Temperature responses of the Rubisco maximum carboxylase activity across domains of life: phylogenetic signals, trade-offs, and importance for carbon gain

Leaf chlorophyll content is the crucial factor for the temporal and spatial variation of global plants leaf maximum carboxylation rate

Photosynthesis plays an important role in the terrestrial carbon and water cycles which are often studied using terrestrial biosphere models (TBMs). The maximum carboxylation rate at 25 °C (Vcmax25) is a key parameter in the photosynthesis module of TBMs, yet the spatiotemporal distribution of Vcmax25 and the driving mechanism are not fully understood. In this study, Enzyme Kinetics response model, leaf chlorophyll content response model and partial correlation analysis were used to analyze the temporal and spatial changes patterns of atmospheric environment, enzyme dynamic and soil nutrition on Vcmax25 and the driving mechanism, and has made a few useful conclusions: (1) Vcmax25 varies significantly with latitude and between- and within-plant function types (PFTs), which mainly dependent on leaf chlorophyll content (LCC). Under the influence of temperature, the contribution of LCC to the seasonal variation of Vcmax25 is very different among the eight main biomes, with an average contribution of 21 %. (2) The relationship between meteorological variables and Vcmax25 was significant, due to the fact that meteorological variables drive the Rubisco enzyme content that have a significant relationship with Vcmax25, rather than directly acting on Vcmax25. (3) Soil nutrient elements had significant influence on the spatiotemporal variation of Vcmax25 and LCC. The results showed that soil total carbon, soil nitrogen and organic carbon not only affect the temporal and spatial pattern of Vcmax25, but also are the key factors of LCC temporal-spatial variation. These findings provide useful information for better parameterization of Vcmax25 in TBMs.

Light and temperature controls of aquatic plant photosynthesis downstream of a hydropower plant and the effect of plant removal

Many rivers worldwide are regulated, and the altered hydrology can lead to mass development of aquatic plants. Plant invasions are often seen as a nuisance for human activities leading to costly remedial actions with uncertain implications for aquatic biodiversity and ecosystem functioning. Mechanical harvesting is often used to remove aquatic plants and knowledge of plant growth rate could improve management decisions. Here, we used a simple light-temperature theoretical model to make a priori prediction of aquatic plant photosynthesis. These predictions were assessed through an open-channel diel change in O2 mass balance approach. A Michaelis-Menten type model was fitted to observed gross primary production (GPP) standardised at 10 °C using a temperature dependence from thermodynamic theory of enzyme kinetics. The model explained 87 % of the variability in GPP of a submerged aquatic plant (Juncus bulbosus L.) throughout an annual cycle in the River Otra, Norway. The annual net plant production was about 2.4 (1.0-3.8) times the standing biomass of J. bulbosus. This suggests a high continuous mass loss due to hydraulic stress and natural mechanical breakage of stems, as the biomass of J. bulbosus remained relatively constant throughout the year. J. bulbosus was predicted to be resilient to mechanical harvesting with photosynthetic capacity recovered within two years following 50-85 % plant removal. The predicted recovery was confirmed through a field experiment where 72 % of J. bulbosus biomass was mechanically removed. We emphasise the value of using a theoretical approach, like metabolic theory, over statistical models where a posteriori results are not always easy to interpret. Finally, the ability to predict ecosystem resilience of aquatic photosynthesis in response to varying management scenarios offers a valuable tool for estimating aquatic ecosystem services, such as carbon regulation. This tool can benefit the EU Biodiversity Strategy and UN Sustainable Development Goals.

Seasonal climate conditions impact the effectiveness of improving photosynthesis to increase soybean yield

Context

Photosynthetic stimulations have shown promising outcomes in improving crop photosynthesis, including soybean. However, it is still unclear to what extent these changes can impact photosynthetic assimilation and yield under long-term field climate conditions.

Objective

In this paper, we present a systematic evaluation of the response of canopy photosynthesis and yield to two critical parameters in leaf photosynthesis: the maximum carboxylation rate of ribulose-1,5-bisphosphate carboxylase/oxygenase (Vcmax) and the maximum electron transport of the ribulose-1,5-bisphosphate regeneration rate (Jmax).

Methods

Using the field-scale crop model Soybean-BioCro and ten years of observed climate data in Urbana, Illinois, U.S., we conducted sensitivity experiments to estimate the changes in canopy photosynthesis, leaf area index, and biomass due to the changes in Vcmax and Jmax.

Results

The results show that 1) Both the canopy photosynthetic assimilation (An) and pod biomass yields were more sensitive to the changes in Jmax, particularly at high atmospheric carbon-dioxide concentrations ([CO2]); 2) Higher [CO2] undermined the effectiveness of increasing the two parameters to improve An and yield; 3) Under the same [CO2], canopy light interception and canopy respiration were key factors that undermined improvements in An and yield; 4) A canopy with smaller leaf area index tended to have a higher yield improvement, and 5) Increases in assimilations and yields were highly dependent on growing-season climatic conditions. The solar radiation, temperature, and relative humidity were the main climate drivers that impacted the yield improvement, and they had opposite correlations with improved yield during the vegetative phase compared to the reproductive phase.

Conclusions

In a world with elevated [CO2], genetic engineering crop photosynthesis should focus more on improving Jmax. Further, long-term climate conditions and seasonal variations must be considered to determine the improvements in soybean canopy photosynthesis and yield at the field scale.

Implications

Quantifying the effectiveness of changing Vcmax and Jmax helps understand their individual and combined contributions to potential improvements in assimilation and yield. This work provides a framework for evaluating how altering the photosynthetic rate parameters impacts soybean yield and assimilation under different seasonal climate scenarios at the field scale.

Temperature-induced changes in Arabidopsis Rubisco activity and isoform expression

In many plant species, expression of the nuclear encoded Rubisco small subunit (SSu) varies with environmental changes, but the functional role of any changes in expression remains unclear. In this study, we investigated the impact of differential expression of Rubisco SSu isoforms on carbon assimilation in Arabidopsis. Using plants grown at contrasting temperatures (10 °C and 30 °C), we confirm the previously reported temperature response of the four RbcS genes and extend this to protein expression, finding that warm-grown plants produce Rubisco containing ~65% SSu-B and cold-grown plants produce Rubisco with ~65% SSu-A as a proportion of the total pool of subunits. We find that these changes in isoform concentration are associated with kinetic changes to Rubisco in vitro: warm-grown plants produce a Rubisco having greater CO2 affinity (i.e. higher SC/O and lower KC) but lower kcatCO2 at warm measurement temperatures. Although warm-grown plants produce 38% less Rubisco than cold-grown plants on a leaf area basis, warm-grown plants can maintain similar rates of photosynthesis to cold-grown plants at ambient CO2 and 30 °C, indicating that the carboxylation capacity of warm-grown Rubisco is enhanced at warmer measurement temperatures, and is able to compensate for the lower Rubisco content in warm-grown plants. This association between SSu isoform expression and maintenance of Rubisco activity at high temperature suggests that SSu isoform expression could impact the temperature response of C3 photosynthesis.

Predicting plant Rubisco kinetics from RbcL sequence data using machine learning

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is responsible for the conversion of atmospheric CO2 to organic carbon during photosynthesis, and often acts as a rate limiting step in the later process. Screening the natural diversity of Rubisco kinetics is the main strategy used to find better Rubisco enzymes for crop engineering efforts. Here, we demonstrate the use of Gaussian processes (GPs), a family of Bayesian models, coupled with protein encoding schemes, for predicting Rubisco kinetics from Rubisco large subunit (RbcL) sequence data. GPs trained on published experimentally obtained Rubisco kinetic datasets were applied to over 9000 sequences encoding RbcL to predict Rubisco kinetic parameters. Notably, our predicted kinetic values were in agreement with known trends, e.g. higher carboxylation turnover rates (Kcat) for Rubisco enzymes from C4 or crassulacean acid metabolism (CAM) species, compared with those found in C3 species. This is the first study demonstrating machine learning approaches as a tool for screening and predicting Rubisco kinetics, which could be applied to other enzymes.

