Gaussian process emulation of an individual-based model simulation of microbial communities

•Highlight the strategy for emulating high-level summary from the individual-based model simulation of microbial communities.•A novel surrogate based technique is developed for incorporating microscale processes in a computationally efficient way into engineered macroscale models of the wastewater plant.•Aggregated characteristics are measured on the microscale simulation data to reduce the dimensionality of the problem.•A dynamic Bayesian surrogate model is proposed (GP emulator) for modelling the interesting morphological characteristics that are essential for the design and performance of wastewater reactor.•Bayesian sensitivity analysis is developed to identify the most influential input parameters.