Applications of individual-based modelling in microbial ecology

Individual-based modelling (IbM) allows description of differences between individuals in a spatially heterogeneous environment - the typical case in microbial ecology. We present the prototype of the first spatially explicit individual-based model of bacterial growth. The simulation reproduced the desired bacterial growth properties correctly. In order to describe the dependence of cell size on growth rate at the single cell level, we implemented a mechanistic version of Donachie's conceptual model of cell division. Surprisingly, it appeared incomplete and had to be replaced by a descriptive version. Random variation of cellular parameters as well as spatial heterogeneity of substrate concentration each led to a complete loss of synchrony of the simulated culture. We propose new measures for growth synchrony and spatial heterogeneity. The model prototype shows the feasibility of this novel approach. It will be extended to become a generic tool for simulating all aspects of microbial growth under real life conditions while our focus will be on social behaviour in biofilms.