New patterns of mixed-substrate utilization during batch growth of Escherichia coli K12

Hierarchical and simultaneous utilization of carbon substrates: mechanistic insights, physiological roles, and ecological consequences

Bacteria grown on a mixture of carbon substrates exhibit two utilization patterns: hierarchical utilization (HU) and simultaneous utilization (SU). How and why cells adopt these different behaviors remains poorly understood despite decades of research. Recent studies address various open questions from multiple viewpoints. From a mechanistic perspective, it was found that flux sensors play a central role in the regulation of substrate utilization, accounting for the known dependences on single-substrate growth rates, substrate concentrations, and the point where the substrate enters central metabolism. From a physiological perspective, several recent studies suggested HU or SU as growth-optimizing strategies through efficient allocation of essential proteome resources. However, other studies demonstrate that a significant fraction of the proteome is dedicated to functions apparently unnecessary for growth, casting doubt on explanations based on slight efficiency gains. From an ecological perspective, recent theoretical studies suggest that HU can help increase species diversity in bacterial communities.

Biofilm Structure Promotes Coexistence of Phage-Resistant and Phage-Susceptible Bacteria

Encounters among bacteria and their viral predators (bacteriophages) are among the most common ecological interactions on Earth. These encounters are likely to occur with regularity inside surface-bound communities that microbes most often occupy in natural environments. Such communities, termed biofilms, are spatially constrained: interactions become limited to near neighbors, diffusion of solutes and particulates can be reduced, and there is pronounced heterogeneity in nutrient access and physiological state. It is appreciated from prior theoretical work that phage-bacteria interactions are fundamentally different in spatially structured contexts, as opposed to well-mixed liquid culture. Spatially structured communities are predicted to promote the protection of susceptible host cells from phage exposure, and thus weaken selection for phage resistance. The details and generality of this prediction in realistic biofilm environments, however, are not known. Here, we explore phage-host interactions using experiments and simulations that are tuned to represent the essential elements of biofilm communities. Our simulations show that in biofilms, phage-resistant cells-as their relative abundance increases-can protect clusters of susceptible cells from phage exposure, promoting the coexistence of susceptible and phage-resistant bacteria under a large array of conditions. We characterize the population dynamics underlying this coexistence, and we show that coexistence is recapitulated in an experimental model of biofilm growth measured with confocal microscopy. Our results provide a clear view into the dynamics of phage resistance in biofilms with single-cell resolution of the underlying cell-virion interactions, linking the predictions of canonical theory to realistic models and in vitro experiments of biofilm growth.IMPORTANCE In the natural environment, bacteria most often live in communities bound to one another by secreted adhesives. These communities, or biofilms, play a central role in biogeochemical cycling, microbiome functioning, wastewater treatment, and disease. Wherever there are bacteria, there are also viruses that attack them, called phages. Interactions between bacteria and phages are likely to occur ubiquitously in biofilms. We show here, using simulations and experiments, that biofilms will in most conditions allow phage-susceptible bacteria to be protected from phage exposure, if they are growing alongside other cells that are phage resistant. This result has implications for the fundamental ecology of phage-bacteria interactions, as well as the development of phage-based antimicrobial therapeutics.

Phototrophic Lactate Utilization by Rhodopseudomonas palustris Is Stimulated by Coutilization with Additional Substrates

