Individual based model links thermodynamics, chemical speciation and environmental conditions to microbial growth

Gogulancea, V. et al. (2019) Individual based model links thermodynamics, chemical speciation and environmental conditions to microbial growth. Frontiers in Microbiology, 10, 1871. (doi: 10.3389/fmicb.2019.01871) (PMID:31456784) (PMCID:PMC6700366)

Abstract

Individual based Models (IbM) must transition from research tools to engineering tools. To make the transition we must aspire to develop large, three dimensional and physically and biologically credible models. Biological credibility can be promoted by grounding, as far as possible, the biology in thermodynamics. Thermodynamic principles are known to have predictive power in microbial ecology. However, this in turn requires a model that incorporates pH and chemical speciation. Physical credibility implies plausible mechanics and a connection with the wider environment. Here, we propose a step toward that ideal by presenting an individual based model connecting thermodynamics, pH and chemical speciation and environmental conditions to microbial growth for 5·105 individuals. We have showcased the model in two scenarios: a two functional group nitrification model and a three functional group anaerobic community. In the former, pH and connection to the environment had an important effect on the outcomes simulated. Whilst in the latter pH was less important but the spatial arrangements and community productivity (that is, methane production) were highly dependent on thermodynamic and reactor coupling. We conclude that if IbM are to attain their potential as tools to evaluate the emergent properties of engineered biological systems it will be necessary to combine the chemical, physical, mechanical and biological along the lines we have proposed. We have still fallen short of our ideals because we cannot (yet) calculate specific uptake rates and must develop the capacity for longer runs in larger models. However, we believe such advances are attainable. Ideally in a common, fast and modular platform. For future innovations in IbM will only be of use if they can be coupled with all the previous advances.

• Item Type: Articles
• Additional Information: The authors acknowledge the support of the EPSRC Frontier Grant A New Frontier in Design: The Simulation of Open Engineered Biological Systems, led by Newcastle University, ref EP/K039083/1.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Gonzalez-Cabaleiro, Dr Rebeca
• Authors: Gogulancea, V., González-Cabaleiro, R., Li, B., Taniguchi, D., Jayathilake, P. G., Chen, J., Wilkinson, D., Swailes, D., McGough, A. S., Zuliani, P., Ofiteru, I. D., and Curtis, T. P.
• College/School: College of Science and Engineering > School of Engineering > Infrastructure and Environment
• Journal Name: Frontiers in Microbiology
• Publisher: Frontiers Media
• ISSN: 1664-302X
• ISSN (Online): 1664-302X
• Copyright Holders: Copyright © 2019 Gogulancea, González-Cabaleiro, Li, Taniguchi, Jayathilake, Chen, Wilkinson, Swailes, McGough, Zuliani, Ofiteru and Curtis
• First Published: First published in Frontiers in Microbiology 10: 1871
• Publisher Policy: Reproduced under a Creative Commons License