Characterization of a novel thermophilic cyanobacterium within Trichocoleusaceae, Trichothermofontia sichuanensis gen. et sp. nov., and its CO2-concentrating mechanism

Thermophiles from extreme thermal environments have shown tremendous potential regarding ecological and biotechnological applications. Nevertheless, thermophilic cyanobacteria remain largely untapped and are rarely characterized. Herein, a polyphasic approach was used to characterize a thermophilic strain, PKUAC-SCTB231 (hereafter B231), isolated from a hot spring (pH 6.62, 55.5°C) in Zhonggu village, China. The analyses of 16S rRNA phylogeny, secondary structures of 16S-23S ITS and morphology strongly supported strain B231 as a novel genus within Trichocoleusaceae. Phylogenomic inference and three genome-based indices further verified the genus delineation. Based on the botanical code, the isolate is herein delineated as Trichothermofontia sichuanensis gen. et sp. nov., a genus closely related to a validly described genus Trichocoleus. In addition, our results suggest that Pinocchia currently classified to belong to the family Leptolyngbyaceae may require revision and assignment to the family Trichocoleusaceae. Furthermore, the complete genome of Trichothermofontia B231 facilitated the elucidation of the genetic basis regarding genes related to its carbon-concentrating mechanism (CCM). The strain belongs to β-cyanobacteria according to its β-carboxysome shell protein and 1B form of Ribulose bisphosphate Carboxylase-Oxygenase (RubisCO). Compared to other thermophilic strains, strain B231contains a relatively low diversity of bicarbonate transporters (only BicA for HCO₃^- transport) but a higher abundance of different types of carbonic anhydrase (CA), β-CA (ccaA) and γ-CA (ccmM). The BCT1 transporter consistently possessed by freshwater cyanobacteria was absent in strain B231. Similar situation was occasionally observed in freshwater thermal Thermoleptolyngbya and Thermosynechococcus strains. Moreover, strain B231 shows a similar composition of carboxysome shell proteins (ccmK1-4, ccmL, -M, -N, -O, and -P) to mesophilic cyanobacteria, the diversity of which was higher than many thermophilic strains lacking at least one of the four ccmK genes. The genomic distribution of CCM-related genes suggests that the expression of some components is regulated as an operon and others in an independently controlled satellite locus. The current study also offers fundamental information for future taxogenomics, ecogenomics and geogenomic studies on distribution and significance of thermophilic cyanobacteria in the global ecosystem.

Neglecting acclimation of photosynthesis under drought can cause significant errors in predicting leaf photosynthesis in wheat

Extreme climatic events, such as heat waves, cold snaps and drought spells, related to global climate change, have become more frequent and intense in recent years. Acclimation of plant physiological processes to changes in environmental conditions is a key component of plant adaptation to climate change. We assessed the temperature response of leaf photosynthetic parameters in wheat grown under contrasting water regimes and growth temperatures (T_growth ). Two independent experiments were conducted under controlled conditions. In Experiment 1, two wheat genotypes were subjected to well-watered or drought-stressed treatments; in Experiment 2, the two water regimes combined with high, medium and low T_growth were imposed on one genotype. Parameters of a biochemical C₃ -photosynthesis model were estimated at six leaf temperatures for each factor combination. Photosynthesis acclimated more to drought than to T_growth . Drought affected photosynthesis by lowering its optimum temperature (T_opt ) and the values at T_opt of light-saturated net photosynthesis, stomatal conductance, mesophyll conductance, the maximum rate of electron transport (J_max ) and the maximum rate of carboxylation by Rubisco (V_cmax ). T_opt for V_cmax was up to 40°C under well-watered conditions but 24-34°C under drought. The decrease in photosynthesis under drought varied among T_growth but was similar between genotypes. The temperature response of photosynthetic quantum yield under drought was partly attributed to photorespiration but more to alternative electron transport. All these changes in biochemical parameters could not be fully explained by the changed leaf nitrogen content. Further model analysis showed that both diffusional and biochemical parameters of photosynthesis and their thermal sensitivity acclimate little to T_growth , but acclimate considerably to drought and the combination of drought and T_growth . The commonly used modelling approaches, which typically consider the response of diffusional parameters, but ignore acclimation responses of biochemical parameters to drought and T_growth , strongly overestimate leaf photosynthesis under variable temperature and drought.

Features of Temperature Adaptation of Phaeodactylum tricornutum, Nitzschia sp., and Skeletonema costatum (Bacillariophyceae) under Different Light Conditions

Two types of possible adaptive response of the photosynthetic apparatus of diatoms to the changes in growth temperature conditions are shown. The first type is a temperature-dependent change in the content of chlorophyll in the cell, aimed at matching the rates of light and dark reactions of photosynthesis (noted in Phaeodactylum tricornutum and Nitzschia sp. 3). At the limiting light intensity, a temperature decrease from 20 to 5°C leads to an increase in the initial slope of light dependence of the C/Chl ratio; under the optimal light conditions at a temperature decrease from 20 to 10°C and from 10 to 5°C, the C/Chl ratio increases 1.5-fold in both species. The second type of response to the changes in growth temperature conditions was observed in Skeletonema costatum, for which the chlorophyll content in the cell does not depend on the temperature in the range of 10-20°C. The adaptation of the photosynthetic apparatus in this case probably occurs due to the changes in the activity of enzyme systems and in the rate of enzyme processes. The potential productivity of all studied species of algae at 10°C, calculated as the increase in biomass per unit of chlorophyll per day, does not differ significantly. Under the conditions of light inhibition, a temperature decrease leads to a progressive decrease in the content of chlorophyll in the cells of all algal species under study due to a decrease in the rate of pigment synthesis against the background of its intense photooxidation.

A photosynthetic rate prediction model using improved RBF neural network

A photosynthetic prediction rate model is a theoretical basis for light environmental regulation, and the existing photosynthetic rate prediction models are limited by low modeling speed and prediction accuracy. Therefore, this paper analyses effects of light quality on photosynthesis rate, and proposes a method based on Radial basis function (RBF) optimized by Quantum genetic algorithm (QGA) to establish photosynthetic rate prediction model. We selected "golden embryo² formula 98-1F1" cucumber seedlings as experimental material and used LI-6800 to record the photosynthetic rates under different temperatures, light intensities and light quality. Experimental data is used to train and test the proposed model. The determinant coefficient of the model between the predicted and the measured values is 0.996, the straight slope of linear fitting is 1.000, and the straight intercept of linear fitting is 0.061. Moreover, the proposed method is compared with 6 artificial intelligence algorithms. The comparison results also validate that the proposed model has the highest accuracy compared with other algorithms.

Comparative Genomic Analysis Revealed Distinct Molecular Components and Organization of CO2-Concentrating Mechanism in Thermophilic Cyanobacteria

Cyanobacteria evolved an inorganic carbon-concentrating mechanism (CCM) to perform effective oxygenic photosynthesis and prevent photorespiratory carbon losses. This process facilitates the acclimation of cyanobacteria to various habitats, particularly in CO₂-limited environments. To date, there is limited information on the CCM of thermophilic cyanobacteria whose habitats limit the solubility of inorganic carbon. Here, genome-based approaches were used to identify the molecular components of CCM in 17 well-described thermophilic cyanobacteria. These cyanobacteria were from the genus Leptodesmis, Leptolyngbya, Leptothermofonsia, Thermoleptolyngbya, Thermostichus, and Thermosynechococcus. All the strains belong to β-cyanobacteria based on their β-carboxysome shell proteins with 1B form of Rubisco. The diversity in the C_i uptake systems and carboxysome composition of these thermophiles were analyzed based on their genomic information. For C_i uptake systems, two CO₂ uptake systems (NDH-1₃ and NDH-1₄) and BicA for HCO₃^– transport were present in all the thermophilic cyanobacteria, while most strains did not have the Na⁺/HCO₃^– Sbt symporter and HCO₃^– transporter BCT1 were absent in four strains. As for carboxysome, the β-carboxysomal shell protein, ccmK2, was absent only in Thermoleptolyngbya strains, whereas ccmK3/K4 were absent in all Thermostichus and Thermosynechococcus strains. Besides, all Thermostichus and Thermosynechococcus strains lacked carboxysomal β-CA, ccaA, the carbonic anhydrase activity of which may be replaced by ccmM proteins as indicated by comparative domain analysis. The genomic distribution of CCM-related genes was different among the thermophiles, suggesting probably distinct expression regulation. Overall, the comparative genomic analysis revealed distinct molecular components and organization of CCM in thermophilic cyanobacteria. These findings provided insights into the CCM components of thermophilic cyanobacteria and fundamental knowledge for further research regarding photosynthetic improvement and biomass yield of thermophilic cyanobacteria with biotechnological potentials.