The phototrophic purple nonsulfur bacterium Rhodopseudomonas palustris is known for its metabolic versatility and is of interest for various industrial and environmental applications. Despite decades of research on R. palustris growth under diverse conditions, patterns of R. palustris growth and carbon utilization with mixtures of carbon substrates remain largely unknown. R. palustris readily utilizes most short-chain organic acids but cannot readily use lactate as a sole carbon source. Here we investigated the influence of mixed-substrate utilization on phototrophic lactate consumption by R. palustris We found that lactate was simultaneously utilized with a variety of other organic acids and glycerol in time frames that were insufficient for R. palustris growth on lactate alone. Thus, lactate utilization by R. palustris was expedited by its coutilization with additional substrates. Separately, experiments using carbon pairs that did not contain lactate revealed acetate-mediated inhibition of glycerol utilization in R. palustris This inhibition was specific to the acetate-glycerol pair, as R. palustris simultaneously utilized acetate or glycerol when either was paired with succinate or lactate. Overall, our results demonstrate that (i) R. palustris commonly employs simultaneous mixed-substrate utilization, (ii) mixed-substrate utilization expands the spectrum of readily utilized organic acids in this species, and (iii) R. palustris has the capacity to exert carbon catabolite control in a substrate-specific manner.IMPORTANCE Bacterial carbon source utilization is frequently assessed using cultures provided single carbon sources. However, the utilization of carbon mixtures by bacteria (i.e., mixed-substrate utilization) is of both fundamental and practical importance; it is central to bacterial physiology and ecology, and it influences the utility of bacteria as biotechnology. Here we investigated mixed-substrate utilization by the model organism Rhodopseudomonas palustris Using mixtures of organic acids and glycerol, we show that R. palustris exhibits an expanded range of usable carbon substrates when provided substrates in mixtures. Specifically, coutilization enabled the prompt consumption of lactate, a substrate that is otherwise not readily used by R. palustris Additionally, we found that R. palustris utilizes acetate and glycerol sequentially, revealing that this species has the capacity to use some substrates in a preferential order. These results provide insights into R. palustris physiology that will aid the use of R. palustris for industrial and commercial applications.

Hierarchy of non-glucose sugars in Escherichia coli

BACKGROUND

Understanding how cells make decisions, and why they make the decisions they make, is of fundamental interest in systems biology. To address this, we study the decisions made by E. coli on which genes to express when presented with two different sugars. It is well-known that glucose, E. coli's preferred carbon source, represses the uptake of other sugars by means of global and gene-specific mechanisms. However, less is known about the utilization of glucose-free sugar mixtures which are found in the natural environment of E. coli and in biotechnology.

RESULTS

Here, we combine experiment and theory to map the choices of E. coli among 6 different non-glucose carbon sources. We used robotic assays and fluorescence reporter strains to make precise measurements of promoter activity and growth rate in all pairs of these sugars. We find that the sugars can be ranked in a hierarchy: in a mixture of a higher and a lower sugar, the lower sugar system shows reduced promoter activity. The hierarchy corresponds to the growth rate supported by each sugar- the faster the growth rate, the higher the sugar on the hierarchy. The hierarchy is 'soft' in the sense that the lower sugar promoters are not completely repressed. Measurement of the activity of the master regulator CRP-cAMP shows that the hierarchy can be quantitatively explained based on differential activation of the promoters by CRP-cAMP. Comparing sugar system activation as a function of time in sugar pair mixtures at sub-saturating concentrations, we find cases of sequential activation, and also cases of simultaneous expression of both systems. Such simultaneous expression is not predicted by simple models of growth rate optimization, which predict only sequential activation. We extend these models by suggesting multi-objective optimization for both growing rapidly now and preparing the cell for future growth on the poorer sugar.

CONCLUSION

We find a defined hierarchy of sugar utilization, which can be quantitatively explained by differential activation by the master regulator cAMP-CRP. The present approach can be used to understand cell decisions when presented with mixtures of conditions.

The decoupling between genetic structure and metabolic phenotypes in Escherichia coli leads to continuous phenotypic diversity

To assess the extent of intra-species diversity and the links between phylogeny, lifestyle (habitat and pathogenicity) and phenotype, we assayed the growth yield on 95 carbon sources of 168 Escherichia strains. We also correlated the growth capacities of 14 E. coli strains with the presence/absence of enzyme-coding genes. Globally, we found that the genetic distance, based on multilocus sequence typing data, was a weak indicator of the metabolic phenotypic distance. Besides, lifestyle and phylogroup had almost no impact on the growth yield of non-Shigella E. coli strains. In these strains, the presence/absence of the metabolic pathways, which was linked to the phylogeny, explained most of the growth capacities. However, few discrepancies blurred the link between metabolic phenotypic distance and metabolic pathway distance. This study shows that a prokaryotic species structured into well-defined genetic and lifestyle groups can yet exhibit continuous phenotypic diversity, possibly caused by gene regulatory effects.

