INDISIM-Paracoccus, an individual-based and thermodynamic model for a denitrifying bacterium

We have developed an individual-based model for denitrifying bacteria. The model, called INDISIM-Paracoccus, embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM, and is designed to simulate the bacterial cell population behavior and the product dynamics within the culture. The INDISIM-Paracoccus model assumes a culture medium containing succinate as a carbon source, ammonium as a nitrogen source and various electron acceptors such as oxygen, nitrate, nitrite, nitric oxide and nitrous oxide to simulate in continuous or batch culture the different nutrient-dependent cell growth kinetics of the bacterium Paracoccus denitrificans. The individuals in the model represent microbes and the individual-based model INDISIM gives the behavior-rules that they use for their nutrient uptake and reproduction cycle. Three previously described metabolic pathways for P. denitrificans were selected and translated into balanced chemical equations using a thermodynamic model. These stoichiometric reactions are an intracellular model for the individual behavior-rules for metabolic maintenance and biomass synthesis and result in the release of different nitrogen oxides to the medium. The model was implemented using the NetLogo platform and it provides an interactive tool to investigate the different steps of denitrification carried out by a denitrifying bacterium. The simulator can be obtained from the authors on request. The individual-based model approach with the thermodynamics embedded as an intracellular model defines the behavior-rule of the individual cell for maintenance and biomass generation to study the denitrification products dynamics, especially the greenhouse gas N2O, carried out by denitrifying bacterium Paracoccus denitrificans. [Display omitted] •An IBM to study denitrification that uses thermodynamics for the cellular activity.•The simulator facilitates interaction between modelers and experts in denitrification.•The thermodynamic properties embedded into individual cells for modeling.