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

Hadrien Delattre, Jing Chen, Matthew Wade, View ORCID ProfileOrkun S Soyer
doi: https://doi.org/10.1101/857276
Hadrien Delattre
1School of Life Sciences, University of Warwick, UK
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  • For correspondence: o.soyer@warwick.ac.uk
Jing Chen
1School of Life Sciences, University of Warwick, UK
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Matthew Wade
2School of Engineering, Newcastle University, Newcastle-upon-Tyne NE1 7RU UK
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Orkun S Soyer
1School of Life Sciences, University of Warwick, UK
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  • ORCID record for Orkun S Soyer
  • For correspondence: o.soyer@warwick.ac.uk
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ABSTRACT

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 accounting explicitly for metabolic activities of composing microbes, system pH, and chemical exchanges. We 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 experimental population dynamics of these synthetic communities that feature relevant species utilising low-energy growth pathways. Furthermore, they provide the first estimates for minimum energy requirements of methanogenesis and elaborates on previous estimates of lactate fermentation by sulfate reducers. 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.

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  • https://github.com/OSS-Lab/micodymora

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 27, 2019.
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Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis
Hadrien Delattre, Jing Chen, Matthew Wade, Orkun S Soyer
bioRxiv 857276; doi: https://doi.org/10.1101/857276
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Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis
Hadrien Delattre, Jing Chen, Matthew Wade, Orkun S Soyer
bioRxiv 857276; doi: https://doi.org/10.1101/857276

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