A comparative analysis of transcriptomic, biochemical, and physiological responses to elevated ozone identifies species-specific mechanisms of resilience in legume crops

Unraveling the underlying mechanisms of biochemical, physiological, and growth responses of two pea (Pisum sativum L.) cultivars under simulated acid rain-induced oxidative stress

The current experiment was designed to evaluate the ramifications of simulated acid rain (SAR) on two pea (Pisum sativum L.) cultivars, Kashi Samridhi (Samridhi) and Kashi Nandini (Nandini), to decipher the intraspecific variations in defence mechanism considering the current scenario of rapid anthropogenic activities leading to increase in rain acidity. The pea cultivars were subjected to SAR of pH 7 (Control), 5.6, 5.0, and 4.5 under field conditions. SAR increased active oxygen species and malondialdehyde content due to increased lipid peroxidation in both cultivars; however, the increment intensity was more remarkable in Samridhi at the later growth stage. Ascorbic acid, thiol, and flavonoids were significantly increased in cultivar Nandini, along with increased peroxidase and superoxide dismutase activities. Total phenolics, glutathione reductase, and ascorbate peroxidase activities were enhanced considerably in Samridhi than in Nandini under SAR treatments. Higher stomatal density and stomatal size in Samridhi prompted greater acidic particles influx which further damaged the chloroplast and mitochondria. The present study concludes that cultivar Nandini is more proficient in inducing defence responses by elevating non-enzymatic antioxidants than Samridhi. Non-enzymatic linked defence mechanisms are more metabolically expensive, leading to less biomass accumulation in Nandini. The study depicted that innate defence responses, particularly the role of non-enzymatic antioxidants, governed the sensitivity level of cultivars towards SAR stress. Further, findings also contribute to bridging the knowledge gap regarding the responses of tropical and subtropical crops to acid rain.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01494-x.

Urban Air Pollution and Plant Tolerance: Omics Responses to Ozone, Nitrogen Oxides, and Particulate Matter

Urban air pollution is a crucial global challenge, mainly originating from urbanization and industrial activities, which are continuously increasing. Vegetation serves as a natural air filter for air pollution, but adverse effects on plant health, photosynthesis, and metabolism can occur. Recent omics technologies have revolutionized the study of molecular plant responses to air pollution, overcoming previous limitations. This review synthesizes the latest advancements in molecular plant responses to major air pollutants, emphasizing ozone (O3), nitrogen oxides (NOX), and particulate matter (PM) research. These pollutants induce stress responses common to other abiotic and biotic stresses, including the activation of reactive oxygen species (ROSs)-scavenging enzymes and hormone signaling pathways. New evidence has shown the central role of antioxidant phenolic compound biosynthesis, via the phenylpropanoid pathway, in air pollution stress responses. Transcription factors like WRKY, AP2/ERF, and MYB, which connect hormone signaling to antioxidant biosynthesis, were also affected. To date, research has predominantly focused on laboratory studies analyzing individual pollutants. This review highlights the need for comprehensive field studies and the identification of molecular tolerance traits, which are crucial for the identification of tolerant plant species, aimed at the development of sustainable nature-based solutions (NBSs) to mitigate urban air pollution.

Effect of tropospheric ozone and its protectants on gas exchange parameters, antioxidant enzymes and quality of Garlic (Allium sativum. L)

