Temperature as competitive strategy determining factor in pulse-fed aerobic bioreactors

Stouten, Gerben Roelandt; Hogendoorn, Carmen; Douwenga, Sieze; Kilias, Estelle; Muyzer, Gerard; Kleerebezem, Robbert

doi:10.1038/s41396-019-0495-8

Cited by 20 publications

(27 citation statements)

References 44 publications

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“…The Particle Filter can be utilized for any biological system where the respiration data reflects the biological processes. In future work, the Particle Filter may be extended with detailed process models involving different microbial functionalities, and variable abundance of microorganisms, thereby attempting to model microbial ecosystem development, which in turn can be linked with molecular data on the development of the microbial community in the process (34).…”

Section: R a F Tmentioning

confidence: 99%

System characterization of dynamic biological cultivations through improved data analysis

Stouten

Douwenga²,

Hogendoorn

et al. 2021

Preprint

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Determining the functional development and dominant competitive strategy in microbial community enrichments is complicated by the extensive measurement campaigns required for off-line system analysis. This study demonstrates that detailed system characterization of aerobic pulse fed enrichments can be established using on-line measurements combined with automated data analysis. By incorporating the physicochemical processes in on-line data processing with a Particle Filter and kinetic process model, an accurate reconstruction of the dominant biological rates can be made. We hereby can differentiate between storage compound production and biomass growth in sequencing batch bioreactors. The method proposed allows for close monitoring of changes in functional behavior of long-running enrichment cultures, without the need for off-line samples, therewith enabling the identification of new insights in process dynamics with a minimal experimental effort. Even though a specific example application of the method proposed is described here, the approach can readily be extended to a wide range of dynamic experimental systems that can be characterized based on on-line measurements.

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Section: R a F Tmentioning

confidence: 99%

System characterization of dynamic biological cultivations through improved data analysis

Stouten

Douwenga²,

Hogendoorn

et al. 2021

Preprint

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“…Functionally, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${\textit{SBR}_{HCl}}$\end{document} showed the typical hoarding strategy (Stouten et al . 2019 ). During the feast phase, carbon was converted into PHA within 40 minutes, and negligible growth occurred during substrate uptake as reflected in negligible ammonium uptake and a constant respiration rate (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The taxa-based microbial community composition of the enriched cultures was determined by amplicon sequencing of the 16S rRNA gene following the procedure described in (Stouten et al . 2019 ) and the sequences are available at NCBI under BioProject accession number [PRJNA577272].…”

Section: Methodsmentioning

confidence: 99%

“… 2014 ; Marang, van Loosdrecht, and Kleerebezem 2016 ; Stouten et al . 2019 ). Typically, the enrichment of P. acidivorans from activated sludge can be established within 30 generations (Stouten et al .…”

Section: Introductionmentioning

confidence: 99%

“…Typically, the enrichment of P. acidivorans from activated sludge can be established within 30 generations (Stouten et al . 2019 ). In a new attempt to enrich for P. acidivorans we operated a Sequencing Batch Bioreactor (SBR) for more than 60 generations.…”

Section: Introductionmentioning

confidence: 99%

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Seemingly trivial secondary factors may determine microbial competition: a cautionary tale on the impact of iron supplementation through corrosion

Stouten

Hamers

Tatenhove‐Pel

et al. 2021

FEMS Microbiology Ecology

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Microbial community engineering aims for enrichment of a specific microbial trait by imposing specific cultivation conditions. This work demonstrates that things may be more complicated than typically presumed and that microbial competition can be affected by seemingly insignificant variables, like in this case the type of acid used for pH control. Aerobic bioreactors pulse fed with acetate operated with hydrochloric acid resulted in the enrichment of Plasticicumulans acidivorans, and changing the pH controlling agent to sulfuric acid shifted the community towards Zoogloea sp. Further research demonstrated that the change in community structure was not directly caused by the change in acid used for pH control, but resulted from the difference in corrosive strength of both acids and the related iron leaching from the bioreactor piping. Neither system was iron deficient, suggesting that the biological availability of iron is affected by the leaching process. Our results demonstrate that microbial competition and process development can be affected dramatically by secondary factors related to nutrient supply and bioavailability, and is way more complex than generally assumed in a single carbon substrate limited process.

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Microbioreactors for nutrient‐controlled microbial cultures: Bridging the gap between bioprocess development and industrial use

Totlani

Tatenhove‐Pel

Kreutzer

et al. 2023

Biotechnology Journal

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It is common practice in the development of bioprocesses to genetically modify a microorganism and study a large number of resulting mutants in order to select the ones that perform best for use at the industrial scale. At industrial scale, strict nutrientcontrolled growth conditions are imposed to control the metabolic activity and growth rate of the microorganism, thereby enhancing the expression of the product of interest. Although it is known that microorganisms that perform best under these strictly controlled conditions are not the same as the ones that perform best under uncontrolled batch conditions, screening, and selection is predominantly performed under batch conditions. Tools that afford high throughput on the one hand and dynamic control over cultivation conditions on the other hand are not yet available. Microbioreactors offer the potential to address this problem, resolving the gap between bioprocess development and industrial scale use. In this review, we highlight the current state-of-the-art of microbioreactors that offer the potential to screen microorganisms under dynamically controlled conditions. We classify them into: (i) microtiter plate-based platforms, (ii) microfluidic chamber-based platforms, and (iii) microfluidic droplet-based platforms. We conclude this review by discussing the opportunities of nutrient-fed microbioreactors in the field of biotechnology.

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Temperature as competitive strategy determining factor in pulse-fed aerobic bioreactors

Cited by 20 publications

References 44 publications

System characterization of dynamic biological cultivations through improved data analysis

System characterization of dynamic biological cultivations through improved data analysis

Seemingly trivial secondary factors may determine microbial competition: a cautionary tale on the impact of iron supplementation through corrosion

Microbioreactors for nutrient‐controlled microbial cultures: Bridging the gap between bioprocess development and industrial use

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