From a thin film model for passive suspensions towards the description of osmotic biofilm spreading

Biofilms are ubiquitous macro-colonies of bacteria that develop at various interfaces (solid-liquid, solid-gas or liquid-gas). The formation of biofilms starts with the attachment of individual bacteria to an interface, where they proliferate and produce a slimy polymeric matrix - two processes that result in colony growth and spreading. Recent experiments on the growth of biofilms on agar substrates under air have shown that for certain bacterial strains, the production of the extracellular matrix and the resulting osmotic influx of nutrient-rich water from the agar into the biofilm are more crucial for the spreading behaviour of a biofilm than the motility of individual bacteria. We present a model which describes the biofilm evolution and the advancing biofilm edge for this spreading mechanism. The model is based on a gradient dynamics formulation for thin films of biologically passive liquid mixtures and suspensions, supplemented by bioactive processes which play a decisive role in the osmotic spreading of biofilms. It explicitly includes the wetting properties of the biofilm on the agar substrate via a disjoining pressure and can therefore give insight into the interplay between passive surface forces and bioactive growth processes

Modeling of the Bacillus subtilis Bacterial Biofilm Growing on an Agar Substrate

Bacterial biofilms are organized communities composed of millions of microorganisms that accumulate on almost any kinds of surfaces. In this paper, a biofilm growth model on an agar substrate is developed based on mass conservation principles, Fick's first law, and Monod's kinetic reaction, by considering nutrient diffusion between biofilm and agar substrate. Our results show biofilm growth evolution characteristics such as biofilm thickness, active biomass, and nutrient concentration in the agar substrate. We quantitatively obtain biofilm growth dependence on different parameters. We provide an alternative mathematical method to describe other kinds of biofilm growth such as multiple bacterial species biofilm and also biofilm growth on various complex substrates

The Effect of Cell Death on the Stability of a Growing Biofilm

In this paper, we investigate the role of cell death in promoting pattern formation within bacterial biofilms. To do this we utilise an extension of the model proposed by Dockery and Klapper [13], and consider the effects of two distinct death rates. Equations describing the evolution of a moving biofilm interface are derived, and properties of steady state solutions are examined. In particular, a comparison of the planar behaviour of the biofilm interface in the different cases of cell death is investigated. Linear stability analysis is carried out at steady state solutions of the interface, and it is shown that, under certain conditions, instabilities may arise. Analysis determines that, while the emergence of patterns is a possibility in `deep’ biofilms, it is unlikely that pattern formation will arise in `shallow’ biofilms

A Computation Study of Biofilm Development and Dispersal

Bacterial biofilms are a structured population of bacteria adhered to a biotic or abiotic surface. Bacteria establish a biofilm by encasing themselves in a self-secreted matrix of extra polymeric substance. The matrix, composed primarily of polysaccharides and protein, confers to the individual bacterium enhanced protection from environmental insults. These insults would otherwise be detrimental to the bacteria if they were not part of the biofilm. To properly time when it is most beneficial to establish a biofilm and carry out other process, bacteria have developed a means to communicate using signaling molecules termed autoinducers. These signaling molecules help bacteria to make coordinated decisions. One such decision is phenotype switching, where some bacteria in the colony change their phenotypes to ensure their survival or the survival of an entire colony. Some species of bacteria exhibit a clear delineated spatiotemporal pattern of changing their phenotype. In particular, Bacillus Subtilis forms a biofilm that exhibits spatiotemporal patterning during its development. Using an agent-based model that includes thresholds on environmental cues we reproduced the spatiotemporal behavior observed from experiments. Specifically, we incorporate thresholds on the concentration on the level of nutrient and autoinducer to reproduce the experimental pattern. This model represents the first attempt using an agent-based model to reproduce the spatiotemporal pattern exhibited experimentally where phenotype switching is induced by both nutrient and the autoinducer. The model allows us to gain an understand of the interrelatedness between autoinducer levels and nutrient availability. The end stage of biofilm development inevitably leads to some members of the community dying or leaving through a variety of dispersal mechanisms. We developed another agent-based model to study biofilm dispersal. Dispersal is caused by the weakening of cohesive bonds within the biofilm. We study dispersal under the condition where cohesive forces are weakened to induce dispersion. The weakening of cohesive force allows us to gain insight on the benefits if any dispersal has on the development of a biofilm

