In search of a thermodynamic description of biomass yields for the chemotrophic growth of microorganisms

Correlations for the prediction of biomass yields are valuable, and many proposals based on a number of parameters (Y(ATP), Y(Ave), eta(o), Y(c), Gibbs energy efficiencies, and enthalpy efficiencies) have been published. This article critically examines the properties of the proposed parameters with respect to the general applicability to chemotrophic growth systems, a clear relation to the Second Law of Thermodynamics, the absence of intrinsic problems, and a requirement of only black box information. It appears that none of the proposed parameters satisfies all these requirements. Particularly, the various energetic efficiency parameters suffer from major intrinsic problems. However, this article will show that the Gibbs energy dissipation per amount of produced biomass (kJ/C-mod) is a parameter which satisfies the requirements without having intrinsic problems. A simple correlation is found which provides the Gibbs energy dissipation/C-mol biomass as a function of the nature of the C-source (expressed as the carbon chain length and the degree of reduction). This dissipation appears to be nearly independent of the nature of the electron acceptor (e.g., O(2), No(3) (-), fermentation). Hence, a single correlation can describe a very wide range of microbial growth systems. In this respect, Gibbs energy dissipation is much more useful than heat production/C-mol biomass, which is strongly dependent on the electron acceptor used. Evidence is presented that even a net heat-uptake can occur in certain growth systems.The correlation of Gibbs energy dissipation thus obtained shows that dissipation/C-mol biomass increases for C-sources with smaller chain length (C(6) --> C(1)), and increases for both higher and lower degrees of reduction than 4. It appears that the dissipation/C-mol biomass can be regarded as a simple thermodynamic measure of the amount of biochemical "work" required to convert the carbon source into biomass by the proper irreversible carbon-carbon coupling and oxidation/reduction reactions. This is supported by the good correlation between the theoretical ATP requirement for biomass formation on different C-sources and the dissipation values (kJ/C-mol biomass) found. The established correlation for the Gibbs energy dissipation allows the prediction of the chemotrophic biomass yield on substrate with an error of 13% in the yield range 0.01 to 0.80 C-mol biomass/(C)-mol substrate for aerobic/anaerobic/denitrifying growth systems.     

森林生态系统发展和植物种群变化的热力学过程

随着生态学的发展,人们对自然生态系统的认识逐渐从对自然现象的记录、描述,发展为对机制的系统认识。热力学定律为人们提供了认识系统发展规律的理论基础,但在生态系统中的应用还处于起步阶段。基于前人关于生态系统可用能的研究。探讨了森林生态系统和植物种群变化的热力学过程。在生态系统水平上,把可用能耗散分为了植物耗散和环境耗散两个部分,并探讨了这两个过程之间的关系。第一次明确地提出蒸散是植物耗散的主要部分。在植物种群水平上,“可用能储存”与“可用能耗散”是决定植物竞争力的关键因子,在同一区域相同条件下,拥有更大可用能耗散能力的物种应当被优先选择。因此,群落中的优势物种应当比同层次的伴生种具有相对高的生长速度和更强的蒸腾能力。研究试图在热力学理论体系与实际生态系统的生理生态过程之间建立了纽带和桥梁,为开展森林生态系统的健康评估、深刻认识植物与环境的关系、以及评价物种竞争能力提供新的理论视野。     

Thermodynamic Analysis of Energy Transfer in Acidogenic Cultures

A global thermodynamic analysis, normally used for pure cultures, has been performed for steady‐state data sets from acidogenic mixed cultures. This analysis is a combination of two different thermodynamic approaches, based on tabulated standard Gibbs energy of formation, global stoichiometry and medium compositions. It takes into account the energy transfer efficiency, ?, together with the Gibbs free energy dissipation, ΔG_o, analysis of the different data. The objective is to describe these systems thermodynamically without any heat measurement. The results show that ? is influenced by environmental conditions, where increasing hydraulic retention time increases its value all cases. The pH effect on ? is related to metabolic shifts and osmoregulation. Within the environmental conditions analyzed, ? ranges from 0.23 for a hydraulic retention time of 20 h and pH 4, to 0.42 for a hydraulic retention time of 8 h and a pH ranging from 7–8.5. The estimated values of ΔG_o are comparable to standard Gibbs energy of dissipation reported in the literature. For the data sets analyzed, ΔG_o ranges from –1210 kJ/mol_x, corresponding to a stirring velocity of 300 rpm, pH 6 and a hydraulic retention time of 6 h, to –20744 kJ/mol_x for pH 4 and a hydraulic retention time of 20 h. For average conclusions, the combined approach based on standard Gibbs energy of formation and global stoichiometry, used in this thermodynamic analysis, allows for the estimation of Gibbs energy dissipation values from the extracellular medium compositions in acidogenic mixed cultures. Such estimated values are comparable to the standard Gibbs energy dissipation values reported in the literature. It is demonstrated that ? is affected by the environmental conditions, i.e., stirring velocity, hydraulic retention time and pH. However, a relationship that relates this parameter to environmental conditions was not found and will be the focus of further research.     

