Elizabeth A. Ainsworth

Free-air CO(2) enrichment (FACE) experiments allow study of the effects of elevated [CO(2)] on plants and ecosystems grown under natural conditions without enclosure. Data from 120 primary, peer-reviewed articles describing physiology and production in the 12 large-scale FACE experiments (475-600 ppm) were collected and summarized using meta-analytic techniques. The results confirm some results from previous chamber experiments: light-saturated carbon uptake, diurnal C assimilation, growth and above-ground production increased, while specific leaf area and stomatal conductance decreased in elevated [CO(2)]. There were differences in FACE. Trees were more responsive than herbaceous species to elevated [CO(2)]. Grain crop yields increased far less than anticipated from prior enclosure studies. The broad direction of change in photosynthesis and production in elevated [CO(2)] may be similar in FACE and enclosure studies, but there are major quantitative differences: trees were more responsive than other functional types; C(4) species showed little response; and the reduction in plant nitrogen was small and largely accounted for by decreased Rubisco. The results from this review may provide the most plausible estimates of how plants in their native environments and field-grown crops will respond to rising atmospheric [CO(2)]; but even with FACE there are limitations, which are also discussed.

This review summarizes current understanding of the mechanisms that underlie the response of photosynthesis and stomatal conductance to elevated carbon dioxide concentration ([CO2]), and examines how downstream processes and environmental constraints modulate these two fundamental responses. The results from free-air CO2 enrichment (FACE) experiments were summarized via meta-analysis to quantify the mean responses of stomatal and photosynthetic parameters to elevated [CO2]. Elevation of [CO2] in FACE experiments reduced stomatal conductance by 22%, yet, this reduction was not associated with a similar change in stomatal density. Elevated [CO2] stimulated light-saturated photosynthesis (Asat) in C3 plants grown in FACE by an average of 31%. However, the magnitude of the increase in Asat varied with functional group and environment. Functional groups with ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)-limited photosynthesis at elevated [CO2] had greater potential for increases in Asat than those where photosynthesis became ribulose-1,5-bisphosphate (RubP)-limited at elevated [CO2]. Both nitrogen supply and sink capacity modulated the response of photosynthesis to elevated [CO2] through their impact on the acclimation of carboxylation capacity. Increased understanding of the molecular and biochemical mechanisms by which plants respond to elevated [CO2], and the feedback of environmental factors upon them, will improve our ability to predict ecosystem responses to rising [CO2] and increase our potential to adapt crops and managed ecosystems to future atmospheric [CO2].

▪ Abstract Atmospheric CO 2 concentration ([CO 2 ]) is now higher than it was at any time in the past 26 million years and is expected to nearly double during this century. Terrestrial plants with the C 3 photosynthetic pathway respond in the short term to increased [CO 2 ] via increased net photosynthesis and decreased transpiration. In the longer term this increase is often offset by downregulation of photosynthetic capacity. But much of what is currently known about plant responses to elevated [CO 2 ] comes from enclosure studies, where the responses of plants may be modified by size constraints and the limited life-cycle stages that are examined. Free-Air CO 2 Enrichment (FACE) was developed as a means to grow plants in the field at controlled elevation of CO 2 under fully open-air field conditions. The findings of FACE experiments are quantitatively summarized via meta-analytic statistics and compared to findings from chamber studies. Although trends agree with parallel summaries of enclosure studies, important quantitative differences emerge that have important implications both for predicting the future terrestrial biosphere and understanding how crops may need to be adapted to the changed and changing atmosphere.

Model projections suggest that although increased temperature and decreased soil moisture will act to reduce global crop yields by 2050, the direct fertilization effect of rising carbon dioxide concentration ([CO 2 ]) will offset these losses. The CO 2 fertilization factors used in models to project future yields were derived from enclosure studies conducted approximately 20 years ago. Free-air concentration enrichment (FACE) technology has now facilitated large-scale trials of the major grain crops at elevated [CO 2 ] under fully open-air field conditions. In those trials, elevated [CO 2 ] enhanced yield by ∼50% less than in enclosure studies. This casts serious doubt on projections that rising [CO 2 ] will fully offset losses due to climate change.

Plant responses to the projected future levels of CO(2) were first characterized in short-term experiments lasting days to weeks. However, longer term acclimation responses to elevated CO(2) were subsequently discovered to be very important in determining plant and ecosystem function. Free-Air CO(2) Enrichment (FACE) experiments are the culmination of efforts to assess the impact of elevated CO(2) on plants over multiple seasons and, in the case of crops, over their entire lifetime. FACE has been used to expose vegetation to elevated concentrations of atmospheric CO(2) under completely open-air conditions for nearly two decades. This review describes some of the lessons learned from the long-term investment in these experiments. First, elevated CO(2) stimulates photosynthetic carbon gain and net primary production over the long term despite down-regulation of Rubisco activity. Second, elevated CO(2) improves nitrogen use efficiency and, third, decreases water use at both the leaf and canopy scale. Fourth, elevated CO(2) stimulates dark respiration via a transcriptional reprogramming of metabolism. Fifth, elevated CO(2) does not directly stimulate C(4) photosynthesis, but can indirectly stimulate carbon gain in times and places of drought. Finally, the stimulation of yield by elevated CO(2) in crop species is much smaller than expected. While many of these lessons have been most clearly demonstrated in crop systems, all of the lessons have important implications for natural systems.

The current trajectory for crop yields is insufficient to nourish the world's population by 20501. Greater and more consistent crop production must be achieved against a backdrop of climatic stress that limits yields, owing to shifts in pests and pathogens, precipitation, heat-waves and other weather extremes. Here we consider the potential of plant sciences to address post-Green Revolution challenges in agriculture and explore emerging strategies for enhancing sustainable crop production and resilience in a changing climate. Accelerated crop improvement must leverage naturally evolved traits and transformative engineering driven by mechanistic understanding, to yield the resilient production systems that are needed to ensure future harvests.

Tropospheric ozone (O 3 ) is a global air pollutant that causes billions of dollars in lost plant productivity annually. It is an important anthropogenic greenhouse gas, and as a secondary air pollutant, it is present at high concentrations in rural areas far from industrial sources. It also reduces plant productivity by entering leaves through the stomata, generating other reactive oxygen species and causing oxidative stress, which in turn decreases photosynthesis, plant growth, and biomass accumulation. The deposition of O 3 into vegetation through stomata is an important sink for tropospheric O 3 , but this sink is modified by other aspects of environmental change, including rising atmospheric carbon dioxide concentrations, rising temperature, altered precipitation, and nitrogen availability. We review the atmospheric chemistry governing tropospheric O 3 mass balance, the effects of O 3 on stomatal conductance and net primary productivity, and implications for agriculture, carbon sequestration, and climate change.

Abstract The northern hemisphere temperate and boreal forests currently provide an important carbon sink; however, current tropospheric ozone concentrations ([O 3 ]) and [O 3 ] projected for later this century are damaging to trees and have the potential to reduce the carbon sink strength of these forests. This meta‐analysis estimated the magnitude of the impacts of current [O 3 ] and future [O 3 ] on the biomass, growth, physiology and biochemistry of trees representative of northern hemisphere forests. Current ambient [O 3 ] (40 ppb on average) significantly reduced the total biomass of trees by 7% compared with trees grown in charcoal‐filtered (CF) controls, which approximate preindustrial [O 3 ]. Above‐ and belowground productivity were equally affected by ambient [O 3 ] in these studies. Elevated [O 3 ] of 64 ppb reduced total biomass by 11% compared with trees grown at ambient [O 3 ] while elevated [O 3 ] of 97 ppb reduced total biomass of trees by 17% compared with CF controls. The root‐to‐shoot ratio was significantly reduced by elevated [O 3 ] indicating greater sensitivity of root biomass to [O 3 ]. At elevated [O 3 ], trees had significant reductions in leaf area, Rubisco content and chlorophyll content which may underlie significant reductions in photosynthetic capacity. Trees also had lower transpiration rates, and were shorter in height and had reduced diameter when grown at elevated [O 3 ]. Further, at elevated [O 3 ], gymnosperms were significantly less sensitive than angiosperms. There were too few observations of the interaction of [O 3 ] with elevated [CO 2 ] and drought to conclusively project how these climate change factors will alter tree responses to [O 3 ]. Taken together, these results demonstrate that the carbon‐sink strength of northern hemisphere forests is likely reduced by current [O 3 ] and will be further reduced in future if [O 3 ] rises. This implies that a key carbon sink currently offsetting a significant portion of global fossil fuel CO 2 emissions could be diminished or lost in the future.

Abstract While increasing temperatures and altered soil moisture arising from climate change in the next 50 years are projected to decrease yield of food crops, elevated CO2 concentration ([CO2]) is predicted to enhance yield and offset these detrimental factors. However, C4 photosynthesis is usually saturated at current [CO2] and theoretically should not be stimulated under elevated [CO2]. Nevertheless, some controlled environment studies have reported direct stimulation of C4 photosynthesis and productivity, as well as physiological acclimation, under elevated [CO2]. To test if these effects occur in the open air and within the Corn Belt, maize (Zea mays) was grown in ambient [CO2] (376 μmol mol−1) and elevated [CO2] (550 μmol mol−1) using Free-Air Concentration Enrichment technology. The 2004 season had ideal growing conditions in which the crop did not experience water stress. In the absence of water stress, growth at elevated [CO2] did not stimulate photosynthesis, biomass, or yield. Nor was there any CO2 effect on the activity of key photosynthetic enzymes, or metabolic markers of carbon and nitrogen status. Stomatal conductance was lower (−34%) and soil moisture was higher (up to 31%), consistent with reduced crop water use. The results provide unique field evidence that photosynthesis and production of maize may be unaffected by rising [CO2] in the absence of drought. This suggests that rising [CO2] may not provide the full dividend to North American maize production anticipated in projections of future global food supply.

Abstract Rice is arguably the most important food source on the planet and is consumed by over half of the world's population. Considerable increases in yield are required over this century to continue feeding the world's growing population. This meta‐analysis synthesizes the research to date on rice responses to two elements of global change, rising atmospheric carbon dioxide concentration ([CO 2 ]) and rising tropospheric ozone concentration ([O 3 ]). On an average, elevated [CO 2 ] (627 ppm) increased rice yields by 23%. Modest increases in grain mass and larger increases in panicle and grain number contributed to this response. The response of rice to elevated [CO 2 ] varied with fumigation technique. The more closely the fumigation conditions mimicked field conditions, the smaller was the stimulation of yield by elevated [CO 2 ]. Free air concentration enrichment (FACE) experiments showed only a 12% increase in rice yield. The rise in atmospheric [CO 2 ] will be accompanied by increases in tropospheric O 3 and temperature. When compared with rice grown in charcoal‐filtered air, rice exposed to 62 ppb O 3 showed a 14% decrease in yield. Many determinants of yield, including photosynthesis, biomass, leaf area index, grain number and grain mass, were reduced by elevated [O 3 ]. While there have been too few studies of the interaction of CO 2 and O 3 for meta‐analysis, the interaction of temperature and CO 2 has been studied more widely. Elevated temperature treatments negated any enhancement in rice yield at elevated [CO 2 ], which suggests that identifying high temperature tolerant germplasm will be key to realizing yield benefits in the future.

Abstract The effects of elevated [CO 2 ] on 25 variables describing soybean physiology, growth and yield are reviewed using meta‐analytic techniques. This is the first meta‐analysis to our knowledge performed on a single crop species and summarizes the effects of 111 studies. These primary studies include numerous soybean growth forms, various stress and experimental treatments, and a range of elevated [CO 2 ] levels (from 450 to 1250 p.p.m.), with a mean of 689 p.p.m. across all studies. Stimulation of soybean leaf CO 2 assimilation rate with growth at elevated [CO 2 ] was 39%, despite a 40% decrease in stomatal conductance and a 11% decrease in Rubisco activity. Increased leaf CO 2 uptake combined with an 18% stimulation in leaf area to provide a 59% increase in canopy photosynthetic rate. The increase in total dry weight was lower at 37%, and seed yield still lower at 24%. This shows that even in an agronomic species selected for maximum investment in seed, several plant level feedbacks prevent additional investment in reproduction, such that yield fails to reflect fully the increase in whole plant carbon uptake. Large soil containers (> 9 L) have been considered adequate for assessing plant responses to elevated [CO 2 ]. However, in open‐top chamber experiments, soybeans grown in large pots showed a significant threefold smaller stimulation in yield than soybeans grown in the ground. This suggests that conclusions about plant yield based on pot studies, even when using very large containers, are a poor reflection of performance in the absence of any physical restriction on root growth. This review supports a number of current paradigms of plant responses to elevated [CO 2 ]. Namely, stimulation of photosynthesis is greater in plants that fix N and have additional carbohydrate sinks in nodules. This supports the notion that photosynthetic capacity decreases when plants are N‐limited, but not when plants have adequate N and sink strength. The root : shoot ratio did not change with growth at elevated [CO 2 ], sustaining the charge that biomass allocation is unaffected by growth at elevated [CO 2 ] when plant size and ontogeny are considered.

ABSTRACT The surface concentration of ozone ([O 3 ]) has risen from less than 10 ppb prior to the industrial revolution to a day‐time mean concentration of approximately 40 ppb over much of the northern temperate zone. If current global emission trends continue, surface [O 3 ] is projected to rise a further 50% over this century, with larger increases in many locations including Northern Hemisphere forests. This review uses statistical meta‐analysis to determine mean effects, and their confidence limits, of both the current and projected elevations of [O 3 ] on light‐saturated photosynthetic CO 2 uptake ( A sat ) and stomatal conductance ( g s ) in trees. In total, 348 measurements of A sat from 61 studies and 266 measures of g s from 55 studies were reviewed. Results suggested that the elevation of [O 3 ] that has occurred since the industrial revolution is depressing A sat and g s by 11% (CI 9–13%) and 13% (CI 11–15%), respectively, where CI is the 95% confidence interval. In contrast to angiosperms, gymnosperms were not significantly affected. Both drought and elevated [CO 2 ] significantly decreased the effect of ambient [O 3 ]. Younger trees (<4 years) were affected less than older trees. Elevation of [O 3 ] above current levels caused progressively larger losses of A sat and g s , including gymnosperms. Results are consistent with the expectation that damage to photosynthesis depends on the cumulative uptake of ozone (O 3 ) into the leaf. Thus, factors that lower g s lessen damage. Where both g s and [O 3 ] were recorded, an overall decline in A sat of 0.21% per mmol m −2 of estimated cumulative O 3 uptake was calculated. These findings suggest that rising [O 3 ], an often overlooked aspect of global atmospheric change, is progressively depressing the ability of temperate and boreal forests to assimilate carbon and transfer water vapour to the atmosphere, with significant potential effects on terrestrial carbon sinks and regional hydrologies.

Abstract We quantitatively evaluated the effects of elevated concentration of ozone (O 3 ) on growth, leaf chemistry, gas exchange, grain yield, and grain quality relative to carbon‐filtered air (CF) by means of meta‐analysis of published data. Our database consisted of 53 peer‐reviewed studies published between 1980 and 2007, taking into account wheat type, O 3 fumigation method, rooting environment, O 3 concentration ([O 3 ]), developmental stage, and additional treatments such as drought and elevated carbon dioxide concentration ([CO 2 ]). The results suggested that elevated [O 3 ] decreased wheat grain yield by 29% (CI: 24–34%) and aboveground biomass by 18% (CI: 13–24%), where CI is the 95% confidence interval. Even in studies where the [O 3 ] range was between 31 and 59 ppb (average 43 ppb), there was a significant decrease in the grain yield (18%) and biomass (16%) relative to CF. Despite the increase in the grain protein content (6.8%), elevated [O 3 ] significantly decreased the grain protein yield (−18%). Relative to CF, elevated [O 3 ] significantly decreased photosynthetic rates (−20%), Rubisco activity (−19%), stomatal conductance (−22%), and chlorophyll content (−40%). For the whole plant, rising [O 3 ] induced a larger decrease in belowground (−27%) biomass than in aboveground (−18%) biomass. There was no significant response difference between spring wheat and winter wheat. Wheat grown in the field showed larger decreases in leaf photosynthesis parameters than wheat grown in < 5 L pots. Open‐top chamber fumigation induced a larger reduction than indoor growth chambers, when plants were exposed to elevated [O 3 ]. The detrimental effect was progressively greater as the average daily [O 3 ] increased, with very few exceptions. The impact of O 3 increased with developmental stages, with the largest detrimental impact during grain filling. Both drought and elevated [CO 2 ] significantly ameliorated the detrimental effects of elevated [O 3 ], which could be explained by a significant decrease in O 3 uptake resulting from decreased stomatal conductance.

