Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

Abstract

<jats:p> Microbial communities are complex dynamical systems harbouring many species interacting together to implement higher-level functions. Among these higher-level functions, conversion of organic matter into simpler building blocks by microbial communities underpins biogeochemical cycles and animal and plant nutrition, and is exploited in biotechnology. A prerequisite to predicting the dynamics and stability of community-mediated metabolic conversions is the development and calibration of appropriate mathematical models. Here, we present a generic, extendable thermodynamic model for community dynamics and calibrate a key parameter of this thermodynamic model, the minimum energy requirement associated with growth-supporting metabolic pathways, using experimental population dynamics data from synthetic communities composed of a sulfate reducer and two methanogens. Our findings show that accounting for thermodynamics is necessary in capturing the experimental population dynamics of these synthetic communities that feature relevant species using low energy growth pathways. Furthermore, they provide the first estimates for minimum energy requirements of methanogenesis (in the range of −30 kJ mol <jats:sup>−1</jats:sup> ) and elaborate on previous estimates of lactate fermentation by sulfate reducers (in the range of −30 to −17 kJ mol <jats:sup>−1</jats:sup> depending on the culture conditions). The open-source nature of the developed model and demonstration of its use for estimating a key thermodynamic parameter should facilitate further thermodynamic modelling of microbial communities. </jats:p>

Energy-based Modelling of the Feedback Control of Biomolecular Systems with Cyclic Flow Modulation

“…An important potential result of combining control theory with energy-based modelling is to identify performance/energy trade-offs. This is important to both evolutionary theory [28] and synthetic biology [29].…”

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

“…However, despite a considerable amount of research on the application of thermodynamics to microbial systems, there are relatively few examples of direct application to the anaerobic digestion process itself. Oh and Martin used principles of thermodynamic equilibrium with chemical activity and fugacity together with a stoichiometric model to study energetic requirements of methanogensis [158], and recently Delattre et al have proposed a kinetic-thermodynamic model to characterise a synthetic anaerobic tri-culture community performing sulphate reduction and methanogenesis [159]. Despite this, it is certain that as more consistent approaches are developed and theory more widely understood, appropriate thermodynamic models will be developed and tested for application to AD systems with the aim to improve performance and understand energetic limitations of different metabolic pathways.…”

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

“…However, despite the considerable amount of research on the application of thermodynamics to microbial systems, there are relatively few examples of direct application to the anaerobic digestion process itself. Oh and Martin used principles of thermodynamic equilibrium with chemical activity and fugacity together with a stoichiometric model to study energetic requirements of methanogensis [154], and recently Delattre et al have proposed a kinetic-thermodynamic model to characterise a synthetic anaerobic tri-culture community performing sulphate reduction and methanogenesis [155]. Despite this, it is certain that as more consistent approaches are developed and theory more widely understood, appropriate thermodynamic models will be developed and tested for application to AD systems with the aim to improve performance and understand energetic limitations of different metabolic pathways.…”