Why small fluxes matter: the case and approaches for improving measurements of photosynthesis and (photo)respiration

Accurate photosynthetic parameter estimation at low stomatal conductance: effects of cuticular conductance and instrumental noise

Accurate estimation of photosynthetic parameters is essential for understanding plant physiological limitations and responses to environmental factors from the leaf to the global scale. Gas exchange is a useful tool to measure responses of net CO2 assimilation (A) to internal CO2 concentration (Ci), a necessary step in estimating photosynthetic parameters including the maximum rate of carboxylation (Vcmax) and the electron transport rate (Jmax). However, species and environmental conditions of low stomatal conductance (gsw) reduce the signal-to-noise ratio of gas exchange, challenging estimations of Ci. Previous works showed that not considering cuticular conductance to water (gcw) can lead to significant errors in estimating Ci, because it has a different effect on total conductance to CO2 (gtc) than does gsw. Here we present a systematic assessment of the need for incorporating gcw into Ci estimates. In this study we modeled the effect of gcw and of instrumental noise and quantified these effects on photosynthetic parameters in the cases of four species with varying gsw and gcw, measured using steady-state and constant ramping techniques, like the rapid A/Ci response method. We show that not accounting for gcw quantitatively influences Ci and the resulting Vcmax and Jmax, particularly when gcw exceeds 7% of the total conductance to water. The influence of gcw was not limited to low gsw species, highlighting the importance of species-specific knowledge before assessing A/Ci curves. Furthermore, at low gsw instrumental noise can affect Ci estimation, but the effect of instrumental noise can be minimized using constant-ramping rather than steady-state techniques. By incorporating these considerations, more precise measurements and interpretations of photosynthetic parameters can be obtained in a broader range of species and environmental conditions.

The Dynamic Assimilation Technique measures photosynthetic CO2 response curves with similar fidelity to steady-state approaches in half the time

The net CO2 assimilation (A) response to intercellular CO2 concentration (Ci) is a fundamental measurement in photosynthesis and plant physiology research. The conventional A/Ci protocols rely on steady-state measurements and take 15-40 min per measurement, limiting data resolution or biological replication. Additionally, there are several CO2 protocols employed across the literature, without clear consensus as to the optimal protocol or systematic biases in their estimations. We compared the non-steady-state Dynamic Assimilation Technique (DAT) protocol and the three most used CO2 protocols in steady-state measurements, and tested whether different CO2 protocols lead to systematic differences in estimations of the biochemical limitations to photosynthesis. The DAT protocol reduced the measurement time by almost half without compromising estimation accuracy or precision. The monotonic protocol was the fastest steady-state method. Estimations of biochemical limitations to photosynthesis were very consistent across all CO2 protocols, with slight differences in Rubisco carboxylation limitation. The A/Ci curves were not affected by the direction of the change of CO2 concentration but rather the time spent under triose phosphate utilization (TPU)-limited conditions. Our results suggest that the maximum rate of Rubisco carboxylation (Vcmax), linear electron flow for NADPH supply (J), and TPU measured using different protocols within the literature are comparable, or at least not systematically different based on the measurement protocol used.

Combined leaf gas-exchange system for model assessment

Leaf gas-exchange measurements are useful in assessing plant environmental responses. However, uncertainties in the leaf gas-exchange model potentially limit its application. The main challenge in the model-dependent calculations is to detect violations of assumptions. Here, we developed a system that integrates into one instrument the direct measurement of leaf intercellular CO2 concentration and the standard open-flow (OF) and novel open-diffusion (OD) systems for flux measurement. In the OD system, a gas-permeable membrane between the leaf ambient air and outside air creates CO2 and H2O differentials, rather than the air flow in the OF chamber. We measured hypostomatous and amphistomatous leaves of several species with different photosynthetic capacities [sunflower (Helianthus annuus), grape (Vitis vinifera), lemon (Citrus limon), and cherry (Prunus avium)]. The CO2 and H2O differentials in the OD system strictly depend on the flux measured by the OF system. The lower permeability of the membrane resulted in a larger differential per flux, indicating that the OD system can increase the resolution for a small flux. An analysis of the conductance model along with observations suggested that cuticle and leaf intercellular conductances and the unsaturation of leaf humidity contributed to discrepancies between the direct measurement and standard calculation. The combined system developed here provides an opportunity to address these overlooked concepts in leaf gas exchange.

A guide to photosynthetic gas exchange measurements: Fundamental principles, best practice and potential pitfalls

Gas exchange measurements enable mechanistic insights into the processes that underpin carbon and water fluxes in plant leaves which in turn inform understanding of related processes at a range of scales from individual cells to entire ecosytems. Given the importance of photosynthesis for the global climate discussion it is important to (a) foster a basic understanding of the fundamental principles underpinning the experimental methods used by the broad community, and (b) ensure best practice and correct data interpretation within the research community. In this review, we outline the biochemical and biophysical parameters of photosynthesis that can be investigated with gas exchange measurements and we provide step-by-step guidance on how to reliably measure them. We advise on best practices for using gas exchange equipment and highlight potential pitfalls in experimental design and data interpretation. The Supporting Information contains exemplary data sets, experimental protocols and data-modelling routines. This review is a community effort to equip both the experimental researcher and the data modeller with a solid understanding of the theoretical basis of gas-exchange measurements, the rationale behind different experimental protocols and the approaches to data interpretation.

