Predicting the impact of temperature on metabolic fluxes using resource allocation modelling: Application to polyphosphate accumulating organisms

The understanding of microbial communities and the biological regulation of its members is crucial for implementation of novel technologies using microbial ecology. One poorly understood metabolic principle of microbial communities is resource allocation and biosynthesis. Resource allocation theory in polyphosphate accumulating organisms ...

Predicting the influence of combined oxygen and glucose gradients based on scale-down and modelling approaches for the scale-up of penicillin fermentations

In large scale fermentors the cultivated cells are exposed to dynamic changes in the nutrient concentrations due to imperfect mixing. Based on the characterization of these nutrient gradients in space and time, a rational scale down design can be obtained. This study focuses on the combined gradients of dissolved sugar and oxygen...

Stochastic parcel tracking in an Euler–Lagrange compartment model for fast simulation of fermentation processes

The compartment model (CM) is a well-known approach for computationally affordable, spatially resolved hydrodynamic modeling of unit operations. Recent implementations use flow profiles based on Computational Fluid Dynamics (CFD) simulations, and several authors included microbial kinetics to simulate gradients in bioreactors. However, these...

Influence of oxygen concentration on the metabolism of Penicillium chrysogenum

In large-scale bioreactors, there is often insufficient mixing and as a consequence, cells experience uneven substrate and oxygen levels that influence product formation. In this study, the influence of dissolved oxygen (DO) gradients on the primary and secondary metabolism of a high producing industrial strain of Penicillium chrysogenum was...

Modeling the energy trade-off between glycogen and polyphosphate use in phosphate accumulating organisms

Phosphate accumulating organisms (PAOs) perform a storage polymer metabolism within an anaerobic-aerobic cycle. Anaerobically, PAOs take up volatile fatty acids (VFA) and store them as poly-ẞ-hydroxyalkanoates (PHA). The energy (mainly ATP) necessary for the transport and storage of VFA (and general maintenance) is obtained through the cleavage...

Looking for Options to Sustainably Fixate Nitrogen. Are Molecular Metal Oxides Catalysts a Viable Avenue?

Fast and reliable industrial production of ammonia (NH₃) is fundamentally sustaining modern society. Since the early 20^th Century, NH₃ has been synthesized via the Haber–Bosch process, running at conditions of around 350–500°C and 100–200 times atmospheric pressure (15–20 MPa). Industrial ammonia production is...

Investigating the chemolithoautotrophic and formate metabolism of nitrospira moscoviensis by constraint-based metabolic modeling and ¹³C-tracer analysis

Nitrite-oxidizing bacteria belonging to the genus Nitrospira mediate a key step in nitrification and play important roles in the biogeochemical nitrogen cycle and wastewater treatment. While these organisms have recently been shown to exhibit metabolic flexibility beyond their chemolithoautotrophic lifestyle, including the use of simple...

Prospects for multi-omics in the microbial ecology of water engineering

Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions – including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful...

From industrial fermentor to CFD-guided downscaling: what have we learned?

Euler–Lagrange computational fluid dynamics simulations offer great potential for the integration of transport dynamics and metabolic dynamics in fermentation systems. Since the seminal work of Lapin et al. [1,2], progress has been made, mainly in the analysis of CFD data and translation to laboratory setup designs. Different large-scale...

Computational fluid dynamics simulation of an industrial P. chrysogenum fermentation with a coupled 9-pool metabolic model: Towards rational scale-down and design optimization

We assess the effect of substrate heterogeneity on the metabolic response of P. chrysogenum in industrial bioreactors via the coupling of a 9-pool metabolic model with Euler-Lagrange CFD simulations. In this work, we outline how this coupled hydrodynamic-metabolic modeling can be utilized in 5 steps. (1) A model response study with a fixed...

Lagrangian modeling of hydrodynamic–kinetic interactions in (bio)chemical reactors: Practical implementation and setup guidelines

Large substrate concentration gradients can exist in chemical or biochemical reactions, resulting from a large circulation time compared to the turnover time of substrates. The influence of such gradients on the microbial metabolism can significantly compromise optimal bioreactor performance. Lapin et al. (2004) proposed an Euler–Lagrange CFD...

Metabolic modeling of denitrification in Agrobacterium tumefaciens: A tool to study inhibiting and activating compounds for the denitrification pathway

Metabolic modeling of denitrification in Agrobacterium tumefaciens: A tool to study inhibiting and activating compounds for the denitrification pathway

A metabolic network model for facultative denitrification was developed based on experimental data obtained with Agrobacterium tumefaciens. The model includes kinetic regulation at the enzyme level and transcription regulation at the enzyme synthesis level. The objective of this work was to study the key factors regulating the metabolic response...

Application and assessment of experimental methods to study the cytosolic primary metabolism of yeast

Although a large part of the metabolism of the yeast Saccharomyces cerevisiae, has been clarified, there are a number of issues that still limit the predictive power of metabolic models for this organism. The dissertation aims to improve the collection of data for metabolic models through application and assessment of different experimental...