Modeling substrate inhibition of microbial growth

This article presents a general equation for substrate inhibition of microbial growth using a statistical thermodynamic approach. Existing empirical models adapted from enzyme kinetics, for example, the Haldane-Andrews equation, often criticized for not being physically based for microbial growth, are shown to derive from the general equation in this article, and their empirical parameters are shown to be well defined physically. Three sets of experimental data from the literature are used to test the modeling abilities of the general equation to represent experimental data. The results are compared with those obtained by fitting the same data set to a widely used empirical model existing in the literature. The general equation is found to represent all three experimental data sets better than the alternative model tested. In addition, a graphical method existing in enzyme kinetics is successfully adapted and further developed to determine the number of inhibition sites of a basic functional unit of a bacterial cell. (c) 1996 John Wiley & Sons, Inc.     

Methane as a carbon substrate for the production of microbial cells

The cultivation of aerobic, methane-utilizing, microbial cells by submerged culture techniques, in an entirely mineral salts medium, with a view to their use as an edible protein source is discussed. Particular emphasis is placed on the potentially explosive nature of gaseous mixtures containing methane and oxygen. The experiments described investigate if fully safe operation at all times, by oxygen concentration control, is possible in agitated and sparged batch fermentors. Appreciable wastage of methane is prevented by gaseous-phase recirculation. It is concluded that fully safe operation is possible, cultures being able to grow exponentially without substrate limitation by the gaseous-phase nutrients.     

Solid substrate fermentation of Monascus purpureus: growth, carbon balance, and consistency analysis

Solid substrate fermentation (SSF) of Monascus purpureus on rice is a promising new technology for obtaining natural pigments. However, before attempts can be made at maximizing pigment yield, all significant macroscopic compounds should be assayed. Here, Monascus purpureus has been grown on rice in batch mode, and the evolution of the main components, biomass, residual rice, O(2), CO(2), ethanol, acetic acid, and pigments, have been followed. This set of data, never previously studied for Monascus SSF, allowed both the performance of a macroscopic elemental balance, which accounted for 83-94% of the initial substrate carbon, and a check of data consistency. Standard consistency analysis showed a significant underestimation of the nitrogen fraction of biomass, but it was unable to discriminate the errors in the carbon balance as a result of the simultaneous presence of two gross errors in the system. A simple stoichiometric model in tandem with consistency analysis explained unaccounted carbon as an underestimation of CO(2) and ethanol. Using the simplified method to estimate ethanol, the macroscopic balance accounted for 87-99% of the initial carbon.     

Correlation between cell composition and carbon conversion efficiency in microbial growth: a theoretical study

Summary As the macromolecular composition of microorganisms varies during their life cycle it was asked whether, and to what extent such changes exert any influence on substrate consumption, i.e. growth yield and carbon conversion efficiency, respectively. This question was dealt with in a theoretical study by use of the Y _APT ^max -concept. The growth substrates considered were methanol, acetate and glucose; the latter was assumed to be assimilated via both the glycolytic and the oxidative hexosemonophosphate pathway. Five fictitious biomasses were used which were altered in their proportion of polysaccharides, proteins, lipids, RNA and DNA. As a result, only small variations in the individual biomass formulae were obtained. On the basis of the energy balances for the syntheses of all cell constituents it was found that variations in the macromolecular composition of microbial biomass have only a slight effect on carbon conversion efficiency, amounting to maximally 3%. From the material balances it could be calculated that the upper, solely metabolism-determined limit of carbon conversion efficiency is 85% for substrates assimilated glycolytically via phosphoglycerate; for gluconeogenetic substrates, the upper limit was 75%. These limits are essentially determined by carbon loss on the way to amino acid syntheses.Abbreviations Ac acetate - CCE carbon conversion efficiency (%) - EMP Embden-Meyerhof-Parnas (glycolytic) pathway - Gluc glucose - HMP oxidative hexosemonophosphate pathway - m _e maintenance coefficient (mmol g^-1 h^-1) - MeOH methanol - PGA phosphoglycerate, Y, growth yield (g dry weight per g substrate) - Y _ATP growth yield (g dry weight per mole ATP) - specific growth rate (h^-1)     