Dynamic metabolic flux analysis demonstrated on cultures where the limiting substrate is changed from carbon to nitrogen and vice versa

The main requirement for metabolic flux analysis (MFA) is that the cells are in a pseudo-steady state, that there is no accumulation or depletion of intracellular metabolites. In the past, the applications of MFA were limited to the analysis of continuous cultures. This contribution introduces the concept of dynamic MFA and extends MFA so that it is applicable to transient cultures. Time series of concentration measurements are transformed into flux values. This transformation involves differentiation, which typically increases the noisiness of the data. Therefore, a noise-reducing step is needed. In this work, polynomial smoothing was used. As a test case, dynamic MFA is applied on Escherichia coli cultivations shifting from carbon limitation to nitrogen limitation and vice versa. After switching the limiting substrate from N to C, a lag phase was observed accompanied with an increase in maintenance energy requirement. This lag phase did not occur in the C- to N-limitation case.

Modeling with a view to target identification in metabolic engineering: a critical evaluation of the available tools

The state of the art tools for modeling metabolism, typically used in the domain of metabolic engineering, were reviewed. The tools considered are stoichiometric network analysis (elementary modes and extreme pathways), stoichiometric modeling (metabolic flux analysis, flux balance analysis, and carbon modeling), mechanistic and approximative modeling, cybernetic modeling, and multivariate statistics. In the context of metabolic engineering, one should be aware that the usefulness of these tools to optimize microbial metabolism for overproducing a target compound depends predominantly on the characteristic properties of that compound. Because of their shortcomings not all tools are suitable for every kind of optimization; issues like the dependence of the target compound's synthesis on severe (redox) constraints, the characteristics of its formation pathway, and the achievable/desired flux towards the target compound should play a role when choosing the optimization strategy.

Gene regulation in continuous cultures: a unified theory for bacteria and yeasts

During batch growth on mixtures of two growth-limiting substrates, microbes consume the substrates either sequentially (diauxie) or simultaneously. The ubiquity of these growth patterns suggests that they may be driven by a universal mechanism common to all microbial species. Recently, we showed that a minimal model accounting only for enzyme induction and dilution, the two processes that occur in all microbes, explains the phenotypes observed in batch cultures of various wild-type and mutant/recombinant cells (Narang and Pilyugin in J. Theor. Biol. 244:326-348, 2007). Here, we examine the extension of the minimal model to continuous cultures. We show that: (1) Several enzymatic trends, attributed entirely to cross-regulatory mechanisms, such as catabolite repression and inducer exclusion, can be quantitatively explained by enzyme dilution. (2) The bifurcation diagram of the minimal model for continuous cultures, which classifies the substrate consumption pattern at any given dilution rate and feed concentrations, provides a precise explanation for the empirically observed correlations between the growth patterns in batch and continuous cultures. (3) Numerical simulations of the model are in excellent agreement with the data. The model captures the variation of the steady state substrate concentrations, cell densities, and enzyme levels during the single- and mixed-substrate growth of bacteria and yeasts at various dilution rates and feed concentrations. This variation is well approximated by simple analytical expressions that furnish deep physical insights. (4) Since the minimal model describes the behavior of the cells in the absence of cross-regulatory mechanisms, it provides a rigorous framework for quantifying the effect of these mechanisms. We illustrate this by analyzing several data sets from the literature.

