Biofilms are colonies of microorganisms, usually growing on solid-liquid interfaces, consisting of cells and a matrix of extracellular polymeric substances (EPS). Such colonies are often elaborately structured and highly dynamic, expanding through cell division and recruitment of cells from outside, and contracting via individual cells or flocs (groups of cells and biofilm matrix) detachment from the biofilm surface. Even amongst simplest single species bacterial biofilms, the behaviour (phenotype) of individual cells is highly heterogenous across the biofilm due to microenvironment variation (e.g. nutrient concentration, pH) and cell-cell signalling (quorum sensing); consequently, many researchers consider biofilms as more akin to multi-cellular organisms rather than a colony of autonomous individual cells.

We revisit the well-known chemostat model, considering that bacteria can be attached together in aggregates or flocs. We distinguish explicitly free and attached compartments in the model and give sufficient conditions for coexistence of these two forms. We then study the case of fast attachment and detachment and show how it is related to density-dependent growth functions. Finally, we give some insights concerning the cases of multi-specific flocs and different removal rates.

In industrialized nations, potable water is often provided through sophisticated water distribution systems. If pathogenic bacteria are introduced into the water distribution network, the presence of a biofilm can lead to biofilm-assisted retention of the pathogens, affecting the potability of the water. To study the dynamics of planktonic and biofilm-bound pathogens within the large network of pipes in a water distribution system, we develop a network model governing the concentration of introduced pathogens within the bulk fluid and the biofilms lining the pipes. Under time-constant flow regimes within the network, we prove that the long-time behaviour of the entire network is dependent on the Lyapunov exponents for each connection in the network when viewed in isolation and the network connectivity. An efficient algorithm is developed for predicting the long-time behaviour of the pathogen population within large networks using the network's topological ordering. The algorithm's predictions are validated using numerical simulations of the full non-linear system on a range of water distribution network sizes.

Biofilms, and collections of embedded microbial communities, present structural heterogeneities with functional consequences for important processes, such as transport. The origin of such structures has been unclear. Here, we propose that they can arise as a consequence of diffusive transport limitation. To illustrate, a model allowing internal heterogeneity is developed. Linear analysis is applied to a simplified version of the model suggesting that heterogeneity forms on (or below) the active layer length, a length scale that may not be suitable for homogenization, with non-trivial implications for system scale properties such as reduction in system-wide diffusive transport efficiency. Numerics suggest that the simplified model provides useful insight into behaviour of the full model. We then show examples based on microcolony formation in host domains and argue that internal heterogeneity can be related to community function.

We propose a numerical method for the simulation of a quasi-linear parabolic biofilm model that exhibits three non-linear diffusion effects: (i) a power law degeneracy, (ii) a super diffusion singularity and (iii) non-linear cross-diffusion. The method is based on a spatial Finite Volume discretisation in which cross-diffusion terms are formally treated as convection terms. Time-integration of the resulting semi-discretised system is carried out using an error-controlled, time-adaptive, embedded Rosenbrock–Wanner method. We compare several variants of the method and two variants of the model to investigate how details such as the choice cross-diffusion coefficients, and specific variants of the time integrator affect simulation time.

We present a model for the force acting to fragment a biofilm-seeded microbial aggregate in shear flow, which we derive by coupling an existing model for the shape and orientation of a deforming ellipsoid with one for the surface force density on a solid ellipsoid. The model can be used to simulate the motion, shape, surface force density, and breakage of colloidal aggregates in shear flow. We apply the model to the case of exhaustive fragmentation of microbial aggregates in order to compute a post-fragmentation density function, indicating the likelihood of a fragmenting aggregate yielding daughter aggregates of a certain size.

The work presents the analysis of the free boundary value problem related to the one-dimensional invasion model of new species in biofilm reactors. In the framework of continuum approach to mathematical modelling of biofilm growth, the problem consists of a system of non-linear hyperbolic partial differential equations governing the microbial species growth and a system of semi-linear elliptic partial differential equations describing the substrate trends. The model is completed with a system of elliptic partial differential equations governing the diffusion and reaction of planktonic cells, which are able to switch their mode of growth from planktonic to sessile when specific environmental conditions are found. Two systems of non-linear differential equations for the substrate and planktonic cells mass balance within the bulk liquid are also considered. The free boundary evolution is governed by a differential equation that accounts for detachment. The qualitative analysis is performed and a uniqueness and existence result is presented. Furthermore, two special models of biological and engineering interest are discussed numerically. The invasion of Anammox bacteria in a constituted biofilm inhabiting the deammonification units of the wastewater treatment plants is simulated. Numerical simulations are run to evaluate the influence of the colonization process on biofilm structure and activity.

We derive a macroscopic model for biofilm formation in a porous medium reactor to investigate the role of suspended bacteria on reactor performance. The starting point is the mesoscopic one-dimensional Wanner–Gujer biofilm model. The following processes are included: hydrodynamics and transport of substrate in the reactor, biofilm and suspended bacteria growth in the pore space, attachment of suspended cells to the biofilm, and detachment of biofilm cells. The mesoscopic equations are up-scaled from the biofilm scale to the reactor scale, yielding a stiff system of balance laws, which we study numerically. We find that suspended bacteria and attachment can have a significant effect on biofilm reactor performance.

Biofilms are communities of bacteria that exhibit a multitude of multiscale biomechanical behaviours. Recent experimental advances have led to characterisations of these behaviours in terms of measurements of the viscoelastic moduli of biofilms grown in bioreactors and the fracture and fragmentation properties of biofilms. These properties are macroscale features of biofilms; however, a previous work by our group has shown that heterogeneous microscale features are critical in predicting biofilm rheology. In this paper, we use tools from statistical physics to develop a generative statistical model of the positions of bacteria in biofilms. Specifically, the model is a type of pairwise interaction model (PIM). We show through simulation that the macroscopic mechanical properties of biofilms depend on the choice of microscale spatial model. A key finding is that uniform and non-uniform sets of points lead to differing mechanical properties. This distinction appears not to have been previously considered in mathematical biofilm literature. We also found that realisations of a biologically informed PIM have realistic in silico mechanical properties, and have statistical properties that closely match experimental data. We also note that a Poisson spatial point process of suitable number density also yields realistic mechanical properties, but that the spatial distribution of points does not reflect those occurring in our experimentally observed biofilm.