Experimental and theoretical discrepancies in growth yields of Acinetobacter calcoaceticus: a correction of published data

Acinetobacter calcoaceticus can incompletely oxidize aldose sugars to the corresponding aldonic acids. This reaction can serve as an auxiliary energy source for the organism. An increase in biomass yields is observed in acetate-limited chemostat cultures grown in the presence of, for example, xylose. However, experimental and theoretical discrepancies exist with respect to the magnitude of the yield enhancement as a result of xylose addition. We previously observed increases in cell yields that were unexpectedly high. In contrast, other data were in agreement with the theoretical predictions. In this paper, evidence is presented indicating that this discrepancy is likely to be due to errors in the methodology used for our previous investigation, in particular with respect to the determination of biomass concentrations. Correspondence to: J. P. van Dijken     

Microbial growth by a net heat up-take: a calorimetric and thermodynamic study on acetotrophic methanogenesis by Methanosarcina barkeri

To answer the intriguing question whether or not endothermic microbial growth exists, and in particular, to verify Heijnen and van Dijken's prediction (1992), acetotrophic methanogen, Methanosarcina barkeri, has been cultivated in a highly sensitive bench-scale calorimeter (an improved Bio-RC1 reaction calorimeter) in a pH auxostat fashion. A growth yield of 0.043 C-mol C-mol(-1) has been obtained and a cell density as high as 3 g L(-1) was attained. Heat uptake during growth has indeed been quantitatively measured with calorimetry, resulting in a heat yield of +145 kJ C-mol(-1). Thermodynamics of the growth of acetotrophic methanogens was analyzed in detail. The changes in Gibbs energy, enthalpy, and entropy during growth of M. barkeri were compared with some typical aerobic and anaerobic growth processes of different microorganisms on various substrates. In the growth of M. barkeri on acetate, the retarding effect of the positive enthalpy change on the driving force of growth is overcompensated by the large positive entropy change, resulting from converting one organic molecule (acetic acid) to two gaseous products, CH(4) and CO(2). Both the enthalpy and the entropy increases are due partially to the transition of these two products into the gaseous phase. The thermodynamic role of this phase transition for the growth process is analyzed. Microbial growth characterized by enthalpy increase and correspondingly by a large increase in entropy may be called enthalpy-retarded growth.     

The strategy of ecosystem development: specific dissipation as an indicator of ecosystem maturity

The ratio of entropy generation rate to entropy embodied in structures relatively to the surroundings can be considered as an indicator of the ability of a self-organizing dissipative system to maintain itself far from equilibrium by pumping out entropy. The higher the ratio (which may be called the specific entropy production or the specific dissipation of a system), the lower the capacity of a system to convert the incoming low-entropy energy into internal organization. It appears that the ratio attains special significance for interpreting the evolution of biological systems, as the maximum expression of self-organizing systems, from the sub-cellular to the ecosystem scale. This paper proposes specific dissipation, written as the ratio of biological entropy production to exergy stored in the living biomass, as a thermodynamic orientor as well as an indicator of the development state of ecological systems. After having presented a method for estimating the specific dissipation in lakes, the adequacy of the proposed indicator is discussed and also tested by comparing its response to those of some classical ecological attributes (successional sequences of species, biodiversity, individual body size, structural organization and generation time of organisms) throughout the seasonal progression of the plankton community in Lake Trasimeno (Umbria, Italy). The results support the hypothesis that the minimization of specific dissipation is a primary criterion of evolution of ecological systems and also sustain the use of specific dissipation as an indicator of ecological maturity.     

