The effect of photosynthesis time scales on microalgae productivity

Microalgae are often seen as a potential biofuel producer. In order to predict achievable productivities in the so called raceway culturing system, the dynamics of photosynthesis has to be taken into account. In particular, the dynamical effect of inhibition by an excess of light (photoinhibition) must be represented. We propose a model considering both photosynthesis and growth dynamics. This model involves three different time scales. We study the response of this model to fluctuating light with different frequencies by slow/fast approximations. Therefore, we identify three different regimes for which a simplified expression for the model can be derived. These expressions give a hint on productivity improvement which can be expected by stimulating photosynthesis with a faster hydrodynamics.     

A dynamic model of photosynthesis in varying light taking account of stomatal conductance, C3-cycle intermediates, photorespiration and Rubisco activation

Abstract. A dynamic model of whole leaf C₃ photosynthesis is constructed using a modified version of the Farquliar-von Caemmerer approach. The model is designed to provide a physiological basis to understand observations of assimilation in environments with varying photon flux densities, including induction phenomena. The model couples the effect of light activation and dark deactivation of enzymes, stomatal conductance responses, and variations in the pools of carbon cycle intermediates. The dynamic components are viewed on three time scales, the slowest of which (min to h) involves changes in stomatal conductance and the activation stale of Rubisco. On a time scale of seconds to a few minutes, adjustments in pools of biochemical components of the photosynthetic pathway occurs. The most rapid time scale corresponds to the equilibration time of intercelluar CO₂ concentration through gaseous diffusion and is here assumed to occur instantaneously. The model form includes a single pool for reduced intermediates including RuBP, a single pool for components of the glycolate pathway, and a third component corresponding to the activation state of Rubisco. This is coupled to a previously described model for the dynamics of stomatal conductance, giving a final model form consisting of six non-linear ordinary differential equations, of which three control conductance dynamics and three control assimilation. The coupling between these occurs through the variable p_i, the intercellular partial pressure of CO_2. Only three of the parameters for the assimilation portion of the model require dynamic data to estimate. The remaining parameters are estimated from steady-state data. The model is calibrated using previously collected data on the tropical understory plant Alocasia macrorrhiza and is shown to have qualitatively similar behaviour to that of experimental measurements using simple changes in PFD, as well as a complex sequence of such changes.     

Under slow flow conditions,daily rates of canopy photosynthesis of marine macrophytes were insensitive to model choice and flow‐rate

Water motion drives the flux of suspended and dissolved material (e.g., nutrients, gametes, and dissolved oxygen) to and from macrophyte canopies, and is one of the most important mechanisms that can regulate the growth, survival, and persistence of marine macrophytes populations. At small spatial scales (e.g., lamina or leaves and individuals), increasing flow‐rates have been demonstrated to enhance physiological processes, especially photosynthesis rates, and we expected a similar response at the canopy scale. We conducted seven experiments over 25 days using a pair of open‐air flow‐chambers under natural light, temperature, and seawater conditions. In the four marine macrophyte (Sargassum piluliferum, S. siliquastrum, S. thunbergii, and Zostera marina) canopies examined, an increase in flow‐rate did not enhance photosynthesis rates. The odds that daily gross photosynthesis rates increase with a decrease in flow‐rates was 1.77 to 1. We also examined if two non‐linear equations and one linear equation, often used to describe the relationship between photosynthesis to photosynthetic photon flux density (PPFD), biased estimates of the daily rates of photosynthesis and respiration. It was revealed that the functional form of the equation strongly influenced photosynthesis and respiration rate estimates at short time scales (i.e., minutes), however, daily rates were insensitive to the type of equation used to model the relationship between photosynthesis and PPFD. We suggest that the predominance of photosynthesis rates occurring in under‐saturating PPFD conditions (> 40 % of daylight hours) may be one of the reasons for this insensitivity.     

Photosynthesis and Ribulose 1,5-Bisphosphate Concentrations in Intact Leaves of Xanthium strumarium L

