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How do energy gradients shape microbial communities? Study of the Microbial Transition State (MTS) approach for modelling microbial ecosystems dynamics and its application to environmental biotechnology processes

Abstract : Microbial communities play a key role in geochemical cycles and environmental bioprocesses. Despite their importance, the mechanisms involved in their structuration remain elusive and are poorly captured in current models. The modelling approach developed during this thesis stands as an alternative to the current empirical approaches. It relies on a novel theory of microbial growth (the MTS theory), which introduce a flux/force relationship between the microbial growth rate and the free energy gradients available in the biotope. The purpose of this thesis is to characterize the dynamic properties of the MTS model and to determine, through simulations, the part of the microbial communities’ spatio-temporal structuration that is intrinsically captured by the MTS theory and which does not pertain to parameters adjustment.Simulations firstly reveal that a characteristic of the MTS model is its ability to account for the simultaneous growth limitation by many resources of different kinds (electron acceptor/donor, but also nutrients), and to integrate them as stoichiometric limitations, giving rise to coherent populations dynamics.In a second stage, the MTS model has been used to predict the dynamics of microbial communities. Those studies revealed that the thermodynamics constraints on which the MTS kinetic theory is built intrinsically give rise to consistent ecological successions without the need to adjust specifically the parameters of each population. In the case of a simplified activated sludge ecosystem, after calibration using respirometric data, the model was able to reproduce ecosystem dynamics quantitatively with a reduced number of parameters compared to current Activated Sludge Models (ASM).In a third stage, a large database of experimental growth yield observations has been compiled from literature. The relationship between multiple physicochemical parameters characterizing the metabolisms (reduction degrees, catabolic energy...) and the growth yield has been investigated using statistical methods. This work confirms that microbial growth yields can be accurately predicted solely on thermodynamic properties of metabolic reactions. The growth yields predictor could be included in future developments of the MTS models.More generally, the work undertaken during this thesis evidenced that the MTS model proposes a formalization of the coupling between thermodynamic and dynamic variables of a microbial ecosystem. The simulated microbial populations and ecosystems display coherent dynamic behaviors. The model is able to account, by construction, for well-known ecological successions, without specific parameter adjustment. This model is peculiarly adapted to the prediction of the functional structure of communities in ecosystems dominated by selection by competition, rather than on species dispersion, diversification or genetic drift.Those results encourage the development of microbial ecosystems based on firmer theoretical grounds. Such models are necessary to the development of bioprocesses able to answer to the new technological and environmental challenges.
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  • HAL Id : tel-03392364, version 1

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Hadrien Delattre. How do energy gradients shape microbial communities? Study of the Microbial Transition State (MTS) approach for modelling microbial ecosystems dynamics and its application to environmental biotechnology processes. Biotechnology. Institut agronomique, vétérinaire et forestier de France, 2018. English. ⟨NNT : 2018IAVF0011⟩. ⟨tel-03392364⟩

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