The influence of cultivation methods on Shewanella oneidensis physiology and proteome expression

High-throughput analyses that are central to microbial systems biology and ecophysiology research benefit from highly homogeneous and physiologically well-defined cell cultures. While attention has focused on the technical variation associated with high-throughput technologies, biological variation introduced as a function of cell cultivation methods has been largely overlooked. This study evaluated the impact of cultivation methods, controlled batch or continuous culture in bioreactors versus shake flasks, on the reproducibility of global proteome measurements in Shewanellaoneidensis MR-1. Variability in dissolved oxygen concentration and consumption rate, metabolite profiles, and proteome was greater in shake flask than controlled batch or chemostat cultures. Proteins indicative of suboxic and anaerobic growth (e.g., fumarate reductase and decaheme c-type cytochromes) were more abundant in cells from shake flasks compared to bioreactor cultures, a finding consistent with data demonstrating that “aerobic” flask cultures were O₂ deficient due to poor mass transfer kinetics. The work described herein establishes the necessity of controlled cultivation for ensuring highly reproducible and homogenous microbial cultures. By decreasing cell to cell variability, higher quality samples will allow for the interpretive accuracy necessary for drawing conclusions relevant to microbial systems biology research.

Dynamics of Escherichia coli at elevated temperatures: effect of temperature history and medium

AIMS

The dynamics of Escherichia coli near the maximum temperature for growth in a rich medium are analysed. The effects of temperature history, medium composition and physiological state of the inoculum are evaluated.

METHODS AND RESULTS

Kinetics of E. coli K12 MG1655 is studied in 'brain-heart infusion' broth in a temperature controlled environment. Based on viable counts, 'smooth' growth curves are observed at 40, 41, 42 and 43 degrees C. The exponential growth phase at 44 and 45 degrees C is interrupted. At 46 degrees C, a period of exponential growth is followed by inactivation. Neither the physiological state of the inoculum nor medium enrichment alters the dynamics, whilst temperature pre-adaptation or chemical chaperones restore regular cell growth and division ('smooth' exponential growth).

CONCLUSIONS

Atypical, nonexponential growth at 44, 45 and 46 degrees C seems related to protein destabilization and can (partly) be restored by an appropriate medium design (i.e. addition of chemical chaperones) or temperature history (i.e. selection of a more resistant subpopulation).

SIGNIFICANCE AND IMPACT OF THE STUDY

This study indicates that the maximum temperature for growth is dependent on the temperature history and the chemical environment. These observations and the nonexponential kinetics have important implications for the development of predictive models for food safety and quality.

Quantitative steps in the evolution of metabolic organisation as specified by the Dynamic Energy Budget theory

The Dynamic Energy Budget (DEB) theory quantifies the metabolic organisation of organisms on the basis of mechanistically inspired assumptions. We here sketch a scenario for how its various modules, such as maintenance, storage dynamics, development, differentiation and life stages could have evolved since the beginning of life. We argue that the combination of homeostasis and maintenance induced the development of reserves and that subsequent increases in the maintenance costs came with increases of the reserve capacity. Life evolved from a multiple reserves - single structure system (prokaryotes, many protoctists) to systems with multiple reserves and two structures (plants) or single reserve and single structure (animals). This had profound consequences for the possible effects of temperature on rates. We present an alternative explanation for what became known as the down-regulation of maintenance at high growth rates in microorganisms; the density of the limiting reserve increases with the growth rate, and reserves do not require maintenance while structure-specific maintenance costs are independent of the growth rate. This is also the mechanism behind the variation of the respiration rate with body size among species. The DEB theory specifies reserve dynamics on the basis of the requirements of weak homeostasis and partitionability. We here present a new and simple mechanism for this dynamics which accounts for the rejection of mobilised reserve by busy maintenance/growth machinery. This module, like quite a few other modules of DEB theory, uses the theory of Synthesising Units; we review recent progress in this field. The plasticity of membranes that evolved in early eukaryotes is a major step forward in metabolic evolution; we discuss quantitative aspects of the efficiency of phagocytosis relative to the excretion of digestive enzymes to illustrate its importance. Some processes of adaptation and gene expression can be understood in terms of allocation linked to the relative workload of metabolic modules in (unicellular) prokaryotes and organs in (multicellular) eukaryotes. We argue that the evolution of demand systems can only be understood in the light of that of supply systems. We illustrate some important points with data from the literature.