The Enzymology of Ocean Global Change

A small subset of marine microbial enzymes and surface transporters have a disproportionately important influence on the cycling of carbon and nutrients in the global ocean. As a result, they largely determine marine biological productivity and have been the focus of considerable research attention from microbial oceanographers. Like all biological catalysts, the activity of these keystone biomolecules is subject to control by temperature and pH, leaving the crucial ecosystem functions they support potentially vulnerable to anthropogenic environmental change. We summarize and discuss both consensus and conflicting evidence on the effects of sea surface warming and ocean acidification for five of these critical enzymes [carbonic anhydrase, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), nitrogenase, nitrate reductase, and ammonia monooxygenase] and one important transporter (proteorhodopsin). Finally, we forecast how the responses of these few but essential biocatalysts to ongoing global change processes may ultimately help to shape the microbial communities and biogeochemical cycles of the future greenhouse ocean.

Analyzing the causes of method-to-method variability among Rubisco kinetic traits: from the first to the current measurements

Due to the importance of Rubisco in the biosphere, its kinetic parameters have been measured by different methodologies in a large number of studies over the last 60 years. These parameters are essential to characterize the natural diversity in the catalytic properties of the enzyme and they are also required for photosynthesis and cross-scale crop modeling. The present compilation of Rubisco kinetic parameters in model species revealed a wide intraspecific laboratory-to-laboratory variability, which was partially solved by making corrections to account for differences in the assay buffer composition and in the acidity constant of dissolved CO2, as well as for differences in the CO2 and O2 solubilities. Part of the intraspecific variability was also related to the different analytical methodologies used. For instance, significant differences were found between the two main methods for the determination of the specificity factor (Sc/o), and also between Rubisco quantification methods, Rubisco purification versus crude extracts, and single-point versus CO2 curve measurements for the carboxylation turnover rate (kcatc) determination. Causes of the intraspecific laboratory-to-laboratory variability for Rubisco catalytic traits are discussed. This study provides a normalized kinetic dataset for model species to be used by the scientific community. Corrections and recommendations are also provided to reduce measurement variability, allowing the comparison of kinetic data obtained in different laboratories using different assay conditions.

Enhanced photosynthetic nitrogen use efficiency and increased nitrogen allocation to photosynthetic machinery under cotton domestication

Domestication involves dramatic phenotypic and physiological diversifications due to successive selection by breeders toward high yield and quality. Although photosynthetic nitrogen use efficiency (PNUE) is a major trait for understanding leaf nitrogen economy, it is unclear whether PNUE of cotton has been improved under domestication. Here, we investigated the effect of domestication on nitrogen allocation to photosynthetic machinery and PNUE in 25 wild and 37 domesticated cotton genotypes. The results showed that domesticated genotypes had higher nitrogen content per mass (N_m), net photosynthesis under saturated light (A_sat), and PNUE but similar nitrogen content per area (N_a) compared with wild genotypes. As expected, in both genotypes, PNUE was positively related to A_sat but negatively correlated with N_a. However, the relative contribution of A_sat to PNUE was greater than the contribution from N_a. Domesticated genotypes had higher nitrogen allocation to light-harvesting (N_L, nitrogen in light-harvesting chlorophyll-protein complex), to bioenergetics (N_b, total nitrogen of cytochrome f, ferredoxin NADP reductase, and the coupling factor), and to Rubisco (N_r) than wild genotypes; however, the two genotype groups did not differ in PNUE_p, the ratio of A_sat to N_p (itself the sum of N_L, N_b, and N_r). Our results suggest that more nitrogen allocation to photosynthetic machinery has boosted A_sat under cotton domestication. Improving the efficiency of nitrogen use in photosynthetic machinery might be future aim to enhance A_sat of cotton.

Eco-evolutionary optimality as a means to improve vegetation and land-surface models

Global vegetation and land-surface models embody interdisciplinary scientific understanding of the behaviour of plants and ecosystems, and are indispensable to project the impacts of environmental change on vegetation and the interactions between vegetation and climate. However, systematic errors and persistently large differences among carbon and water cycle projections by different models highlight the limitations of current process formulations. In this review, focusing on core plant functions in the terrestrial carbon and water cycles, we show how unifying hypotheses derived from eco-evolutionary optimality (EEO) principles can provide novel, parameter-sparse representations of plant and vegetation processes. We present case studies that demonstrate how EEO generates parsimonious representations of core, leaf-level processes that are individually testable and supported by evidence. EEO approaches to photosynthesis and primary production, dark respiration and stomatal behaviour are ripe for implementation in global models. EEO approaches to other important traits, including the leaf economics spectrum and applications of EEO at the community level are active research areas. Independently tested modules emerging from EEO studies could profitably be integrated into modelling frameworks that account for the multiple time scales on which plants and plant communities adjust to environmental change.

A procedure to introduce point mutations into the Rubisco large subunit gene in wild-type plants

Photosynthetic inefficiencies limit the productivity and sustainability of crop production and the resilience of agriculture to future societal and environmental challenges. Rubisco is a key target for improvement as it plays a central role in carbon fixation during photosynthesis and is remarkably inefficient. Introduction of mutations to the chloroplast-encoded Rubisco large subunit rbcL is of particular interest for improving the catalytic activity and efficiency of the enzyme. However, manipulation of rbcL is hampered by its location in the plastome, with many species recalcitrant to plastome transformation, and by the plastid's efficient repair system, which can prevent effective maintenance of mutations introduced with homologous recombination. Here we present a system where the introduction of a number of silent mutations into rbcL within the model plant Nicotiana tabacum facilitates simplified screening via additional restriction enzyme sites. This system was used to successfully generate a range of transplastomic lines from wild-type N. tabacum with stable point mutations within rbcL in 40% of the transformants, allowing assessment of the effect of these mutations on Rubisco assembly and activity. With further optimization the approach offers a viable way forward for mutagenic testing of Rubisco function in planta within tobacco and modification of rbcL in other crops where chloroplast transformation is feasible. The transformation strategy could also be applied to introduce point mutations in other chloroplast-encoded genes.

The effect of increasing temperature on crop photosynthesis: from enzymes to ecosystems

As global land surface temperature continues to rise and heatwave events increase in frequency, duration, and/or intensity, our key food and fuel cropping systems will likely face increased heat-related stress. A large volume of literature exists on exploring measured and modelled impacts of rising temperature on crop photosynthesis, from enzymatic responses within the leaf up to larger ecosystem-scale responses that reflect seasonal and interannual crop responses to heat. This review discusses (i) how crop photosynthesis changes with temperature at the enzymatic scale within the leaf; (ii) how stomata and plant transport systems are affected by temperature; (iii) what features make a plant susceptible or tolerant to elevated temperature and heat stress; and (iv) how these temperature and heat effects compound at the ecosystem scale to affect crop yields. Throughout the review, we identify current advancements and future research trajectories that are needed to make our cropping systems more resilient to rising temperature and heat stress, which are both projected to occur due to current global fossil fuel emissions.

Mechanisms underlying photosynthetic acclimation to high temperature are different between Vitis vinifera cv. Syrah and Grenache

Photosynthesis acclimation to high temperature differs among and within species. Grapevine intra-specific variation in photosynthetic acclimation to elevated temperature has been scarcely assessed. Our objectives were to (i) evaluate the mechanisms underlying long-term acclimation of photosynthesis to elevated temperature in grapevine, and (ii) determine whether these responses are similar among two varieties. A warming experiment with well irrigated Grenache and Syrah field-grown plants was performed during two growing seasons comparing plants exposed at ambient temperature (control) with plants in open-top chambers (heating) that increased mean air temperature between 1.5 and 3.6°C. Photosynthetic acclimation was assessed through the response of net assimilation (An), Rubisco carboxylation rate (Vcmax) and electron transport rate (Jmax), at leaf temperatures from 20 to 40°C. Our results evidenced different mechanisms for photosynthetic acclimation to elevated temperature. Compared with control, Grenache heated increased An, maintaining higher Vcmax and Jmax at temperatures above 35°C. By contrast, Syrah heated and control presented similar values of An, Vcmax and Jmax, evidencing an adjustment of photosynthesis without increasing C assimilation. Both varieties increased the optimum temperature for An, but to a lesser extent when growth temperature was higher. Our study provides evidence that grapevine varieties present different acclimation mechanisms to expected warming.