An experimental study was conducted to assess the detrimental effect of ground-level ozone (O3) on garlic physiology and to find out appropriate control measures against ground-level O3, at TNAU-Horticultural Research farm, Udhagamandalam. Elevated ground ozone levels significantly decreased garlic leaf chlorophyll, photosynthetic rate, stomatal conductance, total soluble solids and pungency. The garlic chlorophyll content was highest in ambient ozone level and lowest in elevated ozone@200 ppb, highest stomatal conductance was recorded in ambient ozone with foliar spray of 3%Panchagavya, and the lowest was observed in elevated ozone@200 ppb. Since the elevated O3 had reduced in garlic photosynthetic rate significantly the lowest was observed in elevated O3@200 ppb and the highest photosynthetic rate was observed in ambient Ozone with foliar spray 3% of panchagavya after a week. The antioxidant enzymes of garlic were increased with increased concentration of tropospheric ozone. The highest catalase (60.97 µg of H2O2/g of leaf) and peroxidase (9.13 ΔA/min/g of leaf) concentration was observed at 200 ppb elevated ozone level. Garlic pungency content was highest in ambient ozone with foliar spray of 0.1% ascorbic acid and the lowest was observed under elevated O3@200 ppb. Highest total soluble solids were observed in ambient ozone with foliar spray of 3%Panchagavya and the lowest observed in elevated ozone@200 ppb. Thus, tropospheric ozone has a detrimental impact on the physiology of crops, which reduced crop growth and yield. Under elevated O3 levels, ascorbic acid performed well followed by panchagavya and neem oil. The antioxidant such as catalase and peroxidase had positive correlation among themselves and had negative correlation with chlorophyll content, stomatal conductance, photosynthetic rate, pungency and TSS. The photosynthetic rate has high positive correlation with chlorophyll content, pungency and TSS. Correlation analysis confirmed the negative effects of tropospheric ozone and garlic gas exchange parameters and clove quality. The ozone protectants will reduce stomatal opening by which the entry of O3 in to the cell will be restricted and other hand they also will alleviate ROS and allied stresses.

Elevated tropospheric ozone and crop production: potential negative effects and plant defense mechanisms

Ozone (O3) levels on Earth are increasing because of anthropogenic activities and natural processes. Ozone enters plants through the leaves, leading to the overgeneration of reactive oxygen species (ROS) in the mesophyll and guard cell walls. ROS can damage chloroplast ultrastructure and block photosynthetic electron transport. Ozone can lead to stomatal closure and alter stomatal conductance, thereby hindering carbon dioxide (CO2) fixation. Ozone-induced leaf chlorosis is common. All of these factors lead to a reduction in photosynthesis under O3 stress. Long-term exposure to high concentrations of O3 disrupts plant physiological processes, including water and nutrient uptake, respiration, and translocation of assimilates and metabolites. As a result, plant growth and reproductive performance are negatively affected. Thus, reduction in crop yield and deterioration of crop quality are the greatest effects of O3 stress on plants. Increased rates of hydrogen peroxide accumulation, lipid peroxidation, and ion leakage are the common indicators of oxidative damage in plants exposed to O3 stress. Ozone disrupts the antioxidant defense system of plants by disturbing enzymatic activity and non-enzymatic antioxidant content. Improving photosynthetic pathways, various physiological processes, antioxidant defense, and phytohormone regulation, which can be achieved through various approaches, have been reported as vital strategies for improving O3 stress tolerance in plants. In plants, O3 stress can be mitigated in several ways. However, improvements in crop management practices, CO2 fertilization, using chemical elicitors, nutrient management, and the selection of tolerant crop varieties have been documented to mitigate O3 stress in different plant species. In this review, the responses of O3-exposed plants are summarized, and different mitigation strategies to decrease O3 stress-induced damage and crop losses are discussed. Further research should be conducted to determine methods to mitigate crop loss, enhance plant antioxidant defenses, modify physiological characteristics, and apply protectants.

Adapting crop production to climate change and air pollution at different scales

Air pollution and climate change are tightly interconnected and jointly affect field crop production and agroecosystem health. Although our understanding of the individual and combined impacts of air pollution and climate change factors is improving, the adaptation of crop production to concurrent air pollution and climate change remains challenging to resolve. Here we evaluate recent advances in the adaptation of crop production to climate change and air pollution at the plant, field and ecosystem scales. The main approaches at the plant level include the integration of genetic variation, molecular breeding and phenotyping. Field-level techniques include optimizing cultivation practices, promoting mixed cropping and diversification, and applying technologies such as antiozonants, nanotechnology and robot-assisted farming. Plant- and field-level techniques would be further facilitated by enhancing soil resilience, incorporating precision agriculture and modifying the hydrology and microclimate of agricultural landscapes at the ecosystem level. Strategies and opportunities for crop production under climate change and air pollution are discussed.

