Stochastic models to study the impact of mixing on a fed-batch culture of Saccharomyces cerevisiae

The mechanisms of interaction between microorganisms and their environment in a stirred bioreactor can be modeled by a stochastic approach. The procedure comprises two submodels: a classical stochastic model for the microbial cell circulation and a Markov chain model for the concentration gradient calculus. The advantage lies in the fact that the core of each submodel, i.e., the transition matrix (which contains the probabilities to shift from a perfectly mixed compartment to another in the bioreactor representation), is identical for the two cases. That means that both the particle circulation and fluid mixing process can be analyzed by use of the same modeling basis. This assumption has been validated by performing inert tracer (NaCl) and stained yeast cells dispersion experiments that have shown good agreement with simulation results. The stochastic model has been used to define a characteristic concentration profile experienced by the microorganisms during a fermentation test performed in a scale-down reactor. The concentration profiles obtained in this way can explain the scale-down effect in the case of a Saccharomyces cerevisiae fed-batch process. The simulation results are analyzed in order to give some explanations about the effect of the substrate fluctuation dynamics on S. cerevisiae.     

Influence of bioreactor hydraulic characteristics on a Saccharomyces cerevisiae fed-batch culture: hydrodynamic modelling and scale-down investigations

Yeast is a widely used microorganism at the industrial level because of its biomass and metabolite production capabilities. However, due to its sensitivity to the glucose effect, problems occur during scale-up to the industrial scale. Hydrodynamic conditions are not ideal in large-scale bioreactors, and glucose concentration gradients can arise when these bioreactors are operating in fed-batch mode. We have studied the effects of such gradients in a scale-down reactor, which consists of a mixed part linked to a non-mixed part by a recirculation pump, in order to mimic the hydrodynamic conditions encountered at the large scale. During the fermentation tests in the scale-down reactor, there was a drop in both biomass yield (ratio between the biomass produced and the glucose added) and trehalose production and an increase in both fermentation time (time between inoculation and beginning of stationary phase) and ethanol production. We have developed a stochastic model which explains these effects as the result of an induction process determined mainly by the hydrodynamic conditions. The concentration profiles experienced by the microorganisms during the scale-down tests were expressed and linked to the biomass yields of the scale-down tests.     

Scale down of recombinant protein production: a comparative study of scaling performance

A large bioreactor is heterogeneous with respect to concentration gradients of substrates fed to the reactor such as oxygen and growth limiting carbon source. Gradient formation will highly depend on the fluid dynamics and mass transfer capacity of the reactor, especially in the area in which the substrate is added. In this study, some production-scale (12 m³ bioreactor) conditions of a recombinant Escherichia coli process were imitated on a laboratory scale. From the large-scale cultivations, it was shown that locally high concentration of the limiting substrate fed to the process, in this case glucose, existed at the level of the feedpoint. The large-scale process was scaled down from: (i) mixing time experiments performed in the large-scale bioreactor in order to identify and describe the oscillating environment and (ii) identification of two distinct glucose concentration zones in the reactor. An important parameter obtained from mixing time experiments was the residence time in the feed zone of about 10 seconds. The size of the feed zone was estimated to 10%. Based on these observations the scale-down reactor with two compartments was designed. It was composed of one stirred tank reactor and an aerated plug flow reactor, in which the effect of oscillating glucose concentration on biomass yield and acetate formation was studied. Results from these experiments indicated that the lower biomass yield and higher acetate formation obtained on a large scale compared to homogeneous small-scale cultivations were not directly caused by the cell response to the glucose oscillation. This was concluded since no acetate was accumulated during scale-down experiments. An explanation for the differences in results between the two reactor scales may be a secondary effect of high glucose concentration resulting in an increased glucose metabolism causing an oxygen consumption rate locally exceeding the transfer rate. The results from pulse response experiments and glucose concentration measurements, at different locations in the reactor, showed a great consistency for the two feeding/pulse positions used in the large-scale bioreactor. Furthermore, measured periodicity from mixing data agrees well with expected circulation times for each impeller volume. Conclusions are drawn concerning the design of the scale-down reactor.     