The quandary of sources and sinks of CO2 efflux in tree stems-new insights and future directions

Stem respiration (RS) substantially contributes to the return of photo assimilated carbon to the atmosphere and, thus, to the tree and ecosystem carbon balance. Stem CO2 efflux (ECO2) is often used as a proxy for RS. However, this metric has often been challenged because of the uncertain origin of CO2 emitted from the stem due to post-respiratory processes. In this Insight, we (i) describe processes affecting the quantification of RS, (ii) review common methodological approaches to quantify and model RS and (iii) develop a research agenda to fill the most relevant knowledge gaps that we identified. Dissolution, transport and accumulation of respired CO2 away from its production site, reassimilation of respired CO2 via stem photosynthesis and the enzyme phosphoenolpyruvate carboxylase, axial CO2 diffusion in the gas phase, shifts in the respiratory substrate and non-respiratory oxygen (O2) consumption are the most relevant processes causing divergence between RS and measured stem gas exchange (ECO2 or O2 influx, IO2). Two common methodological approaches to estimate RS, namely the CO2 mass balance approach and the O2 consumption technique, circumvent some of these processes but have yielded inconsistent results regarding the fate of respired CO2. Stem respiration modelling has recently progressed at the organ and tree levels. However, its implementation in large-scale models, commonly operated from a source-driven perspective, is unlikely to reflect adequate mechanisms. Finally, we propose hypotheses and approaches to advance the knowledge of the stem carbon balance, the role of sap pH on RS, the reassimilation of respired CO2, RS upscaling procedures, large-scale RS modelling and shifts in respiratory metabolism during environmental stress.

Stomatal closure in maize is mediated by subsidiary cells and the PAN2 receptor

Stomata are epidermal pores that facilitate plant gas exchange. Grasses have fast stomatal movements, likely due to their dumbbell-shaped guard cells and lateral subsidiary cells. Subsidiary cells reciprocally exchange water and ions with guard cells. However, the relative contribution of subsidiary cells during stomatal closure is unresolved. We compared stomatal gas exchange and stomatal aperture dynamics in wild-type and pan1, pan2, and pan1;pan2 Zea mays (L.) (maize) mutants, which have varying percentages of aberrantly formed subsidiary cells. Stomata with 1 or 2 defective subsidiary cells cannot close properly, indicating that subsidiary cells are essential for stomatal function. Even though the percentage of aberrant stomata is similar in pan1 and pan2, pan2 showed a more severe defect in stomatal closure. In pan1, only stomata with abnormal subsidiary cells fail to close normally. In pan2, all stomata have stomatal closure defects, indicating that PAN2 has an additional role in stomatal closure. Maize Pan2 is orthologous to Arabidopsis GUARD CELL HYDROGEN PEROXIDE-RESISANT1 (GHR1), which is also required for stomatal closure. PAN2 acts downstream of Ca2+ in maize to promote stomatal closure. This is in contrast to GHR1, which acts upstream of Ca2+ , and suggests the pathways could be differently wired.

Assessing the CO2 concentration at the surface of photosynthetic mesophyll cells

We present a robust estimation of the CO₂ concentration at the surface of photosynthetic mesophyll cells (c_w ), applicable under reasonable assumptions of assimilation distribution within the leaf. We used Capsicum annuum, Helianthus annuus and Gossypium hirsutumas model plants for our experiments. We introduce calculations to estimate c_w using independent adaxial and abaxial gas exchange measurements, and accounting for the mesophyll airspace resistances. The c_w was lower than adaxial and abaxial estimated intercellular CO₂ concentrations (c_i ). Differences between c_w and the c_i of each surface were usually larger than 10 μmol mol^-1 . Differences between adaxial and abaxial c_i ranged from a few μmol mol^-1 to almost 50 μmol mol^-1 , where the largest differences were found at high air saturation deficits (ASD). Differences between adaxial and abaxial c_i and the c_i estimated by mixing both fluxes ranged from -30 to +20 μmol mol^-1 , where the largest differences were found under high ASD or high ambient CO₂ concentrations. Accounting for c_w improves the information that can be extracted from gas exchange experiments, allowing a more detailed description of the CO₂ and water vapor gradients within the leaf.

Into the Shadows and Back into Sunlight: Photosynthesis in Fluctuating Light

Photosynthesis is an important remaining opportunity for further improvement in the genetic yield potential of our major crops. Measurement, analysis, and improvement of leaf CO₂ assimilation (A) have focused largely on photosynthetic rates under light-saturated steady-state conditions. However, in modern crop canopies of several leaf layers, light is rarely constant, and the majority of leaves experience marked light fluctuations throughout the day. It takes several minutes for photosynthesis to regain efficiency in both sun-shade and shade-sun transitions, costing a calculated 10-40% of potential crop CO₂ assimilation. Transgenic manipulations to accelerate the adjustment in sun-shade transitions have already shown a substantial productivity increase in field trials. Here, we explore means to further accelerate these adjustments and minimize these losses through transgenic manipulation, gene editing, and exploitation of natural variation. Measurement andanalysis of photosynthesis in sun-shade and shade-sun transitions are explained. Factors limiting speeds of adjustment and how they could be modified to effect improved efficiency are reviewed, specifically nonphotochemical quenching (NPQ), Rubisco activation, and stomatal responses.

