Theoretical calculations on the influence of the inorganic nitrogen source on parameters for aerobic growth of microorganisms

Interacting Bioenergetic and Stoichiometric Controls on Microbial Growth

Microorganisms function as open systems that exchange matter and energy with their surrounding environment. Even though mass (carbon and nutrients) and energy exchanges are tightly linked, there is a lack of integrated approaches that combine these fluxes and explore how they jointly impact microbial growth. Such links are essential to predicting how the growth rate of microorganisms varies, especially when the stoichiometry of carbon- (C) and nitrogen (N)-uptake is not balanced. Here, we present a theoretical framework to quantify the microbial growth rate for conditions of C-, N-, and energy-(co-) limitations. We use this framework to show how the C:N ratio and the degree of reduction of the organic matter (OM), which is also the electron donor, availability of electron acceptors (EAs), and the different sources of N together control the microbial growth rate under C, nutrient, and energy-limited conditions. We show that the growth rate peaks at intermediate values of the degree of reduction of OM under oxic and C-limited conditions, but not under N-limited conditions. Under oxic conditions and with N-poor OM, the growth rate is higher when the inorganic N (N_Inorg)-source is ammonium compared to nitrate due to the additional energetic cost involved in nitrate reduction. Under anoxic conditions, when nitrate is both EA and N_Inorg-source, the growth rates of denitrifiers and microbes performing the dissimilatory nitrate reduction to ammonia (DNRA) are determined by both OM degree of reduction and nitrate-availability. Consistent with the data, DNRA is predicted to foster growth under extreme nitrate-limitation and with a reduced OM, whereas denitrifiers are favored as nitrate becomes more available and in the presence of oxidized OM. Furthermore, the growth rate is reduced when catabolism is coupled to low energy yielding EAs (e.g., sulfate) because of the low carbon use efficiency (CUE). However, the low CUE also decreases the nutrient demand for growth, thereby reducing N-limitation. We conclude that bioenergetics provides a useful conceptual framework for explaining growth rates under different metabolisms and multiple resource-limitations.

Elemental composition, heat capacity from 2 to 300 K and derived thermodynamic functions of 5 microorganism species

Detailed elemental analysis and low-temperature calorimetric measurement results are reported for the first time for Gram-positive bacteria, Gram-negative bacteria and mold fungi. Microorganism unit carbon formulas (empirical formulas) were calculated. Standard molar heat capacity and entropy were found to be C⁰_p,m = 38.200 J/C-mol K and S⁰_m = 31.234 J/C-mol K for Escherichia coli, C⁰_p,m = 54.188 J/C-mol K and S⁰_m = 47.141 J/C-mol K for Gluconobacter oxydans, C⁰_p,m = 31.475 J/C-mol K and S⁰_m = 33.222 J/C-mol K for Pseudomonas fluorescens, C⁰_p,m = 38.118 J/C-mol K and S⁰_m = 37.042 J/C-mol K for Streptococcus thermophilus, and C⁰_p,m = 35.470 J/C-mol K and S⁰_m = 34.393 J/C-mol K for Penicillium chrysogenum. Microorganism heat capacities below 10 K were best described by an expanded Debye-T³ law. Based on the collected data, empirical formulas and entropies per C-mole of the analyzed organisms were determined. The measured heat capacities were compared to predictions of Kopp's rule and Hurst-Harrison equation, both of which were found to be able to give reasonably accurate predictions. The determined entropies were compared to predictions of Battley and Roels models. The Battley model was found to be more accurate. The measured microorganism entropies lay between the values of their principal macromolecular constituents: DNA, and globular and fibrillar proteins. This indicates that self-assembly of the macromolecular components into cellular structures does not lead to decrease in thermal entropy.