ABSTRACT Surface ozone concentrations ([O 3 ]) during the growing season in much of the northern temperate zone reach mean peak daily concentrations of 60 p.p.b. Concentrations are predicted to continue to rise over much of the globe during the next 50 years. Although these low levels of ozone may not induce visible symptoms on most vegetation, they can result in substantial losses of production and reproductive output. Establishing the vulnerability of vegetation to rising background ozone is complicated by marked differences in findings between individual studies. Ozone effects are influenced by exposure dynamics, nutrient and moisture conditions, and the species and cultivars that are investigated. Meta‐analytic techniques provide an objective means to quantitatively summarize treatment responses. Soybean has been the subject of many studies of ozone effects. It is both the most widely planted dicotyledonous crop and a model for other C 3 annual plants. Meta‐analytic techniques were used to quantitatively summarize the response of soybean to an average, chronic ozone exposure of 70 p.p.b., from 53 peer‐reviewed studies. At maturity, the average shoot biomass was decreased 34% and seed yield was 24% lower. Even in studies where [O 3 ] was < 60 p.p.b., there was a significant decrease in biomass and seed production. At low [O 3 ], decreased production corresponded to a decrease in leaf photosynthesis, but in higher [O 3 ] the larger loss in production was associated with decreases in both leaf photosynthesis and leaf area. The impact of ozone increased with developmental stage, with little effect on vegetative growth and the greatest effect evident at completion of seed filling. Other stress treatments, including UV‐B and drought, did not alter the ozone response. Elevated carbon dioxide significantly decreased ozone‐induced losses, which may be explained by a significant decrease in stomatal conductance.

The phloem is a central component of the plant9s complex vascular system that plays a vital role in moving photoassimilates from sites of primary acquisition to the heterotrophic tissues and organs of the plant. Indeed, as much as 50-80% of the CO2 photoassimilated in a mature leaf is transported out of the leaf in the phloem to satisfy the needs of the non-photosynthetic organs of the plant (Kalt-Torres et al., 1987). In recent years, new data has shown that the phloem also plays a key role in moving information molecules that coordinate many facets of plant growth and development (Turgeon and Wolf, 2009). This update will focus on phloem loading9s contribution to assimilate partitioning, and its role in balancing photosynthetic activity with sink utilization of photoassimilates.

Acclimation of photosynthesis to elevated atmospheric carbon dioxide concentration was tested in lines of soybean (Glycine max) that differed by single genes that altered either the capacity to nodulate or growth habit (determinate or indeterminate growth). Both genetic changes provided, within a uniform genetic background, a test of the “source–sink” hypothesis that down-regulation of photosynthesis in elevated carbon dioxide is a result of inability to form sufficient “sinks” for the additional photosynthate. Plants were grown under ambient and elevated [CO2] (550 μmol mol−1) in the field, using free air gas concentration enrichment (FACE). Mutation of the determinate cultivar, Elf, to an indeterminate form did not result in increased responsiveness to elevated [CO2]. This may reflect a large sink capacity in the selection of determinate cultivars. In elevated [CO2] only the determinate isoline of the indeterminate cultivar (Williams-dt1) and the non-nodulating genotype showed down-regulation of photosynthesis. This resulted from decreases in apparent in vivo Rubisco activity (Vc,max) and maximum rate of electron transport (Jmax). Increase in total non-structural carbohydrate (TNC) content, which is often correlated with down-regulation of photosynthesis, in Williams-dt1 was 80% greater in elevated [CO2] than in ambient [CO2] controls, compared to 40% in the indeterminate line. The results from mutations of the Williams line are consistent with the hypothesis that genetic capacity for the utilization of photosynthate is critical to the ability of plants to sustain increased photosynthesis when grown at elevated [CO2].

Concentrations of ground-level ozone ([O3 ]) over much of the Earth's land surface have more than doubled since pre-industrial times. The air pollutant is highly variable over time and space, which makes it difficult to assess the average agronomic and economic impacts of the pollutant as well as to breed crops for O3 tolerance. Recent modeling efforts have improved quantitative understanding of the effects of current and future [O3 ] on global crop productivity, and experimental advances have improved understanding of the cellular O3 sensing, signaling and response mechanisms. This work provides the fundamental background and justification for breeding and biotechnological approaches for improving O3 tolerance in crops. There is considerable within-species variation in O3 tolerance in crops, which has been used to create mapping populations for screening. Quantitative trait loci (QTL) for O3 tolerance have been identified in model and crop species, and although none has been cloned to date, transcript profiling experiments have identified candidate genes associated with QTL. Biotechnological strategies for improving O3 tolerance are also being tested, although there is considerable research to be done before O3 -tolerant germplasm is available to growers for most crops. Strategies to improve O3 tolerance in crops have been hampered by the lack of translation of laboratory experiments to the field, and the lack of correlation between visual leaf-level O3 damage and yield loss to O3 stress. Future efforts to screen mapping populations in the field and to identify more promising phenotypes for O3 tolerance are needed.

Abstract Free‐air CO 2 enrichment (FACE) allows open‐air elevation of [CO 2 ] without altering the microclimate. Its scale uniquely supports simultaneous study from physiology and yield to soil processes and disease. In 2005 we summarized results of then 28 published observations by meta‐analysis. Subsequent studies have combined FACE with temperature, drought, ozone, and nitrogen treatments. Here, we summarize the results of now almost 250 observations, spanning 14 sites and five continents. Across 186 independent studies of 18 C 3 crops, elevation of [CO 2 ] by ca. 200 ppm caused a ca. 18% increase in yield under non‐stress conditions. Legumes and root crops showed a greater increase and cereals less. Nitrogen deficiency reduced the average increase to 10%, as did warming by ca. 2°C. Two conclusions of the 2005 analysis were that C 4 crops would not be more productive in elevated [CO 2 ], except under drought, and that yield responses of C 3 crops were diminished by nitrogen deficiency and wet conditions. Both stand the test of time. Further studies of maize and sorghum showed no yield increase, except in drought, while soybean productivity was negatively affected by early growing season wet conditions. Subsequent study showed reduced levels of nutrients, notably Zn and Fe in most crops, and lower nitrogen and protein in the seeds of non‐leguminous crops. Testing across crop germplasm revealed sufficient variation to maintain nutrient content under rising [CO 2 ]. A strong correlation of yield response under elevated [CO 2 ] to genetic yield potential in both rice and soybean was observed. Rice cultivars with the highest yield potential showed a 35% yield increase in elevated [CO 2 ] compared to an average of 14%. Future FACE experiments have the potential to develop cultivars and management strategies for co‐promoting sustainability and productivity under future elevated [CO 2 ].

Future agricultural production will encounter multifaceted challenges from global climate change. Carbon dioxide (CO2) and other greenhouse gases are accumulating in the atmosphere at unprecedented rates, causing increased radiative forcing ([Le Quere et al., 2009][1]; [Shindell et al., 2009][2

Soybean (Glycine max Merr.) is the world’s most widely grown leguminous crop and an important source of protein and oil for food and feed. Soybean yields have increased substantially throughout the past century, with yield gains widely attributed to genetic advances and improved cultivars as well as advances in farming technology and practice. Yet, the physiological mechanisms underlying the historical improvements in soybean yield have not been studied rigorously. In this 2-year experiment, 24 soybean cultivars released between 1923 and 2007 were grown in field trials. Physiological improvements in the efficiencies by which soybean canopies intercepted light (εi), converted light energy into biomass (εc), and partitioned biomass into seed (εp) were examined. Seed yield increased by 26.5kg ha–1 year–1, and the increase in seed yield was driven by improvements in all three efficiencies. Although the time to canopy closure did not change in historical soybean cultivars, extended growing seasons and decreased lodging in more modern lines drove improvements in εi. Greater biomass production per unit of absorbed light resulted in improvements in εc. Over 84 years of breeding, soybean seed biomass increased at a rate greater than total aboveground biomass, resulting in an increase in εp. A better understanding of the physiological basis for yield gains will help to identify targets for soybean improvement in the future.

High-throughput, noninvasive field phenotyping has revealed genetic variation in crop morphological, developmental, and agronomic traits, but rapid measurements of the underlying physiological and biochemical traits are needed to fully understand genetic variation in plant-environment interactions. This study tested the application of leaf hyperspectral reflectance (λ = 500-2,400 nm) as a high-throughput phenotyping approach for rapid and accurate assessment of leaf photosynthetic and biochemical traits in maize (Zea mays). Leaf traits were measured with standard wet-laboratory and gas-exchange approaches alongside measurements of leaf reflectance. Partial least-squares regression was used to develop a measure of leaf chlorophyll content, nitrogen content, sucrose content, specific leaf area, maximum rate of phosphoenolpyruvate carboxylation, [CO2]-saturated rate of photosynthesis, and leaf oxygen radical absorbance capacity from leaf reflectance spectra. Partial least-squares regression models accurately predicted five out of seven traits and were more accurate than previously used simple spectral indices for leaf chlorophyll, nitrogen content, and specific leaf area. Correlations among leaf traits and statistical inferences about differences among genotypes and treatments were similar for measured and modeled data. The hyperspectral reflectance approach to phenotyping was dramatically faster than traditional measurements, enabling over 1,000 rows to be phenotyped during midday hours over just 2 to 4 d, and offers a nondestructive method to accurately assess physiological and biochemical trait responses to environmental stress.

We review current knowledge of the processes by which ozone will cause injury and damage to crop plants. We do this both through an understanding of the limitations to ozone uptake (i.e. ozone being transferred from some height in the atmosphere to the leaf boundary layer and subsequent uptake via the stomata) as well as through the internal plant processes that will result in the absorbed ozone dose causing damage and/or injury. We consider these processes across a range of scales by which ozone impacts plants, from cellular metabolism influencing leaf level physiology up to whole canopy and root system processes and feedbacks. We explore how these impacts affect leaf level photosynthesis and senescence (and associated carbon assimilation) as well as whole canopy resource acquisition (e.g. water and nutrients) and ultimately crop growth and yield. We consider these processes from the viewpoint of developing crop growth models capable of incorporating key ozone impact processes within modelling structures that assess crop growth under a variety of different abiotic stresses. These models would provide a dynamic assessment of the impact of ozone within the context of other key variables considered important in determining crop growth and yield. We consider the ability to achieve such modelling through an assessment of the different types of crop model currently available (e.g. empirical, radiation use efficiency, and photosynthesis based crop growth models). Finally, we show how international activities such as the AgMIP (Agricultural Modelling and Improvement Intercomparison Project) could see crop growth modellers collaborate to assess the capabilities of different crop models to simulate the effects of ozone and other stresses. The development of robust crop growth models capable of including ozone effects would substantially improve future national, regional and global risk assessments that aim to assess the role that ozone might play under future climatic conditions in limiting food supply.

Abstract Introduction of high‐performing crop cultivars and crop/soil water management practices that increase the stomatal uptake of carbon dioxide and photosynthesis will be instrumental in realizing the United Nations Sustainable Development Goal ( SDG ) of achieving food security. To date, however, global assessments of how to increase crop yield have failed to consider the negative effects of tropospheric ozone, a gaseous pollutant that enters the leaf stomatal pores of plants along with carbon dioxide, and is increasing in concentration globally, particularly in rapidly developing countries. Earlier studies have simply estimated that the largest effects are in the areas with the highest ozone concentrations. Using a modelling method that accounts for the effects of soil moisture deficit and meteorological factors on the stomatal uptake of ozone, we show for the first time that ozone impacts on wheat yield are particularly large in humid rain‐fed and irrigated areas of major wheat‐producing countries (e.g. United States, France, India, China and Russia). Averaged over 2010–2012, we estimate that ozone reduces wheat yields by a mean 9.9% in the northern hemisphere and 6.2% in the southern hemisphere, corresponding to some 85 Tg (million tonnes) of lost grain. Total production losses in developing countries receiving Official Development Assistance are 50% higher than those in developed countries, potentially reducing the possibility of achieving UN SDG 2. Crucially, our analysis shows that ozone could reduce the potential yield benefits of increasing irrigation usage in response to climate change because added irrigation increases the uptake and subsequent negative effects of the pollutant. We show that mitigation of air pollution in a changing climate could play a vital role in achieving the above‐mentioned UN SDG , while also contributing to other SDG s related to human health and well‐being, ecosystems and climate change.

Significance Although it has long been known that ground-level ozone (O 3 ) damages crops and reduces yield, there has never been an estimate of the total loss attributed to ambient O 3 for field-grown maize and soybean in the United States. Knowing the loss caused by this pollutant would be useful for projecting food supply and setting regulatory standards for pollutant emissions. Here we show that ambient O 3 has reduced maize and soybean yields in rain-fed fields by ∼10% and 5%, respectively, based on historical observations from the past 31 y. Results suggest that air-quality regulations in the United States have been effective in reducing crop production losses to O 3 , and indicate that further reductions in ground-level [O 3 ] would be beneficial in the United States and globally.

Spectroscopy is becoming an increasingly powerful tool to alleviate the challenges of traditional measurements of key plant traits at the leaf, canopy, and ecosystem scales. Spectroscopic methods often rely on statistical approaches to reduce data redundancy and enhance useful prediction of physiological traits. Given the mechanistic uncertainty of spectroscopic techniques, genetic modification of plant biochemical pathways may affect reflectance spectra causing predictive models to lose power. The objectives of this research were to assess over two separate years, whether a predictive model can represent natural and imposed variation in leaf photosynthetic potential for different crop cultivars and genetically modified plants, to assess the interannual capabilities of a partial least square regression (PLSR) model, and to determine whether leaf N is a dominant driver of photosynthesis in PLSR models. In 2016, a PLSR analysis of reflectance spectra coupled with gas exchange data was used to build predictive models for photosynthetic parameters including maximum carboxylation rate of Rubisco (Vc,max ), maximum electron transport rate (Jmax ) and percentage leaf nitrogen ([N]). The model was developed for wild type and genetically modified plants that represent a wide range of photosynthetic capacities. Results show that hyperspectral reflectance accurately predicted Vc,max, Jmax and [N] for all plants measured in 2016. Applying these PLSR models to plants grown in 2017 resulted in a strong predictive ability relative to gas exchange measurements for Vc,max, but not for Jmax, and not for genotypes unique to 2017. Building a new model including data collected in 2017 resulted in more robust predictions, with R2 increases of 17% for Vc,max . and 13% Jmax . Plants generally have a positive correlation between leaf nitrogen and photosynthesis, however, tobacco with reduced Rubisco (SSuD) had significantly higher [N] despite much lower Vc,max. The PLSR model was able to accurately predict both lower Vc,max and higher leaf [N] for this genotype suggesting that the spectral based estimates of Vc,max and leaf nitrogen [N] are independent. These results suggest that the PLSR model can be applied across years, but only to genotypes used to build the model and that the actual mechanism measured with the PLSR technique is not directly related to leaf [N]. The success of the leaf-scale analysis suggests that similar approaches may be successful at the canopy and ecosystem scales but to use these methods across years and between genotypes at any scale, application of accurately populated physical based models based on radiative transfer principles may be required.

Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.

Predictions of yield for the globe's major grain and legume arable crops suggest that, with a moderate temperature increase, production may increase in the temperate zone, but decline in the tropics. In total, global food supply may show little change. This security comes from inclusion of the direct effect of rising carbon dioxide (CO 2 ) concentration, [CO 2 ], which significantly stimulates yield by decreasing photorespiration in C 3 crops and transpiration in all crops. Evidence for a large response to [CO 2 ] is largely based on studies made within chambers at small scales, which would be considered unacceptable for standard agronomic trials of new cultivars or agrochemicals. Yet, predictions of the globe's future food security are based on such inadequate information. Free-Air Concentration Enrichment (FACE) technology now allows investigation of the effects of rising [CO 2 ] and ozone on field crops under fully open-air conditions at an agronomic scale. Experiments with rice, wheat, maize and soybean show smaller increases in yield than anticipated from studies in chambers. Experiments with increased ozone show large yield losses (20%), which are not accounted for in projections of global food security. These findings suggest that current projections of global food security are overoptimistic. The fertilization effect of CO 2 is less than that used in many models, while rising ozone will cause large yield losses in the Northern Hemisphere. Unfortunately, FACE studies have been limited in geographical extent and interactive effects of CO 2 , ozone and temperature have yet to be studied. Without more extensive study of the effects of these changes at an agronomic scale in the open air, our ever-more sophisticated models will continue to have feet of clay.