Cuticular conductance of adaxial and abaxial leaf surfaces and its relation to minimum leaf surface conductance

Cuticular conductance to water (g_cw ) is difficult to quantify for stomatous surfaces due to the complexity of separating cuticular and stomatal transpiration, and additional complications arise for determining adaxial and abaxial g_cw . This has led to the neglect of g_cw as a separate parameter in most common gas exchange measurements. Here, we describe a simple technique to simultaneously estimate adaxial and abaxial values of g_cw , tested in two amphistomatous plant species. What we term the 'Red-Light method' is used to estimate g_cw from gas exchange measurements and a known CO₂ concentration inside the leaf during photosynthetic induction under red light. We provide an easy-to-use web application to assist with the calculation of g_cw . While adaxial and abaxial g_cw varies significantly between leaves of the same species we found that the ratio of adaxial/abaxial g_cw (γ_n ) is stable within a plant species. This has implications for use of generic values of g_cw when analysing gas exchange data. The Red-Light method can be used to estimate total cuticular conductance (g_cw-T ) accurately with the most common setup of gas exchange instruments, i.e. a chamber mixing the adaxial and abaxial gases, allowing for a wide application of this technique.

Evidence for rice tolerance to Tibraca limbativentris (Hemiptera: Pentatomidae)

BACKGROUND

The rice stalk stink bug Tibraca limbativentris (Hemiptera: Pentatomidae) is one of the most important rice pests in Brazil. The search for cultivars that tolerate insect injury is necessary to complement other less aggressive methods of pest suppression. The combination of integrated pest management tactics will reduce insecticide applications and improve the safety of food production. Here, we tested the tolerance response of Xingu, Canela de Ferro and Primavera rice genotypes in glasshouse experiments. In addition, we measured tolerance expressed in a variety of physiological responses, including gas exchange rates, leaf chlorophyll content and reactive oxygen species (ROS) detoxification.

RESULTS

The results showed that the tolerance of the Primavera genotype to rice stalk stink bug damage was higher, due to (a) a lower reduction of photosynthetic activity, (41% reduction only 96 h after infestation) compared to Xingu and Canela de Ferro (56 and 65% reduction at 24 and 48 h after infestation, respectively); (b) the capacity to maintain the chlorophyll content after infestation, while Xingu and Canela de Ferro reduced their chlorophyll content to 20% and 25% at 72 and 48 h after infestation, respectively; (c) the antioxidative defense system being activated in the first 12 h after infestation, in which superoxide dismutase (SOD) showed an increase of 61% in its activity, and (d) the maintenance of its grain yield, number of panicles per plant, number of filled grains, and spikelets sterility.

CONCLUSION

Rice genotypes tolerant to herbivory can be identified by measuring the effect of injury and the plant's physiological response by evaluating attributes such as grain yield and its components, gas exchange, chlorophyll content and ROS detoxification. Therefore, the use of rice genotypes tolerant to stalk stink bugs as a component of integrated pest management has the potential to reduce upland rice yield loss.

An improved theory for calculating leaf gas exchange more precisely accounting for small fluxes

The widely used theory for gas exchange proposed by von Caemmerer and Farquhar (vCF) integrates molar fluxes, mole fraction gradients and ternary effects but does not account for cuticular fluxes, for separation of the leaf surface conditions or for ternary effects within the boundary layer. The magnitude of cuticular conductance to water (g_cw) is a key factor for determining plant survival in drought but is difficult to measure and often neglected in routine gas exchange studies. The vCF ternary effect is applied to the total flux without the recognition of different pathways that are affected by it. These simplifications lead to errors in estimations of stomatal conductance, intercellular carbon dioxide concentration (C_i) and other gas exchange parameters. The theory presented here is a more precise physical approach to the electrical resistance analogy for gas exchange, resulting in a more accurate calculation of gas exchange parameters. Additionally, we extend our theory, using physiological concepts, to create a model that allows us to calculate cuticular conductance to water.

During photosynthetic induction, biochemical and stomatal limitations differ between Brassica crops

Interventions to increase crop radiation use efficiency rely on understanding of how biochemical and stomatal limitations affect photosynthesis. When leaves transition from shade to high light, slow increases in maximum Rubisco carboxylation rate and stomatal conductance limit net CO₂ assimilation for several minutes. However, as stomata open intercellular [CO₂ ] increases, so electron transport rate could also become limiting. Photosynthetic limitations were evaluated in three important Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. Measurements of induction after a period of shade showed that net CO₂ assimilation by B. rapa and B. napus saturated by 10 min. A new method of analyzing limitations to induction by varying intercellular [CO₂ ] showed this was due to co-limitation by Rubisco and electron transport. By contrast, in B. oleracea persistent Rubisco limitation meant that CO₂ assimilation was still recovering 15 min after induction. Correspondingly, B. oleracea had the lowest Rubisco total activity. The methodology developed, and its application here, shows a means to identify the basis of variation in photosynthetic efficiency in fluctuating light, which could be exploited in breeding and bioengineering to improve crop productivity.