Basic leucine zipper gene VvbZIP61 is expressed at a quantitative trait locus for high monoterpene content in grape berries

The widely appreciated muscat flavor of grapes and wine is mainly attributable to the monoterpenes that accumulate in ripe grape berries. To identify quantitative trait loci (QTL) for grape berry monoterpene content, an F1 mapping population was constructed by a cross between two grapevine genotypes, one with neutral aroma berries (cv. 'Beifeng') and the other with a pronounced muscat aroma (elite Vitis vinifera line '3-34'). A high-density genetic linkage map spanning 1563.7 cM was constructed using 3332 SNP markers that were assigned to 19 linkage groups. Monoterpenes were extracted from the berry of the F1 progeny, then identified and quantified by gas chromatography-mass spectrometry. Twelve stable QTLs associated with the amounts of 11 monoterpenes in berries were thus identified. In parallel, the levels of RNA in berries from 34 diverse cultivars were estimated by RNA sequencing and compared to the monoterpene content of the berries. The expression of five genes mapping to stable QTLs correlated well with the monoterpene content of berries. These genes, including the basic leucine zipper VvbZIP61 gene on chromosome 12, are therefore considered as potentially being involved in monoterpene metabolism. Overexpression of VvbZIP61 in Vitis amurensis callus through Agrobacterium-mediated transformation significantly increased the accumulation of several monoterpenes in the callus, including nerol, linalool, geranial, geraniol, β-myrcene, and D-limonene. It is hypothesized that VvbZIP61 expression acts to increase muscat flavor in grapes. These results advance our understanding of the genetic control of monoterpene biosynthesis in grapes and provide important information for the marker-assisted selection of aroma compounds in grape breeding.

Physiological and molecular responses of different rose (Rosa hybrida L.) cultivars to elevated ozone levels

The increasing ground-level ozone (O₃) pollution resulting from rapid global urbanization and industrialization has negative effects on many plants. Nonetheless, many gaps remain in our knowledge of how ornamental plants respond to O₃. Rose (Rosa hybrida L.) is a commercially important ornamental plant worldwide. In this study, we exposed four rose cultivars ("Schloss Mannheim," "Iceberg," "Lüye," and "Spectra") to either unfiltered ambient air (NF), unfiltered ambient air plus 40 ppb O₃ (NF40), or unfiltered ambient air plus 80 ppb O₃ (NF80). Only the cultivar "Schloss Mannheim" showed significant O₃-related effects, including foliar injury, reduced chlorophyll content, reduced net photosynthetic rate, reduced stomatal conductance, and reduced stomatal apertures. In "Schloss Mannheim," several transcription factor genes-HSF, WRKY, and MYB genes-were upregulated by O₃ exposure, and their expression was correlated with that of NCED1, PP2Cs, PYR/PYL, and UGTs, which are related to ABA biosynthesis and signaling. These results suggest that HSF, WRKY, and MYB transcription factors and ABA are important components of the plant response to O₃ stress, suggesting a possible strategy for cultivating O₃-tolerant rose varieties.

The Hidden Potential of High-Throughput RNA-Seq Re-Analysis, a Case Study for DHDPS, Key Enzyme of the Aspartate-Derived Lysine Biosynthesis Pathway and Its Role in Abiotic and Biotic Stress Responses in Soybean

DHDPS is a key enzyme in the aspartate-derived lysine biosynthesis pathway and an evident object of study for biofortification strategies in plants. DHDPS isoforms with novel regulatory properties in Medicago truncatula were demonstrated earlier and hypothesized to be involved in abiotic and biotic stress responses. Here, we present a phylogenetic analysis of the DHPDS gene family in land plants which establishes the existence of a legume-specific class of DHDPS, termed DHDPS B-type, distinguishable from the DHDPS A-type commonly present in all land plants. The G. max genome comprises two A-type DHDPS genes (Gm.DHDPS-A1; Glyma.09G268200, Gm.DHDPS-A2; Glyma.18G221700) and one B-type (Gm.DHDPS-B; Glyma.03G022300). To further investigate the expression pattern of the G. max DHDPS isozymes in different plant tissues and under various stress conditions, 461 RNA-seq experiments were exploited and re-analyzed covering two expression atlases, 13 abiotic and 5 biotic stress studies. Gm.DHDPS-B is seen almost exclusively expressed in roots and nodules in addition to old cotyledons or senescent leaves while both DHDPS A-types are expressed constitutively in all tissues analyzed with the highest expression in mature seeds. Furthermore, Gm.DHDPS-B expression is significantly upregulated in some but not all stress responses including salt stress, flooding, ethylene or infection with Phytophthora sojae and coincides with downregulation of DHDPS A-types. In conclusion, we demonstrate the potential of an in-depth RNA-seq re-analysis for the guidance of future experiments and to expand on current knowledge.