The interacting effects of the rate of ribulose 1,5-bisphosphate (RuBP) regeneration and the rate of RuBP utilization as influenced by the amount and activation of RuBP carboxylase on photosynthesis and RuBP concentrations were resolved in experiments which examined the kinetics of the response of photosynthesis and RuBP concentrations after step changes from a rate-saturating to a rate-limiting light intensity in Xanthium strumarium. Because RuBP carboxylase requires several minutes to deactivate in vivo, it was possible to observe the effect of reducing the rate of RuBP regeneration on the RuBP concentration at constant enzyme activation state by sampling very soon after reducing the light intensity. Samples taken over longer time periods showed the effect of changes in enzyme activation at constant RuBP regeneration rate on RuBP concentration and photosynthetic rate. Within 15 s of lowering the light intensity from 1500 to 600 microEinsteins per square meter per second the RuBP concentration in the leaves dropped below the enzyme active site concentration, indicating that RuBP regeneration rate was limiting for photosynthesis. After longer intervals of time, the RuBP concentration in the leaf increased as the RuBP carboxylase assumed a new steady state activation level. No change in the rate of photosynthesis was observed during the interval that RuBP concentration increased. It is concluded that the rate of photosynthesis at the lower light intensity was limited by the rate of RuBP regeneration and that parallel changes in the activation of RuBP carboxylase occurred such that concentrations of RuBP at steady state were not altered by changes in light intensity.     

A Dynamic Model for Photosynthesis

A dynamic mathematical model of the effect of radiant flux densityand CO₂ concentration on the rate of photosynthesis is proposed.An appropriate dynamic experimental method for ecological studiesof this subject is described. The methodology permits the analysisof numerous problems, including the effect of changes in CO₂concentration on photosynthesis and the effectiveness of energyconversion by a leaf of a plant in different environmental conditions. The dynamic model for photosynthesis is composed of two separateinteracting non-linear parts; one describes the dynamics ofthe complex set of light reactions, and the other describesthe dark reactions. The model explains the dynamics of leafphotosynthesis in a closed circuit flow system, and also explainsthe expressions for the equilibrium states of photosyntheticrate widely used in the literature. photosynthesis, mathematical model, carbon dioxide fixation, light reactions     

木荷种源间光合作用参数分析

基于直角双曲线修正模型估算3个不同纬度的木荷种源(开平、太平和永丰种源)光补偿点、饱和点、最大净光合速率等参数,以便为评价不同木荷种源对环境的适应能力和优良种源选择等提供科学依据。结果表明:在3个不同纬度种源中,开平种源具有最高的净光合速率、最大净光合速率和较高的表观量子效率,且其生长速率最快;太平种源光饱和点最高,但其净光合速率、表观量子效率和最大净光合速率最低,其生长速率也最低;永丰种源具有较高的净光合速率、最大净光合速率和表观量子效率,其生长速率略高于太平种源。3个不同纬度木荷种源中,南部开平种源对当地环境具有较强的适应能力和生长潜力,具有较高的推广应用价值。     

Maintenance of Motility Bias during Cyanobacterial Phototaxis

Signal transduction in bacteria is complex, ranging across scales from molecular signal detectors and effectors to cellular and community responses to stimuli. The unicellular, photosynthetic cyanobacterium Synechocystis sp. PCC6803 transduces a light stimulus into directional movement known as phototaxis. This response occurs via a biased random walk toward or away from a directional light source, which is sensed by intracellular photoreceptors and mediated by Type IV pili. It is unknown how quickly cells can respond to changes in the presence or directionality of light, or how photoreceptors affect single-cell motility behavior. In this study, we use time-lapse microscopy coupled with quantitative single-cell tracking to investigate the timescale of the cellular response to various light conditions and to characterize the contribution of the photoreceptor TaxD1 (PixJ1) to phototaxis. We first demonstrate that a community of cells exhibits both spatial and population heterogeneity in its phototactic response. We then show that individual cells respond within minutes to changes in light conditions, and that movement directionality is conferred only by the current light directionality, rather than by a long-term memory of previous conditions. Our measurements indicate that motility bias likely results from the polarization of pilus activity, yielding variable levels of movement in different directions. Experiments with a photoreceptor (taxD1) mutant suggest a supplementary role of TaxD1 in enhancing movement directionality, in addition to its previously identified role in promoting positive phototaxis. Motivated by the behavior of the taxD1 mutant, we demonstrate using a reaction-diffusion model that diffusion anisotropy is sufficient to produce the observed changes in the pattern of collective motility. Taken together, our results establish that single-cell tracking can be used to determine the factors that affect motility bias, which can then be coupled with biophysical simulations to connect changes in motility behaviors at the cellular scale with group dynamics.     

