Thermodynamic efficiency of bacterial growth calculated from growth yield of Pseudomonas oxalaticus OX1 in the chemostat

Proton pumping complex I increases growth yield in Candida utilis

In living cells, growth is the result of coupling between substrate catabolism and multiple metabolic processes that take place during net biomass formation and cellular maintenance processes. A crucial parameter for growth evaluation is its yield, i.e. the efficiency of the transformation processes. The yeast Candida utilis is of peculiar interest since its mitochondria exhibit a complex I that is proposed to pump protons but also an external NADH dehydrogenase that do not pump protons. Here, we show that in C. utilis cells grown on non-fermentable media, growth yield is 30% higher as compared to that of Saccharomyces cerevisiae that do not exhibit a complex I. Moreover, ADP/O determination in C. utilis shows that electrons coming from internal NADH dehydrogenase go through proton pumping complex I, whereas electrons coming from external NADH dehydrogenases do not go through proton pumping complex I. Furthermore, we show that electron competition strictly depends on extra-mitochondrial NADH concentration, i.e. the higher the extra-mitochondrial NADH concentration, the higher the competition process with a right way for electrons coming from external NADH dehydrogenases. Such a complex regulation in C. utilis allows an increase in growth yield when cytosolic NADH is not plentiful but still favors the cytosolic NADH re-oxidation at high NADH, favoring biomass generation metabolic pathways.

Entropy production of a steady-growth cell with catalytic reactions

Cells generally convert external nutrient resources to support metabolism and growth. Understanding the thermodynamic efficiency of this conversion is essential to determine the general characteristics of cellular growth. Using a simple protocell model with catalytic reaction dynamics to synthesize the necessary enzyme and membrane components from nutrients, the entropy production per unit-cell-volume growth is calculated analytically and numerically based on the rate equation for chemical kinetics and linear nonequilibrium thermodynamics. The minimal entropy production per unit-cell growth is found to be achieved at a nonzero nutrient uptake rate rather than at a quasistatic limit as in the standard Carnot engine. This difference appears because the equilibration mediated by the enzyme exists only within cells that grow through enzyme and membrane synthesis. Optimal nutrient uptake is also confirmed by protocell models with many chemical components synthesized through a catalytic reaction network. The possible relevance of the identified optimal uptake to optimal yield for cellular growth is also discussed.

Uranium bioreduction rates across scales: biogeochemical hot moments and hot spots during a biostimulation experiment at Rifle, Colorado

We aim to understand the scale-dependent evolution of uranium bioreduction during a field experiment at a former uranium mill site near Rifle, Colorado. Acetate was injected to stimulate Fe-reducing bacteria (FeRB) and to immobilize aqueous U(VI) to insoluble U(IV). Bicarbonate was coinjected in half of the domain to mobilize sorbed U(VI). We used reactive transport modeling to integrate hydraulic and geochemical data and to quantify rates at the grid block (0.25 m) and experimental field scale (tens of meters). Although local rates varied by orders of magnitude in conjunction with biostimulation fronts propagating downstream, field-scale rates were dominated by those orders of magnitude higher rates at a few selected hot spots where Fe(III), U(VI), and FeRB were at their maxima in the vicinity of the injection wells. At particular locations, the hot moments with maximum rates negatively corresponded to their distance from the injection wells. Although bicarbonate injection enhanced local rates near the injection wells by a maximum of 39.4%, its effect at the field scale was limited to a maximum of 10.0%. We propose a rate-versus-measurement-length relationship (log R' = -0.63 log L - 2.20, with R' in μmol/mg cell protein/day and L in meters) for orders-of-magnitude estimation of uranium bioreduction rates across scales.