Defensive capabilities of contrasting sorghum genotypes against Atherigona soccata (Rondani) infestation

Plants are equipped with a wide range of defensive mechanisms such as morphophysiological, biochemical, molecular, and hormonal signaling for protecting against insect-pest infestation. The infestation of a devastating pest shoot fly [Atherigona soccata (Rodani)] at seedling stage causes huge loss of sorghum crop productivity. In morphophysiological screening ICSV700, ICSV705, and IS18551 have been categorized as resistant, PSC-4 moderately resistant, SL-44 and SWARNA as susceptible. The present study focused on the role of defensive gene expression and its products viz: superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), glutathione reductase (GR), polyphenol oxidase (PPO), phenyl alanine ammonia lyase (PAL), responsive enzymes, and metabolites restoring redox status in sorghum plants against shoot fly infestation. In both leaf and stem tissue of sorghum genotypes, shoot fly infestation induced SOD, APX, DHAR, GR, PAL, and PPO activities while CAT activity was significantly declined at 15 and 21 days after emergence (DAE). IS18551 with resistant behavior showed upregulation of SOD, GR, APX, and DHAR along with accumulation of ascorbate, glutathione enhancing redox status of the plant during shoot fly infestation at later stage of infestation. While SWARNA with susceptible response exhibited enhanced activity of phenylpropanoid pathway enzymes PAL and PPO which in turn increased the levels of secondary metabolites like o-dihydroxyphenol and other phenols deterring the insect to attack the plant. The qRT-PCR data predicted that stress-responsive genes were initially unregulated in SWARNA; however, at 21 DAE, multifold higher expression of SOD, CAT, APX, and PPO (24.8-, 37.2-, 21.7-, and 17.9-fold respectively) in 1S18551 indicates the resistance behavior of this genotype against insect infestation owing to sustainable development capability.

Plant biochemistry influences tropospheric ozone formation, destruction, deposition, and response

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 O_3; 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.

Novel ozone flux metrics incorporating the detoxification process in the apoplast: An application to Chinese winter wheat

A modified Ball-Berry-Leuning model of stomatal conductance was applied to data from fully open-air ozone (O₃)-enrichment experiments with winter wheat (Triticum aestivum L.). The O₃ fluxes reaching both surface of cell wall (F_cw) and plasmalemma (F_pl) were estimated considering apoplastic ascorbate, a major scavenger of O₃. The difference (D) between F_cw and F_pl was defined as detoxification capacity of O₃ by reaction with ascorbate in the leaf apoplast (ASC_apo). The accumulated stomatal O₃ flux above D nmol O₃ m^-2 s^-1 (AF_stD) and the accumulated F_pl (AF_pl) were calculated over the optimal integration period covering the whole reproductive development of wheat, and used to derive O₃AF_stD yield-response relationships in comparison with POD_Y (phytotoxic O₃ dose above a threshold of Y nmol m^-2 s^-1) and AOT40 (accumulated O₃ dose over a threshold of 40 ppb). There was a good agreement between the observed and modeled values of ASC_apo and stomatal conductance. AF_stD and AF_pl performed better than POD_Y and AOT40 in terms of R² and intercept. However, the AF_stD metric was more suitable for assessing grain yield loss due to lower sensitivity of the regression slope to variations in the input parameters, compared with AF_pl. The average critical level (CL) of four cultivars for 5% grain-yield reduction was 1.53 mmol m^-2 using POD₆ and 2.81 mmol m^-2 using AF_stD, with the latter being well above the POD₆-derived value for European cultivars (1.3 mmol m^-2). The minimum hourly averaged O₃ concentration contributed to CLs was below 20 ppb according to AF_stD, a value that is lower than that suggested by POD₆ (≈27 ppb). O₃ flux-response relationships and CLs on the basis of quantified detoxification capacity shall facilitate the understanding of the different degrees of susceptibility to O₃ among species or cultivars, and improve the assessments of O₃ impacts on plants.

