Special Issue "Metabolic Functionality of Microorganisms under Dynamic Environments"

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Environmental Metabolomics".

Deadline for manuscript submissions: closed (31 May 2022) | Viewed by 1961

Special Issue Editor

Dr. Aljoscha Wahl
E-Mail Website1 Website2
Guest Editor
Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
Interests: metabolic networks; metabolomics; modelling; microbial communities; industrial biotechnology

Special Issue Information

Microbes survive in nearly every niche on the planet, thanks to an enormous metabolic flexibility and capability to adapt. Natural but also engineered environments are highly dynamic, with changes in temperature, pH, oxygen, and substrate concentrations. Examples include day/night cycles, tidal regions, but also wastewater treatment plants or large-scale bioreactors with gradients originating from mass transfer limitations. The speed of dynamics ranges between (sub)seconds and several hours.

Such dynamic environments challenge the metabolism, and tight regulation needs to be in place to ensure a safe transition without energy depletion during famine or acidification of the cytosol after a substrate pulse. Prominent examples include poly phosphate or carbohydrate storage pools that are used to buffer between phases of feast and famine.

This Special Issue invites contributions on microorganisms under dynamic cultivation conditions or describing theoretical approaches to predict metabolic functions.

Keywords

  • Microbial metabolism
  • Metabolic modeling
  • Dynamic environments
  • Metabolomics
  • Systems biology
  • Industrial and environmental biotechnology

Published Papers (2 papers)

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Research

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Article
Effects of Light and Temperature on the Metabolic Profiling of Two Habitat-Dependent Bloom-Forming Cyanobacteria
Metabolites 2022, 12(5), 406; https://doi.org/10.3390/metabo12050406 - 29 Apr 2022
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Abstract
Rapid proliferation of cyanobacteria in both benthic and suspended (planktonic) habitats is a major threat to environmental safety, as they produce nuisance compounds such as cytotoxins and off-flavors, which degrade the safety and quality of water supplies. Temperature and light irradiance are two [...] Read more.
Rapid proliferation of cyanobacteria in both benthic and suspended (planktonic) habitats is a major threat to environmental safety, as they produce nuisance compounds such as cytotoxins and off-flavors, which degrade the safety and quality of water supplies. Temperature and light irradiance are two of the key factors in regulating the occurrence of algal blooms and production of major off-flavors. However, the role of these factors in regulating the growth and metabolism is poorly explored for both benthic and planktonic cyanobacteria. To fill this gap, we studied the effects of light and temperature on the growth and metabolic profiling of both benthic (Hapalosiphon sp. MRB220) and planktonic (Planktothricoides sp. SR001) environmental species collected from a freshwater reservoir in Singapore. Moreover, this study is the first report on the metabolic profiling of cyanobacteria belonging to two different habitats in response to altered environmental conditions. The highest growth rate of both species was observed at the highest light intensity (100 μmol photons/m²/s) and at a temperature of 33 °C. Systematic metabolite profiling analysis suggested that temperature had a more profound effect on metabolome of the Hapalosiphon, whereas light had a greater effect in the case of Planktothricoides. Interestingly, Planktothricoides sp. SR001 showed a specialized adaptation mechanism via biosynthesis of arginine, and metabolism of cysteine and methionine to survive and withstand higher temperatures of 38 °C and higher. Hence, the mode of strategies for coping with different light and temperature conditions was correlated with the growth and alteration in metabolic activities for physiological and ecological adaptations in both species. In addition, we putatively identified a number of unique metabolites with a broad range of antimicrobial activities in both species in response to both light and temperature. These metabolites could play a role in the dominant behavior of these species in suppressing competition during bloom formation. Overall, this study elucidated novel insights into the effects of environmental factors on the growth, metabolism, and adaptation strategies of cyanobacteria from two different habitats, and could be useful in controlling their harmful effects on human health and environmental concerns. Full article
(This article belongs to the Special Issue Metabolic Functionality of Microorganisms under Dynamic Environments)
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Review

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Review
Kinetic Modeling of Saccharomyces cerevisiae Central Carbon Metabolism: Achievements, Limitations, and Opportunities
Metabolites 2022, 12(1), 74; https://doi.org/10.3390/metabo12010074 - 13 Jan 2022
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Abstract
Central carbon metabolism comprises the metabolic pathways in the cell that process nutrients into energy, building blocks and byproducts. To unravel the regulation of this network upon glucose perturbation, several metabolic models have been developed for the microorganism Saccharomyces cerevisiae. These dynamic [...] Read more.
Central carbon metabolism comprises the metabolic pathways in the cell that process nutrients into energy, building blocks and byproducts. To unravel the regulation of this network upon glucose perturbation, several metabolic models have been developed for the microorganism Saccharomyces cerevisiae. These dynamic representations have focused on glycolysis and answered multiple research questions, but no commonly applicable model has been presented. This review systematically evaluates the literature to describe the current advances, limitations, and opportunities. Different kinetic models have unraveled key kinetic glycolytic mechanisms. Nevertheless, some uncertainties regarding model topology and parameter values still limit the application to specific cases. Progressive improvements in experimental measurement technologies as well as advances in computational tools create new opportunities to further extend the model scale. Notably, models need to be made more complex to consider the multiple layers of glycolytic regulation and external physiological variables regulating the bioprocess, opening new possibilities for extrapolation and validation. Finally, the onset of new data representative of individual cells will cause these models to evolve from depicting an average cell in an industrial fermenter, to characterizing the heterogeneity of the population, opening new and unseen possibilities for industrial fermentation improvement. Full article
(This article belongs to the Special Issue Metabolic Functionality of Microorganisms under Dynamic Environments)
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