Linear growth in microbial cultures limited by accumulated substrate

Summary The linear growth phase in cultures limited by intracellular (conservative) substrate is represented by a flat exponential curve. Within the range of experimental errors, the presented model fits well the data from both batch and continuous cultures ofEscherichia coli, whose growth is limited in that way.List of symbols D dilution rate, h^–1 - K_S saturation constant, g.L^–1 - S concentration of the limiting substrate, g.L^–1 - S_i concentration of the limiting substrate accumulated in the cells, g.g^–1 - S_o initial concentration of the limiting substrate, g.L^–1 - t time of cultivation, h - t₁ time of exhaustion of the limiting substrate from medium, h - t_o beginning of exponential phase, h - X biomass concentration, g.L^–1 - X₁ biomass concentration at the time of exhaustion of the limiting substrate from the medium, g.L^–1 - X_o biomass concn. at the beginning of exponential phase, g.L^–1 - biomass concn. at steady-state, g.L^–1 - Y growth yield coefficient (biomass/substrate) - specific growth rate, h^–1 - _m maximum specific growth rate, h^–1     

Calculation of microbial growth efficiency from15N immobilization

Microbial growth rate was estimated by multiplying¹⁵N immobilization by an estimated microbial C:N ratio. This growth rate, in combination with measurements of respiration, was used to calculate growth efficiency. Growth rates and efficiencies were calculated for grassland and cultivated soils of three textures. Calculated efficiencies (Y_c), assuming a microbial C: N ratio of 7, ranged from 32 to 54. Cultivated soils tended to have higher Y_c values than did grassland soils. This calculation depends on several hard-to-verify assumptions, but yields numbers that should be of great interest in comparative studies.     

Simple absolute quantification method correcting for quantitative PCR efficiency variations for microbial community samples

Real-time quantitative PCR (qPCR) is a widely used technique in microbial community analysis, allowing the quantification of the number of target genes in a community sample. Currently, the standard-curve (SC) method of absolute quantification is widely employed for these kinds of analysis. However, the SC method assumes that the amplification efficiency (E) is the same for both the standard and the sample target template. We analyzed 19 bacterial strains and nine environmental samples in qPCR assays, targeting the nifH and 16S rRNA genes. The E values of the qPCRs differed significantly, depending on the template. This has major implications for the quantification. If the sample and standard differ in their E values, quantification errors of up to orders of magnitude are possible. To address this problem, we propose and test the one-point calibration (OPC) method for absolute quantification. The OPC method corrects for differences in E and was derived from the ΔΔC(T) method with correction for E, which is commonly used for relative quantification in gene expression studies. The SC and OPC methods were compared by quantifying artificial template mixtures from Geobacter sulfurreducens (DSM 12127) and Nostoc commune (Culture Collection of Algae and Protozoa [CCAP] 1453/33), which differ in their E values. While the SC method deviated from the expected nifH gene copy number by 3- to 5-fold, the OPC method quantified the template mixtures with high accuracy. Moreover, analyzing environmental samples, we show that even small differences in E between the standard and the sample can cause significant differences between the copy numbers calculated by the SC and the OPC methods.     

Estimation of available efficiency of microbial growth on methanol and ethanol

The balances of reductivity and high-energy bonds (HEB) during microbial growth on glucose (a standard substrate), methanol, and ethanol are reported. Also, numerical values for the quantities of HEB formation in the respiratory metabolism, HEB consumption in the constructive metabolism, as well as in a number of the other intracellular processes are evaluated. Estimations of maximum cell yields by mass and energy are made during growth on methanol and ethanol with regard to peculiar features of different microbe metabolism.     

Preparation and testing of an autolysate of fish viscera as growth substrate for bacteria

The aqueous soluble phase of acidified and autolyzed fish viscera was used as the nitrogen source in a growth medium for bacteria. The bacteria tested grew faster and produced higher yields of cell mass on this growth medium than on corresponding media with standard tryptone preparations as the nitrogen source.     

An improved method for disruption of microbial cells with pressurized carbon dioxide.

Disruption of microbial cells by pressurized carbon dioxide at both subcritical and supercritical temperatures has been previously investigated. This method differs in principle from other disruption techniques and was found to have potential applications for rupture of a variety of microorganisms. However, it is not as effective for some of the microbial cells, including yeast, of which the cell walls are extremely robust and rigid. This work suggests an alternative operation to improve the disruption rates of cells by repeatedly releasing the applied fluid pressure within the cells in the midst of a disruption process. The improvement is substantial at all the experimental conditions studied.     