Heterogeneity of Stomatal Pore Area Is Suppressed by Ambient Aerosol in the Homobaric Species, Vicia faba

Stomatal pore area is heterogeneous across leaf surfaces. This has been considered as "patchy stomatal conductance," and may have substantial implications for photosynthetic efficiency. Aerosols have always been important elements of plant environments, but their effects on stomatal control of plant water relations, and stomatal heterogeneity specifically, have not been considered. Here we evaluate the spatial coordination of pore area in the glabrous and homobaric leaves of Vicia faba grown under two aerosol treatments and measured at four levels of VPD. We construct a large dataset (n > 88,000 discrete comparisons) of paired pore areas and distances between the pores. Plants were grown in ambient urban air and in filtered air (FA) to determine the effect of ambient aerosol on stomatal properties. Pore area exhibited spatial organization, as well as considerable variability among closely co-located pores. The difference between pore areas was positively correlated with the distance between the pores, in both aerosol treatments and at all VPDs. However, aerosol deposition reduced both the magnitude of variability between pores and the rate at which this variability increased with pore separation distance. These data support previous conclusions that deposition of hygroscopic aerosol may create a thin aqueous film across the leaf surface that connects neighboring stomata to each other and to the leaf interior. Aerosol impacts on stomatal heterogeneity and gas exchange are not adequately considered in current assessments of stomatal control.

Guard Cell Metabolism and Stomatal Function

The control of gaseous exchange between the leaf and external atmosphere is governed by stomatal conductance (g_s); therefore, stomata play a critical role in photosynthesis and transpiration and overall plant productivity. Stomatal conductance is determined by both anatomical features and behavioral characteristics. Here we review some of the osmoregulatory pathways in guard cell metabolism, genes and signals that determine stomatal function and patterning, and the recent work that explores coordination between g_s and carbon assimilation (A) and the influence of spatial distribution of functional stomata on underlying mesophyll anatomy. We also evaluate the current literature on mesophyll-driven signals that may coordinate stomatal behavior with mesophyll carbon assimilation and explore stomatal kinetics as a possible target to improve A and water use efficiency. By understanding these processes, we can start to provide insight into manipulation of these regulatory pathways to improve stomatal behavior and identify novel unexploited targets for altering stomatal behavior and improving crop plant productivity.

Two-Source δ18O Method to Validate the CO18O-Photosynthetic Discrimination Model: Implications for Mesophyll Conductance

Theoretical models of photosynthetic isotopic discrimination of CO2 (13C and 18O) are commonly used to estimate mesophyll conductance (g m). This requires making simplifying assumptions and assigning parameter values so that g m can be solved for as the residual term. Uncertainties in g m estimation occur due to measurement noise and assumptions not holding, including parameter uncertainty and model parametrization. Uncertainties in the 13C model have been explored previously, but there has been little testing undertaken to determine the reliability of g m estimates from the 18O model (g m18). In this study, we exploited the action of carbonic anhydrase in equilibrating CO2 with leaf water and manipulated the observed photosynthetic discrimination (Δ18O) by changing the oxygen isotopic composition of the source gas CO2 and water vapor. We developed a two-source δ18O method, whereby two measurements of Δ18O were obtained for a leaf with its gas-exchange characteristics otherwise unchanged. Measurements were performed in broad bean (Vicia faba) and Algerian oak (Quercus canariensis) in response to light and vapor pressure deficit. Despite manipulating the Δ18O by over 100‰, in most cases we observed consistency in the calculated g m18, providing confidence in the measurements and model theory. Where there were differences in g m18 estimates between source-gas measurements, we explored uncertainty associated with two model assumptions (the isotopic composition of water at the sites of CO2-water exchange, and the humidity of the leaf internal airspace) and found evidence for both. Finally, we provide experimental guidelines to minimize the sensitivity of g m18 estimates to measurement errors. The two-source δ18O method offers a flexible tool for model parameterization and provides an opportunity to refine our understanding of leaf water and CO2 fluxes.

Comparing two measures of leaf photorespiration rate across a wide range of light intensities

Suppression of photorespiration by low O₂ concentrations (Method 1) and simultaneous measurements of gas exchange and chlorophyll fluorescence (Method 2) are often used to estimate leaf photorespiration rate (R_p) of C₃ plants. However, it is largely unknown whether Method 1 and Method 2 can be used equivalently in estimating R_p. Using a field experiment on two wheat cultivars (T. aestivum JM22 and T. aestivum Z39-118) whose leaf gas exchange and chlorophyll fluorescence at low and normal O₂ concentrations (2% versus 21% O₂) were simultaneously measured across a wide range of light intensities (I), this study assessed the impacts of the two measures on R_p and its response under changing irradiance conditions. All the above quantities increased with the increasing I until reaching the cultivar-specific maximum values and the corresponding saturation light intensities. However, there were significant differences between R_p estimated by Method 1 and Method 2 at the I range from 150 to 2000 μmol m^-2 s^-1 for T. aestivum JM22 and from 150 to 1000 μmol m^-2 s^-1 for T. aestivum Z39-118. These findings demonstrated that the two methods cannot be used equivalently under changing irradiance conditions.

Contribution and consequences of xylem-transported CO2 assimilation for C3 plants

Traditionally, leaves were thought to be supplied with CO₂ for photosynthesis by the atmosphere and respiration. Recent studies, however, have shown that the xylem also transports a significant amount of inorganic carbon into leaves through the bulk flow of water. However, little is known about the dynamics and proportion of xylem-transported CO₂ that is assimilated, vs simply lost to transpiration. Cut leaves of Populus deltoides and Brassica napus were placed in either KCl or one of three [NaH¹³ CO₃ ] solutions dissolved in water to simultaneously measure the assimilation and the efflux of xylem-transported CO₂ exiting the leaf across light and CO₂ response curves in real-time using a tunable diode laser absorption spectroscope. The rates of assimilation and efflux of xylem-transported CO₂ increased with increasing xylem [¹³ CO₂ *] and transpiration. Under saturating irradiance, rates of assimilation using xylem-transported CO₂ accounted for c. 2.5% of the total assimilation in both species in the highest [¹³ CO₂ *]. The majority of xylem-transported CO₂ is assimilated, and efflux is small compared to respiration. Assimilation of xylem-transported CO₂ comprises a small portion of total photosynthesis, but may be more important when CO₂ is limiting.