Bioreactor mixing efficiency modulates the activity of a prpoS::GFP reporter gene in E. coli

Background  

Extensive studies have shown that up-scaling of bioprocesses has a significant impact on the physiology of the microorganisms. Among the factors associated with the fluid dynamics of the bioreactor, concentration gradients induced by loss of the global mixing efficiency associated with the increasing scale is the main phenomena leading to strong physiological modifications at the level of the microbial population. These changes are not fully understood since they involve complex physiological mechanisms. In this work, we intend to investigate, at the single cell level, the expression of the rpoS gene associated with the stress response of E. coli. The cultures of the reporter strain have been performed in a small scale reactor as well as in a series of scaled-down bioreactors able to induce extracellular perturbations with increasing level of magnitude.     

Substrate gradient formation in the large-scale bioreactor lowers cell yield and increases by-product formation

A heterogeneous micro-environment was identified in a 12 m³ bioreactor with a height-to-diameter ratio of 2.5. The reactor was aerated by a ring sparger and stirred by three Rushton turbines. E. coli cells were cultivated in minimal medium to a cell density in the order of 30?g/l. Samples of glucose, the growth limiting component fed to the process, were taken at three levels in the bioreactor (top/middle/bottom). These showed that glucose concentration declined away from the feedpoint. The gradients depended on the mixing characteristics of the feedpoint, and concentrations of up to 400 times the mean value were found when feed was added to a relatively stagnant mixing zone. This resulted in up to 20% lower biomass yield compared to the bench scale. Gradients also affected the by-product formation, resulting in acetate formation in the large-scale bioreactor. IPTG induction of a recombinant protein was shown to influence important cell parameters and considerably increased the yield of carbon dioxide per glucose added, indicating an increased maintenance. The product formation rate was, however, not notably affected by the scale-up.     

Fast dynamic response of the fermentative metabolism of Escherichia coli to aerobic and anaerobic glucose pulses

The response of Escherichia coli cells to transient exposure (step increase) in substrate concentration and anaerobiosis leading to mixed‐acid fermentation metabolism was studied in a two‐compartment bioreactor system consisting of a stirred tank reactor (STR) connected to a mini‐plug‐flow reactor (PFR: BioScope, 3.5 mL volume). Such a system can mimic the situation often encountered in large‐scale, fed‐batch bioreactors. The STR represented the zones of a large‐scale bioreactor that are far from the point of substrate addition and that can be considered as glucose limited, whereas the PFR simulated the region close to the point of substrate addition, where glucose concentration is much higher than in the rest of the bioreactor. In addition, oxygen‐poor and glucose‐rich regions can occur in large‐scale bioreactors. The response of E. coli to these large‐scale conditions was simulated by continuously pumping E. coli cells from a well stirred, glucose limited, aerated chemostat (D = 0.1 h^?1) into the mini‐PFR. A glucose pulse was added at the entrance of the PFR. In the PFR, a total of 11 samples were taken in a time frame of 92 s. In one case aerobicity in the PFR was maintained in order to evaluate the effects of glucose overflow independently of oxygen limitation. Accumulation of acetate and formate was detected after E. coli cells had been exposed for only 2 s to the glucose‐rich (aerobic) region in the PFR. In the other case, the glucose pulse was also combined with anaerobiosis in the PFR. Glucose overflow combined with anaerobiosis caused the accumulation of formate, acetate, lactate, ethanol, and succinate, which were also detected as soon as 2 s after of exposure of E. coli cells to the glucose and O₂ gradients. This approach (STR‐mini‐PFR) is useful for a better understanding of the fast dynamic phenomena occurring in large‐scale bioreactors and for the design of modified strains with an improved behavior under large‐scale conditions. Biotechnol. Bioeng. 2009; 104: 1153–1161. © 2009 Wiley Periodicals, Inc.     

Mixing in liquid-impelled loop reactors

The liquid-impelled loop reactor is a new column-type bioreactor. The design of this device is based on the principle of the air-lift loop reactor. In the external-loop configuration used in this work, descending perfluorochemical drops bring about circulation of the continuous aqueous phase. Mixing of this continuous phase is characterized per section of the rector. Axial-dispersion coefficients for the tube with two-phase flow are determined and correlated with the energy dissipation in the tube. Comparisons with similar systems such as bubble columns and air-lift loop reactors are made. Overall mixing parameters are derived and used for calculation of the number of circulatins needed to achieve a certain degree of mixing. The hydrodynamic model from previous work is tested for the reactor configurations of this work. It can be useful to calculate circulation times.     