New PhytologistVolume 179, Issue 1 p. 5-9 Free Access FACE-ing the facts: inconsistencies and interdependence among field, chamber and modeling studies of elevated [CO2] impacts on crop yield and food supply Elizabeth A. Ainsworth, Elizabeth A. Ainsworth USDA ARS Photosynthesis Research Unit, 1201 W. Gregory Drive, Urbana, IL 61801, USA; Department of Plant Biology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana IL 61801, USASearch for more papers by this authorAndrew D. B. Leakey, Andrew D. B. Leakey Department of Plant Biology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana IL 61801, USASearch for more papers by this authorDonald R. Ort, Donald R. Ort USDA ARS Photosynthesis Research Unit, 1201 W. Gregory Drive, Urbana, IL 61801, USA; Department of Plant Biology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana IL 61801, USASearch for more papers by this authorStephen P. Long, Corresponding Author Stephen P. Long Department of Plant Biology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana IL 61801, USA(*Author for correspondence: tel +1 (217) 333 2487; fax +1 (217) 244 7563; email [email protected])Search for more papers by this author Elizabeth A. Ainsworth, Elizabeth A. Ainsworth USDA ARS Photosynthesis Research Unit, 1201 W. Gregory Drive, Urbana, IL 61801, USA; Department of Plant Biology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana IL 61801, USASearch for more papers by this authorAndrew D. B. Leakey, Andrew D. B. Leakey Department of Plant Biology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana IL 61801, USASearch for more papers by this authorDonald R. Ort, Donald R. Ort USDA ARS Photosynthesis Research Unit, 1201 W. Gregory Drive, Urbana, IL 61801, USA; Department of Plant Biology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana IL 61801, USASearch for more papers by this authorStephen P. Long, Corresponding Author Stephen P. Long Department of Plant Biology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana IL 61801, USA(*Author for correspondence: tel +1 (217) 333 2487; fax +1 (217) 244 7563; email [email protected])Search for more papers by this author First published: 13 May 2008 https://doi.org/10.1111/j.1469-8137.2008.02500.xCitations: 202AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Rising atmospheric carbon dioxide concentration ([CO2]) is just one aspect of global climate change. However, it is important because it consistently stimulates the growth and harvestable grain production of C3 crops (Kimball et al., 2002; Long et al., 2004; Nowak et al., 2004; Ainsworth & Long, 2005), as well as benefiting C4 crops under drought stress (Ottman et al., 2001; Leakey et al., 2004, 2006). Meanwhile, high temperatures, drought stress and rising ozone concentrations all have negative impacts on crop production (Gitay et al., 2001; Parry et al., 2004). Furthermore, rising [CO2] is unique in being globally almost uniform and so denying spatial proxies for temporal trends. As a result, Parry et al. (2004) singled out its effect as the largest uncertainty in projecting future global food supply. Free-air CO2 enrichment (FACE) experiments currently provide the most realistic measure of the future impact of elevated [CO2] on crop yields. Free-air CO2 enrichment experiments differ from enclosure studies in two salient respects: (1) they are conducted in the open air in farm fields without limiting growing space, or altering microclimate, precipitation or pest/pathogen access; and (2) the scale of the experiments is large enough to be comparable to agronomic trials (typically plots > 300 m2 compared with < 4 m2 in the case of enclosure studies). In Long et al. (2006) and Ainsworth (2008), we reported that stimulation of seed yield in response to elevated [CO2] is lower in FACE experiments than in enclosure studies of the world's four most important food crops. We suggested that the implications of this finding were as follows: modeling studies using CO2 fertilization factors derived from enclosure experiments may have overestimated future food supply; and additional field experiments are needed to understand in greater detail the mechanism of response and to drive research and development efforts to improve crop yields under future climatic conditions. This was argued with the proviso that FACE experiments have been limited in number and geographic range, as well as in the extent to which they currently investigate the interactive effects of the numerous elements of global change. These findings were vigorously challenged and then subsequently dismissed by Tubiello et al. (2007a,b) who argued that the findings of Long et al. (2006) were incorrect for three reasons: a statistically significant difference between FACE and nonFACE data was not adequately tested or proven; results from most crop model simulations are consistent with values from FACE experiments; and lower crop responses to elevated CO2 of the magnitudes in question would not significantly alter projections of world food supply (Tubiello et al., 2007a). This conclusion is in contrast to the findings of Parry et al. (2004), who with similar modeling approaches concluded that whether global food supply remained stable or declined with global change would depend critically on the response of the world's key grain crops to rising [CO2]. The consequences for human welfare will probably be severe if we underestimate the threat of global change to future food supply. This is all the more important given that long lead times will be necessary to produce germplasm better adapted to future growing conditions; typically it may take decades to identify adapted germplasm and then bring it to market in sufficient quantity for these major crops. Consequently, there is an immediate need to evaluate the currently available data correctly and use this to identify the best approaches to predict future food availability and to elucidate the mechanisms of crop responses to elevated [CO2] in order to generate improved germplasm. Statistically significant differences between FACE and nonFACE experiments The statistical validity of comparing the mean response of C3 crops to elevated [CO2] from FACE experiments (Supplementary material Table S1) against the modeled best-fit response of chamber experiments (Long et al., 2006: fig. 2) was criticized because curve-fitting methods and data-pooling choices can bias fair comparisons (Tubiello et al., 2007a). In fact, Tubiello et al. (2007a) recommend that a better approach is to ‘whenever possible, use the observed data – rather than “predicted” from curves lacking full biophysical explanatory power.’ We agree, and given the number of C3 crop studies, it is possible to take a direct approach and limit the comparison of FACE experiments and chamber studies to those with similar ambient [CO2] and similar elevated [CO2] (Supplementary material Tables S1 and S2). The FACE data had an average ambient [CO2] of 367 ppm and an elevated [CO2] of 583 ppm, and were normally distributed with a mean yield response ratio of 1.14 (Fig. 1). The chamber data had an average ambient [CO2] of 373 ppm and an elevated [CO2] of 565 ppm, and a mean yield response ratio of 1.31 (Fig. 1). In contrast to the FACE data, the chamber data were not normally distributed (Shapiro–Wilks P < 0.001) and had a much broader range of responses than the FACE data (Fig. 1). Because the data were not normally distributed and the sample sizes for FACE and chamber studies were unequal, we used the less-sensitive, nonparametric Wilcoxon–Mann–Whitney two-sample test to analyze differences between FACE and chamber studies (Steel et al., 1997). This test revealed a significant difference between the response ratio of yields at elevated [CO2] in FACE studies vs chamber studies (P = 0.016). Consistent with our previous analysis (Long et al., 2006), the magnitude of elevated [CO2] stimulation in FACE experiments was essentially half of the stimulation in chamber studies. Figure 2Open in figure viewerPowerPoint A comparison of stimulation of wheat yields from five different crop models (Demeter, LINTUL, AFRC, mC-wheat, Sirius), and the Maricopa free-air CO2 enrichment (FACE) experiment (FACE observations), modified (with permission) from Tubiello & Ewert (2002). The FACE results show a mean response ratio of 1.08 under well-watered conditions and a mean response ratio of 1.18 under water stress, while the average model outputs estimate a response of 1.18 under well-watered conditions and a response of 1.28 under water stress. Figure 1Open in figure viewerPowerPoint Box plot of the yield response ratios from free-air CO2 enrichment (FACE) and Enclosure yield data (Supplementary material Tables S1 and S2). The thick black line shows the mean, and error bars represent 10th and 90th percentiles. The FACE data have an average ambient [CO2] of 367 ppm and an elevated [CO2] of 583 ppm, and are normally distributed with a mean yield response ratio of 1.14. The enclosure data have an average ambient [CO2] of 373 ppm and elevated [CO2] of 565 ppm, and are not normally distributed, with a mean yield response ratio of 1.31. A Wilcoxon–Mann–Whitney two-sample test for differences revealed a significant difference between FACE and enclosure studies (P = 0.016). The major models do not show good agreement with FACE The best test of model parameterization and model design is validation of model output against observed experimental data. Tubiello et al. (2007a) report that some key models used in climate change impact assessments (AEZ, Fischer et al., 2002; CERES, Tsuji et al., 1994; EPIC, Stockle et al., 1992) have not been evaluated against FACE data, but where this has been carried out, the models reproduce FACE results well. Tubiello & Ewert (2002) summarized the validation of five widely used crop models with wheat grain yield data from the Maricopa FACE experiment, concluding that the models ‘all showed good agreement’, and this work was referred to again by Tubiello et al. (2007a) to justify this point. However, examination of this comparison fails to justify this claim. The models, in fact, project almost twice the yield actually observed in the FACE experiments, in agreement with Long et al. (2006). Using digitizing software (grafula 3 v 2.10; Wesik, SoftHaus, St Petersburg, Russian Federation), we extracted the data from Fig. 3 of Tubiello & Ewert (2002) and replotted the results (Fig. 2). While the FACE results suggest a mean response ratio of 1.08 under well-watered conditions and a mean response ratio of 1.18 under water stress, the average model outputs estimate a response ratio of 1.18 under well-watered conditions and a response ratio of 1.28 under water stress (Fig. 2). Thus, the Demeter, LINTUL, AFRC, mC-wheat, and Sirius models collectively overestimate the [CO2] fertilization effect by 125% under well-watered conditions and by 56% under water stress conditions (Fig. 2). This corresponds with the greater magnitude of yield stimulation by elevated [CO2] in chamber studies compared with FACE studies, which is described in the previous section and reported in Long et al. (2006). In summary, comparison of model parameterization and model validation exercises with data from FACE and nonFACE studies does not support the assertions of Tubiello et al. (2007a,b), but instead supports the concern that there are some important quantitative differences in how crops respond to elevated [CO2] in FACE and chamber experiments. Improving projections will require a better integration of experiments and models. While it is standard for an experimental study to provide sufficient information to allow an exact repetition of the work, this standard has not always been upheld for models projecting future food supply, including those used by the Intergovernmental Panel on Climate Change (IPCC). It is in the mutual interest of experimental and modeling studies that the basis of differences should be understood. Yet, in Tubiello et al. (2007a), the CO2 fertilization factors used in a key model were presented for the first time and referenced with the statement ‘personal communication’. Sensitivity of future food supply to elevated [CO2] Tubiello et al. (2007a) argue that differences in yield response between chamber and FACE experiments are inconsequential because ‘for any specific socio-economic pathway and climate change, including or not including the effects of elevated CO2 on crops changes the global cereal production results by less than 2%’. By contrast, a second modeling study included in the latest IPCC report (Parry et al., 2004), and based on the same economic model, reports that inclusion of CO2 effects reduced the number of undernourished people in 2050 by 12–32%, depending on the climate change scenario (Easterling et al., 2007). By 2080, inclusion of the CO2 effects reduced the number of undernourished people by 18–63% (Easterling et al., 2007). Therefore, it seems unlikely that CO2 effects will only be ‘moderately important’ in the future, as reported by Tubiello et al. (2007a), and we would argue that there is a pressing need to identify crops and genotypes that can maximize the benefits of rising [CO2]. The IPCC report also states that ‘a number of limitations, however, make these model projections highly uncertain’. Including, ‘projections are based on a limited number of crop models, and only one economic model, the latter lacking sufficient evaluation against observations, and thus in need of further improvements’. This further suggests that the evidence presented by Tubiello et al. (2007a) is not adequate to reject the statistically valid difference in yield stimulation between FACE and chamber experiments described above. There is broad agreement that the effects of elevated [CO2] measured in experimental settings lacking the potentially limiting influence of pests, weeds, nutrients, competition for resources, soil water and air quality, may overestimate field responses on the farm (Long et al., 2006; Easterling et al., 2007; Tubiello et al., 2007b). For example, Zavala et al. (2008) reported that elevated [CO2] increased the susceptibility of soybean to two beetle pests by down-regulating gene expression related to defense signaling, which in turn reduced the production of feeding deterrents. This was discovered in a FACE experiment where plants were accessible to pests and pathogens. This type of complex interaction between elevated [CO2] and pest damage could not have been predicted from prior chamber experiments. Such findings are inconsistent with the main conclusions of Tubiello et al. (2007a), that there are no meaningful inconsistencies among data from FACE experiments, nonFACE experiments and modeling studies, and the implication that FACE experiments are not needed to address key knowledge gaps about crop responses to elevated [CO2]. What is the way forward? Free-air CO2 enrichment experiments provide the most realistic conditions for estimating crop yield responses to elevated [CO2]. This is achieved by simulating future atmospheric conditions in the production environment of farm fields, without perturbing the soil–plant–atmosphere continuum, and in plots that are typically an order of magnitude larger than in chamber studies. Extrapolating seed yield responses of crops grown in controlled environments often leads to extremely unrealistic estimates of yield on a meaningful field scale (Supplementary material Table S2). Therefore, controlled environments clearly are not the best experimental facilities for estimating CO2 response ratios of yield. Chamber experiments are particularly valuable as a setting for identifying mechanisms of crop response at the molecular, biochemical and physiological scales. All of the authors of this paper have carried out, and continue to perform, chamber experiments. Long et al. (2006) highlighted, and we repeat here, the concern that a greater number of FACE experiments are needed, in addition to chamber studies, in order to generate the best possible understanding of crop responses to elevated [CO2] and to improve the performance of crops under future conditions. A major assumption of current integrated ecological–economic models of world food supply is that technical progress in crop yields will continue at the past and current pace (Fischer et al., 2005). The importance of investigating the mechanism of plant–environment interactions under realistic field conditions is also recognized by the biotechnology industry when attempting to identify molecular targets for germplasm improvement. For example, Pioneer Hi-Bred has reported, ‘Since we need to target our research effort to the production environment, more emphasis has been placed on field-based profiling experiments, using managed stress environments to generate realistic changes in gene expression’ (Campos et al., 2004). Developing germplasm that responds better to elevated [CO2] is a distant goal and to our knowledge is not a current research priority in industry (Ainsworth et al., 2008). Public research and development is needed to extend capacity beyond the current FACE experiments, which are limited in their geographical distribution, the very narrow range of CO2 concentrations used in the experiments and the inclusion of important interactions with other climate change factors. Supporting Information Table S1 Crop yield from free-air CO2 enrichment (FACE) studies Table S2 Crop yield from chamber studies with ambient &lsqb;CO2&rsqb; of 360–390 ppm and an elevated &lsqb;CO2&rsqb; of 500–650 ppm Please note: Blackwell Publishing are not responsible for the content or functionality of any supplementary materials supplied by the authors. Any queries (other than missing material) should be directed to the journal at New Phytologist Central Office. Filename Description NPH_2500_sm_TablesS1-S2.doc161.5 KB Supporting info item Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. References Ainsworth EA. 2008. Rice production in a changing climate: A meta-analysis of responses to elevated carbon dioxide and elevated ozone concentrations. 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Contribution of Working Group II to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge, UK: Cambridge University Press, 273– 313. Fischer G, Shah M, Tubiello FN, Van Velhuizen H. 2005. Socio-economic and climate change impacts on agriculture: An integrated assessment, 1990–2080. Philosophical Transactions of the Royal Society B 360: 2067– 2083. Fischer G, Van Velhuizen H, Shah M, Nachtergaele FO. 2002. Global agro-ecological assessment for agriculture in the 21st century: methodology and results. IIASA RR-02-02. Laxenburg, Austria: IIASA. Gitay H, Brown S, Easterling W, Jallow B, Antle J, Apps M, Beamish R, Chapin T, Cramer W, Frangi J et al. 2001. Ecosystems and their goods and services. In: JJ McCarthy, OF Canziani, NA Leary, DJ Dokken, KS White, eds. Climate Change 2001: Impacts, Adaptation and Vulnerability to Climate Change. Contribution of Working Group II to the Third Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge, UK, Cambridge University Press, 236– 342. Kimball BA, Kobayashi K, Bindi M. 2002. Responses of agricultural crops to free-air CO2 enrichment. Advances in Agronomy 77: 293– 368. Leakey ADB, Bernacchi CJ, Dohleman FG, Ort DR, Long SP. 2004. Will photosynthesis of maize (Zea mays) in the U.S. Corn Belt increase in future [CO2] rich atmospheres? An analysis of diurnal courses of CO2 uptake under Free-Air Concentration Enrichment (FACE). Global Change Biology 10: 951– 962. Leakey ADB, Uribelarrea M, Ainsworth EA, Naidu SL, Rogers A, Ort DR, Long SP. 2006. Photosynthesis, productivity and yield of Zea mays are not affected by open-air elevation of CO2 concentration in the absence of drought. Plant Physiology 140: 779– 790. Long SP, Ainsworth EA, Leakey ADB, Nösberger J, Ort DR. 2006. Food for thought: Lower-than-expected crop yield stimulation with rising CO2 concentrations. Science 312: 1918– 1921. Long SP, Ainsworth EA, Rogers A, Ort DR. 2004. 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Growth at elevated [CO2] stimulates photosynthesis and increases carbon (C) supply in all C3 species. A sustained and maximal stimulation in productivity at elevated [CO2] requires an enhanced nutrient supply to match the increase in C acquisition. The ability of legumes to exchange C for nitrogen (

Photosynthetic and respiratory exchanges of CO 2 by plants with the atmosphere are significantly larger than anthropogenic CO 2 emissions, and these fluxes will change as growing conditions are altered by climate change. Understanding feedbacks in CO 2 exchange is important to predicting future atmospheric [CO 2 ] and climate change. At the tissue and plant scale, respiration is a key determinant of growth and yield. Although the stimulation of C 3 photosynthesis by growth at elevated [CO 2 ] can be predicted with confidence, the nature of changes in respiration is less certain. This is largely because the mechanism of the respiratory response is insufficiently understood. Molecular, biochemical and physiological changes in the carbon metabolism of soybean in a free-air CO 2 enrichment experiment were investigated over 2 growing seasons. Growth of soybean at elevated [CO 2 ] (550 μmol·mol −1 ) under field conditions stimulated the rate of nighttime respiration by 37%. Greater respiratory capacity was driven by greater abundance of transcripts encoding enzymes throughout the respiratory pathway, which would be needed for the greater number of mitochondria that have been observed in the leaves of plants grown at elevated [CO 2 ]. Greater respiratory quotient and leaf carbohydrate content at elevated [CO 2 ] indicate that stimulated respiration was supported by the additional carbohydrate available from enhanced photosynthesis at elevated [CO 2 ]. If this response is consistent across many species, the future stimulation of net primary productivity could be reduced significantly. Greater foliar respiration at elevated [CO 2 ] will reduce plant carbon balance, but could facilitate greater yields through enhanced photoassimilate export to sink tissues.