Key rules of life and the fading cryosphere: Impacts in alpine lakes and streams

Alpine regions are changing rapidly due to loss of snow and ice in response to ongoing climate change. While studies have documented ecological responses in alpine lakes and streams to these changes, our ability to predict such outcomes is limited. We propose that the application of fundamental rules of life can help develop necessary predictive frameworks. We focus on four key rules of life and their interactions: the temperature dependence of biotic processes from enzymes to evolution; the wavelength dependence of the effects of solar radiation on biological and ecological processes; the ramifications of the non-arbitrary elemental stoichiometry of life; and maximization of limiting resource use efficiency across scales. As the cryosphere melts and thaws, alpine lakes and streams will experience major changes in temperature regimes, absolute and relative inputs of solar radiation in ultraviolet and photosynthetically active radiation, and relative supplies of resources (e.g., carbon, nitrogen, and phosphorus), leading to nonlinear and interactive effects on particular biota, as well as on community and ecosystem properties. We propose that applying these key rules of life to cryosphere-influenced ecosystems will reduce uncertainties about the impacts of global change and help develop an integrated global view of rapidly changing alpine environments. However, doing so will require intensive interdisciplinary collaboration and international cooperation. More broadly, the alpine cryosphere is an example of a system where improving our understanding of mechanistic underpinnings of living systems might transform our ability to predict and mitigate the impacts of ongoing global change across the daunting scope of diversity in Earth's biota and environments.

Adaptive evolution shapes the present-day distribution of the thermal sensitivity of population growth rate

Developing a thorough understanding of how ectotherm physiology adapts to different thermal environments is of crucial importance, especially in the face of global climate change. A key aspect of an organism's thermal performance curve (TPC)-the relationship between fitness-related trait performance and temperature-is its thermal sensitivity, i.e., the rate at which trait values increase with temperature within its typically experienced thermal range. For a given trait, the distribution of thermal sensitivities across species, often quantified as "activation energy" values, is typically right-skewed. Currently, the mechanisms that generate this distribution are unclear, with considerable debate about the role of thermodynamic constraints versus adaptive evolution. Here, using a phylogenetic comparative approach, we study the evolution of the thermal sensitivity of population growth rate across phytoplankton (Cyanobacteria and eukaryotic microalgae) and prokaryotes (bacteria and archaea), 2 microbial groups that play a major role in the global carbon cycle. We find that thermal sensitivity across these groups is moderately phylogenetically heritable, and that its distribution is shaped by repeated evolutionary convergence throughout its parameter space. More precisely, we detect bursts of adaptive evolution in thermal sensitivity, increasing the amount of overlap among its distributions in different clades. We obtain qualitatively similar results from evolutionary analyses of the thermal sensitivities of 2 physiological rates underlying growth rate: net photosynthesis and respiration of plants. Furthermore, we find that these episodes of evolutionary convergence are consistent with 2 opposing forces: decrease in thermal sensitivity due to environmental fluctuations and increase due to adaptation to stable environments. Overall, our results indicate that adaptation can lead to large and relatively rapid shifts in thermal sensitivity, especially in microbes for which rapid evolution can occur at short timescales. Thus, more attention needs to be paid to elucidating the implications of rapid evolution in organismal thermal sensitivity for ecosystem functioning.

Rubisco and carbon-concentrating mechanism co-evolution across chlorophyte and streptophyte green algae

Green algae expressing a carbon-concentrating mechanism (CCM) are usually associated with a Rubisco-containing micro-compartment, the pyrenoid. A link between the small subunit (SSU) of Rubisco and pyrenoid formation in Chlamydomonas reinhardtii has previously suggested that specific RbcS residues could explain pyrenoid occurrence in green algae. A phylogeny of RbcS was used to compare the protein sequence and CCM distribution across the green algae and positive selection in RbcS was estimated. For six streptophyte algae, Rubisco catalytic properties, affinity for CO₂ uptake (K_0.5 ), carbon isotope discrimination (δ¹³ C) and pyrenoid morphology were compared. The length of the βA-βB loop in RbcS provided a phylogenetic marker discriminating chlorophyte from streptophyte green algae. Rubisco kinetic properties in streptophyte algae have responded to the extent of inducible CCM activity, as indicated by changes in inorganic carbon uptake affinity, δ¹³ C and pyrenoid ultrastructure between high and low CO₂ conditions for growth. We conclude that the Rubisco catalytic properties found in streptophyte algae have coevolved and reflect the strength of any CCM or degree of pyrenoid leakiness, and limitations to inorganic carbon in the aquatic habitat, whereas Rubisco in extant land plants reflects more recent selective pressures associated with improved diffusive supply of the terrestrial environment.

Robust leaf trait relationships across species under global environmental changes

Recent studies show coordinated relationships between plant leaf traits and their capacity to predict ecosystem functions. However, how leaf traits will change within species and whether interspecific trait relationships will shift under future environmental changes both remain unclear. Here, we examine the bivariate correlations between leaf economic traits of 515 species in 210 experiments which mimic climate warming, drought, elevated CO₂, and nitrogen deposition. We find divergent directions of changes in trait-pairs between species, and the directions mostly do not follow the interspecific trait relationships. However, the slopes in the logarithmic transformed interspecific trait relationships hold stable under environmental changes, while only their elevations vary. The elevation changes of trait relationship are mainly driven by asymmetrically interspecific responses contrary to the direction of the leaf economic spectrum. These findings suggest robust interspecific trait relationships under global changes, and call for linking within-species responses to interspecific coordination of plant traits.

It is unclear whether rapid global change will lead to unexpected trait combinations. In this global meta-analysis on vascular plants, Cui et al. show that, although within-species responses do not always follow the leaf economic spectrum, the slopes of interspecific trait relationships are robust to rapid environmental change.

A theory of plant function helps to explain leaf-trait and productivity responses to elevation

Several publications have examined leaf-trait and carbon-cycling shifts along an Amazon-Andes transect spanning 3.5 km in elevation and 16°C in mean annual temperature. Photosynthetic capacity was previously shown to increase as temperature declines with increasing elevation, counteracting enzyme-kinetic effects. Primary production declines, nonetheless, due to decreasing light availability. We aimed to predict leaf-trait and production gradients from first principles, using published data to test an emerging theory whereby photosynthetic traits and primary production depend on optimal acclimation and/or adaptation to environment. We re-analysed published data for 210 species at 25 sites, fitting linear relationships to elevation for both predicted and observed photosynthetic traits and primary production. Declining leaf-internal/ambient CO₂ ratio (χ) and increasing carboxylation (V_cmax ) and electron-transport (J_max ) capacities with increasing elevation were predicted. Increases in leaf nitrogen content with elevation were explained by increasing V_cmax and leaf mass-per-area. Leaf and soil phosphorus covaried, but after controlling for elevation, no nutrient metric accounted for any additional variance in photosynthetic traits. Primary production was predicted to decline with elevation. This analysis unifies leaf and ecosystem observations in a common theoretical framework. The insensitivity of primary production to temperature is shown to emerge as a consequence of the optimisation of photosynthetic traits.

Acclimation of leaf respiration consistent with optimal photosynthetic capacity

Plant respiration is an important contributor to the proposed positive global carbon-cycle feedback to climate change. However, as a major component, leaf mitochondrial ('dark') respiration (Rd ) differs among species adapted to contrasting environments and is known to acclimate to sustained changes in temperature. No accepted theory explains these phenomena or predicts its magnitude. Here we propose that the acclimation of Rd follows an optimal behaviour related to the need to maintain long-term average photosynthetic capacity (Vcmax ) so that available environmental resources can be most efficiently used for photosynthesis. To test this hypothesis, we extend photosynthetic co-ordination theory to predict the acclimation of Rd to growth temperature via a link to Vcmax , and compare predictions to a global set of measurements from 112 sites spanning all terrestrial biomes. This extended co-ordination theory predicts that field-measured Rd and Vcmax accessed at growth temperature (Rd,tg and Vcmax,tg ) should increase by 3.7% and 5.5% per degree increase in growth temperature. These acclimated responses to growth temperature are less steep than the corresponding instantaneous responses, which increase 8.1% and 9.9% per degree of measurement temperature for Rd and Vcmax respectively. Data-fitted responses proof indistinguishable from the values predicted by our theory, and smaller than the instantaneous responses. Theory and data are also shown to agree that the basal rates of both Rd and Vcmax assessed at 25°C (Rd,25 and Vcmax,25 ) decline by ~4.4% per degree increase in growth temperature. These results provide a parsimonious general theory for Rd acclimation to temperature that is simpler-and potentially more reliable-than the plant functional type-based leaf respiration schemes currently employed in most ecosystem and land-surface models.