Implementing Process Analytical Technology for the Production of Recombinant Proteins in Escherichia coli Using an Advanced Controller Scheme

The performance of a bioreactor in meeting process goals is affected by the microorganism used, medium composition, and operating conditions. A typical bioreactor uses a supervisory control and data acquisition (SCADA) system for control, and a combination of software and hardware tools for real‐time data analysis. However, when the process is disrupted by utility or instrumentation failure, typical process controllers may be unable to reinstate normal operating conditions before the cells in the reactor shift to unfavorable metabolic regimes. The objective of this study is to examine how the response of a controller affects process recovery when disruptive incidences occur under a process analytical technology (PAT) framework. The process used for this investigation is the production of lethal toxin‐neutralizing factor (LTNF) by Escherichia coli (E. coli), which is controlled by a decoupled input–output‐linearizing controller (DIOLC). The performance of the DIOLC is compared to a proportional integral derivative (PID) controller subjected to the same conditions. The disruptions are introduced manually and the effect of controller action on process recovery and LTNF synthesis is measured in terms of peak purity and concentration. It is observed that DIOLC performs better after reinstating operating conditions and results in a meaningful improvement in performance.     

Turnover characteristics in continuous l-lysine fermentation

The turnover characteristics of a microbial bioreactor were comparatively investigated as a closed (batch) and a continuous stirred tank reactor (CSTR) open system, using a 2-l fermentor. Corynebacterium glutamicum (ATCC 21544) was chosen as the microorganism since it has the ability to produce l-lysine. Parameters measured were l-lysine production rates, glucose consumption rates and biomass production rates as a function of dilution rate, bioreactor volume and biomass concentration. The modes of microbial cell behaviour under steady-state and transition-state conditions were examined. Investigations on scaling properties of the CSTR system were also aimed at comparing scaling or allometry of metabolic rates in organisms that are also open energy dissipative systems.This investigation was first presented at the 10th Dechema-Jahrestagung der Biotechnologen, 1–3 June 1992, Karlsruhe, Germany     

Toward a stochastic formulation of microbial growth in relation to bioreactor performances: case study of an E. coli fed-batch process

A stochastic microbial growth model has been elaborated in the case of the culture of E. coli in fed-batch and scale-down reactors. This model is based on the stochastic determination of the generation time of the microbial cells. The determination of generation time is determined by choosing the appropriate value on a log-normal distribution. The appropriateness of such distribution is discussed and growth curves are obtained that show good agreement compared with the experimental results. The mean and the standard deviation of the log-normal distribution can be considered to be constant during the batch phase of the culture, but they vary when the fed-batch mode is started. It has been shown that the parameters related to the log-normal distribution are submitted to an exponential evolution. The aim of this study is to explore the bioreactor hydrodynamic effect on microbial growth. Thus, in a second time, the stochastic growth model has been reinforced by data coming from a previous stochastic bioreactor mixing model (1). The connection of these hydrodynamic data with the actual stochastic growth model has allowed us to explain the scale-down effect associated with the glucose concentration fluctuations. It is important to point out that the scale-down effect is induced differently according to the feeding strategy involved in the fed-batch experiments.     

Glycogen Metabolism in Aureobasidium Pullulans: A Glycogen Synthetase with Unusual Activation Properties

Abstract

Cultures of filamentous fungi that secrete significant amounts of exopolysaccharides are among the most difficult of fermentation fluids, presenting difficulties in the areas of aeration, agitation, mixing, and control that may in turn impact the physiology of the microorganism in an undesirable manner. The fungus Sclerotium glucanicum, which produces a potentially useful exopolysaccharide known as scleroglucan, illustrates many such difficulties. This review discusses in detail the range of physiological studies on the producing microorganism itself, including those concerning formation of “undesirable” byproducts, principally oxalate, but also, under certain conditions, other TCA cycle acids. In addition, the bioreactor technology in use for production of this type of biopolymer is discussed in relation to the difficulties such fluid types present. The potential of pneumatically agitated reactors for such production is evaluated, and the lack of fundamental studies on such reactors and on the hydrodynamics and mixing behavior of such complex fluids is pointed out.     

