Observers for microbial ecology - How including molecular data into bioprocess modeling?

Dumont, Maxime; Rapaport, Alain; Harmand, Jérôme; Benyahia, Brahim; Godon, Jean‐Jacques

doi:10.1109/med.2008.4602004

Cited by 9 publications

(11 citation statements)

References 6 publications

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“…We consider a multi-species population, represented here by the 21 most abundant OTUs (Dumont et al 2008). The model assumes that these OTUs are in competition on a single limiting substrate.…”

Section: Modeling Approachmentioning

confidence: 99%

Major changes in the composition of a Southern Ocean bacterial community in response to diatom-derived dissolved organic matter

Landa

Blain

Harmand

et al. 2018

FEMS Microbiology Ecology

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In the Southern Ocean, natural iron fertilization in the wake of islands leads to annually occurring spring phytoplankton blooms associated with enhanced heterotrophic activity through the release of labile dissolved organic matter ( OTUs in diatom-DOM compared to winter water conditions. Using a modeling approach, we obtained growth rates for phylogenetically diverse taxa varying between 0.12 and 0.49 d -1 under carbon-limited conditions. Our results identify diatom-DOM as a key factor shaping SouthernOcean winter water bacterial communities and suggest a role for niche partitioning and microbial interactions in organic matter utilization.

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Section: Modeling Approachmentioning

confidence: 99%

Major changes in the composition of a Southern Ocean bacterial community in response to diatom-derived dissolved organic matter

Landa

Blain

Harmand

et al. 2018

FEMS Microbiology Ecology

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“…The tracking problem was applied to data coming from a nitrification process; the experimental conditions are described in [9]. For exploring the hypothesis of interactions as drivers of bioreactors performance environmental conditions should be kept as constant as possible.…”

Section: Application and Discussionmentioning

confidence: 99%

Modelling Interactions of a Microbial Community through an Optimal Tracking Control Approach

Ugalde-Salas¹,

Harmand²,

Quéméner³

2020

2020 European Control Conference (ECC)

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Genetic sequencing measurements of the existing species in a reactor are incorporated into a classic chemostat model through a non linear optimal tracking approach. The framework is applied to data coming from a nitrification process, resulting in a dynamical system with a high dimensional state. The observed ecological dynamics from the bacterial species are able to explain the substrates dynamics.

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“…The tracking problem was applied to data coming from a nitrification process with experimental conditions described in [27]. For exploring the hypothesis of interactions as drivers of bioreactors performance environmental conditions should be kept as constant as possible.…”

Section: Applicationmentioning

confidence: 99%

“…Simulation of system(25) when u = 1, with functions as in(27). Data points are represented by a star.…”

mentioning

confidence: 99%

Microbial Interactions as Drivers of a Nitrification Process in a Chemostat

Ugalde-Salas

Harmand

et al. 2021

Bioengineering

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This article deals with the inclusion of microbial ecology measurements such as abundances of operational taxonomic units in bioprocess modelling. The first part presents the mathematical analysis of a model that may be framed within the class of Lotka–Volterra models fitted to experimental data in a chemostat setting where a nitrification process was operated for over 500 days. The limitations and the insights of such an approach are discussed. In the second part, the use of an optimal tracking technique (developed within the framework of control theory) for the integration of data from genetic sequencing in chemostat models is presented. The optimal tracking revisits the data used in the aforementioned chemostat setting. The resulting model is an explanatory model, not a predictive one, it is able to reconstruct the different forms of nitrogen in the reactor by using the abundances of the operational taxonomic units, providing some insights into the growth rate of microbes in a complex community.

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Observers for microbial ecology - How including molecular data into bioprocess modeling?

Cited by 9 publications

References 6 publications

Major changes in the composition of a Southern Ocean bacterial community in response to diatom-derived dissolved organic matter

Major changes in the composition of a Southern Ocean bacterial community in response to diatom-derived dissolved organic matter

Modelling Interactions of a Microbial Community through an Optimal Tracking Control Approach

Microbial Interactions as Drivers of a Nitrification Process in a Chemostat

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