Abstract A lower than theoretically expected increase in leaf photosynthesis with long‐term elevation of carbon dioxide concentration ([CO 2 ]) is often attributed to limitations in the capacity of the plant to utilize the additional photosynthate, possibly resulting from restrictions in rooting volume, nitrogen supply or genetic constraints. Field‐grown, nitrogen‐fixing soybean with indeterminate flowering might therefore be expected to escape these limitations. Soybean was grown from emergence to grain maturity in ambient air (372 µ mol mol −1 [CO 2 ]) and in air enriched with CO 2 (552 µ mol mol −1 [CO 2 ]) using Free‐Air CO 2 Enrichment (FACE) technology. The diurnal courses of leaf CO 2 uptake ( A ) and stomatal conductance ( g s ) for upper canopy leaves were followed throughout development from the appearance of the first true leaf to the completion of seed filling. Across the growing season the daily integrals of leaf photosynthetic CO 2 uptake ( A ′) increased by 24.6% in elevated [CO 2 ] and the average mid‐day g s decreased by 21.9%. The increase in A ′ was about half the 44.5% theoretical maximum increase calculated from Rubisco kinetics. There was no evidence that the stimulation of A was affected by time of day, as expected if elevated [CO 2 ] led to a large accumulation of leaf carbohydrates towards the end of the photoperiod. In general, the proportion of assimilated carbon that accumulated in the leaf as non‐structural carbohydrate over the photoperiod was small (&lt; 10%) and independent of [CO 2 ] treatment. By contrast to A ′, daily integrals of PSII electron transport measured by modulated chlorophyll fluorescence were not significantly increased by elevated [CO 2 ]. This indicates that A at elevated [CO 2 ] in these field conditions was predominantly ribulose‐1,5‐bisphosphate (RubP) limited rather than Rubisco limited. There was no evidence of any loss of stimulation toward the end of the growing season; the largest stimulation of A ′ occurred during late seed filling. The stimulation of photosynthesis was, however, transiently lost for a brief period just before seed fill. At this point, daytime accumulation of foliar carbohydrates was maximal, and the hexose:sucrose ratio in plants grown at elevated [CO 2 ] was significantly larger than that in plants grown at current [CO 2 ]. The results show that even for a crop lacking the constraints that have been considered to limit the responses of C 3 plants to rising [CO 2 ] in the long term, the actual increase in A over the growing season is considerably less than the increase predicted from theory.

ABSTRACT Photosynthesis is commonly stimulated in grasslands with experimental increases in atmospheric CO 2 concentration ([CO 2 ]), a physiological response that could significantly alter the future carbon cycle if it persists in the long term. Yet an acclimation of photosynthetic capacity suggested by theoretical models and short‐term experiments could completely remove this effect of CO 2 . Perennial ryegrass ( Lolium perenne L. cv. Bastion) was grown under an elevated [CO 2 ] of 600 µ mol mol −1 for 10 years using F ree A ir C O 2 E nrichment ( FACE ), with two contrasting nitrogen levels and abrupt changes in the source : sink ratio following periodic harvests. More than 3000 measurements characterized the response of leaf photosynthesis and stomatal conductance to elevated [CO 2 ] across each growing season for the duration of the experiment. Over the 10 years as a whole, growth at elevated [CO 2 ] resulted in a 43% higher rate of light‐saturated leaf photosynthesis and a 36% increase in daily integral of leaf CO 2 uptake. Photosynthetic stimulation was maintained despite a 30% decrease in stomatal conductance and significant decreases in both the apparent, maximum carboxylation velocity ( V c,max ) and the maximum rate of electron transport ( J max ). Immediately prior to the periodic (every 4–8 weeks) cuts of the L. perenne stands, V c,max and J max, were significantly lower in elevated than in ambient [CO 2 ] in the low‐nitrogen treatment. This difference was smaller after the cut, suggesting a dependence upon the balance between the sources and sinks for carbon. In contrast with theoretical expectations and the results of shorter duration experiments, the present results provide no significant change in photosynthetic stimulation across a 10‐year period, nor greater acclimation in V c,max and J max in the later years in either nitrogen treatment.

Predictions of population growth outpacing agricultural production have been made for the past 200 years ([Malthus, 1817][1]; [Ehrlich, 1968][2]), and though world food supply has more than kept pace with demand, there are over 850 million malnourished people in the world, the vast majority in

ABSTRACT Soybean ( Glycine max Merr.) is the world's most widely grown legume and provides an important source of protein and oil. Global soybean production and yield per hectare increased steadily over the past century with improved agronomy and development of cultivars suited to a wide range of latitudes. In order to meet the needs of a growing world population without unsustainable expansion of the land area devoted to this crop, yield must increase at a faster rate than at present. Here, the historical basis for the yield gains realized in the past 90 years are examined together with potential metabolic targets for achieving further improvements in yield potential. These targets include improving photosynthetic efficiency, optimizing delivery and utilization of carbon, more efficient nitrogen fixation and altering flower initiation and abortion. Optimization of investment in photosynthetic enzymes, bypassing photorespiratory metabolism, engineering the electron transport chain and engineering a faster recovery from the photoprotected state are different strategies to improve photosynthesis in soybean. These potential improvements in photosynthetic carbon gain will need to be matched by increased carbon and nitrogen transport to developing soybean pods and seeds in order to maximize the benefit. Better understanding of control of carbon and nitrogen transport along with improved knowledge of the regulation of flower initiation and abortion will be needed to optimize sink capacity in soybean. Although few single targets are likely to deliver a quantum leap in yields, biotechnological advances in molecular breeding techniques that allow for alteration of the soybean genome and transcriptome promise significant yield gains.

ABSTRACT A rising global population and demand for protein‐rich diets are increasing pressure to maximize agricultural productivity. Rising atmospheric [CO 2 ] is altering global temperature and precipitation patterns, which challenges agricultural productivity. While rising [CO 2 ] provides a unique opportunity to increase the productivity of C 3 crops, average yield stimulation observed to date is well below potential gains. Thus, there is room for improving productivity. However, only a fraction of available germplasm of crops has been tested for CO 2 responsiveness. Yield is a complex phenotypic trait determined by the interactions of a genotype with the environment. Selection of promising genotypes and characterization of response mechanisms will only be effective if crop improvement and systems biology approaches are closely linked to production environments, that is, on the farm within major growing regions. Free air CO 2 enrichment (FACE) experiments can provide the platform upon which to conduct genetic screening and elucidate the inheritance and mechanisms that underlie genotypic differences in productivity under elevated [CO 2 ]. We propose a new generation of large‐scale, low‐cost per unit area FACE experiments to identify the most CO 2 ‐responsive genotypes and provide starting lines for future breeding programmes. This is necessary if we are to realize the potential for yield gains in the future.

Abstract Improvements in carbon assimilation and water-use efficiency lead to increases in maximum leaf area index at elevated carbon dioxide concentration ([CO2]); however, the molecular drivers for this increase are unknown. We investigated the molecular basis for changes in leaf development at elevated [CO2] using soybeans (Glycine max) grown under fully open air conditions at the Soybean Free Air CO2 Enrichment (SoyFACE) facility. The transcriptome responses of rapidly growing and fully expanded leaves to elevated [CO2] were investigated using cDNA microarrays. We identified 1,146 transcripts that showed a significant change in expression in growing versus fully expanded leaves. Transcripts for ribosomal proteins, cell cycle, and cell wall loosening, necessary for cytoplasmic growth and cell proliferation, were highly expressed in growing leaves. We further identified 139 transcripts with a significant [CO2] by development interaction. Clustering of these transcripts showed that transcripts involved in cell growth and cell proliferation were more highly expressed in growing leaves that developed at elevated [CO2] compared to growing leaves that developed at ambient [CO2]. The 327 [CO2]-responsive genes largely suggest that elevated [CO2] stimulates the respiratory breakdown of carbohydrates, which provides increased energy and biochemical precursors for leaf expansion and growth at elevated [CO2]. While increased photosynthesis and carbohydrate production at elevated [CO2] are well documented, this research demonstrates that at the transcript and metabolite level, respiratory breakdown of starch is also increased at elevated [CO2].

ABSTRACT A Free‐Air CO 2 Enrichment (FACE) experiment compared the physiological parameters, transcript and metabolite profiles of Arabidopsis thaliana Columbia‐0 (Col‐0) and Cape Verde Island (Cvi‐0) at ambient (∼0.375 mg g −1 ) and elevated (∼0.550 mg g −1 ) CO 2 ([CO 2 ]). Photoassimilate pool sizes were enhanced in high [CO 2 ] in an ecotype‐specific manner. Short‐term growth at elevated [CO 2 ] stimulated carbon gain irrespective of down‐regulation of plastid functions and altered expression of genes involved in nitrogen metabolism resembling patterns observed under N‐deficiency. The study confirmed well‐known characteristics, but the use of a time course, ecotypic genetic differences, metabolite analysis and the focus on clusters of functional categories provided new aspects about responses to elevated [CO 2 ]. Longer‐term Cvi‐0 responded by down‐regulating functions favouring carbon accumulation, and both ecotypes showed altered expression of genes for defence, redox control, transport, signalling, transcription and chromatin remodelling. Overall, carbon fixation with a smaller commitment of resources in elevated [CO 2 ] appeared beneficial, with the extra C only partially utilized possibly due to disturbance of the C : N ratio. To different degrees, both ecotypes perceived elevated [CO 2 ] as a metabolic perturbation that necessitated increased functions consuming or storing photoassimilate, with Cvi‐0 emerging as more capable of acclimating. Elevated [CO 2 ] in Arabidopsis favoured adjustments in reactive oxygen species (ROS) homeostasis and signalling that defined genotypic markers.

Abstract Tropospheric ozone ( O 3 ) is a harmful air pollutant that can negatively impact plant growth and development. Current O 3 concentrations ([ O 3 ]) decrease forest productivity and crop yields and future [ O 3 ] will likely increase if current emission rates continue. However, the specific effects of elevated [ O 3 ] on reproductive development, a critical stage in the plant's lifecycle, have not been quantitatively reviewed. Data from 128 peer‐reviewed articles published from 1968 to 2010 describing the effects of O 3 on reproductive growth and development were analysed using meta‐analytic techniques. Studies were categorized based on experimental conditions, photosynthetic type, lifecycle, growth habit and flowering class. Current ambient [ O 3 ] significantly decreased seed number (−16%), fruit number (−9%) and fruit weight (−22%) compared to charcoal‐filtered air. In addition, pollen germination and tube growth were decreased by elevated [ O 3 ] compared to charcoal‐filtered air. Relative to ambient air, fumigation with [ O 3 ] between 70 and 100 ppb decreased yield by 27% and individual seed weight by 18%. Reproductive development of both C 3 and C 4 plants was sensitive to elevated [ O 3 ], and lifecycle, flowering class and reproductive growth habit did not significantly affect a plant's response to elevated [ O 3 ] for many components of reproductive development. However, elevated [ O 3 ] decreased fruit weight and fruit number significantly in indeterminate plants, and had no effect on these parameters in determinate plants. While gaps in knowledge remain about the effects of O 3 on plants with different growth habits, reproductive strategies and photosynthetic types, the evidence strongly suggests that detrimental effects of O 3 on reproductive growth and development are compromising current crop yields and the fitness of native plant species.

Rising atmospheric [CO2] is a uniform, global change that increases C3 photosynthesis and could offset some of the negative effects of global climate change on crop yields. Genetic variation in yield responsiveness to rising [CO2] would provide an opportunity to breed more responsive crop genotypes. A multi-year study of 18 soybean (Glycine max Merr.) genotypes was carried out to identify variation in responsiveness to season-long elevated [CO2] (550 ppm) under fully open-air replicated field conditions. On average across 18 genotypes, elevated [CO2] stimulated total above-ground biomass by 22%, but seed yield by only 9%, in part because most genotypes showed a reduction in partitioning of energy to seeds. Over four years of study, there was consistency from year to year in the genotypes that were most and least responsive to elevated [CO2], suggesting heritability of CO2 response. Further analysis of six genotypes did not reveal a photosynthetic basis for the variation in yield response. Although partitioning to seed was decreased, cultivars with the highest partitioning coefficient in current [CO2 ] also had the highest partitioning coefficient in elevated [CO2]. The results show the existence of genetic variation in soybean response to elevated [CO2], which is needed to breed soybean to the future atmospheric environment.

Abstract Heat waves already have a large impact on crops and are predicted to become more intense and more frequent in the future. In this study, heat waves were imposed on soybean using infrared heating technology in a fully open‐air field experiment. Five separate heat waves were applied to field‐grown soybean ( Glycine max ) in central Illinois, three in 2010 and two in 2011. Thirty years of historical weather data from Illinois were analyzed to determine the length and intensity of a regionally realistic heat wave resulting in experimental heat wave treatments during which day and night canopy temperatures were elevated 6 °C above ambient for 3 days. Heat waves were applied during early or late reproductive stages to determine whether and when heat waves had an impact on carbon metabolism and seed yield. By the third day of each heat wave, net photosynthesis ( A ), specific leaf weight ( SLW ), and leaf total nonstructural carbohydrate concentration ( TNC ) were decreased, while leaf oxidative stress was increased. However, A , SLW , TNC , and measures of oxidative stress were no different than the control ca. 12 h after the heat waves ended, indicating rapid physiological recovery from the high‐temperature stress. That end of season seed yield was reduced (~10%) only when heat waves were applied during early pod developmental stages indicates the yield loss had more to do with direct impacts of the heat waves on reproductive process than on photosynthesis. Soybean was unable to mitigate yield loss after heat waves given during late reproductive stages. This study shows that short high‐temperature stress events that reduce photosynthesis and increase oxidative stress resulted in significant losses to soybean production in the Midwest, U.S. The study also suggests that to mitigate heat wave‐induced yield loss, soybean needs improved reproductive and photosynthetic tolerance to high but increasingly common temperatures.

Soybeans (Glycine max Merr.) were grown at elevated carbon dioxide concentration ([CO2]) or chronic elevated ozone concentration ([O3]; 90 ppb), and then exposed to an acute O3 stress (200 ppb for 4 h) in order to test the hypothesis that the atmospheric environment alters the total antioxidant capacity of plants, and their capacity to respond to an acute oxidative stress. Total antioxidant metabolism, antioxidant enzyme activity, and antioxidant transcript abundance were characterized before, immediately after, and during recovery from the acute O3 treatment. Growth at chronic elevated [O3] increased the total antioxidant capacity of plants, while growth at elevated [CO2] decreased the total antioxidant capacity. Changes in total antioxidant capacity were matched by changes in ascorbate content, but not phenolic content. The growth environment significantly altered the pattern of antioxidant transcript and enzyme response to the acute O3 stress. Following the acute oxidative stress, there was an immediate transcriptional reprogramming that allowed for maintained or increased antioxidant enzyme activities in plants grown at elevated [O3]. Growth at elevated [CO2] appeared to increase the response of antioxidant enzymes to acute oxidative stress, but dampened and delayed the transcriptional response. These results provide evidence that the growth environment alters the antioxidant system, the immediate response to an acute oxidative stress, and the timing over which plants return to initial antioxidant levels. The results also indicate that future elevated [CO2] and [O3] will differentially affect the antioxidant system.