Production of capsular polysaccharide from Escherichia coli K4 for biotechnological applications

The production of industrially relevant microbial polysaccharides has recently gained much interest. The capsular polysaccharide of Escherichia coli K4 is almost identical to chondroitin, a commercially valuable biopolymer that is so far obtained from animal tissues entailing complex and expensive extraction procedures. In the present study, the production of capsular polysaccharide by E. coli K4 was investigated taking into consideration a potential industrial application. Strain physiology was first characterized in shake flask experiments to determine the optimal culture conditions for the growth of the microorganism and correlate it to polysaccharide production. Results show that the concentration of carbon source greatly affects polysaccharide production, while the complex nitrogen source is mainly responsible for the build up of biomass. Small-scale batch processes were performed to further evaluate the effect of the initial carbon source concentration and of growth temperatures on polysaccharide production, finally leading to the establishment of the medium to use in following fermentation experiments on a bigger scale. The fed-batch strategy next developed on a 2-L reactor resulted in a maximum cell density of 56 g_cww/L and a titre of capsular polysaccharide equal to 1.4 g/L, approximately ten- and fivefold higher than results obtained in shake flask and 2-L batch experiments, respectively. The release kinetics of K4 polysaccharide into the medium were also explored to gain insight into the mechanisms underlying a complex aspect of the strain physiology.     

Production of immunoglobulin A in different reactor configurations

A murine hybridoma line (Zac3), secreting an IgA monoclonal antibody, was cultivated in different systems: a BALB/c mouse, a T-flask, a stirred-tank bioreactor and a hollow fiber reactor. These systems were characterized in terms of cell metabolism and performances for IgA production. Cultures in T-flask and batch bioreactor were found to be glutamine-limited. Ammonia and lactate were produced in significant amounts. IgA productivity was found to be constant and growth associated. Final IgA concentration was similar in both systems. In fed-batch cultures, supplemented with glutamine and glucose, maximum viable cell concentration was increased by 60% and final IgA concentration by 155%. The hollow fiber reactor was able to produce very large amounts of IgA at very high concentrations, similar to the value found in ascites fluid. The productivity ofZac3 is similar to the values reported for IgG-producing cell lines.     

Performance of tapered column packed-bed bioreactor for ethanol production

A tapered column type of bioreactor system packed with immobilized Saccharomyces cerevisiae was used to study the bioreactor performance as a function of design and operating variables. The performance of tapered column bioreactor system was found to be better than that of the conventional cylindrical column reactor system for the ethanol fermentation. The new bioreactor design alleviated problems associated with carbon dioxide evolution and provided a significantly better flow pattern for both liquid and gas phases in the bioreactor without local channelling. A mathematical simulation model, which takes into account of the axial convection and dispersion, interphase mass transfer, and apparent kinetic design parameters, was developed. The effect of radial concentration gradients on the bioreactor performance was found to be insignificant. For the reactor system studied, the maximum ethanol productivity obtained was 60 g ethanol/L gel/h, and the maximum glucose assimilation rate was 140 g glucose/L gel/h. One of the most important findings from this study was that the apparent kinetic parameters change at the glucose concentration of 2 g/L This change was found to be due to the changes in yeast physiology and metabolism. The values of V(m) (') and V(m) (') decreased from 0.8 to 0.39 g ethanol/g cell/h and from 97mM to 11mM, respectively. The substrate inhibition constant was estimated as 0.76M and the product inhibition constant was determined as 113 g ethanol/L The degree of product inhibition showed practically a linear relationship with an increasing ethanol concentration. Based on the hydro-dynamic analysis of the bioreactor system, it was found that the Peclet number, N(Pe) was not a strong function of the flow velocity at low flow rates through the bioreactor system, but its value decreased somewhat at an interstitial velocity greater than 0.03 cm/s. The tapered column bioreactor system showed a much better flow pattern of gas and liquid phases within the reactor, thereby providing a more homogeneous distribution of gas-liquid-solid phases in the reactor without any phase separation.     