Bacterial gene regulation in diauxic and non-diauxic growth

When bacteria are grown in a batch culture containing a mixture of two growth-limiting substrates, they exhibit a rich spectrum of substrate consumption patterns including diauxic growth, simultaneous consumption, and bistable growth. In previous work, we showed that a minimal model accounting only for enzyme induction and dilution captures all the substrate consumption patterns [Narang, A., 1998a. The dynamical analogy between microbial growth on mixtures of substrates and population growth of competing species. Biotechnol. Bioeng. 59, 116-121, Narang, A., 2006. Comparitive analysis of some models of gene regulation in mixed-substrate microbial growth, J. Theor. Biol. 242, 489-501]. In this work, we construct the bifurcation diagram of the minimal model, which shows the substrate consumption pattern at any given set of parameter values. The bifurcation diagram explains several general properties of mixed-substrate growth. (1) In almost all the cases of diauxic growth, the "preferred" substrate is the one that, by itself, supports a higher specific growth rate. In the literature, this property is often attributed to the optimality of regulatory mechanisms. Here, we show that the minimal model, which accounts for induction and growth only, displays the property under fairly general conditions. This suggests that the higher growth rate of the preferred substrate is an intrinsic property of the induction and dilution kinetics. It can be explained mechanistically without appealing to optimality principles. (2) The model explains the phenotypes of various mutants containing lesions in the regions encoding for the operator, repressor, and peripheral enzymes. A particularly striking phenotype is the "reversal of the diauxie" in which the wild-type and mutant strains consume the very same two substrates in opposite order. This phenotype is difficult to explain in terms of molecular mechanisms, such as inducer exclusion or CAP activation, but it turns out to be a natural consequence of the model. We show furthermore that the model is robust. The key property of the model, namely, the competitive dynamics of the enzymes, is preserved even if the model is modified to account for various regulatory mechanisms. Finally, the model has important implications for the problem of size regulation in development. It suggests that protein dilution may be the mechanism coupling patterning and growth.

Comparative analysis of some models of gene regulation in mixed-substrate microbial growth

Mixed-substrate microbial growth is of fundamental interest in microbiology and bioengineering. Several mathematical models have been developed to account for the genetic regulation of such systems, especially those resulting in diauxic growth. In this work, we compare the dynamics of three such models (Narang, 1998a. The dynamical analogy between microbial growth on mixtures of substrates and population growth of competing species. Biotechnol. Bioeng. 59, 116-121; Thattai and Shraiman, 2003. Metabolic switching in the sugar phosphotransferase system of Escherichia coli. Biophys. J. 85(2), 744-754; Brandt et al., 2004. Modelling microbial adaptation to changing availability of substrates. Water Res. 38, 1004-1013). We show that these models are dynamically similar--the initial motion of the inducible enzymes in all the models is described by the Lotka-Volterra equations for competing species. In particular, the prediction of diauxic growth corresponds to "extinction" of one of the enzymes during the first few hours of growth. The dynamic similarity occurs because in all the models, the inducible enzymes possess properties characteristic of competing species: they are required for their own synthesis, and they inhibit each other. Despite this dynamic similarity, the models vary with respect to the range of dynamics captured. The Brandt et al. model always predicts the diauxic growth pattern, whereas the remaining two models exhibit both diauxic and non-diauxic growth patterns. The models also differ with respect to the mechanisms that generate the mutual inhibition between the enzymes. In the Narang model, mutual inhibition occurs because the enzymes for each substrate enhance the dilution of the enzymes for the other substrate. The Brandt et al. model superimposes upon this dilution effect an additional mechanism of mutual inhibition. In the Thattai and Shraiman model, the mutual inhibition is entirely due to competition for the phosphoryl groups. For quantitative agreement with the data, all models must be modified to account for specific mechanisms of mutual inhibition, such as inducer exclusion.