Phytoplankton blooms in a fluctuating environment: the roles of plankton response time scales and grazing

Our new view of planktonic ecosystems states that the picoplanktoncan outcompete the netplankton for nutrients, but are held toa relatively constant biomass because of the short responsetime scales of their protist grazers. The long response timeof the mesozooplankton grazing the netphytoplankton allows theselarger phytoplankton to respond to environmental fluctuationswith large changes in biomass. There is some ambiguity in theliterature, however, over the relative importance of ‘responsetime scales’ versus grazing in controlling the phytoplanktonbiomass. To address this issue, a simple model including explicitresponse time scales and grazing was formulated. The model wasused to explore the influence of these two dynamics in controllingthe response of phytoplankton to sudden changes in the carryingcapacity of the environment. It was applied to the IronEx IIdata to explore the implications of the two types of control.The model supports the hypothesis that the short response timescale of the protists limits the picoplankton biomass. However,it also shows that the zooplankton grazing rate (here representedby a clearance rate a) has a much stronger effect in determiningthe phytoplankton biomass than the response time scale.     

Seagrass Canopy Photosynthetic Response Is a Function of Canopy Density and Light Environment: A Model for Amphibolis griffithii

A three-dimensional computer model of canopies of the seagrass Amphibolis griffithii was used to investigate the consequences of variations in canopy structure and benthic light environment on leaf-level photosynthetic saturation state. The model was constructed using empirical data of plant morphometrics from a previously conducted shading experiment and validated well to in-situ data on light attenuation in canopies of different densities. Using published values of the leaf-level saturating irradiance for photosynthesis, results show that the interaction of canopy density and canopy-scale photosynthetic response is complex and non-linear, due to the combination of self-shading and the non-linearity of photosynthesis versus irradiance (P-I) curves near saturating irradiance. Therefore studies of light limitation in seagrasses should consider variation in canopy structure and density. Based on empirical work, we propose a number of possible measures for canopy scale photosynthetic response that can be plotted to yield isoclines in the space of canopy density and light environment. These plots can be used to interpret the significance of canopy changes induced as a response to decreases in the benthic light environment: in some cases canopy thinning can lead to an equivalent leaf level light environment, in others physiological changes may also be required but these alone may be inadequate for canopy survival. By providing insight to these processes the methods developed here could be a valuable management tool for seagrass conservation during dredging or other coastal developments.     

Sun‐induced chlorophyll fluorescence from high‐resolution imaging spectroscopy data to quantify spatio‐temporal patterns of photosynthetic function in crop canopies

Passive detection of sun‐induced chlorophyll fluorescence (SIF) using spectroscopy has been proposed as a proxy to quantify changes in photochemical efficiency at canopy level under natural light conditions. In this study, we explored the use of imaging spectroscopy to quantify spatio‐temporal dynamics of SIF within crop canopies and its sensitivity to track patterns of photosynthetic activity originating from the interaction between vegetation structure and incoming radiation as well as variations in plant function. SIF was retrieved using the Fraunhofer Line Depth (FLD) principle from imaging spectroscopy data acquired at different time scales a few metres above several crop canopies growing under natural illumination. We report the first maps of canopy SIF in high spatial resolution. Changes of SIF were monitored at different time scales ranging from quick variations under induced stress conditions to seasonal dynamics. Natural changes were primarily determined by varying levels and distribution of photosynthetic active radiation (PAR). However, this relationship changed throughout the day demonstrating an additional physiological component modulating spatio‐temporal patterns of SIF emission. We successfully used detailed SIF maps to track changes in the canopy's photochemical activity under field conditions, providing a new tool to evaluate complex patterns of photosynthesis within the canopy.     

A generalized,lumped-parameter model of photosynthesis,evapotranspiration and net primary production in temperate and boreal forest ecosystems

Summary PnET is a simple, lumped-parameter, monthlytime-step model of carbon and water balances of forests built on two principal relationships: 1) maximum photosynthetic rate is a function of foliar nitrogen concentration, and 2) stomatal conductance is a function of realized photosynthetic rate. Monthyly leaf area display and carbon and water balances are predicted by combining these with standard equations describing light attenuation in canopies and photosynthetic response to diminishing radiation intensity, along with effects of soil water stress and vapor pressure deficit (VPD). PnET has been validated against field data from 10 well-studied temperate and boreal forest ecosystems, supporting our central hypothesis that aggregation of climatic data to the monthly scale and biological data such as foliar characteristics to the ecosystem level does not cause a significant loss of information relative to long-term, mean ecosystem responses. Sensitivity analyses reveal a diversity of responses among systems to identical alterations in climatic drivers. This suggests that great care should be used in developing generalizations as to how forests will respond to a changing climate. Also critical is the degree to which the temperature responses of photosynthesis and respiration might acclimate to changes in mean temperatures at decadal time scales. An extreme climate change simulation (+3° C maximum temperature, –25% precipitation with no change in minimum temperature or radiation, direct effects of increased atmospheric CO₂ ignored) suggests that major increases in water stress, and reductions in biomass production (net carbon gain) and water yield would follow such a change.     