The Dis1/Stu2/XMAP215 Family Gene FgStu2 Is Involved in Vegetative Growth, Morphology, Sexual and Asexual Reproduction, Pathogenicity and DON Production of Fusarium graminearum

The conserved Dis1/Stu2/XMAP215 microtubule association proteins (MAPs) family plays an important role in microtubule dynamics, nucleation, and kinetochore-microtubule attachments. However, function of Dis1/Stu2/XMAP215 homolog in plant pathogenic fungi has not been determined. Here, we identified and investigated the Dis1/Stu2/XMAP215 homolog (FGSG_10528) in Fusarium graminearum (FgStu2p). Co-localization experiment and co-immunoprecipitation (Co-IP) assay demonstrated that FgStu2p is a microtubule associated protein. Besides, FgStu2 could also interact with Fgγ-tubulin and presumed FgNdc80, which suggested that the FgStu2 gene might associate with microtubule nucleation and kinetochore-microtubule attachments like Dis1/Stu2/XMAP215 homologs in other species. Moreover, the FgStu2 promoter replacement mutants (FgStu2-Si mutants) produced twisted hyphae and decreased growth rate. Microscope examination further showed that the microtubule polymerization was reduced in FgStu2-Si mutants, which could account for the aberrant morphology. Although the microtubule polymerization was affected in FgStu2-Si mutants, the FgStu2-Si mutants didn't show highly increased sensitivity to anti-microtubule fungicide carbendazim (methyl benzimidazol-2-ylcarbamate [MBC]). In addition, the FgStu2-Si mutants exhibited curved conidia, decreased number of conidial production, blocked ability of perithecia production, decreased pathogenicity and deoxynivalenol (DON) production. Taken together, these results indicate that the FgStu2 gene plays a crucial role in vegetative growth, morphology, sexual reproduction, asexual reproduction, virulence and deoxynivalenol (DON) production of F. graminearum, which brings new insights into the functions of Dis1/Stu2/XMAP215 homolog in plant pathogenic fungi.

Thermodynamic properties of microorganisms: determination and analysis of enthalpy, entropy, and Gibbs free energy of biomass, cells and colonies of 32 microorganism species

Thermodynamic analysis is an important part of chemical engineering. However, its application in biotechnology has been hampered by lack of data on thermodynamic properties of microorganism biomass. In this paper, a review was made of methods for estimation of thermodynamic properties of biomass, including standard enthalpy of combustion h_C⁰, enthalpy of formation h_f⁰, entropy s⁰, and Gibbs free energy of formation g_f⁰. These parameters were calculated on molar and mass specific basis for 32 microorganism species, including 14 bacteria, 7 yeast and 11 algae species. It was found that h_f⁰, s⁰, g_f⁰ are, respectively, similar for all the analyzed species, due to the fact that all living organisms have a common ancestor and thus a similar chemical composition. Furthermore, all the analyzed microorganisms have negative h_f⁰, originating from partial oxidation of all other elements by oxygen and nitrogen. A brief review was given of microorganism endogenous and growth metabolic rates. Finally, based on the determined thermodynamic properties, entropy of individual E. coli and Pseudomonas cells were determined and entropy of a Pseudomonas colony during its lifespan was calculated and analyzed. Three periods can be distinguished in the existence of a microorganism colony: (a) accumulation period when cell number, mass and entropy increase, (b) steady state period when they are approximately constant, and (c) decumulation period when they decrease.

Energy metabolism and ATP balance in animal cell cultivation using a stoichiometrically based reaction network

A metabolic reaction network is developed for the estimation of the stoichiometric production of adenosine triphosphate (ATP) in animal cell culture. By using the material balance data from fed-batch and batch cultures of hybridoma cells, the stoichiometric ATP productions are determined with estimated effective P/O ratios of 2 for NADH and 1.2 for FADH(2). A significant percentage of the ATP requirement (16-41%) in hybridoma cells is generated directly from free energy release without the participation of oxygen. The oxidative phosphorylation of NADH accounts for about 60% of the total ATP production in the fed-batch cultures and about 47% in the batch culture. The oxidative phosphorylation of FADH(2) accounts for less then 20% of the total ATP production in all cases.A fractional model is devised to analyze the contribution of each nutrient to the ATP production. Results show that a majority of the ATP is produced from glucose metabolism (60-76%). Less than 30% of the ATP is derived from glutamine, and less than 11% is derived from other essential amino acids. The analysis also shows that the glycolytic pathway generates more ATP in the batch (41%) than in the fed-batch (<27%) cultures. The TCA cycle provides 51-68% of the total ATP production. The calculated stoichiometric oxygen consumption differs among the batch and fed-batch cultures, depending on the glucose concentration. This result suggests that the relationship between the oxygen uptake rate (OUR) and cell growth may change with the culture conditions. However, the calculated respiratory quotient (RQ) is relatively constant in all cases.A linear relationship is obtained between the specific ATP production rate and the specific cell growth rate. The maximum ATP yield and the maintenance ATP requirement are determined based on this linear relationship. The biosynthetic ATP demand estimated from the dry cell weight and cell composition is significantly lower than that calculated from the maximum ATP yield, indicating that the non-growth-associated ATP demand may contain other factors than what is considered in the estimation of the biosynthetic ATP demand.