How do vascular plants perform photosynthesis in extreme environments? An integrative ecophysiological and biochemical story

In this work, we review the physiological and molecular mechanisms that allow vascular plants to perform photosynthesis in extreme environments, such as deserts, polar and alpine ecosystems. Specifically, we discuss the morpho/anatomical, photochemical and metabolic adaptive processes that enable a positive carbon balance in photosynthetic tissues under extreme temperatures and/or severe water-limiting conditions in C₃ species. Nevertheless, only a few studies have described the in situ functioning of photoprotection in plants from extreme environments, given the intrinsic difficulties of fieldwork in remote places. However, they cover a substantial geographical and functional range, which allowed us to describe some general trends. In general, photoprotection relies on the same mechanisms as those operating in the remaining plant species, ranging from enhanced morphological photoprotection to increased scavenging of oxidative products such as reactive oxygen species. Much less information is available about the main physiological and biochemical drivers of photosynthesis: stomatal conductance (g_s ), mesophyll conductance (g_m ) and carbon fixation, mostly driven by RuBisCO carboxylation. Extreme environments shape adaptations in structures, such as cell wall and membrane composition, the concentration and activation state of Calvin-Benson cycle enzymes, and RuBisCO evolution, optimizing kinetic traits to ensure functionality. Altogether, these species display a combination of rearrangements, from the whole-plant level to the molecular scale, to sustain a positive carbon balance in some of the most hostile environments on Earth.

Evolutionary trends in RuBisCO kinetics and their co-evolution with CO2 concentrating mechanisms

RuBisCO-catalyzed CO₂ fixation is the main source of organic carbon in the biosphere. This enzyme is present in all domains of life in different forms (III, II, and I) and its origin goes back to 3500 Mya, when the atmosphere was anoxygenic. However, the RuBisCO active site also catalyzes oxygenation of ribulose 1,5-bisphosphate, therefore, the development of oxygenic photosynthesis and the subsequent oxygen-rich atmosphere promoted the appearance of CO₂ concentrating mechanisms (CCMs) and/or the evolution of a more CO₂ -specific RuBisCO enzyme. The wide variability in RuBisCO kinetic traits of extant organisms reveals a history of adaptation to the prevailing CO₂ /O₂ concentrations and the thermal environment throughout evolution. Notable differences in the kinetic parameters are found among the different forms of RuBisCO, but the differences are also associated with the presence and type of CCMs within each form, indicative of co-evolution of RuBisCO and CCMs. Trade-offs between RuBisCO kinetic traits vary among the RuBisCO forms and also among phylogenetic groups within the same form. These results suggest that different biochemical and structural constraints have operated on each type of RuBisCO during evolution, probably reflecting different environmental selective pressures. In a similar way, variations in carbon isotopic fractionation of the enzyme point to significant differences in its relationship to the CO₂ specificity among different RuBisCO forms. A deeper knowledge of the natural variability of RuBisCO catalytic traits and the chemical mechanism of RuBisCO carboxylation and oxygenation reactions raises the possibility of finding unrevealed landscapes in RuBisCO evolution.

Niche partitioning of microbial communities in riverine floodplains

Riverine floodplains exhibit high floral and faunal diversity as a consequence of their biophysical complexity. Extension of such niche partitioning processes to microbial communities is far less resolved or supported. Here, we evaluated the responses of aquatic biofilms diversity to environmental gradients across ten riverine floodplains with differing degrees of flow alteration and habitat diversity to assess whether complex floodplains support biofilm communities with greater biodiversity and species interactions. No significant evidence was found to support a central role for habitat diversity in promoting microbial diversity across 116 samples derived from 62 aquatic habitats, as neither α (H': 2.8-4.1) nor β (Sørensen: 0.3-0.39) diversity were positively related to floodplain complexity across the ten floodplains. In contrast, our results documented the sensitivity of biofilm communities to regional templates manifested as gradients of carbon, nitrogen, and phosphorous availability. Large-scale conditions reflecting nitrogen limitation increased the relative abundance of N-fixing cyanobacteria (up to 0.34 as fraction of total reads), constrained the total number of interactions among bacterial taxa, and reinforced negative over positive interactions, generating unique microbial communities and networks that reflect large-scale species sorting in response to regional geochemical gradients.

Carbon assimilation in crops at high temperatures

Global temperatures are rising, and higher rates of temperature increase are projected over land areas that encompass the globe's major agricultural regions. In addition to increased growing season temperatures, heat waves are predicted to become more common and severe. High temperatures can inhibit photosynthetic carbon gain of crop plants and thus threaten productivity, the effects of which may interact with other aspects of climate change. Here, we review the current literature assessing temperature effects on photosynthesis in key crops with special attention to field studies using crop canopy heating technology and in combination with other climate variables. We also discuss the biochemical reactions related to carbon fixation that may limit crop photosynthesis under warming temperatures and the current strategies for adaptation. Important progress has been made on several adaptation strategies demonstrating proof-of-concept for translating improved photosynthesis into higher yields. These are now poised to test in important food crops.

Different ways to die in a changing world: Consequences of climate change for tree species performance and survival through an ecophysiological perspective

Anthropogenic activities such as uncontrolled deforestation and increasing greenhouse gas emissions are responsible for triggering a series of environmental imbalances that affect the Earth's complex climate dynamics. As a consequence of these changes, several climate models forecast an intensification of extreme weather events over the upcoming decades, including heat waves and increasingly severe drought and flood episodes. The occurrence of such extreme weather will prompt profound changes in several plant communities, resulting in massive forest dieback events that can trigger a massive loss of biodiversity in several biomes worldwide. Despite the gravity of the situation, our knowledge regarding how extreme weather events can undermine the performance, survival, and distribution of forest species remains very fragmented. Therefore, the present review aimed to provide a broad and integrated perspective of the main biochemical, physiological, and morpho-anatomical disorders that may compromise the performance and survival of forest species exposed to climate change factors, particularly drought, flooding, and global warming. In addition, we also discuss the controversial effects of high CO2 concentrations in enhancing plant growth and reducing the deleterious effects of some extreme climatic events. We conclude with a discussion about the possible effects that the factors associated with the climate change might have on species distribution and forest composition.

Potential improvement of photosynthetic CO2 assimilation in crops by exploiting the natural variation in the temperature response of Rubisco catalytic traits

The enhancement of the photosynthetic capacity of crops by the expression of more efficient Rubisco versions has been a main target in the field of plant photosynthesis improvement. However, such an increase in the photosynthetic efficiency will depend on the environmental conditions and on the responsiveness of Rubisco to temperature and CO₂ availability. After an exhaustive compilation and standardization of the data published so far, a large natural variability in the thermal responses of Rubisco kinetic parameters in higher plant species was revealed. The variability observed was related to the photosynthetic type but a limited adaptation to the species thermal environment was found. We provide theoretical evidence that the existence of distinctive Rubisco responses to varying temperature and CO₂ concentration constitutes a promising avenue for increasing the photosynthetic capacity of important crops under future climatic conditions.

Plant evolutionary history mainly explains the variance in biomass responses to climate warming at a global scale

Evolutionary history shapes the interspecific relatedness and intraspecific variation, which has a profound influence on plant functional traits and productivity. However, it is far from clear how the phylogenetic relatedness among species and intraspecific variation could contribute to the observed variance in plant biomass responses to climate warming. We compiled a dataset with 284 species from warming experiments to explore the relative importance of phylogenetic, intraspecific, experimental and ecological factors to warming effects on plant biomass, using phylogenetic eigenvector regression and variance decomposition. Our results showed that phylogenetic relatedness could account for about half the total variance in biomass responses to warming, which were correlated with leaf economic traits at the family level but not at species level. The intraspecific variation contributed to approximately one-third of the variance, whereas the experimental design and ecological characteristics only explained 7-17%. These results suggest that intrinsic factors (evolutionary history) play more important roles than extrinsic factors (experimental treatment and environment) in determining the responses of plant biomass to warming at the global scale. This highlights the urgent need for land surface models to include evolutionary aspects in predicting ecosystem functions under climate change.