Energy dissipation as a key factor for electroporation of protoplasts

Energy dissipation (ε) during electroporation was theoretically determined to be ε=0.5CV ₀ ² for the various combinations of capacitance (C) and initial voltage (V ₀). Experiments on asparagus protoplasts established that electroporation efficiency (EE) and survival rate were directly proportional to energy dissipation during electroporation. A positive linear relationship exists between energy dissipation per unit volume and EE, whereas energy dissipation per unit volume and survival rate of protoplasts are related in a negative linear manner. At the same energy level, longer time constants were more effective at increasing EE. This suggest that energy dissipation approximating rectangular waveforms is more important than that dissipated as sharply decaying exponential waveforms. With energy as the key parameter, the optimization of electrical parameters for efficient electroporation is greatly simplified, is not machine-dependent, and generally applies to all species.     

Dissipation of Excitation Energy During Development of Photosystem 2 Photochemistry in Helianthus annuus

Etiolated sunflower cotyledons developed in complete darkness and lacking photosystem (PS) 2 were exposed to continuous 200 µmol(photon) m^–2 s^–1 white light for 1, 3, 6, 12, and 18 h prior to evaluations of excitation-energy dissipation using modulated chlorophyll a fluorescence. Photochemical potential of PS2, measured as the dark-adapted quantum efficiency of PS2 (F_V(M)/F_M), and thermal dissipation from the antenna pigment-protein complex, measured as the Stern-Volmer non-photochemical quenching coefficient (NPQ), increased to 12 h of irradiation. Following 12 h of irradiation, thermal dissipation from the antennae pigment-protein complex decreased while the efficiency of excitation capture by PS2 centers (F_V/F_M) and light-adapted quantum efficiency of PS2 (_PS2) continued to increase to 18 h of irradiation. The fraction of the oxidized state of Q_A, measured by the photochemical quenching coefficient (q_P), remained near optimal and was not changed significantly by irradiation time. Hence during the development of maximum photochemical potential of PS2 in sunflower etioplasts, which initially lacked PS2, enhanced thermal dissipation helps limit excitation energy reaching PS2 centers. Changes of the magnitude of thermal dissipation help maintain an optimum fraction of the oxidized state of Q_A during the development of PS2 photochemistry.     

Xanthophyll cycle and light stress in nature: uniform response to excess direct sunlight among higher plant species

Photosystem II (PS II) efficiency, nonphotochemical fluorescence quenching, and xanthophyll cycle composition were determined in situ in the natural environment at midday in (i) a range of differently angled sun leaves ofEuonymus kiautschovicus Loesener and (ii) in sun leaves of a wide range of different plant species, including trees, shrubs, and herbs. Very different degrees of light stress were experienced by these leaves (i) in response to different levels of incident photon flux densities at similar photosynthetic capacities amongEuonymus leaves and (ii) as a result of very different photosynthetic capacities among species at similar incident photon flux densities (that were equivalent to full sunlight). ForEuonymus as well as the interspecific comparison all data fell on one single, close relationship for changes in intrinsic PSII efficiency, nonphotochemical fluorescence quenching, or the levels of zeaxanthin + antheraxanthin in leaves, respectively, as a function of the actual level of light stress. Thus, the same conversion state of the xanthophyll cycle and the same level of energy dissipation were observed for a given degree of light stress independent of species or conditions causing the light stress. Since all increases in thermal energy dissipation were associated with increases in the levels of zeaxanthin + antheraxanthin in these leaves, there was thus no indication of any form of xanthophyll cycle-independent energy dissipation in any of the twenty-four species or varieties of plants examined in their natural environment. It is also concluded that transient diurnal changes in intrinsic PSII efficiency in nature are caused by changes in the efficiency with which excitation energy is delivered from the antennae to PSII centers, and are thus likely to be purely photoprotective. Consequently, the possibility of quantifying the allocation of absorbed light into PSII photochemistry versus energy dissipation in the antennae from changes in intrinsic PSII efficiency is explored.Abbreviations A antheraxanthin - F actual level of fluorescence - F_a, F _o minimal fluorescence in the absence, presence of thylakoid energization - F_m, F _m maximal fluorescence in the absence, presence of thylakoid energization - F_m, - F)/F _m actual PSII efficiency ( = percent of absorbed light utilized in PSII photochemistry) - F_v/F_m, F _v /F_m/ PSII efficiency of open centers in the absence, presence of thylakoid energization - NPQ nonphotochemical fluorescence quenching - F_m/F _m - 1; q_p quenching coefficient for photochemical quenching - V violaxanthin - Z zeaxanthin     