Ozone uptake at night is more damaging to plants than equivalent day-time flux

MAIN CONCLUSION

Plants exposed to equivalent ozone fluxes administered during day-time versus night-time exhibited greater losses in biomass at night and this finding is attributed to night-time depletion of cell wall-localised ascorbate. The present study employed Lactuca sativa and its closest wild relative, L. serriola, to explore the relative sensitivity of plants to ozone-induced oxidative stress during day-time versus night-time. By controlling atmospheric ozone concentration and measuring stomatal conductance, equivalent ozone uptake into leaves was engineered during day and night, and consequences on productivity and net CO2 assimilation rate were determined. Biomass losses attributable to ozone were significantly greater when an equivalent dose of ozone was taken-up by foliage at night compared to the day. Linkages between ozone impacts and ascorbic acid (AA) content, redox status and cellular compartmentation were probed in both species. Leaf AA pools were depleted by exposure of plants to darkness, and then AA levels in the apoplast and symplast were monitored on subsequent transfer of plants to the light. Apoplast AA appeared to be more affected by light-dark transition than the symplast pool. Moreover, equivalent ozone fluxes administered to leaves with contrasting AA levels resulted in contrasting effects on the light-saturated rate of CO2 assimilation (Asat) in both species. Once apoplast AA content recovered to pre-treatment levels, the same ozone flux resulted in no impacts on Asat. The results of the present investigation reveal that plants are significantly more sensitive to equivalent ozone fluxes taken-up at night compared with those during the day and were consistent with diel shifts in apoplast AA content and/or redox status. Furthermore, findings suggest that some thought should be given to weighing regional models of ozone impacts for extraordinary night-time ozone impacts.

Age-dependent increase in α-tocopherol and phytosterols in maize leaves exposed to elevated ozone pollution

Tropospheric ozone is a major air pollutant that significantly damages crop production. Crop metabolic responses to rising chronic ozone stress have not been well studied in the field, especially in C4 crops. In this study, we investigated the metabolomic profile of leaves from two diverse maize (Zea mays) inbred lines and the hybrid cross during exposure to season-long elevated ozone (~100 nl L-1) in the field using free air concentration enrichment (FACE) to identify key biochemical responses of maize to elevated ozone. Senescence, measured by loss of chlorophyll content, was accelerated in the hybrid line, B73 × Mo17, but not in either inbred line (B73 or Mo17). Untargeted metabolomic profiling further revealed that inbred and hybrid lines of maize differed in metabolic responses to ozone. A significant difference in the metabolite profile of hybrid leaves exposed to elevated ozone occurred as leaves aged, but no age-dependent difference in leaf metabolite profiles between ozone conditions was measured in the inbred lines. Phytosterols and α-tocopherol levels increased in B73 × Mo17 leaves as they aged, and to a significantly greater degree in elevated ozone stress. These metabolites are involved in membrane stabilization and chloroplast reactive oxygen species (ROS) quenching. The hybrid line also showed significant yield loss at elevated ozone, which the inbred lines did not. This suggests that the hybrid maize line was more sensitive to ozone exposure than the inbred lines, and up-regulated metabolic pathways to stabilize membranes and quench ROS in response to chronic ozone stress.

Ozone tolerant maize hybrids maintain Rubisco content and activity during long-term exposure in the field

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.

Response of cucumber (Cucumis sativus) to perfluorooctanoic acid in photosynthesis and metabolomics

A mechanistic understanding of perfluorooctanoic acid (PFOA) toxicity to plants is essential for future risk assessment of PFOA in agricultural soil. In this study, soil-grown cucumber (Cucumis sativus) was exposed to 0, 0.2, and 5 mg/kg of PFOA for 60 days. At harvest, contaminant accumulation, cucumber biomass, photosynthesis profiles and metabolites were measured. Results showed that PFOA depressed cucumber biomass and accumulated highest in leaves. Photosynthesis analysis revealed that PFOA at both doses reduced the chlorophyll contents and net photosynthesis rate of cucumber leaves. Gas chromatography-mass spectrometry-based non-targeted metabolomics revealed that PFOA induced metabolic reprogramming in cucumber leaves, including up-regulation of phenols (at 0.2 and 5 mg/kg) and down-regulation of amino acids (at 5 mg/kg), indicating disrupted nitrogen and carbon metabolism. Results revealed how PFOA represses plant growth by down-regulating photosynthetic pigments and disturbing the metabolism of carbohydroxides, phenols and amino acids. These findings provide valuable information for understanding the molecular mechanisms involved in plant responses to PFOA-induced stress.