Determination of the carbon-bound electron composition of microbial cells and metabolites by dichromate oxidation

The applicability of the silver sulfate-acid dichromate oxidation (chemical oxygen demand) method for determining the carbon-bound electron compositions of microbial cells, substrates, and metabolic by-products was evaluated. An approach for approximating the carbon-bound electron composition of microbial cells from CHN data is also presented. Ten aliphatic and aromatic carboxylic acids, 17 amino acids, and 8 sugars generally gave 96 to 101% (mainly >/=98%) recovery with 0.0625 N dichromate (digestion mixture of 10 ml of sample-10 ml of 0.25 N dichromate-20 ml of Ag(2)SO(4)-amended concentrated H(2)SO(4)). Recoveries of nicotinic acid (5%) and methionine (65%) were incomplete; arginine (125%) and two purine and three pyrimidine bases (105 to 120%) were overestimated. The validity of 0.0625 N dichromate for determining the carbon-bound electron composition of bacterial cells was supported by theoretical analysis of the carbon-bound electron composition of hypothetical bacterial cell material (defined monomer composition) and by the compatibility of elemental and dichromate oxidation-derived carbon-bound electron compositions of typical bacterial cells.

Growth, death, and oxygen uptake kinetics of Pichia stipitis on xylose

Pichia stipitis NRRL Y-7124 has potential application in the fermentation of xylose-rich waste streams, produced by wood hydrolysis. Kinetic models of cell growth, death, and oxygen uptake were investigated in batch and oxygen-limited continuous cultures fed a rich synthetic medium. Variables included rates of dilution (D) and oxygen transfer (K(1)a) and concentrations of xylose (X), ethanol (E), and dissolved oxygen (C(ox)). Sustained cell growth required the presence of oxygen. Given excess xylose, specific growth rate (micro) was a Monod function of C(ox). Specific oxygen uptake rate was proportional to mu by a yield coefficient relating biomass production to oxygen consumption; but oxygen uptake for maintenance was negligible. Thus steady-state C(OX) depended only on D, while steady-state biomass concentration was controlled by both D and K(1)a. Given excess oxygen, cells grew subject to Monod limitation by xylose, which became inhibitory above 40 g/L. Ethanol inhibition was consistent with Luong's model, and 64. 3 g/L was the maximum ethanol concentration allowing growth. Actively growing cells died at a rate that was 20% of micro. The dying portion increased with E and X.

The energetics of bacterial growth: a reassessment

The growth yield of microbial cultures can be used to estimate the efficiency of energy generation during a fermentation or respiration. In the past, the assessment of this efficiency in organisms carrying out a respiration has been the subject of many heated debates. This has partly been caused by the complexity of microbial respiratory chains. Strains of Escherichia coli specifically modified in their respiratory chain have been used recently to re-evaluate the energetic efficiency of the bacterial respiration using chemostat cultures. The different strains indeed show different growth efficiencies. The physiological significance of energetically less-efficient branches of the respiratory chain is discussed.