Abstract Crop biomass production is a function of the efficiencies with which sunlight can be intercepted by the canopy and then converted into biomass. Conversion efficiency has been identified as a target for improvement to enhance crop biomass and yield. Greater conversion efficiency in modern soybean [ Glycine max (L.) Merr.] cultivars was documented in recent field trials, and this study explored the physiological basis for this observation. In replicated field trials conducted over three successive years, diurnal leaf gas exchange and photosynthetic CO 2 response curves were measured in 24 soybean cultivars with year of release dates (YOR) from 1923 to 2007. Maximum photosynthetic capacity, mesophyll conductance and nighttime respiration have not changed consistently with cultivar release date. However, daily carbon gain was periodically greater in more recently released cultivars compared with older cultivars. Our analysis suggests that this difference in daily carbon gain primarily occurred when stomatal conductance and soil water content were high. There was also evidence for greater chlorophyll content and greater sink capacity late in the growing season in more recently released soybean varieties. Better understanding of the mechanisms that have improved conversion efficiency in the past may help identify new, promising targets for the future.

Human activities result in a wide array of pollutants being released to the atmosphere. A number of these pollutants have direct effects on plants, including carbon dioxide (CO2 ), which is the substrate for photosynthesis, and ozone (O3 ), a damaging oxidant. How plants respond to changes in these atmospheric air pollutants, both directly and indirectly, feeds back on atmospheric composition and climate, global net primary productivity and ecosystem service provisioning. Here we discuss the past, current and future trends in emissions of CO2 and O3 and synthesise the current atmospheric CO2 and O3 budgets, describing the important role of vegetation in determining the atmospheric burden of those pollutants. While increased atmospheric CO2 concentration over the past 150 years has been accompanied by greater CO2 assimilation and storage in terrestrial ecosystems, there is evidence that rising temperatures and increased drought stress may limit the ability of future terrestrial ecosystems to buffer against atmospheric emissions. Long-term Free Air CO2 or O3 Enrichment (FACE) experiments provide critical experimentation about the effects of future CO2 and O3 on ecosystems, and highlight the important interactive effects of temperature, nutrients and water supply in determining ecosystem responses to air pollution. Long-term experimentation in both natural and cropping systems is needed to provide critical empirical data for modelling the effects of air pollutants on plant productivity in the decades to come.

Rising atmospheric concentrations of CO2 and O3 are key features of global environmental change. To investigate changes in the belowground bacterial community composition in response to elevated CO2 and O3 (eCO2 and eO3) the endosphere, rhizosphere and soil were sampled from soybeans under eCO2 and maize under eO3. The maize rhizosphere and endosphere α-diversity was higher than soybean, which may be due to a high relative abundance of Rhizobiales. Only the rhizosphere microbiome composition of the soybeans changed in response to eCO2, associated with an increased abundance of nitrogen fixing microbes. In maize, the microbiome composition was altered by the genotype and linked to differences in root exudate profiles. The eO3 treatment did not change the microbial communities in the rhizosphere, but altered the soil communities where hybrid maize was grown. In contrast to previous studies that focused exclusively on the soil, this study provides new insights into the effects of plant root exudates on the composition of the belowground microbiome in response to changing atmospheric conditions. Our results demonstrate that plant species and plant genotype were key factors driving the changes in the belowground bacterial community composition in agroecosystems that experience rising levels of atmospheric CO2 and O3.

Due to climate change, heat waves are predicted to become more frequent and severe. While long-term studies on temperature stress have been conducted on important crops such as maize (Zea mays), the immediate or long-term effects of short duration but extreme high temperature events during key developmental periods on physiological and yield parameters are unknown. Therefore, heat waves were applied to field-grown maize in east central Illinois using infrared heating technology. The heat waves warmed the canopy approximately 6 °C above ambient canopy temperatures for three consecutive days during vegetative development (Wv1) and during an early reproductive stage (silking; Wv2). Neither treatment affected aboveground vegetative biomass, and Wv1 did not significantly reduce reproductive biomass. However, Wv2 significantly reduced total reproductive biomass by 16% (p < 0.1) due to significant reductions in cob length (p < 0.1), cob mass (p < 0.05), and husk mass (p < 0.05). Although not statistically significant, seed yield was also reduced by 13% (p = 0.15) and kernel number by 10% (p = 0.16) in the Wv2 treatment. Soil water status was unaffected in both treatments, and leaf water potential and midday photosynthesis were only transiently reduced by heating with complete recovery after the treatment period. Therefore, the reduction in Wv2 reproductive biomass was most likely due to greater sensitivity of reproductive structures to direct effects of high temperature stress.

Elevated atmospheric CO2 concentrations ([CO2 ]) are expected to increase C3 crop yield through the CO2 fertilization effect (CFE) by stimulating photosynthesis and by reducing stomatal conductance and transpiration. The latter effect is widely believed to lead to greater benefits in dry rather than wet conditions, although some recent experimental evidence challenges this view. Here we used a process-based crop model, the Agricultural Production Systems sIMulator (APSIM), to quantify the contemporary and future CFE on soybean in one of its primary production area of the US Midwest. APSIM accurately reproduced experimental data from the Soybean Free-Air CO2 Enrichment site showing that the CFE declined with increasing drought stress. This resulted from greater radiation use efficiency (RUE) and above-ground biomass production at elevated [CO2 ] that outpaced gains in transpiration efficiency (TE). Using an ensemble of eight climate model projections, we found that drought frequency in the US Midwest is projected to increase from once every 5 years currently to once every other year by 2050. In addition to directly driving yield loss, greater drought also significantly limited the benefit from rising [CO2 ]. This study provides a link between localized experiments and regional-scale modeling to highlight that increased drought frequency and severity pose a formidable challenge to maintaining soybean yield progress that is not offset by rising [CO2 ] as previously anticipated. Evaluating the relative sensitivity of RUE and TE to elevated [CO2 ] will be an important target for future modeling and experimental studies of climate change impacts and adaptation in C3 crops.

Abstract Photosynthesis is currently measured using time-laborious and/or destructive methods which slows research and breeding efforts to identify crop germplasm with higher photosynthetic capacities. We present a plot-level screening tool for quantification of photosynthetic parameters and pigment contents that utilizes hyperspectral reflectance from sunlit leaf pixels collected from a plot (~2 m×2 m) in &amp;lt;1 min. Using field-grown Nicotiana tabacum with genetically altered photosynthetic pathways over two growing seasons (2017 and 2018), we built predictive models for eight photosynthetic parameters and pigment traits. Using partial least squares regression (PLSR) analysis of plot-level sunlit vegetative reflectance pixels from a single visible near infra-red (VNIR) (400–900 nm) hyperspectral camera, we predict maximum carboxylation rate of Rubisco (Vc,max, R2=0.79) maximum electron transport rate in given conditions (J1800, R2=0.59), maximal light-saturated photosynthesis (Pmax, R2=0.54), chlorophyll content (R2=0.87), the Chl a/b ratio (R2=0.63), carbon content (R2=0.47), and nitrogen content (R2=0.49). Model predictions did not improve when using two cameras spanning 400–1800 nm, suggesting a robust, widely applicable and more ‘cost-effective’ pipeline requiring only a single VNIR camera. The analysis pipeline and methods can be used in any cropping system with modified species-specific PLSR analysis to offer a high-throughput field phenotyping screening for germplasm with improved photosynthetic performance in field trials.

Agricultural expansion and management have greatly increased global food production and altered Earth's climate by changing physical and biogeochemical properties of terrestrial ecosystems. Few Earth system models represent agricultural management practices due to the complexity of the interactions between human decisions and biological processes on global scales. We describe the new capabilities of representing crop distributions and management in the Community Land Model (CLM) Version 5, which includes time-varying spatial distributions of major crop types and their management through fertilization and irrigation, and temperature-based phenological triggers. Including active crop management increases peak growing season gross primary productivity (GPP), increases the amplitude of Northern Hemisphere net ecosystem exchange, and changes seasonal and annual patterns of latent and sensible heat fluxes. The CLM5 crop model simulates the global observed historical trend of crop yields with relative fidelity from 1850 to 1990. Cropland expansion was important for increasing crop production, especially during the first century of the simulations, while fertilization and irrigation were important for increasing yields from 1950 onward. From 1990 to present day, observed crop production continued to increase while CLM5 production levels off, likely because intensification practices are not represented in the model. Specifically, CLM does not currently include increasing planting density, crop breeding and genetic modification, representations of tillage, or other management practices that may also affect crop-climate and crop-carbon cycle interactions and alter trends in yields. These results highlight the importance of including crop management in Earth system models, particularly as global data sets for parameterization and evaluation become more readily available.

High temperature and accompanying high vapor pressure deficit often stress plants without causing distinctive changes in plant canopy structure and consequential spectral signatures. Sun-induced chlorophyll fluorescence (SIF), because of its mechanistic link with photosynthesis, may better detect such stress than remote sensing techniques relying on spectral reflectance signatures of canopy structural changes. However, our understanding about physiological mechanisms of SIF and its unique potential for physiological stress detection remains less clear. In this study, we measured SIF at a high-temperature experiment, Temperature Free-Air Controlled Enhancement, to explore the potential of SIF for physiological investigations. The experiment provided a gradient of soybean canopy temperature with 1.5, 3.0, 4.5, and 6.0°C above the ambient canopy temperature in the open field environments. SIF yield, which is normalized by incident radiation and the fraction of absorbed photosynthetically active radiation, showed a high correlation with photosynthetic light use efficiency (r = 0.89) and captured dynamic plant responses to high-temperature conditions. SIF yield was affected by canopy structural and plant physiological changes associated with high-temperature stress (partial correlation r = 0.60 and -0.23). Near-infrared reflectance of vegetation, only affected by canopy structural changes, was used to minimize the canopy structural impact on SIF yield and to retrieve physiological SIF yield (ΦF ) signals. ΦF further excludes the canopy structural impact than SIF yield and indicates plant physiological variability, and we found that ΦF outperformed SIF yield in responding to physiological stress (r = -0.37). Our findings highlight that ΦF sensitively responded to the physiological downregulation of soybean gross primary productivity under high temperature. ΦF , if reliably derived from satellite SIF, can support monitoring regional crop growth and different ecosystems' vegetation productivity under environmental stress and climate change.

<h2>Summary</h2> Increasing tropospheric concentrations of ozone (e[O₃]) and carbon dioxide (e[CO₂]) profoundly perturb terrestrial ecosystem functions through carbon and nitrogen cycles, affecting beneficial services such as their capacity to combat climate change and provide food. However, the interactive effects of e[O₃] and e[CO₂] on these functions and services remain unclear. Here, we synthesize the results of 810 studies (9,109 observations), spanning boreal to tropical regions around the world, and show that e[O₃] significantly decreases global net primary productivity and food production as well as the capacity of ecosystems to store carbon and nitrogen, which are stimulated by e[CO₂]. More importantly, simultaneous increases in [CO₂] and [O₃] negate or even overcompensate the negative effects of e[O₃] on ecosystem functions and carbon and nitrogen cycles. Therefore, the negative effects of e[O₃] on terrestrial ecosystems would be overestimated if e[CO₂] impacts are not considered, stressing the need for evaluating terrestrial carbon and nitrogen feedbacks to concurrent changes in global atmospheric composition.

Cover cropping between cash crop growing seasons is a multifunctional conservation practice. Timely and accurate monitoring of cover crop traits, notably aboveground biomass and nutrient content, is beneficial to agricultural stakeholders to improve management and understand outcomes. Currently, there is a scarcity of spatially and temporally resolved information for assessing cover crop growth. Remote sensing has a high potential to fill this need, but conventional empirical regression operated with coarse-resolution multispectral data has large uncertainties. Therefore, this study utilized airborne hyperspectral imaging techniques and developed new process-guided machine learning approaches (PGML) for cover crop monitoring. Specifically, we deployed an airborne hyperspectral system covering visible to shortwave-infrared wavelengths (400–2400 nm) to acquire high spatial (0.5 m) and spectral (3–5 nm) resolution reflectance over 23 cover crop fields across Central Illinois in March and April of 2021. Airborne hyperspectral surface reflectance with high spectral and spatial resolution can be well matched with field data to quantify cover crop traits. Furthermore, the PGML models were pre-trained by synthetic data from soil-vegetation radiative transfer modeling (one million records), and then fine-tuned with field data of cover crop biomass and nutrient content. Results show that airborne hyperspectral data with PGML can achieve high accuracy to predict cover crop aboveground biomass (R2 = 0.72, relative RMSE = 15.16%) and nitrogen content (R2 = 0.69, relative RMSE = 16.59%) through leave-one-field-out cross-validation. Unlike the pure data-driven approach (e.g., partial least-squares regression), PGML incorporated radiative transfer knowledge and obtained higher predictive performance with fewer field data. Meanwhile, with field data for model fine-tuning, PGML predicted biomass more accurately than the inversion of radiative transfer models. We also found that the red edge has a high contribution in quantifying aboveground biomass and nitrogen content, followed by green and shortwave spectra. This study demonstrated the first attempt of utilizing hyperspectral remote sensing to accurately quantify cover crop traits. We highlight the strength of PGML in exploiting sensing data to quantify ecosystem variables to advance agroecosystem monitoring for sustainable agricultural management.

Abstract 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.

Increases in growth at elevated [CO2] may be constrained by a plant's ability to assimilate the nutrients needed for new tissue in sufficient quantity to match the increase in carbon fixation and/or the ability to transport those nutrients and carbon in sufficient quantity to growing organs and tissues. Analysis of metabolites provides an indication of shifts in carbon and nitrogen partitioning due to rising atmospheric [CO2] and can help identify where bottlenecks in carbon utilization occur. In this study, the carbon and nitrogen balance was investigated in growing and fully expanded soybean leaves exposed to elevated [CO2] in a free air CO2 enrichment experiment. Diurnal photosynthesis and diurnal profiles of carbon and nitrogen metabolites were measured during two different crop growth stages. Diurnal carbon gain was increased by c. 20% in elevated [CO2] in fully expanded leaves, which led to significant increases in leaf hexose, sucrose, and starch contents. However, there was no detectable difference in nitrogen-rich amino acids and ureides in mature leaves. By contrast to mature leaves, developing leaves had high concentrations of ureides and amino acids relative to low concentrations of carbohydrates. Developing leaves at elevated [CO2] had smaller pools of ureides compared with developing leaves at ambient [CO2], which suggests N assimilation in young leaves was improved by elevated [CO2]. This work shows that elevated [CO2] alters the balance of carbon and nitrogen pools in both mature and growing soybean leaves, which could have down-stream impacts on growth and productivity.

Crops losses to tropospheric ozone (O3) in the United States are estimated to cost $1–3 billion annually. This challenge is expected to increase as O3 concentrations ([O3]) rise over the next half century. This study tested the hypothesis that there is cultivar variation in the antioxidant, photosynthetic and yield response of soybean to growth at elevated [O3]. Ten cultivars of soybean were grown at elevated [O3] from germination through maturity at the Soybean Free Air Concentration Enrichment facility in 2007 and six were grown in 2008. Photosynthetic gas exchange, leaf area index, chlorophyll content, fluorescence and antioxidant capacity were monitored during the growing seasons in order to determine if changes in these parameters could be used to predict the sensitivity of seed yield to elevated [O3]. Doubling background [O3] decreased soybean yields by 17%, but the variation in response among cultivars and years ranged from 8 to 37%. Chlorophyll content and photosynthetic parameters were positively correlated with seed yield, while antioxidant capacity was negatively correlated with photosynthesis and seed yield, suggesting a trade-off between antioxidant metabolism and carbon gain. Exposure response curves indicate that there has not been a significant improvement in soybean tolerance to [O3] in the past 30 years.

Abstract Current background ozone (O3) concentrations over the northern hemisphere’s midlatitudes are high enough to damage crops and are projected to increase. Soybean (Glycine max) is particularly sensitive to O3; therefore, establishing an O3 exposure threshold for damage is critical to understanding the current and future impact of this pollutant. This study aims to determine the exposure response of soybean to elevated tropospheric O3 by measuring the agronomic, biochemical, and physiological responses of seven soybean genotypes to nine O3 concentrations (38–120 nL L−1) within a fully open-air agricultural field location across 2 years. All genotypes responded similarly, with season-long exposure to O3 causing a linear increase in antioxidant capacity while reducing leaf area, light absorption, specific leaf mass, primary metabolites, seed yield, and harvest index. Across two seasons with different temperature and rainfall patterns, there was a robust linear yield decrease of 37 to 39 kg ha−1 per nL L−1 cumulative O3 exposure over 40 nL L−1. The existence of immediate effects of O3 on photosynthesis, stomatal conductance, and photosynthetic transcript abundance before and after the initiation and termination of O3 fumigation were concurrently assessed, and there was no evidence to support an instantaneous photosynthetic response. The ability of the soybean canopy to intercept radiation, the efficiency of photosynthesis, and the harvest index were all negatively impacted by O3, suggesting that there are multiple targets for improving soybean responses to this damaging air pollutant.

