Rheological characterisation of biofilms in both linear and nonlinear viscoelastic regimes

Abstract

Biofilms are a ubiquitous mode of bacteria proliferation found within aqueous environments. The structure and architecture that a biofilm self assembles into confers mechanical resistance against shear forces. A characteristic trait of biofilm is the production of extra cellular materials which act as the “glue” in the ECM/bacteria composite. The myriad physical properties of biofilm systems result in highly variable mechanical properties, which are studied using rheology. Previous studies about biofilm mechanics were mainly focused on linear viscoelastic regions. However the linear region is unable to provide information regarding the dynamics of deformation and structural rearrangement. Probing the biofilm nonlinear viscoelastic regime and yielding dynamics opens a window to access how the rearrangement behaviour of the EPS network and bacterium network are impacted by EPS composition and bacterial network topology. In addition, to determine the rheological properties of biofilms within the linear viscoelastic regime using the rotational rheometer, this thesis sheds light on utilising high fidelity non-linear rheological techniques and advanced imaging techniques to produce a framework explaining the emergence of characteristic biofilm mechanical behaviours across an array of species, chemical environments and genetic mutations. I have demonstrated the applicability of three types of large amplitude oscillatory shear (LAOS) analysis methodologies to Pseudomonas fluorescens biofilms and the rheological effects of divalent cations and a chaotropic compound. It was shown that by increasing ionic concentration the characteristic behaviour changes from a repulsive glass to an attractive glass. To understand the rheological and architectural effects of capsular polysaccharide secretion in biofilms, I selected the bacterium Pantoea sp. I revealed how the secretion of amylovoren and stewartin causes a characteristic rheological change from viscoelastic liquid to glass and how this is primarily driven by changes in EPS polymer concentration and packing fraction. Finally, I investigated the yielding behaviours across a range of bacteria with different geometries (rods/cocci) and EPS compositions. I identified four different types of yielding behaviour across the tested bacterial strains and used a range of rheological and microscopy data to identify the extent of short- and long-range polymer networks which determine the viscoelastic response of bacterial biofilms. Biofilms are a ubiquitous mode of bacteria proliferation found within aqueous environments. The structure and architecture that a biofilm self assembles into confers mechanical resistance against shear forces. A characteristic trait of biofilm is the production of extra cellular materials which act as the “glue” in the ECM/bacteria composite. The myriad physical properties of biofilm systems result in highly variable mechanical properties, which are studied using rheology. Previous studies about biofilm mechanics were mainly focused on linear viscoelastic regions. However the linear region is unable to provide information regarding the dynamics of deformation and structural rearrangement. Probing the biofilm nonlinear viscoelastic regime and yielding dynamics opens a window to access how the rearrangement behaviour of the EPS network and bacterium network are impacted by EPS composition and bacterial network topology. In addition, to determine the rheological properties of biofilms within the linear viscoelastic regime using the rotational rheometer, this thesis sheds light on utilising high fidelity non-linear rheological techniques and advanced imaging techniques to produce a framework explaining the emergence of characteristic biofilm mechanical behaviours across an array of species, chemical environments and genetic mutations. I have demonstrated the applicability of three types of large amplitude oscillatory shear (LAOS) analysis methodologies to Pseudomonas fluorescens biofilms and the rheological effects of divalent cations and a chaotropic compound. It was shown that by increasing ionic concentration the characteristic behaviour changes from a repulsive glass to an attractive glass. To understand the rheological and architectural effects of capsular polysaccharide secretion in biofilms, I selected the bacterium Pantoea sp. I revealed how the secretion of amylovoren and stewartin causes a characteristic rheological change from viscoelastic liquid to glass and how this is primarily driven by changes in EPS polymer concentration and packing fraction. Finally, I investigated the yielding behaviours across a range of bacteria with different geometries (rods/cocci) and EPS compositions. I identified four different types of yielding behaviour across the tested bacterial strains and used a range of rheological and microscopy data to identify the extent of short- and long-range polymer networks which determine the viscoelastic response of bacterial biofilms. In summary, this thesis demonstrates how contemporary rheological methods and soft matter physics can be used in a reductive approach towards linking biofilm mechanics, microstructure and phenomenology.