In natural environments, microbial communities regularly experience perturbations that can disrupt their stability. Such disturbances may temporarily alter community composition or, in more extreme cases, lead to cell death and species extinction, resulting in a new composition. An important example is the disturbance of soil communities by temperature shifts.

In soil, a majority fraction of the microbial community is dormant. Dormant microbes do not grow but are expected to resist unfavourable perturbations. This 'microbial seed bank' is thought to enhance community resilience (the ability to recover after perturbation), as the resuscitation of dormant cells contributes to community reassembly. Previous experiments with soil communities have demonstrated that resuscitation and microbial dispersal contribute to microbiome recovery following temperature shifts. However, the relative contribution of resuscitation and dispersal to resilience remains an open question. Quantifying the factors driving community reassembly after perturbation is an essential step in helping to restore microbial-contributed ecosystem functions following disturbance.

Mathematical modelling is important in distinguishing the contributions of different factors to microbial community dynamics. Therefore, we have developed an individual-based mathematical model that accounts for individual cells from various species, each with a distinct temperature-dependent response and the ability to switch between active (growth and death) and inactive (dormant) states and to proliferate or die. The model simulates the impact of temperature perturbations on a microbial community. Our model is linked to existing dynamical data on the response of soil microbiomes to temperature shifts and provides insights into how dormancy, growth, mortality, and dispersal impact community structure.

Using this model, we aim to quantify the potential for microbiome restoration via the reactivation of dormant cells and the dispersal of cells following perturbations.