New method for the characterization of the microbial growth in carrageenan gel

A method for the analysis of distributed growth of E. coli in k-carrageenan gel is described. The method uses optical and electron microscopy to determine morphometric data of cell microcolonies in the gel, such as average microcolony volume, distance of microcolonies to gel surface and cell density in the microcolonies. Logarithmic equations describing the distribution of authentic values of volume occupied by cells in gels at different times of incubation were determined. With these equations it is possible to predict the quantitative distribution of cells in the gel and to define some parameters. These parameters can characterize the growth behaviour of the microbial strains in any particular culture condition and can be useful in the future search to improve the industrial applications of immobilized cells.     

Preparation and testing of an autolysate of fish viscera as growth substrate for bacteria.

The aqueous soluble phase of acidified and autolyzed fish viscera was used as the nitrogen source in a growth medium for bacteria. The bacteria tested grew faster and produced higher yields of cell mass on this growth medium than on corresponding media with standard tryptone preparations as the nitrogen source.     

An optimal strategy to model microbial growth in a multiple substrate environment

A comprehensive model is developed based on an optimal strategy describing varied microbial growth phenomenon involving sequential and simultaneous utilization of substrate. The model mimics the complex regulatory process of a cell which results in diverse growth process with the help of simple multi-variable constrained optimization, which aims at maximizing the specific cell growth. The metabolic processes of a cell are represented by simple flux balance equations. The different growth phenomenon exhibited by a microorganism are attributed to different levels of control present inside the cell. Provision is made in the model for these controls, in the form of constraints in the optimization formulation. The model prediction matches well with the experimental data of simultaneous growth of E. coli K12 on a mixture of glucose and organic acids like lactate, pyruvate, and acetate. Moreover, the model predictions are well in agreement with earlier published experimental data for the growth of E. coli K12 on other organic acids like fumarate, alpha-ketoglutarate, and succinate. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 635-644, 1997.     

Biochemical limits to microbial growth yields: An analysis of mixed substrate utilization

A theoretical analysis has been made of carbon conversion efficiency during heterotrophic microbial growth. The expectation was that the maximal growth yield occurs when all the substrate is assimilated and the net flow of carbon through dissimilation is zero. This, however, is not identical to a 100% carbon conversion, since assimilatory pathways lead to a net production of CO(2). It can be shown that the amount of CO(2) produced by way of assimilatory processes is dependent upon the nature of the carbon source, but independent of its degree of reduction and varies between 12 and 29% of the substrate carbon. An analysis of published yield data reveals that nearly complete assimilation can occur during growth on substrates with a high energy content. This holds for substrates with a heat of combustion of ca. 550 kJ/mol C, or a degree of reduction higher than 5 (e.g. ethane, ethanol, and methanol). Complete assimilation can also be achieved on substrates with a lower energy content, provided that an auxiliary energy source is present that cannot be used as a carbon source. This is evident from the cell yields reported for Candida utilis grown on glucose plus formate and for Thiobacillus versutus grown on acetate plus thiosulfate. This evaluation of the carbon conversion efficiency during assimilation also made it possible to compare the energy content of the auxiliary energy substrate added with the quantity of the carbon source it had replaced. It will be shown that utilization of the auxiliary energy source may lead to extreme changes in the efficiency of dissimilatory processes.     

Kinetic model for microbial uptake of insoluble solid-state substrate

A kinetic model for anaerobic digestion of insoluble solid-state substrates was developed. Rate equations for cell growth and substrate consumption were derived based on the assumption that the microorganisms assimilate the substrate mainly at the point of contact where they grow. The model emphasizes effects of substrate particle size, organic loading, and cell concentration on the rates of cell growth and substrate utilization. Batch digestion of a stearic acid emulsion with a mean particle size of 2.0 mum and a biological sludge was conducted at 30 and 37 degrees C to verify the proposed model. Agreement between the experimental and calculated results indicated the validity of the model for describing the microbial degradation of insoluble solid-state substrates. Further examinationof the model revealed that with low cell substrate affinity or at low cell concentration, it coincided with a Michaelis-Menten type kinetics in which the effect of particle size was taken into consideration.     

A rapid electrical method to detect microbial growth automatically

Summary A simple electrical method has been developed which allows the direct enumeration of microorganisms in various substrates without dilution. When this method was compared with a plate count method to enumerate E. coli a correlation coefficient of –0.988 was achieved.