Energetic efficiency of Escherichia coli: effects of mutations in components of the aerobic respiratory chain

The aerobic respiratory chain of Escherichia coli can function with either of two different membrane-bound NADH dehydrogenases (NDH-1 and NDH-2) and with either of two ubiquinol oxidases (bd-type and bo-type). The amounts of each of these enzymes present in the E. coli membrane depend on growth conditions in general and particularly on the dissolved oxygen concentration. Previous in vitro studies have established that NDH-1 and NDH-2 differ in the extent to which they are coupled to the generation of an energy-conserving proton motive force. The same is true for the two ubiquinol oxidases. Hence, the bioenergetic efficiency of the aerobic respiratory chain must depend on the electron flux through each of the specific enzyme components which are being utilized. In this work, the specific rates of oxygen consumption for cells growing under glucose-limited conditions are reported for a series of isogenic strains in which one or more respiratory components are genetically eliminated. The results are compatible with the proton translocation values of the various components reported from in vitro measurements. The data show that (i) the bd-type oxidase is less efficient than is the bo-type oxidase, but the former is still a coupling site in the respiratory chain; and (ii) under the conditions employed, the wild-type strain uses both the NDH-1 and NDH-2 NADH dehydrogenases to a significant degree, but most of the electron flux is directed through the bo-type oxidase.

The effect of the dissolved oxygen concentration and anabolic limitations on the behaviour of Rhizobium ORS571 in chemostat cultures

Chemostat cultures of Rhizobium ORS571 limited by the supply of oxygen or an anabolic substrate contained poly-beta-hydroxybutyrate (PHB). Low amounts of PHB (about 10%) were present in ammonia- or nitrate-limited cultures; higher amounts were found in Mg++-limited cultures (about 20%) and in oxygen-limited nitrogen-fixing cultures (37%). A method is described to calculate YATP values (g PHB-free biomass . mol-1 ATP) from the Ysucc values (g dry wt . mol-1 succinate) measured. Ysucc and YATP values in cultures limited by the supply of an anabolic substrate and in the oxygen-limited ammonia-assimilating culture were much lower than the values found in the PHB-free succinate-limited cultures. This shows that uncoupling of growth and energy production occurred. Therefore, H2/N2 ratio (mol hydrogen formed per mol nitrogen fixed) in nitrogen-fixing cultures could not be calculated from the comparison of the YATP value found in the nitrogen-fixing culture and the value found in the corresponding ammonia-assimilating culture. Although the optimal dissolved oxygen concentration (d.o.c.) for nitrogen-fixing cultures of Rhizobium ORS571 is 5 or 10 microM, nitrogen-fixing cultures could be obtained up to a d.o.c. of 40 microM. Not only nitrogenase but also hydrogenase was active at this d.o.c. However, accumulation of PHB (10%) may indicate that cultures grown at unfavourable oxygen concentrations (15-40 microM O2) were N-limited rather than energy-limited, which may be the result of partial inactivation or repression of nitrogenase at a higher d.o.c.

The NADP(H) redox couple in yeast metabolism

Theoretical calculations of the NADPH requirement for biomass formation indicate that in yeast this parameter is strongly dependent on the carbon and nitrogen sources used for growth. Enzyme surveys of NADPH-generating metabolic pathways and radiorespirometric studies demonstrate that in yeast the HMP pathway is the major source of NADPH. Furthermore, radiorespirometric data suggest that in yeasts the HMP pathway activities are close to the theoretical minimum. It may be concluded that the mitochondrial NADPH oxidation, which in yeasts may yield ATP, is quantitatively not an important process. The inability of C. utilis to utilize the NADH produced in formate oxidation as an extra source of NADPH strongly suggests that transhydrogenase activity is absent. Furthermore, the absence of xylose utilization under anaerobic conditions in most facultatively fermentative yeasts indicates that also in these organisms transhydrogenase activity is absent. This conclusion is supported by the observation that anaerobic xylose utilization is observed only in those yeasts which possess a high activity of an NADH-linked xylose reductase. Hence in these organisms the redox-neutral conversion of xylose to ethanol is possible, since the second step in xylose metabolism is mediated by an NAD+-linked xylitol dehydrogenase.