Modeling and simulation of bacterial biofilm growth

This work has been supported by the Ministerio de Economía y Competitividad grants MTM2014-56948-C2-2-P and MTM2017-84446-C2-2-R.Programa Oficial de Doctorado en Ingeniería MatemáticaPresidente: Fernando Varas Mérida.- Secretario: Manuel Carretero Cerrajero.- Vocal: Elena Cebrián de Barri

Defining early steps in <i>Bacillus subtilis</i> biofilm biosynthesis

ABSTRACT The Bacillus subtilis extracellular biofilm matrix includes an exopolysaccharide (EPS) that is critical for the architecture and function of the community. To date, our understanding of the biosynthetic machinery and the molecular composition of the EPS of B. subtilis remains unclear and incomplete. This report presents synergistic biochemical and genetic studies built from a foundation of comparative sequence analyses targeted at elucidating the activities of the first two membrane-committed steps in the EPS biosynthetic pathway. By taking this approach, we determined the nucleotide sugar donor and lipid-linked acceptor substrates for the first two enzymes in the B. subtilis biofilm EPS biosynthetic pathway. EpsL catalyzes the first phosphoglycosyl transferase step using uridine diphosphate (UDP)-di-N-acetyl bacillosamine as phospho-sugar donor. EpsD is a predicted GT-B fold (GT4 family) retaining glycosyl transferase that catalyzes the second step in the pathway that utilizes the product of EpsL as an acceptor substrate and UDP-N-acetyl glucosamine as the sugar donor. Thus, the study defines the first two monosaccharides at the reducing end of the growing EPS unit. In doing so, we provide the first evidence of the presence of bacillosamine in an EPS synthesized by a Gram-positive bacterium. IMPORTANCE Biofilms are the communal way of life that microbes adopt to increase survival. Key to our ability to systematically promote or ablate biofilm formation is a detailed understanding of the biofilm matrix macromolecules. Here, we identify the first two essential steps in the Bacillus subtilis biofilm matrix exopolysaccharide (EPS) synthesis pathway. Together, our studies and approaches provide the foundation for the sequential characterization of the steps in EPS biosynthesis, using prior steps to enable chemoenzymatic synthesis of the undecaprenyl diphosphate-linked glycan substrates

Impact of Fe2+^{2+} and Shear Stress on the Development and Mesoscopic Structure of Biofilms—A Bacillus subtilis Case Study

Bivalent cations are known to affect the structural and mechanical properties of biofilms. In order to reveal the impact of Fe2+ ions within the cultivation medium on biofilm development, structure and stability, Bacillus subtilis biofilms were cultivated in mini-fluidic flow cells. Two different Fe2+ inflow concentrations (0.25 and 2.5 mg/L, respectively) and wall shear stress levels (0.05 and 0.27 Pa, respectively) were tested. Mesoscopic biofilm structure was determined daily in situ and non-invasively by means of optical coherence tomography. A set of ten structural parameters was used to quantify biofilm structure, its development and change. The study focused on characterizing biofilm structure and development at the mesoscale (mm-range). Therefore, biofilm replicates (n = 10) were cultivated and analyzed. Three hypotheses were defined in order to estimate the effect of Fe2+ inflow concentration and/or wall shear stress on biofilm development and structure, respectively. It was not the intention to investigate and describe the underlying mechanisms of iron incorporation as this would require a different set of tools applied at microscopic levels as well as the use of, i.e., omic approaches. Fe2+ addition influenced biofilm development (e.g., biofilm accumulation) and structure markedly. Experiments revealed the accumulation of FeO(OH) within the biofilm matrix and a positive correlation of Fe2+ inflow concentration and biofilm accumulation. In more detail, independent of the wall shear stress applied during cultivation, biofilms grew approximately four times thicker at 2.5 mg Fe2+/L (44.8 µmol/L; high inflow concentration) compared to the low Fe2+ inflow concentration of 0.25 mg Fe2+/L (4.48 µmol/L). This finding was statistically verified (Scheirer–Ray–Hare test, ANOVA) and hints at a higher stability of Bacillus subtilis biofilms (e.g., elevated cohesive and adhesive strength) when grown at elevated Fe2+ inflow concentrations