INDISIM-Denitrification, an individual-based model for study the denitrification process

  • Pablo Araujo-GrandaEmail author
  • Anna Gras
  • Marta Ginovart
  • Vincent Moulton
Environmental Microbiology - Original Paper


Denitrification is one of the key processes of the global nitrogen (N) cycle driven by bacteria. It has been widely known for more than 100 years as a process by which the biogeochemical N-cycle is balanced. To study this process, we develop an individual-based model called INDISIM-Denitrification. The model embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM and is designed to simulate in aerobic and anaerobic conditions the cell growth kinetics of denitrifying bacteria. INDISIM-Denitrification simulates a bioreactor that contains a culture medium with succinate as a carbon source, ammonium as nitrogen source and various electron acceptors. To implement INDISIM-Denitrification, the individual-based model INDISIM was used to give sub-models for nutrient uptake, stirring and reproduction cycle. Using a thermodynamic approach, the denitrification pathway, cellular maintenance and individual mass degradation were modeled using microbial metabolic reactions. These equations are the basis of the sub-models for metabolic maintenance, individual mass synthesis and reducing internal cytotoxic products. The model was implemented in the open-access platform NetLogo. INDISIM-Denitrification is validated using a set of experimental data of two denitrifying bacteria in two different experimental conditions. This provides an interactive tool to study the denitrification process carried out by any denitrifying bacterium since INDISIM-Denitrification allows changes in the microbial empirical formula and in the energy-transfer-efficiency used to represent the metabolic pathways involved in the denitrification process. The simulator can be obtained from the authors on request.


Denitrification Bacterial yield prediction Individual-based model Thermodynamic electron equivalent model NetLogo INDISIM 



The financial support of the Ecuador National Secretary of Higher Education, Science, Technology and Innovation (SENESCYT) (Grant Convocatoria Abierta 2011—no. 94-2012), to the Universidad Central del Ecuador (Research Project no. 26 according to RHCU.SO.08 No. 0082-2017 in official resolution with date March 21th, 2017) and the Plan Nacional I + D+i from the Spanish Ministerio de Educación y Ciencia (MICINN, CGL2010-20160). We would also like to thank Dr. David Richardson and Dr. Andrew Gates for helpful discussions at early stages in this project and for providing us with the full dataset presented in Felgate et al. [18].

Author contributions

All the authors listed have made substantial, direct and intellectual contribution to the work, and approved it for publication.

Compliance with ethical standards

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Supplementary material

10295_2019_2245_MOESM1_ESM.docx (56 kb)
Supplementary material 1 (DOCX 56 kb)


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Copyright information

© Society for Industrial Microbiology and Biotechnology 2019

Authors and Affiliations

  1. 1.Chemical Engineering FacultyUniversidad Central del Ecuador, Ciudad UniversitariaQuitoEcuador
  2. 2.Department of Agri-Food Engineering and BiotechnologyUniversitat Politècnica de CatalunyaBarcelonaSpain
  3. 3.Department of MathematicsUniversitat Politècnica de CatalunyaBarcelonaSpain
  4. 4.School of Computing SciencesUniversity of East AngliaNorwichUK

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