Quantifying determinants of ozone detoxification by apoplastic ascorbate in peach (Prunus persica) leaves using a model of ozone transport and reaction

Ascorbate in leaf apoplast (ASC_apo ) reacts with ozone (O₃ ) and thereby reduces O₃ flux reaching plasmalemma (F_pl ). Some studies have shown significant protection of cells from O₃ by ASC_apo , while others have questioned its efficacy. Hypothesizing that the protection by ASC_apo depends on other variables, we quantified determinants of O₃ detoxification with a model of O₃ transport and reaction in apoplast. The model determines ascorbic acid concentration in apoplast (AA_apo ) using measured values of O₃ concentration (c_o ), leaf tissue ascorbic acid concentration (AA_leaf ), cell wall thickness (L₃ ), apoplastic pH (pH_apo ), and stomatal conductance (G_sw ). We compared the measured and model-estimated AA_apo in leaves of peach (Prunus persica) grown in open-top chambers under non-filtered air (NF) and elevated (EO₃ : NF + 80 ppb) O₃ concentrations. The estimated AA_apo in individual leaves agreed well with the measured values (R²  = .91). Analyses of the simulation results yielded the following findings: (a) The efficacy of O₃ reduction with ASC_apo as quantified by fractional reduction (ϕ₃ ) of O₃ flux at the surface of plasmalemma (F_pl ) was lowered from 70% in NF to 40% in EO₃ due to the reduction of L₃ . The EO₃ reduced AA_apo , but the lower G_sw and L₃ in EO₃ increased AA_apo resulting in no significant change in AA_apo due to EO₃ . ϕ₃ can be calculated with measured values of AA_apo and L₃ , and F_pl can be estimated with the measurement-based ϕ₃ . (b) When c₀ is increased, F_pl increased curvilinearly with the increase of F_st : nominal O₃ flux via stomatal diffusion, exhibiting apparent threshold on F_st . The deviation of F_pl from F_st became greater when L₃ , pH_apo , and AA_leaf were increased. The quantification of ϕ₃ and F_pl using leaf traits shall facilitate the understanding of the mechanisms of differential plant sensitivity to O₃ and improve quantification of the O₃ impacts on plants.

Transcriptome profiles of Quercus rubra responding to increased O3 stress

BACKGROUND

Climate plays an essential role in forest health, and climate change may increase forest productivity losses due to abiotic and biotic stress. Increased temperature leads to the increased formation of ozone (O3). Ozone is formed by the interaction of sunlight, molecular oxygen and by the reactions of chemicals commonly found in industrial and automobile emissions such as nitrogen oxides and volatile organic compounds. Although it is well known that productivity of Northern red oak (Quercus rubra) (NRO), an ecologically and economically important species in the forests of eastern North America, is reduced by exposure to O3, limited information is available on its responses to exogenous stimuli at the level of gene expression.

RESULTS

RNA sequencing yielded more than 323 million high-quality raw sequence reads. De novo assembly generated 52,662 unigenes, of which more than 42,000 sequences could be annotated through homology-based searches. A total of 4140 differential expressed genes (DEGs) were detected in response to O3 stress, as compared to their respective controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the O3-response DEGs revealed perturbation of several biological pathways including energy, lipid, amino acid, carbohydrate and terpenoid metabolism as well as plant-pathogen interaction.

CONCLUSION

This study provides the first reference transcriptome for NRO and initial insights into the genomic responses of NRO to O3. Gene expression profiling reveals altered primary and secondary metabolism of NRO seedlings, including known defense responses such as terpenoid biosynthesis.

Closing the yield gap: can metabolomics be of help?

This article comments on:

Melandri G, AbdElgawad H, Riewe D, Hageman JA, Asard H, Beemster GTS, Kadam N, Jagadish K, Altmann T, Ruyter-Spira1 C, Bouwmeester H. 2019. Biomarkers for grain yield stability in rice under drought stress. Journal of Experimental Botany 71, 669–683.