Hydrogen oxidation and nitrogen fixation in rhizobia, with special attention focused on strain ORS 571

In this survey we describe the influence of hydrogen oxidation on the physiology of Rhizobium ORS 571. The presence of hydrogen is required for the synthesis of hydrogenase. Carbon substrates do not repress the synthesis of hydrogenase. The respiratory system contains cytrochromes of the b- and c-type. Cytochrome alpha 600 is present after growth at high oxygen tensions. The nature of the terminal oxidases functioning at low oxygen tensions has not been established yet----H+/O values with endogenous substrates are between 6 and 7. The results show the presence of two phosphorylation sites: site 1 (ATP/2e = 1.0) and site 2(ATP/2e = 1.33). By measuring molar growth yields it has been demonstrated that carbon-limited, nitrogen-fixing cultures obtain additional ATP from hydrogen oxidation, and that site 2 of oxidative phosphorylation is passed during hydrogen oxidation. A method is described to calculate ATP/N2 values (the total amount of ATP used by nitrogenase during the fixation of 1 mol N2) and H2/N2 ratios (mol hydrogen formed per mol N2 fixed) in aerobic organisms. For Rhizobium ORS 571 the ATP/N2 value is about 40 and the H2/N2 ratio is between 5 and 7.5. Cells obtained from oxygen-limited nitrogen-fixing cultures contain 30-40% poly-beta-hydroxybutyrate, which explains the high molar growth yields found. Hydrogen has not been detected in the effluent gas of these cultures, which may point to reoxidation of the hydrogen formed at nitrogen fixation. Calculations show that the effect of hydrogen reoxidation on the efficiency of nitrogen fixation (g N fixed X mol-1 substrate converted) is not very large and that the actual H2/N2 ratio is of much more importance. After addition of hydrogen to succinate-limited, ammonia-assimilating cultures, an initial increase of the Ysuccinate value (g dry wt X mol-1 succinate) is followed by a gradual decrease. This is accompanied by a large decrease of the YO2 value, and an increased permeability of the cytoplasmic membrane to protons. The results may be explained by a transition of the culture from an energy-limited state to a carbon-limited state.

Thermodynamics of growth. Non-equilibrium thermodynamics of bacterial growth. The phenomenological and the mosaic approach

Microbial growth is analyzed in terms of mosaic and phenomenological non-equilibrium thermodynamics. It turns out that already existing parameters devised to measure bacterial growth, such as YATP, mu, and Q substrate, have as thermodynamic equivalents flow ratio, output flow and input flow. With this characterisation it becomes possible to apply much of the already existing knowledge of phenomenological non-equilibrium thermodynamics to bacterial growth. One of the conclusions is that the frequent observation that YATP is only 50% of its theoretical maximum does not mean that the microbe corresponds to a thermodynamic system that has been optimized for maximal output power, as has been suggested. Rather, at least in some cases, it corresponds to a system that has been optimized towards maximum growth rate. When the degree of reduction of the (single) carbon source is significantly smaller than that of the biomass produced, the efficiency of biomass synthesis has been kept as high (i.e., about 24%) as is consistent with maximization of the growth rate at optimal efficiency. Mosaic thermodynamics allows an analysis of processes which in microbial metabolism may be responsible for any particular growth behaviour. Equations are derived that predict the effect of uncoupling through leaks, futile cycling, or 'slip' on microbial growth. It turns out that uncoupling is expected to affect both the growth rate-independent and the growth rate-dependent 'maintenance coefficient'. The effect on the latter is different when catabolic substrate limits growth than when anabolic substrate limits growth. In the latter case, the growth rate-dependent maintenance coefficient is negative. It is concluded that mosaic non-equilibrium thermodynamics will be a powerful theoretical tool especially in future experimental analyses of the metabolic basis for microbial growth characteristics and growth regulation.

Application of balancing methods in modeling the penicillin fermentation

This paper shows the application of elementary balancing methods in combination with simple kinetic equations in the formulation of an unstructured model for the fed-batch process for the production of penicillin. The rate of substrate uptake is modeled with a Monod-type relationship. The specific penicillin production rate is assumed to be a function of growth rate. Hydrolysis of penicillin to penicilloic acid is assumed to be first order in penicillin. In simulations with the present model it is shown that the model, although assuming a strict relationship between specific growth rate and penicillin productivity, allows for the commonly observed lag phase in the penicillin concentration curve and the apparent separation between growth and production phase (idiophase-trophophase concept). Furthermore it is shown that the feed rate profile during fermentation is of vital importance in the realization of a high production rate throughout the duration of the fermentation. It is emphasized that the method of modeling presented may also prove rewarding for an analysis of fermentation processes other than the penicillin fermentation.