Net photosynthetic CO2 assimilation: more than just CO2 and O2 reduction cycles

Net photosynthetic assimilation in C₃ plants is mostly viewed as a simple balance between CO₂ fixation by Rubisco-catalyzed carboxylation and CO₂ production by photorespiration (and to a lower extent, by day respiration) that can be easily manipulated during gas exchange experiments using the CO₂  : O₂ ratio of the environment. However, it now becomes clear that it is not so simple, because the photosynthetic response to gaseous conditions involves 'ancillary' metabolisms, even in the short-term. That is, carbon and nitrogen utilization by pathways other than the Calvin cycle and the photorespiratory cycle, as well as rapid signaling events, can influence the observed rate of net photosynthesis. The potential impact of such ancillary metabolisms is assessed as well as how it must be taken into account to avoid misinterpretation of photosynthetic CO₂ response curves or low O₂ effects in C₃ leaves.

Isotope ratio laser spectroscopy to disentangle xylem-transported from locally respired CO2 in stem CO2 efflux

Respired CO2 in woody tissues radially diffuses to the atmosphere or it is transported upward with the transpiration stream, making the origin of CO2 in stem CO2 efflux (EA) uncertain, which may confound stem respiration (RS) estimates. An aqueous 13C-enriched solution was infused into stems of Populus tremula L. trees, and real-time measurements of 13C-CO2 and 12C-CO2 in EA were performed via Cavity Ring Down Laser Spectroscopy (CRDS). The contribution of locally respired CO2 (LCO2) and xylem-transported CO2 (TCO2) to EA was estimated from their different isotopic composition. Mean daily values of TCO2/EA ranged from 13% to 38%, evidencing the notable role that xylem CO2 transport plays in the assessment of stem respiration. Mean daily TCO2/EA did not differ between treatments of drought stress and light exclusion of woody tissues, but they showed different TCO2/EA dynamics on a sub-daily time scale. Sub-daily CO2 diffusion patterns were explained by a light-induced axial CO2 gradient ascribed to woody tissue photosynthesis, and the resistance to radial CO2 diffusion determined by bark water content. Here, we demonstrate the outstanding potential of CRDS paired with 13C-CO2 labelling to advance in the understanding of CO2 movement at the plant-atmosphere interface and the respiratory physiology in woody tissues.

On the minimum leaf conductance: its role in models of plant water use, and ecological and environmental controls

Contents Summary 693 I. Introduction 693 II. Comparison of various definitions and measurement techniques of minimum conductance 694 III. Cuticular conductance 695 IV. Contribution of stomata 696 V. Environmental and ecological variation in minimum conductance 696 VI. Use of minimum conductance in models 698 VII. Conclusions 703 Acknowledgements 703 References 703 SUMMARY: When the rate of photosynthesis is greatly diminished, such as during severe drought, extreme temperature or low light, it seems advantageous for plants to close stomata and completely halt water loss. However, water loss continues through the cuticle and incompletely closed stomata, together constituting the leaf minimum conductance (g_min ). In this review, we critically evaluate the sources of variation in g_min , quantitatively compare various methods for its estimation, and illustrate the role of g_min in models of leaf gas exchange. A literature compilation of g_min as measured by the weight loss of detached leaves is presented, which shows much variation in this trait, which is not clearly related to species groups, climate of origin or leaf type. Much evidence points to the idea that g_min is highly responsive to the growing conditions of the plant, including soil water availability, temperature and air humidity - as we further demonstrate with two case studies. We pay special attention to the role of the minimum conductance in the Ball-Berry model of stomatal conductance, and caution against the usual regression-based method for its estimation. The synthesis presented here provides guidelines for the use of g_min in ecosystem models, and points to clear research gaps for this drought tolerance trait.

Environmental controls on light inhibition of respiration and leaf and canopy daytime carbon exchange in a temperate deciduous forest

Uncertainty in the estimation of daytime ecosystem carbon cycling due to the light inhibition of leaf respiration and photorespiration, and how these small fluxes vary through the growing season in the field, remains a confounding element in calculations of gross primary productivity and ecosystem respiration. Our study focuses on how phenology, short-term temperature changes and canopy position influence leaf-level carbon exchange in Quercus rubra L. (red oak) at Harvard Forest in central Massachusetts, USA. Using leaf measurements and eddy covariance, we also quantify the effect of light inhibition on estimates of daytime respiration at leaf and ecosystem scales. Measured rates of leaf respiration in the light and dark were highest in the early growing season and declined in response to 10-day prior air temperatures (P < 0.01), evidence of within-season thermal acclimation. Leaf respiration was significantly inhibited by light (27.1 ± 2.82% inhibited across all measurements), and this inhibition varied with the month of measurement; greater inhibition was observed in mid-summer leaves compared with early- and late-season leaves. Increases in measurement temperature led to higher rates of respiration and photorespiration, though with a less pronounced positive effect on photosynthesis; as a result, carbon-use efficiency declined with increasing leaf temperature. Over the growing season when we account for seasonally variable light inhibition and basal respiration rates, our modeling approaches found a cumulative 12.9% reduction of leaf-level respiration and a 12.8% reduction of canopy leaf respiration, resulting in a 3.7% decrease in total ecosystem respiration compared with estimates that do not account for light inhibition in leaves. Our study sheds light on the environmental controls of the light inhibition of daytime leaf respiration and how integrating this phenomenon and other small fluxes can reduce uncertainty in current and future projections of terrestrial carbon cycling.