Acclimation and adaptation components of the temperature dependence of plant photosynthesis at the global scale

The temperature response of photosynthesis is one of the key factors determining predicted responses to warming in global vegetation models (GVMs). The response may vary geographically, owing to genetic adaptation to climate, and temporally, as a result of acclimation to changes in ambient temperature. Our goal was to develop a robust quantitative global model representing acclimation and adaptation of photosynthetic temperature responses. We quantified and modelled key mechanisms responsible for photosynthetic temperature acclimation and adaptation using a global dataset of photosynthetic CO₂ response curves, including data from 141 C₃ species from tropical rainforest to Arctic tundra. We separated temperature acclimation and adaptation processes by considering seasonal and common-garden datasets, respectively. The observed global variation in the temperature optimum of photosynthesis was primarily explained by biochemical limitations to photosynthesis, rather than stomatal conductance or respiration. We found acclimation to growth temperature to be a stronger driver of this variation than adaptation to temperature at climate of origin. We developed a summary model to represent photosynthetic temperature responses and showed that it predicted the observed global variation in optimal temperatures with high accuracy. This novel algorithm should enable improved prediction of the function of global ecosystems in a warming climate.

Rubisco carboxylation kinetics and inorganic carbon utilization in polar versus cold-temperate seaweeds

Despite the high productivity and ecological importance of seaweeds in polar coastal regions, little is known about their carbon utilization mechanisms, especially the kinetics of the CO2-fixing enzyme Rubisco. We analyzed Rubisco carboxylation kinetics at 4 °C and 25 °C in 12 diverse polar seaweed species (including cold-temperate populations of the same species) and the relationship with their ability to use bicarbonate, by using 13C isotope discrimination and pH drift experiments. We observed a large variation in Rubisco carboxylation kinetics among the selected species, although no correlation was found between either the Michaelis-Menten constant for CO2 (Kc) or Rubisco content per total soluble protein ([Rubisco]/[TSP]) and the ability to use bicarbonate for non-green seaweeds. This study reports intraspecific Rubisco cold adaptation by means of either higher Rubisco carboxylation turnover rate (kcatc) and carboxylase efficiency (kcatc/Kc) at 4 °C or higher [Rubisco]/[TSP] in some of the analyzed species. Our data point to a widespread ability for photosynthetic bicarbonate usage among polar seaweeds, despite the higher affinity of Rubisco for CO2 and higher dissolved CO2 concentration in cold seawater. Moreover, the reported catalytic variation within form ID Rubisco might avert the canonical trade-off previously observed between Kc and kcatc for plant Rubiscos.

Evaluating the kinetic basis of plant growth from organs to ecosystems

Contents Summary 37 I. Introduction 37 II. Predictions for metabolic kinetics 38 III. Kinetics of net photosynthesis 38 IV. Kinetics of plant growth 40 V. Hypotheses for higher-level kinetic decoupling 41 VI. Conclusions 42 Acknowledgements 42 References 42 SUMMARY: Understanding how temperature influences the scaling of physiological rates through levels of biological organization is critical for predicting plant responses to climate. Metabolic theory predicts that many rates increase exponentially with temperature following an activation energy (E) of 0.32 eV for photosynthesis. Here, I evaluate this prediction for net photosynthesis and organ, individual, and ecosystem growth. Observed E for photosynthesis varied widely but was not statistically different from predictions, while E for organs was greater than predicted, and E for individuals and ecosystems only weakly characterized temperature responses. I review several hypotheses that may underlie these results. Understanding how multiple rate-limiting processes coalesce into a single E that characterizes metabolic responses to temperature, and how to best estimate E from unimodal data, remain important challenges.

Wheat plant selection for high yields entailed improvement of leaf anatomical and biochemical traits including tolerance to non-optimal temperature conditions

Assessment of photosynthetic traits and temperature tolerance was performed on field-grown modern genotype (MG), and the local landrace (LR) of wheat (Triticum aestivum L.) as well as the wild relative species (Aegilops cylindrica Host.). The comparison was based on measurements of the gas exchange (A/c_i, light and temperature response curves), slow and fast chlorophyll fluorescence kinetics, and some growth and leaf parameters. In MG, we observed the highest CO₂ assimilation rate [Formula: see text] electron transport rate (J_max) and maximum carboxylation rate [Formula: see text]. The Aegilops leaves had substantially lower values of all photosynthetic parameters; this fact correlated with its lower biomass production. The mesophyll conductance was almost the same in Aegilops and MG, despite the significant differences in leaf phenotype. In contrary, in LR with a higher dry mass per leaf area, the half mesophyll conductance (g_m) values indicated more limited CO₂ diffusion. In Aegilops, we found much lower carboxylation capacity; this can be attributed mainly to thin leaves and lower Rubisco activity. The difference in CO₂ assimilation rate between MG and others was diminished because of its higher mitochondrial respiration activity indicating more intense metabolism. Assessment of temperature response showed lower temperature optimum and a narrow ecological valence (i.e., the range determining the tolerance limits of a species to an environmental factor) in Aegilops. In addition, analysis of photosynthetic thermostability identified the LR as the most sensitive. Our results support the idea that the selection for high yields was accompanied by the increase of photosynthetic productivity through unintentional improvement of leaf anatomical and biochemical traits including tolerance to non-optimal temperature conditions.

Increasing metabolic potential: C-fixation

Due to the growing world population, crop yields must increase to meet the rising demand. Crop plants also require adaptation to optimize performance in the changing environments caused by climate change. Improving photosynthetic carbon fixation is a promising, albeit technically challenging, strategy whose potential has only just begun to be considered in breeding programmes. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), a fundamental enzyme of carbon fixation, is extremely inefficient and many strategies to improve photosynthesis focus on overcoming the limitations of this enzyme, either by improving Rubisco activity and regulation or by improving the supply of substrates. Although progress is being made, the need to tailor solutions for each crop and their respective environments has been highlighted. Even so, continuing research will be required to achieve these objectives and to grow crops more sustainably in the future.

Positive Selection Driving Cytoplasmic Genome Evolution of the Medicinally Important Ginseng Plant Genus Panax

Panax L. (the ginseng genus) is a shade-demanding group within the family Araliaceae and all of its species are of crucial significance in traditional Chinese medicine. Phylogenetic and biogeographic analyses demonstrated that two rounds of whole genome duplications accompanying with geographic and ecological isolations promoted the diversification of Panax species. However, contributions of the cytoplasmic genomes to the adaptive evolution of Panax species remained largely uninvestigated. In this study, we sequenced the chloroplast and mitochondrial genomes of 11 accessions belonging to seven Panax species. Our results show that heterogeneity in nucleotide substitution rate is abundant in both of the two cytoplasmic genomes, with the mitochondrial genome possessing more variants at the total level but the chloroplast showing higher sequence polymorphisms at the genic regions. Genome-wide scanning of positive selection identified five and 12 genes from the chloroplast and mitochondrial genomes, respectively. Functional analyses further revealed that these selected genes play important roles in plant development, cellular metabolism and adaptation. We therefore conclude that positive selection might be one of the potential evolutionary forces that shaped nucleotide variation pattern of these Panax species. In particular, the mitochondrial genes evolved under stronger selective pressure compared to the chloroplast genes.

Improving models of photosynthetic thermal acclimation: Which parameters are most important and how many should be modified?

Photosynthetic temperature acclimation could strongly affect coupled vegetation-atmosphere feedbacks in the global carbon cycle, especially as the climate warms. Thermal acclimation of photosynthesis can be modelled as changes in the parameters describing the direct effect of temperature on photosynthetic capacity (i.e., activation energy, E_a ; deactivation energy, H_d ; entropy parameter, ΔS) or the basal value of photosynthetic capacity (i.e., photosynthetic capacity measured at 25°C). However, the impact of acclimating these parameters (individually or in combination) on vegetative carbon gain is relatively unexplored. Here we compare the ability of 66 photosynthetic temperature acclimation scenarios to improve the ability of a spatially explicit canopy carbon flux model, MAESTRA, to predict eddy covariance data from a loblolly pine forest. We show that: (1) incorporating seasonal temperature acclimation of basal photosynthetic capacity improves the model's ability to capture seasonal changes in carbon fluxes and outperforms acclimation of other single factors (i.e., E_a or ΔS alone); (2) multifactor scenarios of photosynthetic temperature acclimation provide minimal (if any) improvement in model performance over single factor acclimation scenarios; (3) acclimation of E_a should be restricted to the temperature ranges of the data from which the equations are derived; and (4) model performance is strongly affected by the H_d parameter. We suggest that a renewed effort be made into understanding whether basal photosynthetic capacity, E_a , H_d and ΔS co-acclimate across broad temperature ranges to determine whether and how multifactor thermal acclimation of photosynthesis occurs.

