Individual-based modelling of biofilms

Understanding the emergence of the complex organization of biofilms from th e interactions of its parts, individual cells and their environment, is the aim of the individual-based modelling (IbM) approach. This IbM is version 2 of BacSim, a model of Escherichia coli colony growth, which was developed into a two-dimensional multi-substrate, multi-species model of nitrifying biofilms. it was compared with the established biomass-based model (BbM) of Picioreanu and others. Both models assume that biofilm growth is due to th e processes of diffusion, reaction and growth (including biomass growth, di vision and spreading). In the IbM, each bacterium was a spherical cell in c ontinuous space and had variable growth parameters. Spreading of biomass oc curred by shoving of cells to minimize overlap between cells. In the BbM, b iomass was distributed in a discrete grid and each species had uniform grow th parameters. Spreading of biomass occurred by cellular automata rules. In the IbM, the effect of random variation of growth parameters of individual bacteria was negligible in contrast to the E. coli colony model, because t he heterogeneity of substrate concentrations in the biofilm was more import ant. The growth of a single cell into a clone, and therefore also the growt h of the less abundant species, depended on the randomly chosen site of att achment, owing to the heterogeneity of substrate concentrations in the biof ilm. The IbM agreed with the BbM regarding the overall growth of the biofil m, due to the same diffusion-reaction processes. However, the biofilm shape was different due to the different biomass spreading mechanisms. The IbM b iofilm was more confluent and rounded due to the steady, deterministic and directionally unconstrained spreading of the bacteria. Since the biofilm sh ape is influenced by the spreading mechanism, it is partially independent o f growth, which is driven by diffusion-reaction. Chance in initial attachme nt events modifies the biofilm shape and the growth of single cells because of the high heterogeneity of substrate concentrations in the biofilm, whic h again results from the interaction of diffusion-reaction with spreading. This stresses the primary importance of spreading and chance in addition to diffusion-reaction in the emergence of the complexity of the biofilm commu nity.