Development of a predictive description of an immobilized-cell, three-phase, fluidized-bed bioreactor

A Large bioreactor is an inhomogenous system with concentration gradients which depend on the fluid dynamics and the mass transfer of the reactor, the feeding strategy, the saturation constant, and the cell density. The responses of Escherichia coli cells to short-term oscillations of the carbon/energy substrate in glucose limited fed-batch cultivations were studied in a two-compartment reactor system consisting of a stirred tank reactor (STR) and an aerated plug flow reactor (PFR) as a recycle loop. Short-term glucose excess or starvation in the PFR was simulated by feeding of glucose to the PFR or to the STR alternatively. The cellular response to repeated short-term glucose excess was a transient increase of glucose consumption and acetate formation. But, there was no accumulation of acetate in the culture, because it was consumed in the STR part where the glucose concentration was growth limiting. However, acetate accumulated during the cultivation if the oxygen supply in the PFR was insufficient, causing higher acetate formation. The biomass yield was then negatively influenced, which was also the case if the PFR was used to simulate a glucose starvation zone. The results suggest that short-term heterogeneities influence the cellular physiology and growth, and can be of major importance for the process performance. (c) 1995 John Wiley & Sons, Inc.     

Ethanol production by immobilized whole cells ofZymomonas mobilis in a continuous flow expanded bed bioreactor and a continuous flow stirred tank bioreactor

Continuous ethanol fermentation by immobilized whole cells ofZymomonas mobilis was investigated in an expanded bed bioreactor and in a continuous stirred tank reactor at glucose concentrations of 100, 150 and 200 g L^–1. The effect of different dilution rates on ethanol production by immobilized whole cells ofZymomonas mobilis was studied in both reactors. The maximum ethanol productivity attained was 21 g L^–1 h^–1 at a dilution rate of 0.36 h^–1 with 150 g glucose L^–1 in the continuous expanded bed bioreactor. The conversion of glucose to ethanol was independent of the glucose concentration in both reactors.     

A scale-down two-compartment reactor with controlled substrate oscillations: Metabolic response of Saccharomyces cerevisiae

Substrate concentration gradients are likely to appear during large scale fermentations. To study effects of such gradients on microorganisms, an aerated scale-down reactor system was constructed. It consists of a plug flow reactor (PFR) and a stirred tank reactor (STR), between which the medium is circulated. The PFR, which is an aerated static mixer reactor, was characterized with respect to plug flow behaviour and oxygen transfer. A Bodenstein number of 15–220, depending on residence time and aeration rate, and a k_La of 500–1130 h^–1, depending mainly on aeration rate, were obtained. The biological test system used, was aerobic ethanol production by Saccharomyces cerevisiae, due to sugar excess. The ethanol concentration profile and the yield of biomass were compared in two fed-batch fermentations. In the first case, the feeding point of molasses was located at the inlet of the PFR. This simulates location of the feeding point in the segregated part of a heterogeneous reactor, with local high sugar concentrations. In the second mode of operation, as a control with good mixing conditions, the PFR was disconnected from the STR, into which the substrate was fed. Differences were found: Up to 6% less biomass was produced and a larger amount of ethanol was formed in the two-compartment reactor system, due to the uneven sugar concentration distribution. This emphasizes the importance of the location of, and the mixing conditions at, the feeding point in a bioreactor.     

A fermentation system designed to independently evaluate mixing and/or oxygen tension effects in microbial processes: development,application and performance

In order to evaluate the independent effects of hydrodynamic conditions and/or oxygen tension on culture physiology and productivity, a fermentation system designed to control dissolved oxygen at constant power drawn (P/V) was developed. The system included a fully instrumented 14 l bioreactor coupled to a PC for data acquisition and control. Power drawn was measured (using a commercial torquemeter coupled to the shaft) and maintained constant by varying the agitation speed; while gas blending was used to control dissolved oxygen concentration. To validate the system, rheological-complex fermentations involving xanthan gum production and filamentous fungal cultivation (using Xanthomonas campestris and Trichoderma harzianum) were developed. In both cases, and despite the changing environmental conditions (due to increased broth viscosities and microbial respiration), both variables were controlled at the desired set points. Through such a system, a rigorous evaluation of the hydrodynamic conditions and/or oxygen tension on culture physiology and productivity is now feasible.