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

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 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-1) and elaborate on previous estimates of lactate fermentation by sulfate reducers (in the range of -30 to -17 kJ mol-1 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.

SUBMITTER: Delattre H

PROVIDER: S-EPMC7276542 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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

Delattre Hadrien H Chen Jing J Wade Matthew J MJ Soyer Orkun S OS

Journal of the Royal Society, Interface 20200506 166

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 appropriat ...[more]

PMID: 32370691

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Project description:This paper reports the results of an investigation of industrial requirements for thermodynamic and transport properties carried out during the years 2019-2020. It is a follow-up of a similar investigation performed and published 10 years ago by the Working Party (WP) of Thermodynamics and Transport Properties of European Federation of Chemical Engineering (EFCE).1 The main goal was to investigate the advances in this area over the past 10 years, to identify the limitations that still exist, and to propose future R&D directions that will address the industrial needs. An updated questionnaire, with two new categories, namely, digitalization and comparison to previous survey/changes over the past 10 years, was sent to a broad number of experts in companies with a diverse activity spectrum, in oil and gas, chemicals, pharmaceuticals/biotechnology, food, chemical/mechanical engineering, consultancy, and power generation, among others, and in software suppliers and contract research laboratories. Very comprehensive answers were received by 37 companies, mostly from Europe (operating globally), but answers were also provided by companies in the USA and Japan. The response rate was about 60%, compared to 47% in the year 2010. The paper is written in such a way that both the majority and minority points of view are presented, and although the discussion is focused on needs and challenges, the benefits of thermodynamics and success stories are also reported. The results of the survey are thematically structured and cover changes, challenges, and further needs for a number of areas of interest such as data, models, systems, properties, and computational aspects (molecular simulation, algorithms and standards, and digitalization). Education and collaboration are discussed and recommendations on the future research activities are also outlined. In addition, a few initiatives, books, and reviews published in the past decade are briefly discussed. It is a long paper and, to provide the reader with a more complete understanding of the survey, many (anonymous) quotations (indicated with "..." and italics) from the industrial colleagues who have participated in the survey are provided. To help disseminate the specific information of interest only to particular industrial sectors, the paper has been written in such a way that the individual sections can also be read independently of each other.

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

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

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