Design and in vitro realization of carbon-conserving photorespiration

Photorespiration limits plant carbon fixation by releasing CO₂ and using cellular resources to recycle the product of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) oxygenation, 2-phosphoglycolate. We systematically designed synthetic photorespiration bypasses that combine existing and new-to-nature enzymatic activities and that do not release CO₂. Our computational model shows that these bypasses could enhance carbon fixation rate under a range of physiological conditions. To realize the designed bypasses, a glycolate reduction module, which does not exist in nature, is needed to be engineered. By reshaping the substrate and cofactor specificity of two natural enzymes, we established glycolate reduction to glycolaldehyde. With the addition of three natural enzymes, we observed recycling of glycolate to the key Calvin Cycle intermediate ribulose 1,5-bisphosphate with no carbon loss.

Photorespiration recycles ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) oxygenation product, 2-phosphoglycolate, back into the Calvin Cycle. Natural photorespiration, however, limits agricultural productivity by dissipating energy and releasing CO₂. Several photorespiration bypasses have been previously suggested but were limited to existing enzymes and pathways that release CO₂. Here, we harness the power of enzyme and metabolic engineering to establish synthetic routes that bypass photorespiration without CO₂ release. By defining specific reaction rules, we systematically identified promising routes that assimilate 2-phosphoglycolate into the Calvin Cycle without carbon loss. We further developed a kinetic–stoichiometric model that indicates that the identified synthetic shunts could potentially enhance carbon fixation rate across the physiological range of irradiation and CO₂, even if most of their enzymes operate at a tenth of Rubisco’s maximal carboxylation activity. Glycolate reduction to glycolaldehyde is essential for several of the synthetic shunts but is not known to occur naturally. We, therefore, used computational design and directed evolution to establish this activity in two sequential reactions. An acetyl-CoA synthetase was engineered for higher stability and glycolyl-CoA synthesis. A propionyl-CoA reductase was engineered for higher selectivity for glycolyl-CoA and for use of NADPH over NAD⁺, thereby favoring reduction over oxidation. The engineered glycolate reduction module was then combined with downstream condensation and assimilation of glycolaldehyde to ribulose 1,5-bisphosphate, thus providing proof of principle for a carbon-conserving photorespiration pathway.

Leaf hydraulic vulnerability triggers the decline in stomatal and mesophyll conductance during drought in rice

Understanding the physiological responses of crops to drought is important for ensuring sustained crop productivity under climate change, which is expected to exacerbate the frequency and intensity of periods of drought. Drought responses involve multiple traits, and the correlations between these traits are poorly understood. Using a variety of techniques, we estimated the changes in gas exchange, leaf hydraulic conductance, and leaf turgor in rice (Oryza sativa) in response to both short- and long-term soil drought. We performed a photosynthetic limitation analysis to quantify the contributions of each limiting factor to the resultant overall decrease in photosynthesis during drought. Biomass, leaf area, and leaf width significantly decreased during the 2-week drought treatment, but leaf mass per area and leaf vein density increased. Light-saturated photosynthetic rate declined dramatically during soil drought, mainly due to the decrease in stomatal conductance (gs) and mesophyll conductance (gm). Stomatal modeling suggested that the decline in leaf hydraulic conductance explained most of the decrease in stomatal closure during the drought treatment, and may also trigger the drought-related decrease of stomatal conductance and mesophyll conductance. The results of this study provide insight into the regulation of carbon assimilation under drought conditions.

Ambient aerosol increases minimum leaf conductance and alters the aperture-flux relationship as stomata respond to vapor pressure deficit (VPD)

Aerosols are important components of the global plant environment, with beneficial and deleterious impacts. The direct effects of aerosol deposition on plant-water relationships remain poorly characterized but potentially important. Vicia faba was grown in ambient urban air and in the same air with aerosol excluded, in a moderately polluted environment using two exposure protocols. Simultaneous measurement of gas exchange and stomatal pore aperture was combined with leaf dehydration kinetics and microscopic evaluation of leaf wetness formation and aerosol deposition patterns. The ambient aerosol was shown to be hygroscopic. Aerosol exposure increased minimum leaf conductance, shown by dehydration kinetics, and nocturnal water vapor flux, shown by dark-adapted gas exchange. Aerosol exposure decreased stomatal apertures at each level of vapor pressure deficit (VPD) and increased stomatal conductance at comparable levels of aperture. Overall, these effects were modest, and largest when stomata were wide open. The uncoupling of conductance (flux-based) from aperture (directly measured microscopically) implies that aerosol-induced water loss is not fully under stomatal control. This reduces drought tolerance and may provide a mechanism by which deposited aerosol plays a direct role in stomatal response to VPD.

