Individual Based Model Links Thermodynamics, Chemical Speciation and Environmental Conditions to Microbial Growth

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 5·10 5 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.

NUFEB: A massively parallel simulator for individual-based modelling of microbial communities

“…Nutrient transport is described using the diffusion-advection-reaction equation. To improve the representation of microbial growth, NUFEB also implemented the work proposed in [37] to allow pH dynamics and gas-liquid transfer to be considered. In this section, we briefly address the main ideas of this chemical sub-model.…”

“…Bacteria twitching motility under fluid flow was investigated in [51]. We also successfully applied the tool to study the influence of thermodynamics and pH on microbial growth [37]. In [42] and [52], we used micro-scale NUFEB simulations to emulate the behaviour of biofilm/floc in the macro-scale.…”

Not Just Numbers: Mathematical Modelling and its Contribution to Anaerobic Digestion Processes

“…IbMs have historically been used in macro-ecology, but found significant purchase as a tool for modelling biofilms, building on knowledge gained from spatio-temporal, multi-species biomass based models, such as those briefly mentioned in Section 3 [168,169]. In addition to the microbial growth properties, physical interactions between individuals, motility, environmental gradients, fluid dynamics, thermodynamics, and even stochasticity may also be included as hybrid components to a more comprehensive process, sub-process or reactor scale model [170][171][172]. Such a multi-scale model is highly complex and requires a large degree of multi-disciplinarity to ensure successful implementation.…”

“…Such a multi-scale model is highly complex and requires a large degree of multi-disciplinarity to ensure successful implementation. However, the use of IbMs is becoming more ubiquitous and recent efforts to develop large scale simulators of EBS using hybrid IbM and statistical emulators have established a framework for studying microbial community behaviour at scale [69,173,174], opening the door for application to anaerobic digestion processes [172,175] (See Fig. 5 for an example application of an IbM applied to anaerobic processes).…”

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

“…For instance, the heterogeneity at individual level can be revealed using biomass distributions of the bacteria (or other distributions of cellular contents) and controlling which reactions are more often used than others by the microbes during the temporal evolution of the system (Figure 2). Nowadays, this perspective on the biological heterogeneity in individual behavior has been assumed and treated in other applications [100][101][102] in order to advance our understanding of microbial systems. Using highly controlled experimental conditions has offered the possibility to focus on the individual behavior rules (exception made of the bacterial movement) that are now validated and ready, in the near future, to deal with other medium conditions.…”