A model of dynamics of leaves and nitrogen in a plant canopy: an integration of canopy photosynthesis,leaf life span,and nitrogen use efficiency

A model of dynamics of leaves and nitrogen is developed to predict the effect of environmental and ecophysiological factors on the structure and photosynthesis of a plant canopy. In the model, leaf area in the canopy increases by the production of new leaves, which is proportional to the canopy photosynthetic rate, with canopy nitrogen increasing with uptake of nitrogen from soil. Then the optimal leaf area index (LAI; leaf area per ground area) that maximizes canopy photosynthesis is calculated. If leaf area is produced in excess, old leaves are eliminated with their nitrogen as dead leaves. Consequently, a new canopy having an optimal LAI and an optimal amount of nitrogen is obtained. Repeating these processes gives canopy growth. The model provides predictions of optimal LAI, canopy photosynthetic rates, leaf life span, nitrogen use efficiency, and also the responses of these factors to changes in nitrogen and light availability. Canopies are predicted to have a larger LAI and a higher canopy photosynthetic rate at a steady state under higher nutrient and/or light availabilities. Effects of species characteristics, such as photosynthetic nitrogen use efficiency and leaf mass per area, are also evaluated. The model predicts many empirically observed patterns for ecophysiological traits across species.     

The endogenous circadian pacemaker imparts a scale-invariant pattern of heart rate fluctuations across time scales spanning minutes to 24 hours

Heartbeat fluctuations in mammals display a robust temporal structure characterized by scale-invariant/fractal patterns. These scale-invariant patterns likely confer physiological advantage because they change with cardiovascular disease and these changes are associated with reduced survival. Models of physical systems imply that to produce scale-invariant patterns, factors influencing the system at different time scales must be coupled via a network of feedback interactions. A similar cardiac control network is hypothesized to be responsible for the scale-invariant pattern in heartbeat dynamics, although the essential network components have not been determined. Here is shown that scale-invariant cardiac control occurs across time scales from minutes to approximately 24 h, and that lesioning the mammalian circadian pacemaker (suprachiasmatic nucleus; SCN) completely abolishes the scale-invariant pattern at time scales>or approximately 4 h. At time scales相似文献   

Rapid, reversible alterations in spinach thylakoid appression upon changes in light intensity

Changes in light quantity and quality cause structural changes within the thylakoid membrane; long‐term responses have been described for so‐called ‘sun’ and ‘shade’ leaves. Many leaves, however, experience changes in irradiance on a time scale of minutes due to self‐shading and sun flecks. In this study, mature, attached spinach leaves were grown at 300 µmol photons m^?2 s^?1 then rapidly switched to a different light treatment. The treatment irradiances were 10, 800 or 1500 µmol m^?2 s^?1 for 10 min, or 10 or 20 min of self‐shading (about 10 µmol m^?2 s^?1). Image analysis of transmission electron micrographs revealed that a 10 min switch to a lower light intensity increased grana size and number per chloroplast profile by 10–20%. Returning the leaves to 300 µmol m^?2 s^?1 for 10 min reversed the phenomenon. Chlorophyll fluorescence measurements of detached, intact leaves at 77 K were suggestive of a transition from state 2 to state 1 upon shading. Diurnal ultrastructural measurements of granal size and number did not reveal a significant net change in ultrastructure over the time scale of hours. It is concluded that spinach chloroplasts can alter the degree of thylakoid appression in response to irradiance changes on a time scale of minutes. These ultrastructural responses are caused by biochemical and biophysical adjustments within the thylakoid membrane that serve to maximize photosynthesis and minimize photo‐inhibition under rapidly fluctuating light environments.     