One-third of the plastid genes evolved under positive selection in PACMAD grasses

We demonstrate that rbcL underwent strong positive selection during the C ₃ -C ₄ photosynthetic transitions in PACMAD grasses, in particular the 3' end of the gene. In contrast, selective pressures on other plastid genes vary widely and environmental drivers remain to be identified. Plastid genomes have been widely used to infer phylogenetic relationships among plants, but the selective pressures driving their evolution have not been systematically investigated. In our study, we analyse all protein-coding plastid genes from 113 species of PACMAD grasses (Poaceae) to evaluate the selective pressures driving their evolution. Our analyses confirm that the gene encoding the large subunit of RubisCO (rbcL) evolved under strong positive selection after C₃-C₄ photosynthetic transitions. We highlight new codons in rbcL that underwent parallel changes, in particular those encoding the C-terminal part of the protein. C₃-C₄ photosynthetic shifts did not significantly affect the evolutionary dynamics of other plastid genes. Instead, while two-third of the plastid genes evolved under purifying selection or neutrality, 25 evolved under positive selection across the PACMAD clade. This set of genes encode for proteins involved in diverse functions, including self-replication of plastids and photosynthesis. Our results suggest that plastid genes widely adapt to changing ecological conditions, but factors driving this evolution largely remain to be identified.

Short-term thermal photosynthetic responses of C4 grasses are independent of the biochemical subtype

C4 photosynthesis evolved independently many times, resulting in multiple biochemical pathways; however, little is known about how these different pathways respond to temperature. We investigated the photosynthetic responses of eight C4 grasses belonging to three biochemical subtypes (NADP-ME, PEP-CK, and NAD-ME) to four leaf temperatures (18, 25, 32, and 40 °C). We also explored whether the biochemical subtype influences the thermal responses of (i) in vitro PEPC (Vpmax) and Rubisco (Vcmax) maximal activities, (ii) initial slope (IS) and CO2-saturated rate (CSR) derived from the A-Ci curves, and (iii) CO2 leakage out of the bundle sheath estimated from carbon isotope discrimination. We focussed on leakiness and the two carboxylases because they determine the coordination of the CO2-concentrating mechanism and are important for parameterizing the semi-mechanistic C4 photosynthesis model. We found that the thermal responses of Vpmax and Vcmax, IS, CSR, and leakiness varied among the C4 species independently of the biochemical subtype. No correlation was observed between Vpmax and IS or between Vcmax and CSR; while the ratios Vpmax/Vcmax and IS/CSR did not correlate with leakiness among the C4 grasses. Determining mesophyll and bundle sheath conductances in diverse C4 grasses is required to further elucidate how C4 photosynthesis responds to temperature.

Engineering photosynthesis: progress and perspectives

Photosynthesis is the basis of primary productivity on the planet. Crop breeding has sustained steady improvements in yield to keep pace with population growth increases. Yet these advances have not resulted from improving the photosynthetic process per se but rather of altering the way carbon is partitioned within the plant. Mounting evidence suggests that the rate at which crop yields can be boosted by traditional plant breeding approaches is wavering, and they may reach a “yield ceiling” in the foreseeable future. Further increases in yield will likely depend on the targeted manipulation of plant metabolism. Improving photosynthesis poses one such route, with simulations indicating it could have a significant transformative influence on enhancing crop productivity. Here, we summarize recent advances of alternative approaches for the manipulation and enhancement of photosynthesis and their possible application for crop improvement.

Metabolic compensation constrains the temperature dependence of gross primary production

Gross primary production (GPP) is the largest flux in the carbon cycle, yet its response to global warming is highly uncertain. The temperature dependence of GPP is directly linked to photosynthetic physiology, but the response of GPP to warming over longer timescales could also be shaped by ecological and evolutionary processes that drive variation in community structure and functional trait distributions. Here, we show that selection on photosynthetic traits within and across taxa dampens the effects of temperature on GPP across a catchment of geothermally heated streams. Autotrophs from cold streams had higher photosynthetic rates and after accounting for differences in biomass among sites, biomass-specific GPP was independent of temperature in spite of a 20 °C thermal gradient. Our results suggest that temperature compensation of photosynthetic rates constrains the long-term temperature dependence of GPP, and highlights the importance of considering physiological, ecological and evolutionary mechanisms when predicting how ecosystem-level processes respond to warming.

Photosynthetic limitations in two Antarctic vascular plants: importance of leaf anatomical traits and Rubisco kinetic parameters

Particular physiological traits allow the vascular plants Deschampsia antarctica Desv. and Colobanthus quitensis (Kunth) Bartl. to inhabit Antarctica. The photosynthetic performance of these species was evaluated in situ, focusing on diffusive and biochemical constraints to CO2 assimilation. Leaf gas exchange, Chl a fluorescence, leaf ultrastructure, and Rubisco catalytic properties were examined in plants growing on King George and Lagotellerie islands. In spite of the species- and population-specific effects of the measurement temperature on the main photosynthetic parameters, CO2 assimilation was highly limited by CO2 diffusion. In particular, the mesophyll conductance (gm)-estimated from both gas exchange and leaf chlorophyll fluorescence and modeled from leaf anatomy-was remarkably low, restricting CO2 diffusion and imposing the strongest constraint to CO2 acquisition. Rubisco presented a high specificity for CO2 as determined in vitro, suggesting a tight co-ordination between CO2 diffusion and leaf biochemistry that may be critical ultimately to optimize carbon balance in these species. Interestingly, both anatomical and biochemical traits resembled those described in plants from arid environments, providing a new insight into plant functional acclimation to extreme conditions. Understanding what actually limits photosynthesis in these species is important to anticipate their responses to the ongoing and predicted rapid warming in the Antarctic Peninsula.

Evidence that higher [CO2] increases tree growth sensitivity to temperature: a comparison of modern and paleo oaks

To test tree growth sensitivity to temperature under different ambient CO₂ concentrations, we determined stem radial growth rates as they relate to variation in temperature during the last deglacial period, and compare these to modern tree growth rates as they relate to spatial variation in temperature across the modern species distributional range. Paleo oaks were sampled from Northern Missouri, USA and compared to a pollen-based, high-resolution paleo temperature reconstruction from Northern Illinois, USA. Growth data were from 53 paleo bur oak log cross sections collected in Missouri. These oaks were preserved in river and stream sediments and were radiocarbon-dated to a period of rapid climate change during the last deglaciation (10.5 and 13.3 cal kyr BP). Growth data from modern bur oaks were obtained from increment core collections paired with USDA Forest Service Forest Inventory and Analysis data collected across the Great Plains, Midwest, and Upper Great Lakes regions. For modern oaks growing at an average [CO₂] of 330 ppm, growth sensitivity to temperature (i.e., the slope of growth rate versus temperature) was about twice that of paleo oaks growing at an average [CO₂] of 230 ppm. These data help to confirm that leaf-level predictions that photosynthesis and thus growth will be more sensitive to temperature at higher [CO₂] in mature trees-suggesting that tree growth forest productivity will be increasingly sensitive to temperature under projected global warming and high-[CO₂] conditions.

A roadmap for improving the representation of photosynthesis in Earth system models

Accurate representation of photosynthesis in terrestrial biosphere models (TBMs) is essential for robust projections of global change. However, current representations vary markedly between TBMs, contributing uncertainty to projections of global carbon fluxes. Here we compared the representation of photosynthesis in seven TBMs by examining leaf and canopy level responses of photosynthetic CO₂ assimilation (A) to key environmental variables: light, temperature, CO₂ concentration, vapor pressure deficit and soil water content. We identified research areas where limited process knowledge prevents inclusion of physiological phenomena in current TBMs and research areas where data are urgently needed for model parameterization or evaluation. We provide a roadmap for new science needed to improve the representation of photosynthesis in the next generation of terrestrial biosphere and Earth system models.