Unsaturation of vapour pressure inside leaves of two conifer species

Stomatal conductance (g_s) impacts both photosynthesis and transpiration, and is therefore fundamental to the global carbon and water cycles, food production, and ecosystem services. Mathematical models provide the primary means of analysing this important leaf gas exchange parameter. A nearly universal assumption in such models is that the vapour pressure inside leaves (e_i) remains saturated under all conditions. The validity of this assumption has not been well tested, because so far e_i cannot be measured directly. Here, we test this assumption using a novel technique, based on coupled measurements of leaf gas exchange and the stable isotope compositions of CO₂ and water vapour passing over the leaf. We applied this technique to mature individuals of two semiarid conifer species. In both species, e_i routinely dropped below saturation when leaves were exposed to moderate to high air vapour pressure deficits. Typical values of relative humidity in the intercellular air spaces were as low 0.9 in Juniperus monosperma and 0.8 in Pinus edulis. These departures of e_i from saturation caused significant biases in calculations of g_s and the intercellular CO₂ concentration. Our results refute the longstanding assumption of saturated vapour pressure in plant leaves under all conditions.

Direct measurement of intercellular CO2 concentration in a gas-exchange system resolves overestimation using the standard method

Intercellular CO2 concentration of leaves (Ci) is a critical parameter in photosynthesis. Nevertheless, uncertainties in calculating Ci arise as stomata close. Here, by modifying the assimilation chamber of a commercial gas-exchange equipment to directly measure Ci, we demonstrate overestimation of calculated Ci (i.e. Ci(c)) without stimulating stomatal closure. Gas exchange was measured on one side of the leaf while measured Ci (Ci(m)) was acquired simultaneously on the other side of the leaf in hypostomatous passion fruit (Passiflora edulis Sims) and amphistomatous sunflower (Helianthus annuus L.) and common bean (Phaseolus vulgaris L.). The adaxial surface showed comparable Ci(c) and Ci(m) in sunflower, whereas in common bean, where the adaxial surface has a low stomatal density, Ci(c) markedly differed from Ci(m) when the stomata remained open. However, the latter discrepancy disappeared when measuring the leaf flipped upside down so that the gas exchange was measured (i.e. Ci was calculated) on the abaxial side, which has a much higher stomatal density. The passion fruit showed the largest discrepancy on the astomatous side, indicating that the cuticle has a large impact on the calculation. Direct measurement of Ci is recommended as a more accurate estimate than the calculation when stomatal gas transport is restricted. Occurrence of overestimation and prospects for direct measurement are discussed.

Phenotypic Trait Identification Using a Multimodel Bayesian Method: A Case Study Using Photosynthesis in Brassica rapa Genotypes

Agronomists have used statistical crop models to predict yield on a genotype-by-genotype basis. Mechanistic models, based on fundamental physiological processes common across plant taxa, will ultimately enable yield prediction applicable to diverse genotypes and crops. Here, genotypic information is combined with multiple mechanistically based models to characterize photosynthetic trait differentiation among genotypes of Brassica rapa. Infrared leaf gas exchange and chlorophyll fluorescence observations are analyzed using Bayesian methods. Three advantages of Bayesian approaches are employed: a hierarchical model structure, the testing of parameter estimates with posterior predictive checks and a multimodel complexity analysis. In all, eight models of photosynthesis are compared for fit to data and penalized for complexity using deviance information criteria (DIC) at the genotype scale. The multimodel evaluation improves the credibility of trait estimates using posterior distributions. Traits with important implications for yield in crops, including maximum rate of carboxylation (V_cmax ) and maximum rate of electron transport (J_max ) show genotypic differentiation. B. rapa shows phenotypic diversity in causal traits with the potential for genetic enhancement of photosynthesis. This multimodel screening represents a statistically rigorous method for characterizing genotypic differences in traits with clear biophysical consequences to growth and productivity within large crop breeding populations with application across plant processes.

Development of pGEMINI, a Plant Gateway Destination Vector Allowing the Simultaneous Integration of Two cDNA via a Single LR-Clonase Reaction

Gateway technology has been used to facilitate the generation of a large number of constructs for the modification of plants for research purposes. However, many of the currently available vectors only allow the integration of a single cDNA of interest into an expression clone. The ability to over-express multiple genes in combination is essential for the study of plant development where several transcripts have a role to play in one or more metabolic processes. The tools to carry out such studies are limited, and in many cases rely on the incorporation of cDNA into expression systems via conventional cloning, which can be both time consuming and laborious. To our knowledge, this study reports on the first development of a vector allowing the simultaneous integration of two independent cDNAs via a single LR-clonase reaction. This vector “pGEMINI” represents a powerful molecular tool offering the ability to study the role of multi-cDNA constructs on plant development, and opens up the process of gene stacking and the study of gene combinations through transient or stable transformation procedures.

Screening for Natural Variation in Water Use Efficiency Traits in a Diversity Set of Brassica napus L. Identifies Candidate Variants in Photosynthetic Assimilation

Seed yield and quality of crop species are significantly reduced by water deficit. Stable isotope screening (δ13C) of a diversity set of 147 accessions of Brassica napus grown in the field identified several accessions with extremes in water use efficiency (WUE). We next conducted an investigation of the physiological characteristics of selected natural variants with high and low WUE to understand how these characteristics translate to differences in WUE. We identified an interesting Spring accession, G302 (Mozart), that exhibited the highest WUE in the field and high CO2 assimilation rates coupled with an increased electron transport capacity (Jmax) under the imposed conditions. Differences in stomatal density and stomatal index did not translate to differences in stomatal conductance in the investigated accessions. Stomatal conductance response to exogenous ABA was analyzed in selected high and low WUE accessions. Spring lines showed little variation in response to exogenous ABA, while one Semi-Winter line (SW047) showed a significantly more rapid response to exogenous ABA, that corresponded to the high WUE indicated by δ13C measurements. This research illustrates the importance of examining natural variation at a physiological level for investigation of the underlying mechanisms influencing the diversity of carbon isotope discrimination values in the field and identifies natural variants in B. napus with improved WUE and potential relevant traits.