ABSTRACT Antioxidant metabolism is responsive to environmental conditions, and is proposed to be a key component of ozone (O 3 ) tolerance in plants. Tropospheric O 3 concentration ([O 3 ]) has doubled since the Industrial Revolution and will increase further if precursor emissions rise as expected over this century. Additionally, atmospheric CO 2 concentration ([CO 2 ]) is increasing at an unprecedented rate and will surpass 550 ppm by 2050. This study investigated the molecular, biochemical and physiological changes in soybean exposed to elevated [O 3 ] in a background of ambient [CO 2 ] and elevated [CO 2 ] in the field. Previously, it has been difficult to demonstrate any link between antioxidant defences and O 3 stress under field conditions. However, this study used principle components analysis to separate variability in [O 3 ] from variability in other environmental conditions (temperature, light and relative humidity). Subsequent analysis of covariance determined that soybean antioxidant metabolism increased with increasing [O 3 ], in both ambient and elevated [CO 2 ]. The transcriptional response was dampened at elevated [CO 2 ], consistent with lower stomatal conductance and lower O 3 flux into leaves. Energetically expensive increases in antioxidant metabolism and tetrapyrrole synthesis at elevated [O 3 ] were associated with greater transcript levels of enzymes involved in respiratory metabolism.

Elevated concentrations of ground-level ozone (O3) are frequently measured over farmland regions in many parts of the world. While numerous experimental studies show that O3 can significantly decrease crop productivity, independent verifications of yield losses at current ambient O3 concentrations in rural locations are sparse. In this study, soybean crop yield data during a 5-year period over the Midwest of the United States were combined with ground and satellite O3 measurements to provide evidence that yield losses on the order of 10% could be estimated through the use of a multiple linear regression model. Yield loss trends based on both conventional ground-based instrumentation and satellite-derived tropospheric O3 measurements were statistically significant and were consistent with results obtained from open-top chamber experiments and an open-air experimental facility (SoyFACE, Soybean Free Air Concentration Enrichment) in central Illinois. Our analysis suggests that such losses are a relatively new phenomenon due to the increase in background tropospheric O3 levels over recent decades. Extrapolation of these findings supports previous studies that estimate the global economic loss to the farming community of more than $10 billion annually.

A key finding from elevated [CO2] field experiments is that the impact of elevated [CO2] on plant and ecosystem function is highly dependent upon other environmental conditions, namely temperature and the availability of nutrients and soil moisture. In addition, there is significant variation in the response to elevated [CO2] among plant functional types, species and crop varieties. However, experimental data on plant and ecosystem responses to elevated [CO2] are strongly biased to economically and ecologically important systems in the temperate zone. There is a multi-biome gap in experimental data that is most severe in the tropics and subtropics, but also includes high latitudes. Physiological understanding of the environmental conditions and species found at high and low latitudes suggest they may respond differently to elevated [CO2] than well-studied temperate systems. Addressing this knowledge gap should be a high priority as it is vital to understanding 21st century food supply and ecosystem feedbacks on climate change.

Abstract The rising trend in concentrations of ground‐level ozone (O 3 ) – a common air pollutant and phytotoxin – currently being experienced in some world regions represents a threat to agricultural yield. Soybean ( Glycine max (L.) Merr.) is an O 3 ‐sensitive crop species and is experiencing increasing global demand as a dietary protein source and constituent of livestock feed. In this study, we collate O 3 exposure‐yield data for 49 soybean cultivars, from 28 experimental studies published between 1982 and 2014, to produce an updated dose–response function for soybean. Different cultivars were seen to vary considerably in their sensitivity to O 3 , with estimated yield loss due to O 3 ranging from 13.3% for the least sensitive cultivar to 37.9% for the most sensitive, at a 7‐h mean O 3 concentration (M7) of 55 ppb – a level frequently observed in regions of the USA , India and China in recent years. The year of cultivar release, country of data collection and type of O 3 exposure used were all important explanatory variables in a multivariate regression model describing soybean yield response to O 3 . The data show that the O 3 sensitivity of soybean cultivars increased by an average of 32.5% between 1960 and 2000, suggesting that selective breeding strategies targeting high yield and high stomatal conductance may have inadvertently selected for greater O 3 sensitivity over time. Higher sensitivity was observed in data from India and China compared to the USA , although it is difficult to determine whether this effect is the result of differential cultivar physiology, or related to local environmental factors such as co‐occurring pollutants. Gaining further understanding of the underlying mechanisms that govern the sensitivity of soybean cultivars to O 3 will be important in shaping future strategies for breeding O 3 ‐tolerant cultivars.

Abstract Rising atmospheric carbon dioxide concentration ([ CO 2 ]) has the potential to positively impact C 3 food crop production by directly stimulating photosynthetic carbon gain ( A ), which leads to increased crop biomass and yield. Further stimulation of A and yield can result from an indirect mechanism in which elevated [ CO 2 ] decreases stomatal conductance and canopy water use, ameliorating drought stress. Experiments in open top chambers ( OTC ) and free air CO 2 enrichment ( FACE ) facilities have enabled investigation of crop responses to elevated [ CO 2 ] in near natural, field conditions. Mechanistic understanding of physiological responses to elevated [ CO 2 ] has led to predictions that the stimulation of A , biomass production, and economic yield will vary with the temperature and water supply experienced by the crop. This study tested current assumptions about the relationships between relative responses of yield and biomass to elevated [ CO 2 ] and variation in growing season temperature and water inputs (precipitation plus irrigation). Growing season average temperature was not a good predictor of the magnitude of biomass and yield responses to elevated [ CO 2 ], contradicting the prediction that responses to elevated [ CO 2 ] would increase with increasing temperature due to the greater benefit from decreasing photorespiration. However, the prediction that the relative stimulation of yield by elevated [ CO 2 ] would be greatest in dry conditions was generally supported. Thus, a simple CO 2 fertilization value is not appropriate for modeling future crop productivity under varying environmental conditions. Further studies are necessary across a broader range of environmental conditions in order to accurately predict how rising [ CO 2 ] will interact with temperature and drought stress and alter future crop production.

Abstract The photosynthetic capacity or the CO2-saturated photosynthetic rate (Vmax), chlorophyll, and nitrogen are closely linked leaf traits that determine C4 crop photosynthesis and yield. Accurate, timely, rapid, and non-destructive approaches to predict leaf photosynthetic traits from hyperspectral reflectance are urgently needed for high-throughput crop monitoring to ensure food and bioenergy security. Therefore, this study thoroughly evaluated the state-of-the-art physically based radiative transfer models (RTMs), data-driven partial least squares regression (PLSR), and generalized PLSR (gPLSR) models to estimate leaf traits from leaf-clip hyperspectral reflectance, which was collected from maize (Zea mays L.) bioenergy plots with diverse genotypes, growth stages, treatments with nitrogen fertilizers, and ozone stresses in three growing seasons. The results show that leaf RTMs considering bidirectional effects can give accurate estimates of chlorophyll content (Pearson correlation r=0.95), while gPLSR enabled retrieval of leaf nitrogen concentration (r=0.85). Using PLSR with field measurements for training, the cross-validation indicates that Vmax can be well predicted from spectra (r=0.81). The integration of chlorophyll content (strongly related to visible spectra) and nitrogen concentration (linked to shortwave infrared signals) can provide better predictions of Vmax (r=0.71) than only using either chlorophyll or nitrogen individually. This study highlights that leaf chlorophyll content and nitrogen concentration have key and unique contributions to Vmax prediction.

Ozone (O3 ) is a damaging air pollutant to crops. As one of the most reactive oxidants known, O3 rapidly forms other reactive oxygen species (ROS) once it enters leaves through stomata. Those ROS in turn can cause oxidative stress, reduce photosynthesis, accelerate senescence, and decrease crop yield. To improve and adapt our feed, fuel, and food supply to rising O3 pollution, a number of Free Air Concentration Enrichment (O3 -FACE) facilities have been developed around the world and have studied key staple crops. In this review, we provide an overview of the FACE facilities and highlight some of the lessons learned from the last two decades of research. We discuss the differences between C3 and C4 crop responses to elevated O3 , the possible trade-off between productivity and protection, genetic variation in O3 response within and across species, and how we might leverage this observed variation for crop improvement. We also highlight the need to improve understanding of the interaction between rising O3 pollution and other aspects of climate change, notably drought. Finally, we propose the use of globally modeled O3 data that are available at increasing spatial and temporal resolutions to expand upon the research conducted at the limited number of global O3 -FACE facilities.

Tropospheric ozone (O3) is among the most damaging air pollutant to plants. Plants alter the atmospheric O3 concentration in two distinct ways: (i) by the emission of volatile organic compounds (VOCs) that are precursors of O3; and (ii) by dry deposition, which includes diffusion of O3 into vegetation through stomata and destruction by nonstomatal pathways. Isoprene, monoterpenes, and higher terpenoids are emitted by plants in quantities that alter tropospheric O3. Deposition of O3 into vegetation is related to stomatal conductance, leaf structural traits, and the detoxification capacity of the apoplast. The biochemical fate of O3 once it enters leaves and reacts with aqueous surfaces is largely unknown, but new techniques for the tracking and identification of initial products have the potential to open the black box.

Abstract On-farm soybean yield has increased considerably in the last 50 years in southern Brazil, but there is still little information about how selection and breeding for yield increase has changed the agronomic attributes of cultivars. The objectives of this study were to evaluate the changes in soybean yield, seed oil and protein concentration, and changes in plant attributes that might be associated with yield improvement of 26 soybean cultivars released over the past 50 years in southern Brazil, sown simultaneously in a common field environment for two growing seasons. The average rate of yield gain was 45.9 kg ha −1 yr −1 (2.1% ha −1 yr −1 ), mainly due increased seed number per area and harvest index. Over year of cultivar release, cultivars became less susceptible to lodging, as well as plant mortality reduced. Meanwhile, the seed oil concentration increased, and seed protein concentration decreased, which could have negative consequences for soybeans use and requires further attention for breeding of future cultivars. Breeders have successfully contributed to the annual rate of soybean yield increase in southern Brazil. By our results, as well as the official on-farm production data, there is no evidence of soybean yield reaching a plateau in the near future in southern Brazil.

Abstract Gas exchange techniques revolutionized plant research and advanced understanding, including associated fluxes and efficiencies, of photosynthesis, photorespiration, and respiration of plants from cellular to ecosystem scales. These techniques remain the gold standard for inferring photosynthetic rates and underlying physiology/biochemistry, although their utility for high-throughput phenotyping (HTP) of photosynthesis is limited both by the number of gas exchange systems available and the number of personnel available to operate the equipment. Remote sensing techniques have long been used to assess ecosystem productivity at coarse spatial and temporal resolutions, and advances in sensor technology coupled with advanced statistical techniques are expanding remote sensing tools to finer spatial scales and increasing the number and complexity of phenotypes that can be extracted. In this review, we outline the photosynthetic phenotypes of interest to the plant science community and describe the advances in high-throughput techniques to characterize photosynthesis at spatial scales useful to infer treatment or genotypic variation in field-based experiments or breeding trials. We will accomplish this objective by presenting six lessons learned thus far through the development and application of proximal/remote sensing-based measurements and the accompanying statistical analyses. We will conclude by outlining what we perceive as the current limitations, bottlenecks, and opportunities facing HTP of photosynthesis.

• Ozone (O₃) causes significant agricultural losses, with soybean (Glycine max) being highly sensitive to this oxidant. Here we assess the effect of elevated seasonal O₃ exposure on the total and redox proteomes of soybean. • To understand the molecular responses to O₃ exposure, soybean grown at the Soybean Free Air Concentration Enrichment facility under ambient (37 ppb), moderate (58 ppb), and high (116 ppb) O₃ concentrations was examined by redox-sensitive thiol labeling, mass spectrometry, and targeted enzyme assays. • Proteomic analysis of soybean leaf tissue exposed to high O₃ concentrations reveals widespread changes. In the high-O₃ treatment leaf, 35 proteins increased up to fivefold in abundance, 22 proteins showed up to fivefold higher oxidation, and 22 proteins increased in both abundance and oxidation. These changes occurred in carbon metabolism, photosynthesis, amino acid synthesis, flavonoid and isoprenoid biosynthesis, signaling and homeostasis, and antioxidant pathways. • This study shows that seasonal O₃ exposure in soybean alters the abundance and oxidation state of redox-sensitive multiple proteins and that these changes reflect a combination of damage effects and adaptive responses that influence a wide range of metabolic processes, which in some cases may help mitigate oxidative stress.

Current concentrations of tropospheric ozone ([O3]) pollution negatively impact plant metabolism, which can result in decreased crop yields. Interspecific variation in the physiological response of plants to elevated [O3] exists; however, the underlying cellular responses explaining species-specific differences are largely unknown. Here, a physiological screen has been performed on multiple varieties of legume species. Three varieties of garden pea (Pisum sativum L.) were resilient to elevated [O3]. Garden pea showed no change in photosynthetic capacity or leaf longevity when exposed to elevated [O3], in contrast to varieties of soybean (Glycine max (L.) Merr.) and common bean (Phaseolus vulgaris L.). Global transcriptomic and targeted biochemical analyses were then done to examine the mechanistic differences in legume responses to elevated [O3]. In all three species, there was an O3-mediated reduction in specific leaf weight and total non-structural carbohydrate content, as well as increased abundance of respiration-related transcripts. Differences specific to garden pea included a pronounced increase in the abundance of GLUTATHIONE REDUCTASE transcript, as well as greater contents of foliar glutathione, apoplastic ascorbate, and sucrose in elevated [O3]. These results suggest that garden pea may have had greater capacity for detoxification, which prevented net losses in CO2 fixation in an elevated [O3] environment.

In omics experiments, variable selection involves a large number of metabolites/ genes and a small number of samples (the n < p problem). The ultimate goal is often the identification of one, or a few features that are different among conditions- a biomarker. Complicating biomarker identification, the p variables often contain a correlation structure due to the biology of the experiment making identifying causal compounds from correlated compounds difficult. Additionally, there may be elements in the experimental design (blocks, batches) that introduce structure in the data. While this problem has been discussed in the literature and various strategies proposed, the over fitting problems concomitant with such approaches are rarely acknowledged. Instead of viewing a single omics experiment as a definitive test for a biomarker, an unrealistic analytical goal, we propose to view such studies as screening studies where the goal of the study is to reduce the number of features present in the second round of testing, and to limit the Type II error. Using this perspective, the performance of LASSO, ridge regression and Elastic Net was compared with the performance of an ANOVA via a simulation study and two real data comparisons. Interestingly, a dramatic increase in the number of features had no effect on Type I error for the ANOVA approach. ANOVA, even without multiple test correction, has a low false positive rates in the scenarios tested. The Elastic Net has an inflated Type I error (from 10 to 50%) for small numbers of features which increases with sample size. The Type II error rate for the ANOVA is comparable or lower than that for the Elastic Net leading us to conclude that an ANOVA is an effective analytical tool for the initial screening of features in omics experiments.

Exposure to elevated tropospheric ozone concentration ([O3 ]) accelerates leaf senescence in many C3 crops. However, the effects of elevated [O3 ] on C4 crops including maize (Zea mays L.) are poorly understood in terms of physiological mechanism and genetic variation in sensitivity. Using free air gas concentration enrichment, we investigated the photosynthetic response of 18 diverse maize inbred and hybrid lines to season-long exposure to elevated [O3 ] (~100 nl L-1 ) in the field. Gas exchange was measured on the leaf subtending the ear throughout the grain filling period. On average over the lifetime of the leaf, elevated [O3 ] led to reductions in photosynthetic CO2 assimilation of both inbred (-22%) and hybrid (-33%) genotypes. There was significant variation among both inbred and hybrid lines in the sensitivity of photosynthesis to elevated [O3 ], with some lines showing no change in photosynthesis at elevated [O3 ]. Based on analysis of inbred line B73, the reduced CO2 assimilation at elevated [O3 ] was associated with accelerated senescence decreasing photosynthetic capacity and not altered stomatal limitation. These findings across diverse maize genotypes could advance the development of more O3 tolerant maize and provide experimental data for parameterization and validation of studies modeling how O3 impacts crop performance.

Ozone is the most damaging air pollutant to crops, currently reducing Midwest US maize production by up to 10%, yet there has been very little effort to adapt germplasm for ozone tolerance. Ozone enters plants through stomata, reacts to form reactive oxygen species in the apoplast and ultimately decreases photosynthetic C gain. In this study, 10 diverse inbred parents were crossed in a half-diallel design to create 45 F1 hybrids, which were tested for ozone response in the field using free air concentration enrichment (FACE). Ozone stress increased the heritability of photosynthetic traits and altered genetic correlations among traits. Hybrids from parents Hp301 and NC338 showed greater sensitivity to ozone stress, and disrupted relationships among photosynthetic traits. The physiological responses underlying sensitivity to ozone differed in hybrids from the two parents, suggesting multiple mechanisms of response to oxidative stress. FACE technology was essential to this evaluation because genetic variation in photosynthesis under elevated ozone was not predictable based on performance at ambient ozone. These findings suggest that selection under elevated ozone is needed to identify deleterious alleles in the world's largest commodity crop.