Thermodynamic perspectives on genetic instructions, the laws of biology and diseased states

This article examines in a broad perspective entropy and some examples of its relationship to evolution, genetic instructions and how we view diseases. Living organisms are programmed by functional genetic instructions (FGI), through cellular communication pathways, to grow and reproduce by maintaining a variety of hemistable, ordered structures (low entropy). Living organisms are far from equilibrium with their surrounding environmental systems, which tends towards increasing disorder (increasing entropy). Organisms free themselves from high entropy (high disorder) to maintain their cellular structures for a period of time sufficient to allow reproduction and the resultant offspring to reach reproductive ages. This time interval varies for different species. Bacteria, for example need no sexual parents; dividing cells are nearly identical to the previous generation of cells, and can begin a new cell cycle without delay under appropriate conditions. By contrast, human infants require years of care before they can reproduce. Living organisms maintain order in spite of their changing surrounding environment that decreases order according to the second law of thermodynamics. These events actually work together since living organisms create ordered biological structures by increasing local entropy. From a disease perspective, viruses and other disease agents interrupt the normal functioning of cells. The pressure for survival may result in mechanisms that allow organisms to resist attacks by viruses, other pathogens, destructive chemicals and physical agents such as radiation. However, when the attack is successful, the organism can be damaged until the cell, tissue, organ or entire organism is no longer functional and entropy increases.

Thermodynamic evaluation of energy metabolism in mixed substrate catabolism: modeling studies of stationary and oscillatory states

Thermodynamic and kinetic calculations were performed in a model of mixed substrate metabolism. The model simulates the catabolic breakdown of a first substrate, glucose (S(1)), in the presence of a second substrate, formate (S(2)), which acts as an additional source of free energy. The principal results obtained with different relative rates of uptake of S(2) allow to predict and interpret the following experimental observations: (1) the existence of increased ATP yields by mixed substrate utilization with a maximum ATP yield and optimum input (or molar) ratio for both substrates; (2) a greater assimilation of S(1) which may be interpreted as a decreasing fraction of energy required for assimilation; (3) a decrease in ATP yields due to increasing energy demand for transport; (4) an increased assimilation of the carbon source (S(1)) as a function of increasing inputs of the additional energy source; (5) thermodynamic efficiency (eta) defined as the ratio between the output power of ATP synthesis and the input catabolic power, increases for S(2)/S(1) ratios ranging between 0.08 and 2 while for ratios higher than two a slight decrease of eta was noticed; and (6) the observed maximum in ATP yield for optimum molar ratio of the two substrates corresponds to high eta predicting that higher biomass yields may be obtained through a variable, high, eta by chanelling fluxes through catabolic pathways with different ATP yields. During oscillatory behavior, maxima in fluxes were almost coincident with maxima in forces. Thus, the pattern of dissipation was not so advantageous as in the single substrate model under starvation conditions.

Effects of physical and geochemical heterogeneities on mineral transformation and biomass accumulation during biostimulation experiments at Rifle, Colorado

Electron donor amendment for bioremediation often results in precipitation of secondary minerals and the growth of biomass, both of which can potentially change flow paths and the efficacy of bioremediation. Quantitative estimation of precipitate and biomass distribution has remained challenging, partly due to the intrinsic heterogeneities of natural porous media and the scarcity of field data. In this work, we examine the effects of physical and geochemical heterogeneities on the spatial distributions of mineral precipitates and biomass accumulated during a biostimulation field experiment near Rifle, Colorado. Field bromide breakthrough data were used to infer a heterogeneous distribution of hydraulic conductivity through inverse transport modeling, while the solid phase Fe(III) content was determined by assuming a negative correlation with hydraulic conductivity. Validated by field aqueous geochemical data, reactive transport modeling was used to explicitly keep track of the growth of the biomass and to estimate the spatial distribution of precipitates and biomass. The results show that the maximum mineral precipitation and biomass accumulation occurs in the vicinity of the injection wells, occupying up to 5.4vol.% of the pore space, and is dominated by reaction products of sulfate reduction. Accumulation near the injection wells is not strongly affected by heterogeneities present in the system due to the ubiquitous presence of sulfate in the groundwater. However, accumulation in the down-gradient regions is dominated by the iron-reducing reaction products, whose spatial patterns are strongly controlled by both physical and geochemical heterogeneities. Heterogeneities can lead to localized large accumulation of mineral precipitates and biomass, increasing the possibility of pore clogging. Although ignoring the heterogeneities of the system can lead to adequate prediction of the average behavior of sulfate-reducing related products, it can also lead to an overestimation of the overall accumulation of iron-reducing bacteria, as well as the rate and extent of iron reduction. Surprisingly, the model predicts that the total amount of uranium being reduced in the heterogeneous 2D system was similar to that in the 1D homogeneous system, suggesting that the overall uranium bioremediation efficacy may not be significantly affected by the heterogeneities of Fe(III) content in the down-gradient regions. Rather, the characteristics close to the vicinity of the injection wells might be crucial in determining the overall efficacy of uranium bioremediation. These findings have important implications not only for uranium bioremediation at the Rifle site and for bioremediation of other redox sensitive contaminants at sites with similar characteristics, but also for the development of optimal amendment delivery strategies in other settings.