The rapid A-Ci response: photosynthesis in the phenomic era

Phenotyping for photosynthetic gas exchange parameters is limiting our ability to select plants for enhanced photosynthetic carbon gain and to assess plant function in current and future natural environments. This is due, in part, to the time required to generate estimates of the maximum rate of ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) carboxylation (V_c,max ) and the maximal rate of electron transport (J_max ) from the response of photosynthesis (A) to the CO₂ concentration inside leaf air spaces (C_i ). To relieve this bottleneck, we developed a method for rapid photosynthetic carbon assimilation CO₂ responses [rapid A-C_i response (RACiR)] utilizing non-steady-state measurements of gas exchange. Using high temporal resolution measurements under rapidly changing CO₂ concentrations, we show that RACiR techniques can obtain measures of V_c,max and J_max in ~5 min, and possibly even faster. This is a small fraction of the time required for even the most advanced gas exchange instrumentation. The RACiR technique, owing to its increased throughput, will allow for more rapid screening of crops, mutants and populations of plants in natural environments, bringing gas exchange into the phenomic era.

Uncertainty in measurements of the photorespiratory CO2 compensation point and its impact on models of leaf photosynthesis

Rates of carbon dioxide assimilation through photosynthesis are readily modeled using the Farquhar, von Caemmerer, and Berry (FvCB) model based on the biochemistry of the initial Rubisco-catalyzed reaction of net C3 photosynthesis. As models of CO2 assimilation rate are used more broadly for simulating photosynthesis among species and across scales, it is increasingly important that their temperature dependencies are accurately parameterized. A vital component of the FvCB model, the photorespiratory CO2 compensation point (Γ *), combines the biochemistry of Rubisco with the stoichiometry of photorespiratory release of CO2. This report details a comparison of the temperature response of Γ * measured using different techniques in three important model and crop species (Nicotiana tabacum, Triticum aestivum, and Glycine max). We determined that the different Γ * determination methods produce different temperature responses in the same species that are large enough to impact higher-scale leaf models of CO2 assimilation rate. These differences are largest in N. tabacum and could be the result of temperature-dependent increases in the amount of CO2 lost from photorespiration per Rubisco oxygenation reaction.

Inside out: efflux of carbon dioxide from leaves represents more than leaf metabolism

High concentrations of inorganic carbon in the xylem, produced from root, stem, and branch respiration, travel via the transpiration stream and eventually exit the plant through distant tissues as CO2. Unlike previous studies that focused on the efflux of CO2 from roots and woody tissues, we focus on efflux from leaves and the potential effect on leaf respiration measurements. We labeled transported inorganic carbon, spanning reported xylem concentrations, with 13C and then manipulated transpiration rates in the dark in order to vary the rates of inorganic carbon supply to cut leaves from Brassica napus and Populus deltoides. We used tunable diode laser absorbance spectroscopy to directly measure the rate of gross 13CO2 efflux, derived from inorganic carbon supplied from outside of the leaf, relative to gross 12CO2 efflux generated from leaf cells. These experiemnts showed that 13CO2 efflux was dependent upon the rate of inorganic carbon supply to the leaf and the rate of transpiration. Our data show that the gross leaf efflux of xylem-transported CO2 is likely small in the dark when rates of transpiration are low. However, gross leaf efflux of xylem-transported CO2 could approach half the rate of leaf respiration in the light when transpiration rates and branch inorganic carbon concentrations are high, irrespective of the grossly different petiole morphologies in our experiment.

Variable Mesophyll Conductance among Soybean Cultivars Sets a Tradeoff between Photosynthesis and Water-Use-Efficiency

Photosynthetic efficiency is a critical determinant of crop yield potential, although it remains below the theoretical optimum in modern crop varieties. Enhancing mesophyll conductance (i.e. the rate of carbon dioxide diffusion from substomatal cavities to the sites of carboxylation) may increase photosynthetic and water use efficiencies. To improve water use efficiency, mesophyll conductance should be increased without concomitantly increasing stomatal conductance. Here, we partition the variance in mesophyll conductance to within- and among-cultivar components across soybean (Glycine max) grown under both controlled and field conditions and examine the covariation of mesophyll conductance with photosynthetic rate, stomatal conductance, water use efficiency, and leaf mass per area. We demonstrate that mesophyll conductance varies more than 2-fold and that 38% of this variation is due to cultivar identity. As expected, mesophyll conductance is positively correlated with photosynthetic rates. However, a strong positive correlation between mesophyll and stomatal conductance among cultivars apparently impedes positive scaling between mesophyll conductance and water use efficiency in soybean. Contrary to expectations, photosynthetic rates and mesophyll conductance both increased with increasing leaf mass per area. The presence of genetic variation for mesophyll conductance suggests that there is potential to increase photosynthesis and mesophyll conductance by selecting for greater leaf mass per area. Increasing water use efficiency, though, is unlikely unless there is simultaneous stabilizing selection on stomatal conductance.