Bacillus subtilis was conducted during its development. We have highlighted the emergence of a particular texture of the floating pellicle exhibiting a characteristic wavelength. The parameters of this structure (wavelength, amplitude, ...) vary depending on the experimental conditions and on the strain of Bacillus subtilis studied.

We now wish to establish the link between the collective phenomena observed in the bulk of the growth medium and the emergence of a particular structure on the surface of the liquid. The development of a theoretical model in agreement with the experimental studies will highlight the environmental parameters crucial for the development of the biofilms. These results may help to develop strategies to control their growth: either by inhibiting them or by stimulating them, depending on the application.

This work has been subject to oral communications in international conferences or seminars in front of experts in the field. Also, a number of publications in journals with peer review are under preparation and shall appear in a near future.

Bacteria are unicellular prokaryotic microorganisms. They are ubiquitous and constitute a large part of the terrestrial biomass. They live as individuals interacting with their environment during the planktonic phase but most of the time they self-organize in a collective manner in complex architectures adsorbed on interfaces, the so-called “biofilms”. Because bacteria embedded in biofilms exhibit an increased resistance to antibiotics as well as to environmental stresses, they have a large impact in the medical, ecology, environment and food industry fields.

Up to now, the vast majority of studies that have been carried out on biofilms are proteomic studies of molecular or genetic mechanisms (in terms of protein expression and function). These studies have shown that for bacterial microorganisms such as E. Coli and B. Subtilis, motility is needed for the development of biofilms. However, very few physical approaches of the bacterial behavior (and especially of their motility) were adopted to study the formation of biofilms. The goal of this project is to study the role of the cell dynamics correlated with environmental parameters (oxygen, temperature, food…) on the structure of biofilms. This project, at the physics and biology interface, combines physics, instrumentation, computation, biochemistry, and microbiology.

The scientific program will be developed in two steps: first the study of the biofilm at the early stages of its development when its structure remains bi-dimensional. And then, we will study thicker mature biofilms. We will set-up optical microscopy experiments that will allow us to observe the cell dynamics and the local and overall structures of biofilms over their development. We will develop new analysis techniques to extract the characteristics that define biofilms from the recorded images and videos. We will particularly focus our attention on the different physico-chemical measurable parameters known to affect significantly the biofilm growth such as cell motility, oxygen gradient distribution, temperature… Additionally, different theoretical approaches will be tested to identify the minimal set of parameters that is required to numerically reproduce and predict the structure of the cell self-assembly. Experimentally finding correlations between these parameters will allow us to simplify the theoretical model. Scientific breakthroughs on the fundamental structure of biofilms could help to develop future strategies to inhibit or at the contrary to accelerate its growth, depending on the different requirements of the applications.

This project will be developed at the Laboratoire de Physique des Solides (UMR8502) at Orsay University where a research activity on biofilms has just started in 2009. Research domains on soft matter developed in this lab (tissue and biological fibers, polymeric systems, self-organized soft matter…) constitute assets for the development of this project. Additionally, the research centers of INRA (Massy), CNRS of Gif-sur-Yvette and Danone research center will be partners of choice for the forthcoming collaborations.