Summary Plants are characterized by the iso/anisohydry continuum depending on how they regulate leaf water potential (Ψ L ). However, how iso/anisohydry changes over time in response to year‐to‐year variations in environmental dryness and how such responses vary across different regions remains poorly characterized. We investigated how dryness, represented by aridity index, affects the interannual variability of ecosystem iso/anisohydry at the regional scale, estimated using satellite microwave vegetation optical depth (VOD) observations. This ecosystem‐level analysis was further complemented with published field observations of species‐level Ψ L . We found different behaviors in the directionality and sensitivity of isohydricity (σ) with respect to the interannual variation of dryness in different ecosystems. These behaviors can largely be differentiated by the average dryness of the ecosystem itself: in mesic ecosystems, σ decreases in drier years with a higher sensitivity to dryness; in xeric ecosystems, σ increases in drier years with a lower sensitivity to dryness. These results were supported by the species‐level synthesis. Our study suggests that how plants adjust their water use across years – as revealed by their interannual variability in isohydricity – depends on the dryness of plants’ living environment. This finding advances our understanding of plant responses to drought at regional scales.

Nitrogen is an essential nutrient that directly affects plant photosynthesis, crop yield, and biomass production for bioenergy crops, but excessive application of nitrogen fertilizers can cause environmental degradation. To achieve sustainable nitrogen fertilizer management for precision agriculture, there is an urgent need for nondestructive and high spatial resolution monitoring of crop nitrogen and its allocation to photosynthetic proteins as that changes over time. Here, we used visible to shortwave infrared (400–2400 nm) airborne hyperspectral imaging with high spatial (0.5 m) and spectral (3–5 nm) resolutions to accurately estimate critical crop traits, i.e., nitrogen, chlorophyll, and photosynthetic capacity (CO2-saturated photosynthesis rate, Vmax,27), at leaf and canopy scales, and to assess nitrogen deficiency on crop yield. We conducted three airborne campaigns over a maize (Zea mays L.) field during the growing season of 2019. Physically based soil-canopy Radiative Transfer Modeling (RTM) and data-driven approaches i.e. Partial-Least Squares Regression (PLSR) were used to retrieve crop traits from hyperspectral reflectance, with ground truth of leaf nitrogen, chlorophyll, Vmax,27, Leaf Area Index (LAI), and harvested grain yield. To improve computational efficiency of RTMs, Random Forest (RF) was used to mimic RTM simulations to generate machine learning surrogate models RTM-RF. The results show that prior knowledge of soil background and leaf angle distribution can significantly reduce the ill-posed RTM retrieval. RTM-RF achieved a high accuracy to predict leaf chlorophyll content (R2 = 0.73) and LAI (R2 = 0.75). Meanwhile, PLSR exhibited better accuracy to predict leaf chlorophyll content (R2 = 0.79), nitrogen concentration (R2 = 0.83), nitrogen content (R2 = 0.77), and Vmax,27 (R2 = 0.69) but required measured traits for model training. We also found that canopy structure signals can enhance the use of spectral data to predict nitrogen related photosynthetic traits, as combining RTM-RF LAI and PLSR leaf traits well predicted canopy-level traits (leaf traits × LAI) including canopy chlorophyll (R2 = 0.80), nitrogen (R2 = 0.85) and Vmax,27 (R2 = 0.82). Compared to leaf traits, we further found that canopy-level photosynthetic traits, particularly canopy Vmax,27, have higher correlation with maize grain yield. This study highlights the potential for synergistic use of process-based and data-driven approaches of hyperspectral imaging to quantify crop traits that facilitate precision agricultural management to secure food and bioenergy production.

Abstract Sun-induced chlorophyll fluorescence (SIF) measurements have shown unique potential for quantifying plant physiological stress. However, recent investigations found canopy structure and radiation largely control SIF, and physiological relevance of SIF remains yet to be fully understood. This study aims to evaluate whether the SIF-derived physiological signal improves quantification of crop responses to environmental stresses, by analyzing data at three different spatial scales within the U.S. Corn Belt, i.e. experiment plot, field, and regional scales, where ground-based portable, stationary and space-borne hyperspectral sensing systems are used, respectively. We found that, when controlling for variations in incoming radiation and canopy structure, crop SIF signals can be decomposed into non-physiological (i.e. canopy structure and radiation, 60% ∼ 82%) and physiological information (i.e. physiological SIF yield, Φ F , 17% ∼ 31%), which confirms the contribution of physiological variation to SIF. We further evaluated whether Φ F indicated plant responses under high-temperature and high vapor pressure deficit (VPD) stresses. The plot-scale data showed that Φ F responded to the proxy for physiological stress (partial correlation coefficient, r p = 0.40, p &lt; 0.001) while non-physiological signals of SIF did not respond ( p &gt; 0.1). The field-scale Φ F data showed water deficit stress from the comparison between irrigated and rainfed fields, and Φ F was positively correlated with canopy-scale stomatal conductance, a reliable indicator of plant physiological condition (correlation coefficient r = 0.60 and 0.56 for an irrigated and rainfed sites, respectively). The regional-scale data showed Φ F was more strongly correlated spatially with air temperature and VPD ( r = 0.23 and 0.39) than SIF ( r = 0.11 and 0.34) for the U.S. Corn Belt. The lines of evidence suggested that Φ F reflects crop physiological responses to environmental stresses with greater sensitivity to stress factors than SIF, and the stress quantification capability of Φ F is spatially scalable. Utilizing Φ F for physiological investigations will contribute to improve our understanding of vegetation responses to high-temperature and high-VPD stresses.

Leaf-level gas exchange data support the mechanistic understanding of plant fluxes of carbon and water. These fluxes inform our understanding of ecosystem function, are an important constraint on parameterization of terrestrial biosphere models, are necessary to understand the response of plants to global environmental change, and are integral to efforts to improve crop production. Collection of these data using gas analyzers can be both technically challenging and time consuming, and individual studies generally focus on a small range of species, restricted time periods, or limited geographic regions. The high value of these data is exemplified by the many publications that reuse and synthesize gas exchange data, however the lack of metadata and data reporting conventions make full and efficient use of these data difficult. Here we propose a reporting format for leaf-level gas exchange data and metadata to provide guidance to data contributors on how to store data in repositories to maximize their discoverability, facilitate their efficient reuse, and add value to individual datasets. For data users, the reporting format will better allow data repositories to optimize data search and extraction, and more readily integrate similar data into harmonized synthesis products. The reporting format specifies data table variable naming and unit conventions, as well as metadata characterizing experimental conditions and protocols. For common data types that were the focus of this initial version of the reporting format, i.e., survey measurements, dark respiration, carbon dioxide and light response curves, and parameters derived from those measurements, we took a further step of defining required additional data and metadata that would maximize the potential reuse of those data types. To aid data contributors and the development of data ingest tools by data repositories we provided a translation table comparing the outputs of common gas exchange instruments. Extensive consultation with data collectors, data users, instrument manufacturers, and data scientists was undertaken in order to ensure that the reporting format met community needs. The reporting format presented here is intended to form a foundation for future development that will incorporate additional data types and variables as gas exchange systems and measurement approaches advance in the future. The reporting format is published in the U.S. Department of Energy's ESS-DIVE data repository, with documentation and future development efforts being maintained in a version control system.

The initial stimulation of photosynthesis observed on elevation of [CO 2 ] in grasslands has been predicted to be a transient phenomenon constrained by the loss of photosynthetic capacity due to other limitations, notably nutrients and sinks for carbohydrates.Legumes might be expected partially to escape these feedbacks through symbiotic N 2 ®xation.The Free-Air Carbon dioxide Enrichment (FACE) experiment at Eschikon, Switzerland, has been the longest running investigation of the effects of open-air elevation of [CO 2 ] on vegetation.The prediction of a long-term loss of photosynthetic capacity was tested by analysing photosynthesis in Trifolium repens L. (cv.Milkanova) in the spring and autumn of the eighth, ninth and tenth years of treatment.A high and low N treatment also allowed a test of the signi®cance of exogenous N-supply in maintaining a stimulation of photosynthetic capacity in the long-term.Prior work in this Free Air CO 2 Enrichment (FACE) experiment has revealed that elevated [CO 2 ] increased both vegetative and reproductive growth of T. repens independent of N treatment.It is shown here that the photosynthetic response of T. repens was also independent of N fertilization under both current ambient and elevated (600 mmol mol ±1 ) [CO 2 ].There was a strong effect of season on photosynthesis, with lightsaturated rates (A sat ) 37% higher in spring than in autumn.Higher A sat in the spring was supported by higher maximum Rubisco carboxylation rates (V c,max ) and maximum rates of electron transport (J max ) contributing to RuBP regeneration.Elevated [CO 2 ] increased A sat by 37% when averaged across all measurement periods and both N fertilization levels, and decreased stomatal conductance by 25%.In spring, there was no effect of elevated [CO 2 ] on photosynthetic capacity of leaves, but in autumn both V c,max and J max were reduced by approximately 20% in elevated [CO 2 ].The results show that acclimation of photosynthetic capacity can occur in a nitrogen-®xing species, in the ®eld where there are no arti®cial restrictions on sink capacity.However, even with acclimation there was a highly signi®cant increase in photosynthesis at elevated [CO 2 ].

Rising atmospheric carbon dioxide concentration ([CO2]) in this century will alter crop yield quantity and quality. It is important to understand the magnitude of the expected changes and the mechanisms involved in crop responses to elevated [CO2] in order to adapt our food systems to the committed change in atmospheric [CO2] and to accurately model future food supply. Free-Air CO2 Enrichment (FACE) allows for crops to be grown in their production environment, under fully open air conditions, at elevated [CO2]. Current best estimates for the response of the staple crops wheat, soybean and rice from FACE experiments are that grain yield will increase by 13% at 550 ppm CO2. For the C4 species, sorghum and maize, grain yield is not expected to increase at elevated [CO2] if water supply is adequate. Grain quality is adversely affected by elevated [CO2]. On average, protein content decreases by 10–14% in non-leguminous grain crops and concentrations of minerals, such as iron and zinc decrease by 15–30%. While these represent our best estimate of changes in crop yield quantity and quality, most studies have been done in temperate regions, and do not account for possible interactions of rising [CO2] with other aspects of climate change, including increased temperature, drought stress and tropospheric ozone concentration.

Current forest Free Air CO2 Enrichment (FACE) experiments are reaching completion. Therefore, it is time to define the scientific goals and priorities of future experimental facilities. In this opinion article, we discuss the following three overarching issues (i) What are the most urgent scientific questions and how can they be addressed? (ii) What forest ecosystems should be investigated? (iii) Which other climate change factors should be coupled with elevated CO2 concentrations in future experiments to better predict the effects of climate change? Plantations and natural forests can have conflicting purposes for high productivity and environmental protection. However, in both cases the assessment of carbon balance and how this will be affected by elevated CO2 concentrations and the interacting climate change factors is the most pressing priority for future experiments. Current forest Free Air CO2 Enrichment (FACE) experiments are reaching completion. Therefore, it is time to define the scientific goals and priorities of future experimental facilities. In this opinion article, we discuss the following three overarching issues (i) What are the most urgent scientific questions and how can they be addressed? (ii) What forest ecosystems should be investigated? (iii) Which other climate change factors should be coupled with elevated CO2 concentrations in future experiments to better predict the effects of climate change? Plantations and natural forests can have conflicting purposes for high productivity and environmental protection. However, in both cases the assessment of carbon balance and how this will be affected by elevated CO2 concentrations and the interacting climate change factors is the most pressing priority for future experiments.

Improving plant energy conversion efficiency (εc) is crucial for increasing food and bioenergy crop production and yields. Using a meta-analysis, the effects of greenhouse gases, weather-related stresses projected to intensify due to climate change, and management practices including inputs, shading, and intercropping on εc were statistically quantified from 140 published studies to identify where improvements would have the largest impact on closing yield gaps. Variation in the response of εc to treatment type and dosage, plant characteristics, and growth conditions were also examined. Significant mean increases in εc were caused by elevated [CO2] (20%), shade (18%), and intercropping (15%). εc increased curvilinearly up to 55% with nitrogen additions whereas phosphorus application was most beneficial at low levels. Significant decreases in εc of -8.4% due to elevated [O3], -16.8% due to water stress, and -6.5% due to foliar damage were found. A non-significant decrease in εc of -17.3% was caused by temperature stress. These results identify the need to engineer greater stress tolerance and enhanced responses to positive factors such as [CO2] and nitrogen to improve average yields and yield potential. Optimizing management strategies will also enhance the benefits possible with intercropping, shade, and pest resilience. To determine optimal practices for εc improvement, further studies should be conducted in the field since several responses were exaggerated by non-field experimental conditions.

Abstract Both elevated ozone ( O 3 ) and limiting soil nitrogen (N) availability negatively affect crop performance. However, less is known about how the combination of elevated O 3 and limiting N affect crop growth and metabolism. In this study, we grew tobacco ( Nicotiana sylvestris ) in ambient and elevated O 3 at two N levels (limiting and sufficient). Results at the whole plant, leaf, and cellular level showed that primary metabolism was reduced by growth in limiting N, and that reduction was exacerbated by exposure to elevated O 3 . Limiting N reduced the rates of photosynthetic CO 2 uptake by 40.8% in ambient O 3 ‐exposed plants, and by 58.6% in elevated O 3 ‐exposed plants, compared with plants grown with sufficient N. Reductions in photosynthesis compounded to cause large differences in leaf and whole plant parameters including leaf number, leaf area, and leaf and root biomass. These results were consistent with our meta‐analysis of all published studies of plant responses to elevated O 3 and N availability. In tobacco, N uptake and allocation was also affected by growth in limiting N and elevated O 3 , and there was an O 3 ‐induced compensatory response that resulted in increased N recycling from senescing leaves. In addition, transcript‐based markers were used to track the progress through senescence, and indicated that limiting N and elevated O 3 , separately and in combination, caused an acceleration of senescence. These results suggest that reductions in crop productivity in growing regions with poor soil fertility will be exacerbated by rising background O 3 .

Traditional gas exchange measurements are cumbersome, which makes it difficult to capture variation in biochemical parameters, namely the maximum rate of carboxylation measured at a reference temperature (Vcmax25 ) and the maximum electron transport at a reference temperature (Jmax25 ), in response to growth temperature over time from days to weeks. Hyperspectral reflectance provides reliable measures of Vcmax25 and Jmax25 ; however, the capability of this method to capture biochemical acclimations of the two parameters to high growth temperature over time has not been demonstrated. In this study, Vcmax25 and Jmax25 were measured over multiple growth stages during two growing seasons for field-grown soybeans using both gas exchange techniques and leaf spectral reflectance under ambient and four elevated canopy temperature treatments (ambient+1.5, +3, +4.5, and +6°C). Spectral vegetation indices and machine learning methods were used to build predictive models for Vcmax25 and Jmax25 , based on the leaf reflectance. Results showed that these models yielded an R2 of 0.57-0.65 and 0.48-0.58 for Vcmax25 and Jmax25 , respectively. Hyperspectral reflectance captured biochemical acclimation of leaf photosynthesis to high temperature in the field, improving spatial and temporal resolution in the ability to assess the impact of future warming on crop productivity.

Abstract There is tremendous interspecific variability in O 3 sensitivity among C 3 species, but variation among C 4 species has been less clearly documented. It is also unclear whether stomatal conductance and leaf structure such as leaf mass per area (LMA) determine the variation in sensitivity to O 3 across species. In this study, we investigated leaf morphological, chemical, and photosynthetic responses of 22 genotypes of four C 4 bioenergy species (switchgrass, sorghum, maize, and miscanthus) to elevated O 3 in side‐by‐side field experiments using free‐air O 3 concentration enrichment (FACE). The C 4 species varied largely in leaf morphology, physiology, and nutrient composition. Elevated O 3 did not alter leaf morphology, nutrient content, stomatal conductance, chlorophyll fluorescence, and respiration in most genotypes but reduced net CO 2 assimilation in maize and photosynthetic capacity in sorghum and maize. Species with lower LMA and higher stomatal conductance tended to show greater losses in photosynthetic rate and capacity in elevated O 3 compared with species with higher LMA and lower stomatal conductance. Stomatal conductance was the strongest determinant of leaf photosynthetic rate and capacity. The response of both area‐ and mass‐based leaf photosynthetic rate and capacity to elevated O 3 were not affected by LMA directly but negatively influenced by LMA indirectly through stomatal conductance. These results demonstrate that there is significant variation in O 3 sensitivity among C 4 species with maize and sorghum showing greater sensitivity of photosynthesis to O 3 than switchgrass and miscanthus. Interspecific variation in O 3 sensitivity was determined by direct effects of stomatal conductance and indirect effects of LMA. This is the first study to provide a test of unifying theories explaining variation in O 3 sensitivity in C 4 bioenergy grasses. These findings advance understanding of O 3 tolerance in C 4 grasses and could aid in optimal placement of diverse C 4 bioenergy feedstock across a polluted landscape.