Bacterial growth yields on EDTA, NTA, and their biodegradation intermediates

Ethylenediaminetetraacetic acid (EDTA) and nitrilotriacetic acid (NTA) are widely used anthropogenic chelating agents for control of metal speciation and are ubiquitous in natural waters and wastewaters. This is the first report of systematic measurement of the growth yields of a mixed culture (BNC1-BNC2) on EDTA and its biodegradation intermediates, and of Aminobacter aminovorans (aka Chelatobacter heintzii) ATCC 29600 on NTA and its biodegradation intermediates. The yields measured for BNC1-BNC2 co-culture were 75.0 g of cell dry weight (CDW) (mole of EDTA)(-1), 68.6 g of CDW (mole of ED3 A)(-1), 51.2 g of CDW (mole of N,N'-EDDA)(-1), 34.5 g of CDW (mole of ED)(-1), 26.3 g of CDW (mole of IDA)(-1), 12.2 g of CDW (mole of glycine)(-1), and 9.7 g of CDW (mole of glyoxylate)(-1). The yields measured for A. aminovorans were 44.3 g of CDW (mole of NTA)(-1), 37.9 g of CDW (mole of IDA)(-1), 15.2 g of CDW (mole of glycine)(-1), and 10.4 g of CDW (mole of glyoxylate)(-1). The biodegradation pathways of EDTA, NTA, and several of their metabolic intermediates include reactions catalyzed by oxygenase enzymes, which may reduce energy available for cell synthesis. Comparison of measured yields with predicted yields indicates that the effect of oxygenase reaction on cell yield can be quantified experimentally as well as modeled based on thermodynamics.

Expanded thermodynamic model for microbial true yield prediction

Thermodynamic methods to predict true yield and stoichiometry of bacterial reactions have been widely used in biotechnology and environmental engineering. However, yield predictions are often inaccurate for certain simple organic compounds. This work evaluates an existing method and identifies the cause of prediction errors for compounds with low degree of reductance of carbon. For these compounds, carbon, not energy or reducing equivalents, constrains growth. Existing thermodynamically-based models do not account for the potential of carbon-limited growth. The improved method described here consists of four balances: carbon balance, nitrogen balance, electron balance, and energy balance. Two efficiency terms, K1 and K2 are defined and estimated from a priori analysis. The results show that K1 and K2 are nearly the same in value so that only one coefficient, K = 0.41 is used in the modified model. Comparisons with observed yields show that use of the new model and parameters results in significantly improved yield estimation based on inclusion of the carbon balance. The average estimation error is less than 6% for the data set presented.