The ideal free distribution and bacterial growth on two substrates

A population dynamical model describing growth of bacteria on two substrates is analyzed. The model assumes that bacteria choose substrates in order to maximize their per capita population growth rate. For batch bacterial growth, the model predicts that as the concentration of the preferred substrate decreases there will be a time at which both substrates provide bacteria with the same fitness and both substrates will be used simultaneously thereafter. Preferences for either substrate are computed as a function of substrate concentrations. The predicted time of switching is calculated for some experimental data given in the literature and it is shown that the fit between predicted and observed values is good. For bacterial growth in the chemostat, the model predicts that at low dilution rates bacteria should feed on both substrates while at higher dilution rates bacteria should feed on the preferred substrate only. Adaptive use of substrates permits bacteria to survive in the chemostat at higher dilution rates when compared with non-adaptive bacteria.

Predicting stability of mixed microbial cultures from single species experiments: 2. Physiological model

In this paper, we study the equilibria of a physiological model describing the continuous culture in which two microbial populations compete for two substitutable resources. This work is an extension of the stability analysis of the phenomenological model of mixed microbial growth [M.M. Ballyk, G.S.K. Wolkowicz, Exploitative competition in the chemostat for two perfectly substitutable resources, Math. Biosci. 118 (1993) 127-180; S.S. Pilyugin, G.T. Reeves, A. Narang, Predicting stability of mixed microbial cultures from single species experiments: 2. Phenomenological model]. Here, we investigate the influence of the peripheral enzymes that catabolize the substrate uptake on the stability of the mixed culture. We show that, under steady state conditions, an increase in the concentration of one substrate inhibits the uptake of the other substrate(s). We present the criteria for existence, uniqueness, and stability of various types of equilibria. We formulate these criteria in terms of growth isoclines and consumption curves for each of the competing species. Since both types of curves can be obtained from a single species experiment, our approach provides a direct connection between theory and experiment and allows one to infer the dynamics of mixed cultures from the dynamics of single species cultures. By expressing the stability criteria in terms of intracellular properties, the model establishes a link between ecology and molecular biology.

Effect of preculturing conditions on growth of Lactobacillus rhamnosus on medium containing glucose and citrate

Lactobacillus rhamnosus can metabolize citrate through a citrate inducible transport system. The growth curves of L. rhamnosus on medium containing glucose and citrate was found to be highly dependent on preculturing conditions. It exhibited diauxic growth when precultured on glucose, but demonstrated simultaneous consumption when cultured on citrate. The maximum specific growth rate for cells growing on glucose + citrate was 0.38 h-1, which was higher than the growth rate on individual substrates (0.28 h-1). Simultaneous consumption also yielded higher net flavour compounds, diacetyl and acetoin. Flux analysis indicated that L. rhamnosus requires oxygen for balancing excess NADH through NADH oxidase. The flux analysis provided insights into the metabolic network of L. rhamnosus.

Validation of bacterial growth inhibition models based on molecular properties of organic acids

Organic acids occur naturally in foods and have been used in many food products as preservatives because they inhibit the growth of most microorganisms. The acids commonly found in foods differ greatly in both their structure and inhibitory effects for different bacteria. A way to represent relationships between different acids was previously described in which principal components analysis (PCA) was applied to 11 physical and chemical properties of 17 organic acids, to arrive at principal properties. These were used for development of regression models that related the minimum inhibitory concentrations (MICs) of organic acids to their principal properties. Separate MIC models were constructed for six different bacteria. The objective of the present study was to test the predictive capabilities of the organism models using different organic acids from the ones used to construct the original models. MIC predictions were made for three acids for each of the six bacteria for which models were previously constructed. MIC determinations for these acids were then carried out and compared with the predictions; these were in good agreement, thus validating the models. The new data were combined with that obtained previously to produce similar, but slightly stronger models. These had R(2) values between 0.861 and 0.992.