Abstract Improvements in genetics, technology, and agricultural intensification have increased soybean yields; however, adverse climate conditions may prevent these gains from being fully realized in the future. Higher growing season temperatures reduce soybean yields in key production regions including the US Midwest, and better understanding of the developmental and physiological mechanisms that constrain soybean yield under high temperature conditions is needed. This study tested the response of two soybean cultivars to four elevated temperature treatments (+1.7, +2.6, +3.6, and +4.8 °C) in the field over three growing seasons and identified threshold temperatures for response and linear versus non-linear trait responses to temperature. Yield declined non-linearly to temperature, with decreases apparent when canopy temperature exceeded 20.9 °C for the locally adapted cultivar and 22.7°C for a cultivar adapted to more southern locations. While stem node number increased with increasing temperature, leaf area index decreased substantially. Pod production, seed size, and harvest index significantly decreased with increasing temperature. The seasonal average temperature of even the mildest treatment exceeded the threshold temperatures for yield loss, emphasizing the importance of improving temperature tolerance in soybean germplasm with intensifying climate change.

Transfer learning refers to the transfer of knowledge or information from a relevant source domain to a target domain. However, most existing transfer learning theories and algorithms focus on IID tasks, where the source/target samples are assumed to be independent and identically distributed. Very little effort is devoted to theoretically studying the knowledge transferability on non-IID tasks, e.g., cross-network mining. To bridge the gap, in this paper, we propose rigorous generalization bounds and algorithms for cross-network transfer learning from a source graph to a target graph. The crucial idea is to characterize the cross-network knowledge transferability from the perspective of the Weisfeiler-Lehman graph isomorphism test. To this end, we propose a novel Graph Subtree Discrepancy to measure the graph distribution shift between source and target graphs. Then the generalization error bounds on cross-network transfer learning, including both cross-network node classification and link prediction tasks, can be derived in terms of the source knowledge and the Graph Subtree Discrepancy across domains. This thereby motivates us to propose a generic graph adaptive network (GRADE) to minimize the distribution shift between source and target graphs for cross-network transfer learning. Experimental results verify the effectiveness and efficiency of our GRADE framework on both cross-network node classification and cross-domain recommendation tasks.

The deleterious effects of ozone (O3) pollution on crop physiology, yield, and productivity are widely acknowledged. It has also been assumed that C4 crops with a carbon concentrating mechanism and greater water use efficiency are less sensitive to O3 pollution than C3 crops. This assumption has not been widely tested. Therefore, we compiled 46 journal articles and unpublished datasets that reported leaf photosynthetic and biochemical traits, plant biomass, and yield in five C3 crops (chickpea, rice, snap bean, soybean, and wheat) and four C4 crops (sorghum, maize, Miscanthus × giganteus, and switchgrass) grown under ambient and elevated O3 concentration ([O3]) in the field at free-air O3 concentration enrichment (O3-FACE) facilities over the past 20 y. When normalized by O3 exposure, C3 and C4 crops showed a similar response of leaf photosynthesis, but the reduction in chlorophyll content, fluorescence, and yield was greater in C3 crops compared with C4 crops. Additionally, inbred and hybrid lines of rice and maize showed different sensitivities to O3 exposure. This study quantitatively demonstrates that C4 crops respond less to elevated [O3] than C3 crops. This understanding could help maintain cropland productivity in an increasingly polluted atmosphere.

Abstract The use of genomic techniques to address ecological questions is emerging as the field of genomic ecology. Experimentation under environmentally realistic conditions to investigate the molecular response of plants to meaningful changes in growth conditions and ecological interactions is the defining feature of genomic ecology. Because the impact of global change factors on plant performance are mediated by direct effects at the molecular, biochemical, and physiological scales, gene expression analysis promises important advances in understanding factors that have previously been consigned to the ‘black box’ of unknown mechanism. Various tools and approaches are available for assessing gene expression in model and nonmodel species as part of global change biology studies. Each approach has its own unique advantages and constraints. A first generation of genomic ecology studies in managed ecosystems and mesocosms have provided a testbed for the approach and have begun to reveal how the experimental design and data analysis of gene expression studies can be tailored for use in an ecological context.

Summary Here, we investigated the effects of increasing concentrations of ozone ([O 3 ]) on soybean canopy‐scale fluxes of heat and water vapor, as well as water use efficiency (WUE), at the Soybean Free Air Concentration Enrichment (SoyFACE) facility. Micrometeorological measurements were made to determine the net radiation ( R n ), sensible heat flux ( H ), soil heat flux ( G 0 ) and latent heat flux ( λET ) of a commercial soybean ( Glycine max ) cultivar (Pioneer 93B15), exposed to a gradient of eight daytime average ozone concentrations ranging from approximately current ( c . 40 ppb) to three times current ( c . 120 ppb) levels. As [O 3 ] increased, soybean canopy fluxes of λET decreased and H increased, whereas R n and G 0 were not altered significantly. Exposure to increased [O 3 ] also resulted in warmer canopies, especially during the day. The lower λET decreased season total evapotranspiration ( ET ) by c . 26%. The [O 3 ]‐induced relative decline in ET was half that of the relative decline in seed yield, driving a 50% reduction in seasonal WUE. These results suggest that rising [O 3 ] will alter the canopy energy fluxes that drive regional climate and hydrology, and have a negative impact on productivity and WUE, key ecosystem services.

RNA sequencing (RNA-Seq) is emerging as a highly accurate method to quantify transcript abundance. However, analyses of the large data sets obtained by sequencing the entire transcriptome of organisms have generally been performed by bioinformatics specialists. Here we provide a step-by-step guide and outline a strategy using currently available statistical tools that results in a conservative list of differentially expressed genes. We also discuss potential sources of error in RNA-Seq analysis that could alter interpretation of global changes in gene expression. When comparing statistical tools, the negative binomial distribution-based methods, edgeR and DESeq, respectively identified 11,995 and 11,317 differentially expressed genes from an RNA-seq dataset generated from soybean leaf tissue grown in elevated O3. However, the number of genes in common between these two methods was only 10,535, resulting in 2,242 genes determined to be differentially expressed by only one method. Upon analysis of the non-significant genes, several limitations of these analytic tools were revealed, including evidence for overly stringent parameters for determining statistical significance of differentially expressed genes as well as increased type II error for high abundance transcripts. Because of the high variability between methods for determining differential expression of RNA-Seq data, we suggest using several bioinformatics tools, as outlined here, to ensure that a conservative list of differentially expressed genes is obtained. We also conclude that despite these analytical limitations, RNA-Seq provides highly accurate transcript abundance quantification that is comparable to qRT-PCR.

Understanding how intensification of abiotic stress due to global climate change affects crop yields is important for continued agricultural productivity. Coupling genomic technologies with physiological crop responses in a dynamic field environment is an effective approach to dissect the mechanisms underpinning crop responses to abiotic stress. Soybean (Glycine max L. Merr. cv. Pioneer 93B15) was grown in natural production environments with projected changes to environmental conditions predicted for the end of the century, including decreased precipitation, increased tropospheric ozone concentrations ([O3]), or increased temperature. All three environmental stresses significantly decreased leaf-level photosynthesis and stomatal conductance, leading to significant losses in seed yield. This was driven by a significant decrease in the number of pods per node for all abiotic stress treatments. To understand the underlying transcriptomic response involved in the yield response to environmental stress, RNA-Sequencing analysis was performed on the soybean seed coat, a tissue that plays an essential role in regulating carbon and nitrogen transport to developing seeds. Gene expression analysis revealed 49, 148 and 1,576 differentially expressed genes in the soybean seed coat in response to drought, elevated [O3] and elevated temperature, respectively. Elevated [O3] and drought did not elicit substantive transcriptional changes in the soybean seed coat. However, this may be due to the timing of sampling and does not preclude impacts of those stresses on different tissues or different stages in seed coat development. Expression of genes involved in DNA replication and metabolic processes were enriched in the seed coat under high temperate stress, suggesting that the timing of events that are important for cell division and proper seed development were altered in a stressful growth environment.

Abstract The atmospheric [ CO 2 ] in which crops grow today is greater than at any point in their domestication history and represents an opportunity for positive effects on seed yield that can counteract the negative effects of greater heat and drought this century. In order to maximize yields under future atmospheric [ CO 2 ], we need to identify and study crop cultivars that respond most favorably to elevated [ CO 2 ] and understand the mechanisms contributing to their responsiveness. Soybean ( Glycine max Merr.) is a widely grown oilseed crop and shows genetic variation in response to elevated [ CO 2 ]. However, few studies have studied the physiological basis for this variation. Here, we examined canopy light interception, photosynthesis, respiration and radiation use efficiency along with yield and yield parameters in two cultivars of soybean (Loda and HS 93‐4118) previously reported to have similar seed yield at ambient [ CO 2 ], but contrasting responses to elevated [ CO 2 ]. Seed yield increased by 26% at elevated [ CO 2 ] (600 μmol/mol) in the responsive cultivar Loda, but only by 11% in HS 93‐4118. Canopy light interception and leaf area index were greater in HS 93‐4118 in ambient [ CO 2 ], but increased more in response to elevated [ CO 2 ] in Loda. Radiation use efficiency and harvest index were also greater in Loda than HS 93‐4118 at both ambient and elevated [ CO 2 ]. Daily C assimilation was greater at elevated [ CO 2 ] in both cultivars, while stomatal conductance was lower. Electron transport capacity was also greater in Loda than HS 93‐4118, but there was no difference in the response of photosynthetic traits to elevated [ CO 2 ] in the two cultivars. Overall, this greater understanding of leaf‐ and canopy‐level photosynthetic traits provides a strong conceptual basis for modeling genotypic variation in response to elevated [ CO 2 ].

By mid-century, global atmospheric carbon dioxide concentration ([CO2]) is predicted to reach 600 μmol mol−1 with global temperatures rising by 2 °C. Rising [CO2] and temperature will alter the growth and productivity of major food and forage crops across the globe. Although the impact is expected to be greatest in tropical regions, the impact of climate-change has been poorly studied in those regions. This experiment aimed to understand the effects of elevated [CO2] (600 μmol mol−1) and warming (+ 2 °C), singly and in combination, on Panicum maximum Jacq. (Guinea grass) metabolite and transcript profiles. We created a de novo assembly of the Panicum maximum transcriptome. Leaf samples were taken at two time points in the Guinea grass growing season to analyze transcriptional and metabolite profiles in plants grown at ambient and elevated [CO2] and temperature, and statistical analyses were used to integrate the data. Elevated temperature altered the content of amino acids and secondary metabolites. The transcriptome of Guinea grass shows a clear time point separations, with the changes in the elevated temperature and [CO2] combination plots. Field transcriptomics and metabolomics revealed that elevated temperature and [CO2] result in alterations in transcript and metabolite profiles associated with environmental response, secondary metabolism and stomatal function. These metabolic responses are consistent with greater growth and leaf area production under elevated temperature and [CO2]. These results show that tropical C4 grasslands may have unpredicted responses to global climate change, and that warming during a cool growing season enhances growth and alleviates stress.

There remains limited information to characterize the solar-induced chlorophyll fluorescence (SIF)-gross primary production (GPP) relationship in C4 cropping systems. The annual C4 crop corn and perennial C4 crop miscanthus differ in phenology, canopy structure and leaf physiology. Investigating the SIF-GPP relationships in these species could deepen our understanding of SIF-GPP relationships within C4 crops. Using in situ canopy SIF and GPP measurements for both species along with leaf-level measurements, we found considerable differences in the SIF-GPP relationships between corn and miscanthus, with a stronger SIF-GPP relationship and higher slope of SIF-GPP observed in corn compared to miscanthus. These differences were mainly caused by leaf physiology. For miscanthus, high non-photochemical quenching (NPQ) under high light, temperature and water vapor deficit (VPD) conditions caused a large decline of fluorescence yield (ΦF), which further led to a SIF midday depression and weakened the SIF-GPP relationship. The larger slope in corn than miscanthus was mainly due to its higher GPP in mid-summer, largely attributed to the higher leaf photosynthesis and less NPQ. Our results demonstrated variation of the SIF-GPP relationship within C4 crops and highlighted the importance of leaf physiology in determining canopy SIF behaviors and SIF-GPP relationships.

The concentration of CO2 ([CO2]) in the atmosphere is projected to exceed 550 ppm by 2050. C3 plants respond directly to growth at elevated [CO2] by stimulation of photosynthesis and reduced stomatal conductance. The stimulation of photosynthesis is the result of increased velocity of carboxylation of CO2 by Rubisco and inhibition of the competing oxygenation reaction. Long-term exposure of C3 plants to elevated [CO2] can also lead to photosynthetic acclimation in which allocation of resources to components of the photosynthetic machinery, including Rubisco, is altered to optimize metabolic efficiency. The decrease in stomatal conductance that occurs in all plants at elevated [CO2] can reduce canopy water use and indirectly enhance carbon gain by ameliorating drought stress. However, canopy micrometeorology constrains reductions in water use at the whole-plant level compared to the leaf level. C4 photosynthesis is not directly stimulated by free-air concentration enrichment (FACE) of CO2 in the field. However, reduced water use can indirectly enhance carbon gain by ameliorating stress in times and places of drought. There are commonalities and important distinctions between plant responses to growth at elevated [CO2] under FACE versus controlled environment chambers. In FACE experiments: (1) the enhancement of photosynthesis and productivity by elevated [CO2] is sustained over time; (2) the decrease in carboxylation capacity and leaf N characteristic of photosynthetic acclimation to elevated [CO2] is consistent with an optimization of metabolic efficiency rather than a general down-regulation of metabolism, and (3) the enhancement effect of elevated [CO2] is greatest for photosynthesis, intermediate for biomass accumulation, and lowest for crop yield. Plant responses to elevated [CO2] have the potential to influence the global carbon cycle and climate in the future, but the complexity of scaling from the leaf to whole plant, canopy, ecosystem and biosphere make it unclear to what extent this will be realized. Elevated [CO2] will probably offset some of the future losses in crop yield caused by increased temperature and drought stress, but not to the extent previously thought. Expanding FACE experimentation to consider multiple elements of global change across a wider geographic range and more ecosystem types should be a priority if we are to minimize the problems, and maximize the benefits, of climate change impacts on ecosystem good and services.

Abstract This study tested the hypothesis that inoculation of soybean ( G lycine max M err.) with a B radyrhizobium japonicum strain ( USDA 110) with greater N 2 fixation rates would enhance soybean response to elevated [ CO 2 ]. In field experiments at the S oybean F ree A ir CO 2 Enrichment facility, inoculation of soybean with USDA 110 increased nodule occupancy from 5% in native soil to 54% in elevated [ CO 2 ] and 34% at ambient [ CO 2 ]. Despite this success, inoculation with USDA 110 did not result in greater photosynthesis, growth or seed yield at ambient or elevated [ CO 2 ] in the field, presumably due to competition from native rhizobia. In a growth chamber experiment designed to study the effects of inoculation in the absence of competition, inoculation with USDA 110 in sterilized soil resulted in nodule occupation of &gt;90%, significantly greater 15 N 2 fixation, photosynthetic capacity, leaf N and total plant biomass compared with plants grown with native soil bacteria. However, there was no interaction of rhizobium fertilization with elevated [ CO 2 ]; inoculation with USDA 110 was equally beneficial at ambient and elevated [ CO 2 ]. These results suggest that selected rhizobia could potentially stimulate soybean yield in soils with little or no history of prior soybean production, but that better quality rhizobia do not enhance soybean responses to elevated [ CO 2 ].

Abstract Ozone pollution is a damaging air pollutant that reduces maize yields equivalently to nutrient deficiency, heat, and aridity stress. Therefore, understanding the physiological and biochemical responses of maize to ozone pollution and identifying traits predictive of ozone tolerance is important. In this study, we examined the physiological, biochemical and yield responses of six maize hybrids to elevated ozone in the field using Free Air Ozone Enrichment. Elevated ozone stress reduced photosynthetic capacity, in vivo and in vitro, decreasing Rubisco content, but not activation state. Contrary to our hypotheses, variation in maize hybrid responses to ozone was not associated with stomatal limitation or antioxidant pools in maize. Rather, tolerance to ozone stress in the hybrid B73 × Mo17 was correlated with maintenance of leaf N content. Sensitive lines showed greater ozone‐induced senescence and loss of photosynthetic capacity compared to the tolerant line.