A Mathematical Model for Leaf Photosynthesis of Mulberry

A mathematical model of leaf photosynthesis has been established. In this model, the processes of photosynthesis are divided into two parts, ie., the carboxylation process driven by light which is dependent on temperature and CO2 concentration, and the diffusion of CO2 from atmosphere to the carboxylation site. Finatly, CO2 uptake by the leaf is understood as dependent on 1), the CO2 response curve of the leaf mesophyll and 2). the CO2 partial pressure in the intercellular space in leaf. The COs response curve of the leaf photosynthesis is described mathematically in terms of carboxylation efficiency (Ca) or its initial slope and the photosynthetic capacity (Pm) or the CO2-saturated uptake rate of CO2 uptake, and dark respiration (Rd). The dependency of photosynthesis on leaf temperature and incident light intensity is incorporated into variations of those parameters which establish an appropriate response to internal CO2 pressure for particular light and temperature conditions prevailing at any time. Secondly the interactiion of stomata with photosynthesis is represented as an empirical relation between stomatal conductance and a combined environmental physiological index, APn·Hx/CaThe parameters used in the modelwere estimated with Marquardt-Newton method for non-linear function. Field measurements of mulberry leaf photosynthesis provided a data set for model testing. The resuks show that the simulated values of the model agree well with observed data. The model was used to analyse the response surface of leaf conductance and photosynthesis to environmental factors—Applications and limitations of the model are discussed     

An improved dynamic model of photosynthesis for estimation of carbon gain in sunfleck light regimes

A dynamic model of leaf photosynthesis for C₃ plants has been developed for examination of the role of the dynamic properties of the photosynthetic apparatus in regulating CO₂ assimilation in variable light regimes. The model is modified from the Farquhar-von Caemmerer-Berry model by explicitly including metabolite pools and the effects of light activation and deactivation of Calvin cycle enzymes. It is coupled to a dynamic stomatal conductance model, with the assimilation rate at any time being determined by the joint effects of the dynamic biochemical model and the stomatal conductance model on the intercellular CO₂ pressure. When parametrized for each species, the model was shown to exhibit responses to step changes in photon flux density that agreed closely with the observed responses for both the understory plant Alocasia macrorrhiza and the crop plant Glycine max. Comparisons of measured and simulated photosynthesis under simulated light regimes having natural patterns of lightfleck frequencies and durations showed that the simulated total for Alocasia was within ±4% of the measured total assimilation, but that both were 12–50% less than the predictions from a steady–state solution of the model. Agreement was within ±10% for Glycine max, and only small differences were apparent between the dynamic and steady–state predictions. The model may therefore be parametrized for quite different species, and is shown to reflect more accurately the dynamics of photosynthesis than earlier dynamic models.     

Micro-environmentally restricted cell growth dynamics – modeling considerations

Various modeling approaches have been applied to describe the rearrangement of immobilized cell clusters within the extracellular matrix. The cell rearrangement has been related with the micro-environmental restrictions to cell growth. Herein, an attempt is made to discuss and connect various modeling approaches on various time scales which have been proposed in the literature in order to shed further light to this complex phenomenon which induces micro-environmental restrictions to cell growth. The rearrangement is driven by internal stress generated within the cluster. The internal stress represents a consequence of the matrix rheological response to cell expansion. The rearrangement includes the interplay between the processes of: (1) single and collective cell migrations, (2) cell deformation and orientation, (3) decrease of cell-to-cell separation distances and (4) cell growth. It has been considered on two time scales: a short time scale (i.e. the rearrangement time) and a long time scale (i.e. the growing time). The results indicate that short and long times cell rearrangement induces energy dissipation. The dissipation provokes biological responses of cells which cause the resistance effects to cell growth. Deeper insight in the anomalous nature of the energy dissipation would be useful for understanding the biological mechanisms which causes the resistance effects to cell growth.     

Exploring the role of structure and dynamics in the function of chymotrypsin inhibitor 2

Increasing awareness of the possible role of internal dynamics in protein function has led to the development of new methods for experimentally characterizing protein dynamics across multiple time scales, especially using NMR spectroscopy. A few analyses of the conformational dynamics of proteins ranging from nonallosteric single domains to multidomain allosteric enzymes are now available; however, demonstrating a connection between dynamics and function remains difficult on account of the comparative lack of studies examining both changes in dynamics and changes in function in response to the same perturbations. In previous work, we characterized changes in structure and dynamics on the ps–ns time scale resulting from hydrophobic core mutations in chymotrypsin inhibitor 2 and found that there are moderate, persistent global changes in dynamics in the absence of gross structural changes (Whitley et al., Biochemistry 2008;47:8566–8576). Here, we assay those and additional mutants for inhibitory ability toward the serine proteases elastase and chymotrypsin to determine the effects of mutation on function. Results indicate that core mutation has only a subtle effect on CI2 function. Using chemical shifts, we also studied the effect of complex formation on CI2 structure and found that perturbations are greatest at the complex interface but also propagate toward CI2's hydrophobic core. The structure–dynamics–function data set completed here suggests that dynamics plays a limited role in the function of this small model system, although we do observe a correlation between nanosecond-scale reactive loop motions and inhibitory ability for mutations at one key position in the hydrophobic core.