Dynamic flux balance analysis of diauxic growth in Escherichia coli

Flux Balance Analysis (FBA) has been used in the past to analyze microbial metabolic networks. Typically, FBA is used to study the metabolic flux at a particular steady state of the system. However, there are many situations where the reprogramming of the metabolic network is important. Therefore, the dynamics of these metabolic networks have to be studied. In this paper, we have extended FBA to account for dynamics and present two different formulations for dynamic FBA. These two approaches were used in the analysis of diauxic growth in Escherichia coli. Dynamic FBA was used to simulate the batch growth of E. coli on glucose, and the predictions were found to qualitatively match experimental data. The dynamic FBA formalism was also used to study the sensitivity to the objective function. It was found that an instantaneous objective function resulted in better predictions than a terminal-type objective function. The constraints that govern the growth at different phases in the batch culture were also identified. Therefore, dynamic FBA provides a framework for analyzing the transience of metabolism due to metabolic reprogramming and for obtaining insights for the design of metabolic networks.

Quantitative analysis of the regulation scheme of invertase expression in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, the expression of invertase, which is the hydrolyzing enzyme of sucrose, is controlled by the presence of monosaccharides, such as glucose and fructose, and referred to as carbon catabolite repression. To date, efforts have been made to identify the mechanism by which cells sense extracellular monosaccharide concentrations and trigger the genes involved in the repression pathway. The aim of the present work was to quantitatively investigate the cellular regulation of invertase expression in the wild-type strain S. cerevisiae CEN.PK113-7D during batch growth containing mixed sugar substrates under different initial conditions. Because of the high frequency and accurate online analysis of multiple components, a tight control of invertase expression could be observed, and threshold concentrations of the monosaccharides for derepression could be determined to 0.5 gl(-1) for glucose and 2 gl(-1) for fructose. Also, the existence of a hitherto undescribed regulatory state, in which cells regulate invertase expression very precisely and operate over long periods at monosaccharide concentrations lower than the above thresholds, could be demonstrated. All experimental observations could be summarized in a formulation of the cellular regulation scheme of invertase expression. A simple kinetic model could show that the regulation scheme explains the observed behavior very well. Additionally, the model was able to explain consequences of the regulation on the global metabolism.

Effect of nitrate exposure history on the oxygen/nitrate diauxic growth of Pseudomonas denitrificans

Pseudomonas denitrificans pre-cultured (revived from agar plates) under varying conditions (nitrate absent or present; dissolved oxygen absent or present) was subsequently grown aerobically with or without nitrate present, and finally exposed to anoxic conditions (i.e., aeration stopped and dissolved oxygen stripped from solution). The occurrence and length of diauxic lags following transition from aerobic to anoxic conditions were affected strongly by the nitrate and oxygen exposure history of the biomass.

The dynamical analogy between microbial growth on mixtures of substrates and population growth of competing species

There is a similarity between the metabolic dynamics of a microbial species growing on a mixture of two substrates and the dynamics of growth of two competing populations. Specifically, the enzymes catalyzing the uptake and catabolism of substrates exhibit phenomena analogous to extinction and coexistence."Extinction" of the enzymes associated with one of the substrates results in sequential utilization of the substrates (diauxie) (Monod, 1942). "Coexistence" of the enzymes associated with the substrates results in simultaneous utilization of the substrates (Egli, 1995). Here, we formulate a simple model that shows the basis for this dynamical similarity: The equations describing the evolution of the enzyme levels are dynamical analogs of the Lotka-Volterra model for two competing species. The analogy suggests ways of capturing the experimentally observed preculture-dependent growth patterns, i.e., growth patterns that vary depending on the physiological state of the preculture.