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Register a new userVerticalization of bacterial biofilms
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Biofilms are communities of bacteria adhered to surfaces. Recently, biofilms of rod-shaped bacteria were observed at single-cell resolution and shown to develop from a disordered, two-dimensional layer of founder cells into a three-dimensional structure with a vertically-aligned core. Here, we elucidate the physical mechanism underpinning this transition using a combination of agent-based and continuum modeling. We find that verticalization proceeds through a series of localized mechanical instabilities on the cellular scale. For short cells, these instabilities are primarily triggered by cell division, whereas long cells are more likely to be peeled off the surface by nearby vertical cells, creating an inverse domino effect. The interplay between cell growth and cell verticalization gives rise to an exotic mechanical state in which the effective surface pressure becomes constant throughout the growing core of the biofilm surface layer. This dynamical isobaricity determines the expansion speed of a biofilm cluster and thereby governs how cells access the third dimension. In particular, theory predicts that a longer average cell length yields more rapidly expanding, flatter biofilms. We experimentally show that such changes in biofilm development occur by exploiting chemicals that modulate cell length.
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We develop a theory of thermodynamic instabilities for complex fluids composed of many interacting species organised in families. This model includes partially structured and partially random interactions and can be solved exactly using tools from random matrix theory. Depending on the parameters of the model, we detect and characterise analytically family condensation, family demixing at finite critical density, and random demixing. We apply the theory to phase separation of proteins triggered by a change of pH.
The ability of many living systems to actively self-propel underlies critical biomedical, environmental, and industrial processes. While such active transport is well-studied in uniform settings, environmental complexities such as geometric constraints, mechanical cues, and external stimuli such as chemical gradients and fluid flow can strongly influence transport. In this chapter, we describe recent progress in the study of active transport in such complex environments, focusing on two prominent biological systems -- bacteria and eukaryotic cells -- as archetypes of active matter. We review research findings highlighting how environmental factors can fundamentally alter cellular motility, hindering or promoting active transport in unexpected ways, and giving rise to fascinating behaviors such as directed migration and large-scale clustering. In parallel, we describe specific open questions and promising avenues for future research. Furthermore, given the diverse forms of active matter -- ranging from enzymes and driven biopolymer assemblies, to microorganisms and synthetic microswimmers, to larger animals and even robots -- we also describe connections to other active systems as well as more general theoretical/computational models of transport processes in complex environments.
We propose a modeling approach to study how mature biofilms spread and colonize new surfaces by predicting the formation and growth of satellite colonies generated by dispersing biofilms. This model provides the basis for better understanding the fate and behavior of dispersal cells, phenomenon that cannot, as yet, be predicted from knowledge of the genome. The model results were promising as supported by the experimental results. The proposed approach allows for further improvements through more detailed sub-models for front propagation, seeding, availability and depletion of resources. The present study was a successful proof-of-concept in answering the following questions: Can we predict the colonization of new sites following biofilm dispersal? Can we generate patterns in space and time to shed light on seeding dispersal? That are fundamental issues for developing novel approaches to manipulate biofilm formation in industrial, environmental and medical applications.
Inspired by recent experiments on the effects of cytosolic crowders on the organization of bacterial chromosomes, we consider a feather-boa type model chromosome in the presence of non-additive crowders, encapsulated within a cylindrical cell. We observe spontaneous emergence of complementary helicity of the confined polymer and crowders. This feature is reproduced within a simplified effective model of the chromosome. This latter model further establishes the occurrence of longitudinal and transverse spatial segregation transitions between the chromosome and crowders upon increasing crowder size.
Bacterial processes ranging from gene expression to motility and biofilm formation are constantly challenged by internal and external noise. While the importance of stochastic fluctuations has been appreciated for chemotaxis, it is currently believed that deterministic long-range fluid dynamical effects govern cell-cell and cell-surface scattering - the elementary events that lead to swarming and collective swimming in active suspensions and to the formation of biofilms. Here, we report the first direct measurements of the bacterial flow field generated by individual swimming Escherichia coli both far from and near to a solid surface. These experiments allowed us to examine the relative importance of fluid dynamics and rotational diffusion for bacteria. For cell-cell interactions it is shown that thermal and intrinsic stochasticity drown the effects of long-range fluid dynamics, implying that physical interactions between bacteria are determined by steric collisions and near-field lubrication forces. This dominance of short-range forces closely links collective motion in bacterial suspensions to self-organization in driven granular systems, assemblages of biofilaments, and animal flocks. For the scattering of bacteria with surfaces, long-range fluid dynamical interactions are also shown to be negligible before collisions; however, once the bacterium swims along the surface within a few microns after an aligning collision, hydrodynamic effects can contribute to the experimentally observed, long residence times. As these results are based on purely mechanical properties, they apply to a wide range of microorganisms.
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