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

Authored by Marta Ginovart, Anna Gras, Granda Pablo Araujo, Vincent Moulton

Date Published: 2016

DOI: 10.1016/j.jtbi.2016.05.017

Sponsors: Spanish Ministry of Education (Ministerio de Educación) Ecuador National Secretary of Science and Technology (SENESCYT)

Platforms: NetLogo

Model Documentation: ODD Flow charts

Model Code URLs: Model code not found

Abstract

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 R 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. (C) 2016 Elsevier Ltd. All rights reserved.
Tags
Simulation carbon Sensitivity-analysis Denitrification Pathways Cell-population dynamics True yield prediction Chemotropic growth Oxide reductase Nitrous-oxide