Thermodynamics of microbial growth and metabolism: an analysis of the current situation

This paper attempts to review in how far thermodynamic analysis can be used to understand and predict the performance of microorganisms with respect to growth and bio-product synthesis. In the first part, a simple thermodynamic model of microbial growth is developed which explains the relationship between the driving force for growth in terms of Gibbs energy dissipation and biomass yield. From the currently available literature, it appears that the Gibbs energy dissipation per C-mol of biomass grown, which represents the driving force for chemotrophic growth, may have been adapted by evolutionary processes to strike a reasonable compromise between metabolic rate and growth efficiency. Based on empirical correlations of the C-molar Gibbs energy dissipation, the wide variety of biomass yields observed in nature can be explained and roughly predicted. This type of analysis may be highly useful in environmental applications, where such wide variations occur. It is however not able to predict biomass yields in very complex systems such as mammalian cells nor is it able to predict or to assess bio-product or recombinant protein yields. For this purpose, a much more sophisticated treatment that accounts for individual metabolic pathways separately is required. Based on glycolysis as a test example, it is shown in the last part that simple thermodynamic analysis leads to erroneous conclusions even in well-known, simple cases. Potential sources for errors have been analyzed and can be used to identify the most important needs for future research.     

On the relationship between dissipation and the rate of spontaneous entropy production from linear irreversible thermodynamics

When systems are far from equilibrium, the temperature, the entropy and the thermodynamic entropy production are not defined and the Gibbs entropy does not provide useful information about the physical properties of a system. Furthermore, far from equilibrium, or if the dissipative field changes in time, the spontaneous entropy production of linear irreversible thermodynamics becomes irrelevant. In 2000 we introduced a definition for the dissipation function and showed that for systems of arbitrary size, arbitrarily near or far from equilibrium, the time integral of the ensemble average of this quantity can never decrease. In the low-field limit, its ensemble average becomes equal to the spontaneous entropy production of linear irreversible thermodynamics. We discuss how these quantities are related and why one should use dissipation rather than entropy or entropy production for non-equilibrium systems.     

Photosystem II efficiency and mechanisms of energy dissipation in iron-deficient,field-grown pear trees (Pyrus communis L.)

The dark-adapted Photosystem II efficiency of field-grown pear leaves, estimated by the variable to maximum chlorophyll fluorescence ratio, was little affected by moderate and severe iron deficiency. Only extremely iron-deficient leaves showed a decreased Photosystem II efficiency after dark adaptation. Midday depressions in Photosystem II efficiency were still found after short-term dark-adaptation in iron-deficient leaves, indicating that Photosystem II down-regulation occurred when the leaves were illuminated by excessive irradiance. The actual Photosystem II efficiency at steady-state photosynthesis was decreased by iron deficiency both early in the morning and at midday, due to closure of Photosystem II reaction centers and decreases of the intrinsic Photosystem II efficiency. Iron deficiency decreased the amount of light in excess of that which can be used in photosynthesis not only by decreasing absorptance, but also by increasing the relative amount of light dissipated thermally by the Photosystem II antenna. When compared to the controls, iron-deficient pear leaves dissipated thermally up to 20% more of the light absorbed by the Photosystem II, both early in the morning and at midday. At low light iron-deficient leaves with high violaxanthin cycle pigments to chlorophyll ratios had increases in pigment de-epoxidation, non-photochemical quenching and thermal dissipation. Our data suggest that pH could be the major factor controlling thermal energy dissipation, and that large (more than 10-fold) changes in the zeaxanthin plus antheraxanthin to chlorophyll molar ratio caused by iron deficiency were associated only to moderate increases in the extent of photoprotection.This revised version was published online in October 2005 with corrections to the Cover Date.     