Engineering chloroplasts to improve Rubisco catalysis: prospects for translating improvements into food and fiber crops

494 I. 495 II. 496 III. 496 IV. 499 V. 499 VI. 501 VII. 501 VIII. 502 IX. 505 X. 506 507 References 507 SUMMARY: The uncertainty of future climate change is placing pressure on cropping systems to continue to provide stable increases in productive yields. To mitigate future climates and the increasing threats against global food security, new solutions to manipulate photosynthesis are required. This review explores the current efforts available to improve carbon assimilation within plant chloroplasts by engineering Rubisco, which catalyzes the rate-limiting step of CO₂ fixation. Fixation of CO₂ and subsequent cycling of 3-phosphoglycerate through the Calvin cycle provides the necessary carbohydrate building blocks for maintaining plant growth and yield, but has to compete with Rubisco oxygenation, which results in photorespiration that is energetically wasteful for plants. Engineering improvements in Rubisco is a complex challenge and requires an understanding of chloroplast gene regulatory pathways, and the intricate nature of Rubisco catalysis and biogenesis, to transplant more efficient forms of Rubisco into crops. In recent times, major advances in Rubisco engineering have been achieved through improvement of our knowledge of Rubisco synthesis and assembly, and identifying amino acid catalytic switches in the L-subunit responsible for improvements in catalysis. Improving the capacity of CO₂ fixation in crops such as rice will require further advances in chloroplast bioengineering and Rubisco biogenesis.

Warm preconditioning protects against acute heat-induced respiratory dysfunction and delays bleaching in a symbiotic sea anemone

Preconditioning to non-stressful warming can protect some symbiotic cnidarians against the high temperature-induced collapse of their mutualistic endosymbiosis with photosynthetic dinoflagellates (Symbiodinium spp.), a process known as bleaching. Here, we sought to determine whether such preconditioning is underpinned by differential regulation of aerobic respiration. We quantified in vivo metabolism and mitochondrial respiratory enzyme activity in the naturally symbiotic sea anemone Exaiptasia pallida preconditioned to 30°C for >7 weeks as well as anemones kept at 26°C. Preconditioning resulted in increased Symbiodinium photosynthetic activity and holobiont (host+symbiont) respiration rates. Biomass-normalised activities of host respiratory enzymes [citrate synthase and the mitochondrial electron transport chain (mETC) complexes I and IV] were higher in preconditioned animals, suggesting that increased holobiont respiration may have been due to host mitochondrial biogenesis and/or enlargement. Subsequent acute heating of preconditioned and 'thermally naive' animals to 33°C induced dramatic increases in host mETC complex I and Symbiodinium mETC complex II activities only in thermally naive E. pallida These changes were not reflected in the activities of other respiratory enzymes. Furthermore, bleaching in preconditioned E. pallida (defined as the significant loss of symbionts) was delayed by several days relative to the thermally naive group. These findings suggest that changes to mitochondrial biogenesis and/or function in symbiotic cnidarians during warm preconditioning might play a protective role during periods of exposure to stressful heating.

Temperature responses of Rubisco from Paniceae grasses provide opportunities for improving C3 photosynthesis

Enhancing the catalytic properties of the CO₂-fixing enzyme Rubisco is a target for improving agricultural crop productivity. Here, we reveal extensive diversity in the kinetic response between 10 and 37 °C by Rubisco from C₃ and C₄ species within the grass tribe Paniceae. The CO₂ fixation rate (kcatc) for Rubisco from the C₄ grasses with nicotinamide adenine dinucleotide (NAD) phosphate malic enzyme (NADP-ME) and phosphoenolpyruvate carboxykinase (PCK) photosynthetic pathways was twofold greater than the kcatc of Rubisco from NAD-ME species across all temperatures. The declining response of CO₂/O₂ specificity with increasing temperature was less pronounced for PCK and NADP-ME Rubisco, which would be advantageous in warmer climates relative to the NAD-ME grasses. Modelled variation in the temperature kinetics of Paniceae C₃ Rubisco and PCK Rubisco differentially stimulated C₃ photosynthesis relative to tobacco above and below 25 °C under current and elevated CO₂. Amino acid substitutions in the large subunit that could account for the catalytic variation among Paniceae Rubisco are identified; however, incompatibilities with Paniceae Rubisco biogenesis in tobacco hindered their mutagenic testing by chloroplast transformation. Circumventing these bioengineering limitations is critical to tailoring the properties of crop Rubisco to suit future climates.

Acclimation of Biochemical and Diffusive Components of Photosynthesis in Rice, Wheat, and Maize to Heat and Water Deficit: Implications for Modeling Photosynthesis

The impact of the combined effects of heat stress, increased vapor pressure deficit (VPD) and water deficit on the physiology of major crops needs to be better understood to help identifying the expected negative consequences of climate change and heat waves on global agricultural productivity. To address this issue, rice, wheat, and maize plants were grown under control temperature (CT, 25°C, VPD 1.8 kPa), and a high temperature (HT, 38°C, VPD 3.5 kPa), both under well-watered (WW) and water deficit (WD) conditions. Gas-exchange measurements showed that, in general, WD conditions affected the leaf conductance to CO2, while growth at HT had a more marked effect on the biochemistry of photosynthesis. When combined, HT and WD had an additive effect in limiting photosynthesis. The negative impacts of the imposed treatments on the processes governing leaf gas-exchange were species-dependent. Wheat presented a higher sensitivity while rice and maize showed a higher acclimation potential to increased temperature. Rubisco and PEPC kinetic constants determined in vitro at 25°C and 38°C were used to estimate Vcmax, Jmax, and Vpmax in the modeling of C3 and C4 photosynthesis. The results here obtained reiterate the need to use species-specific and temperature-specific values for Rubisco and PEPC kinetic constants for a precise parameterization of the photosynthetic response to changing environmental conditions in different crop species.

A compendium of temperature responses of Rubisco kinetic traits: variability among and within photosynthetic groups and impacts on photosynthesis modeling

The present study provides a synthesis of the in vitro and in vivo temperature responses of Rubisco Michaelis-Menten constants for CO2 (Kc) and O2 (Ko), specificity factor (Sc,o) and maximum carboxylase turnover rate (kcatc) for 49 species from all the main photosynthetic kingdoms of life. Novel correction routines were developed for in vitro data to remove the effects of study-to-study differences in Rubisco assays. The compilation revealed differences in the energy of activation (∆Ha) of Rubisco kinetics between higher plants and other photosynthetic groups, although photosynthetic bacteria and algae were under-represented and very few species have been investigated so far. Within plants, the variation in Rubisco temperature responses was related to species' climate and photosynthetic mechanism, with differences in ∆Ha for kcatc among C3 plants from cool and warm environments, and in ∆Ha for kcatc and Kc among C3 and C4 plants. A negative correlation was observed among ∆Ha for Sc/o and species' growth temperature for all data pooled, supporting the convergent adjustment of the temperature sensitivity of Rubisco kinetics to species' thermal history. Simulations of the influence of varying temperature dependences of Rubisco kinetics on Rubisco-limited photosynthesis suggested improved photosynthetic performance of C3 plants from cool habitats at lower temperatures, and C3 plants from warm habitats at higher temperatures, especially at higher CO2 concentration. Thus, variation in Rubisco kinetics for different groups of photosynthetic organisms might need consideration to improve prediction of photosynthesis in future climates. Comparisons between in vitro and in vivo data revealed common trends, but also highlighted a large variability among both types of Rubisco kinetics currently used to simulate photosynthesis, emphasizing the need for more experimental work to fill in the gaps in Rubisco datasets and improve scaling from enzyme kinetics to realized photosynthesis.

Temperature effects on fish production across a natural thermal gradient

Global warming is widely predicted to reduce the biomass production of top predators, or even result in species loss. Several exceptions to this expectation have been identified, however, and it is vital that we understand the underlying mechanisms if we are to improve our ability to predict future trends. Here, we used a natural warming experiment in Iceland and quantitative theoretical predictions to investigate the success of brown trout as top predators across a stream temperature gradient (4-25 °C). Brown trout are at the northern limit of their geographic distribution in this system, with ambient stream temperatures below their optimum for maximal growth, and above it in the warmest streams. A five-month mark-recapture study revealed that population abundance, biomass, growth rate, and production of trout all increased with stream temperature. We identified two mechanisms that contributed to these responses: (1) trout became more selective in their diet as stream temperature increased, feeding higher in the food web and increasing in trophic position; and (2) trophic transfer through the food web was more efficient in the warmer streams. We found little evidence to support a third potential mechanism: that external subsidies would play a more important role in the diet of trout with increasing stream temperature. Resource availability was also amplified through the trophic levels with warming, as predicted by metabolic theory in nutrient-replete systems. These results highlight circumstances in which top predators can thrive in warmer environments and contribute to our knowledge of warming impacts on natural communities and ecosystem functioning.