The calorimetric-respirometric ratio is an on-line marker of enthalpy efficiency of yeast cells growing on a non-fermentable carbon source

Although on-line calorimetry has been widely used to detect transitions in global metabolic activity during the growth of microorganisms, the relationships between oxygen consumption flux and heat production are poorly documented. In this work, we developed a respirometric and calorimetric approach to determine the enthalpy efficiency of respiration-linked energy transformation of isolated yeast mitochondria and yeast cells under growing and resting conditions. On isolated mitochondria, the analysis of different phosphorylating and non-phosphorylating steady states clearly showed that the simultaneous measurements of heat production and oxygen consumption rates can lead to the determination of both the enthalpy efficiency and the ATP/O yield of oxidative phosphorylation. However, these determinations were made possible only when the net enthalpy change associated with the phosphorylating system was different from zero. On whole yeast cells, it is shown that the simultaneous steady state measurements of the heat production and oxygen consumption rates allow the enthalpy growth efficiency (i.e. the amount of energy conserved as biomass compared to the energy utilised for complete catabolism plus anabolism) to be assessed. This method is based on the comparison between the calorimetric-respirometric ratio (CR ratio) determined under growth versus resting conditions during a purely aerobic metabolism. Therefore, in contrast to the enthalpy balance approach, this method does not rely on the exhaustive and tedious determinations of the metabolites and elemental composition of biomass. Thus, experiments can be performed in the presence of non-limiting amounts of carbon substrate, an approach which has been successfully applied to slow growing cells such as yeast cells expressing wild-type or a mutant rat uncoupling protein-1.

Quantification of multiple-substrate controlled growth--simultaneous ammonium and glucose limitation in chemostat cultures of Klebsiella pneumoniae

In chemostat cultures of Klebsiella pneumoniae (K. aerogenes) NCTC 418 we measured the concentrations of glucose and ammonium and we varied the ratio of the (limiting) concentrations of glucose and ammonium in the feed medium. By doing this at different dilution rates we found a range where growth rate varies with either concentration in the culture when the other concentration in the culture is held constant. This proves that within this range, dual-substrate controlled growth occurs. Dual substrate-controlled growth was accompanied by yield coefficients for glucose and for ammonium that were intermediate between the yield coefficients obtained for single glucose or single ammonium limitation. We quantified the control by either substrate in terms of the flux control coefficient with respect to that substrate, where flux refers to growth rate. Dual-substrate controlled growth is reflected by the finding that both flux control coefficients exceed zero, simultaneously. In the transition of glucose to ammonium limitation, the control gradually shifts from glucose to ammonium.

Effect of concentration of substrates and products on the growth of Klebsiella pneumoniae in chemostat cultures

Non-equilibrium thermodynamics (NET) can be used to describe microbial growth. In this description, the concentrations of products contribute to the driving forces of the metabolic processes (anabolism and catabolism). Thus, in contrast to the model of bacterial growth of Monod (Recherches sur la Croissance les Cultures Bactériennes (1942) Herman et Cie, Paris), it is predicted that the growth rate of a bacterial chemostat culture is, in principle, dependent on the concentration of the catabolic product (for instance HCO3-) during catabolite limitation and on the concentration of the anabolic product (for instance biomass) during anabolite limitation. In order to test this prediction, Klebsiella pneumoniae was grown in aerobic citrate-limited, glucose-limited or ammonia-limited chemostat cultures. Ammonia-limited cultures were considered to be essentially anabolite-limited, whereas citrate limitation was used as a representative for catabolite limitation. In ammonia-limited or in glucose-limited cultures it was found that the growth rate was independent of the biomass concentration present. In the NET description this means that the 'back' reaction (i.e., in the direction from biomass to substrates) is saturated with respect to biomass. On the other hand, in citrate-limited cultures, the steady-state concentration of citrate increased with the concentration of the catabolic product HCO3-. At relatively low concentrations of HCO3-, 'thermodynamic back-pressure' of growth (i.e., increase in product concentration was compensated by an increase in substrate concentration so that the driving force for growth remained almost constant) was demonstrated as predicted by the NET model. At concentrations above 40 mM, a kinetic (allosteric) effect of HCO3- was detected. This was concluded from a reduced growth yield on citrate, and from a significant decrease in the maximal growth rate and the maximal oxygen consumption rate after relief of the citrate limitation.