紫茎泽兰光合特性对生长环境光强的适应

测定了不同光强下生长的紫茎泽兰叶片最大净光合速率(Pmax)、叶绿素荧光参数、光合色素含量和比叶重(SLW),探讨了其光适应能力及生理生态学机制．强光下(100％相对光强)紫茎泽兰发生了轻度光抑制,Pmax、SLW、类胡萝卜素含量和日间热耗散升高,但热耗散能力没有提高．强光下紫茎泽兰通过：1)加强日间热耗散和活性氧清除能力以及光系统Ⅱ反应中心可逆失活来耗散过剩光能;2)增大P～以增加光能利用;3)提高SLW,降低单位干重叶绿素含量以减少光能吸收3个途径避免了光合机构光破坏．弱光下(36％、12．5％和4．5％相对光强)紫茎泽兰日间热耗散很小,SLW降低,但P～较高,这有利于其增加光能吸收和利用效率．紫茎泽兰能在很大的光强范围内有效地维持光合系统正常运转,这可能是其表现较强入侵性的原因之一．     

Correlation between persistent forms of zeaxanthin-dependent energy dissipation and thylakoid protein phosphorylation

High light stress induced not only a sustained form of xanthophyll cycle-dependent energy dissipation but also sustained thylakoid protein phosphorylation. The effect of protein phosphatase inhibitors (fluoride and molybdate ions) on recovery from a 1-h exposure to a high PFD was examined in leaf discs of Parthenocissus quinquefolia (Virginia creeper). Inhibition of protein dephosphorylation induced zeaxanthin retention and sustained energy dissipation (NPQ) upon return to low PFD for recovery, but had no significant effects on pigment and Chl fluorescence characteristics under high light exposure. In addition, whole plants of Monstera deliciosa and spinach grown at low to moderate PFDs were transferred to high PFDs, and thylakoid protein phosphorylation pattern (assessed with anti-phosphothreonine antibody) as well as pigment and Chl fluorescence characteristics were examined over several days. A correlation was obtained between dark-sustained D1/D2 phosphorylation and dark-sustained zeaxanthin retention and maintenance of PS II in a state primed for energy dissipation in both species. The degree of these dark-sustained phenomena was more pronounced in M. deliciosa compared with spinach. Moreover, M. deliciosa but not spinach plants showed unusual phosphorylation patterns of Lhcb proteins with pronounced dark-sustained Lhcb phosphorylation even under low PFD growth conditions. Subsequent to the transfer to a high PFD, dark-sustained Lhcb protein phosphorylation was further enhanced. Thus, phosphorylation patterns of D1/D2 and Lhcb proteins differed from each other as well as among plant species. The results presented here suggest an association between dark-sustained D1/D2 phosphorylation and sustained retention of zeaxanthin and energy dissipation (NPQ) in light-stressed, and particularly photoinhibited, leaves. Functional implications of these observations are discussed.This revised version was published online in October 2005 with corrections to the Cover Date.     

Quantifying energy dissipation by grazing animals in harsh environments

Grazing systems in harsh environments are common throughout the world, and animal production is the mainstay of the livelihoods of many resource-poor farmers. The energy cost of the various activities involved in the process of harvesting the pasture to transform it into animal product can be estimated through an energy balance. This cost would be the difference between the metabolizable energy intake (MEI) and the energy expenditures for maintenance (MEm), temperature regulation (MEtr), and the energy for production (MEp). Each of the ME has its own net energy (NE) and its associated efficiency (K). When MEI>MEm+MEtr+MEp, the difference is attributable to the energy dissipated during grazing. The efficiency of converting the energy consumed into animal products depends on the magnitude of the dissipation. The inefficiency is associated with the energy spent in locomotion and the stress produced when there is low availability of energy in the pasture. This paper presents a method to quantify the dissipation of energy by grazing animals by considering it as a function of available energy. Such an understanding is required in order to develop management strategies to increase conversion efficiency.     

Thermal dissipation of light energy is regulated differently and by different mechanisms in lichens and higher plants

Modulated chlorophyll fluorescence was used to compare dissipation of light energy as heat in photosystem II of homoiohydric and poikilohydric photosynthetic organisms which were either hydrated or dehydrated. In hydrated chlorolichens with an alga as the photobiont, fluorescence quenching revealed a dominant mechanism of energy dissipation which was based on a protonation reaction when zeaxanthin was present. CO2 was effective as a weak protonating agent and actinic light was not necessary. In a hydrated cyanobacterial lichen, protonation by CO2 was ineffective to initiate energy dissipation. This was also true for leaves of higher plants. Thus, regulation of zeaxanthin-dependent energy dissipation by protonation was different in leaves and in chlorolichens. A mechanism of energy dissipation different from that based on zeaxanthin became apparent on dehydration of both lichens and leaves. Quenching of maximum or Fm fluorescence increased strongly during dehydration. In lichens, this was also true for so-called basal or Fo fluorescence. In contrast to zeaxanthin-dependent quenching, dehydration-induced quenching could not be inhibited by dithiothreitol. Both zeaxanthin-dependent and dehydration-induced quenching cooperated in chlorolichens to increase thermal dissipation of light energy if desiccation occurred in the light. In cyanolichens, which do not possess a zeaxanthin cycle, only desiccation-induced thermal energy dissipation was active in the dry state. Fluorescence emission spectra of chlorolichens revealed stronger desiccation-induced suppression of 685-nm fluorescence than of 720-nm fluorescence. In agreement with earlier reports of , fluorescence excitation data showed that desiccation reduced flow of excitation energy from chlorophyll b of the light harvesting complex II to emitting centres more than flow from chlorophyll a of core pigments. The data are discussed in relation to regulation and localization of thermal energy dissipation mechanisms. It is concluded that desiccation-induced fluorescence quenching of lichens results from the reversible conversion of energy-conserving to energy-dissipating photosystem II core complexes.     

基于热消散探针法的植物水分运输的研究进展

液流是分析树木耗水特性、研究树木水分传输机制的重要途径之一,热消散探针法已广泛用于树干液流变化的监测.热消散探针法是目前研究不同时空尺度上植物蒸腾耗水特性较为灵活、可靠、经济的一种方法.但由于物种特性的差异,可能造成试验过程中出现测量值与实际值相比偏低的状况.此外,相当一部分植物依赖树干储存水进行蒸腾,因此木材含水量的...     

不同生态习性热带雨林树种的幼苗对光能的利用与耗散

研究了生长于100％、25％和8％光照条件下的热带雨林先锋树种团花、演替顶极阶段的冠层树种绒毛番龙眼和中下层树种滇南风吹楠幼苗的光合能力及光能分配特性对光强的响应。与绒毛番龙眼和滇南风吹楠相比,团花具有较高的最大光合速率和最大电子传递速率,从光能分配对光强的响应曲线可以看出,随着光强的增加,3个树种幼苗叶片吸收的光能分配到光化学反应的比例减少,分配到热耗散的比例增加,光能在光化学反应与热耗散之间的分配呈显著负相关,与其它两个种相比,100％光下的团花幼苗将较多的光能分配到光化学反应中,热耗散较弱且未达到饱和。过剩光能少,没有引起长期光抑制,绒毛番龙眼和滇南风吹楠将叶片吸收的较多光能分配到热耗散中,但生长于100％光下的幼苗过剩光能仍然较多,导致幼苗遭受长期光抑制,结果表明,不同生态习性热带雨林树种幼苗更新对光环境的要求与这些幼苗对光能的利用和耗散特性密切相关。     

Transition metals as catalysts of "autoxidation" reactions

Superoxide (O2-), hydrogen peroxide (H2O2), and hydroxyl radical (.OH) produced from the "autoxidation" of biomolecules, such as ascorbate, catecholamines, or thiols, have been implicated in numerous toxicities. However, the direct reaction of dioxygen with the vast majority of biomolecules, including those listed above, is spin forbidden, a condition which imposes a severe kinetic limitation on this reaction pathway. Therefore, an alternate mechanism must be invoked to explain the "autoxidations" reactions frequently reported. Transition metals are efficient catalysts of redox reactions and their reactions with dioxygen are not spin restricted. Therefore it is likely that the "autoxidation" observed for many biomolecules is, in fact, metal catalyzed. In this paper we discuss: 1) the quantum mechanic, thermodynamic, and kinetic aspects of the reactions of dioxygen with biomolecules; 2) the involvement of transition metals in biomolecule oxidation; and 3) the biological implications of metal catalyzed oxidations. We hypothesize that true autoxidation of biomolecules does not occur in biological systems, instead the "autoxidation" of biomolecules is the result of transition metals bound by the biomolecules.