Dynamics of plant responses to combinations of air pollutants

The focus of this review is on how plants respond to combinations of multiple air pollutants. Global pollution trends, plant physiological responses and ecological perspectives in natural and agricultural systems are all discussed. In particular, we highlight the importance of studying sequential or simultaneous exposure of plants to pollutants, rather than exposure to individual pollutants in isolation, and explore how these responses may interfere with the way plants interact with their biotic community. Air pollutants can alter the normal physiology and metabolic functioning of plants. Here we describe how the phenotypic and molecular changes in response to multiple pollutants can differ compared to those elicited by single pollutants, and how different responses have been observed between plants in the field and in controlled laboratory conditions and between trees and crop plants. From an ecological perspective, we discuss how air pollution can result in greater susceptibility to biotic stressors and in direct or indirect effects on interactions with organisms that occupy higher trophic levels. Finally, we provide an overview of the potential uses of plants to mitigate air pollution, exploring the feasibility for pollution removal via the processes of bio-accumulation and phytoremediation. We conclude by proposing some new directions for future research in the field.

Molecular response of poplar to single and combined ozone and drought

High concentration in ground-level ozone (O₃) and water deficit affect forest ecosystems service. Previously we found intercellular CO₂ concentration and isoprene emission were affected by the combination of O₃ and drought, but the molecular mechanisms controlling these phenotypes are still open questions. In this study, we investigated the stomatal conductance (g_s) and transcriptome changes in an O₃-sensitive hybrid poplar exposed to two O₃ levels [charcoal-filtered ambient air (CF) and non-filtered ambient air plus 40 ppb (NF40)] and two water conditions [well-watered (W) and moderate drought (D)]. NF40 reduced the g_s more under D than W. We identified the differentially expressed genes (DEGs) from pairwise comparisons and found the poplar's molecular response to drought was counteracted by elevated O₃. From nine clusters obtained through K-means clustering, 12 core transcription factors were identified. DEGs involved in isoprene biosynthesis and phytohormones signal pathways indicate the molecular response and stomatal closure of poplar under O₃ and/or drought might be through MEP/DOXP and ABA-dependent pathways. In addition, 102 Helitrons capturing DEGs were involved in response to O₃ and/or drought and related with ABA-dependent pathway. This integrated analysis provides multi-dimensional insights to understand the molecular response to the combination of O₃ and drought.

Increase of apoplastic ascorbate induced by ozone is insufficient to remove the negative effects in tobacco, soybean and poplar

Apoplastic ascorbate (ASCapo) is an important contributor to the detoxification of ozone (O3). The objective of the study is to explore whether ASCapo is stimulated by elevated O3 concentrations. The detoxification of O3 by ASCapo was quantified in tobacco (Nicotiana L), soybean (Glycine max (L.) Merr.) and poplar (Populus L), which were exposed to charcoal-filtered air (CF) and elevated O3 treatments (E-O3). ASCapo in the three species were significantly increased by E-O3 compared with the values in the filtered treatment. For all three species, E-O3 significantly increased the malondialdehyde (MDA) content and decreased light-saturated rate of photosynthesis (Asat), suggesting that high O3 has induced injury/damage to plants. E-O3 significantly increased redox state in the apoplast (redox stateapo) for all species, whereas no effect on the apoplastic dehydroascorbate (DHAapo) was observed. In leaf tissues, E-O3 significantly enhanced reduced-ascorbate (ASC) and total ascorbate (ASC+DHA) in soybean and poplar, but significantly reduced these in tobacco, indicating different antioxidative capacity to the high O3 levels among the three species. Total antioxidant capacity in the apoplast (TACapo) was significantly increased by E-O3 in tobacco and poplar, but leaf tissue TAC was significantly enhanced only in tobacco. Leaf tissue superoxide anion (O2•-) in poplar and hydrogen peroxide (H2O2) in tobacco and soybean were significantly increased by E-O3. The diurnal variation of ASCapo, with maximum values occurring in the late morning and lower values experienced in the afternoon, appeared to play an important role in the harmful effects of O3 on tobacco, soybean and poplar.

Ethylenediurea (EDU) mitigates the negative effects of ozone in rice: Insights into its mode of action

Monitoring of ozone damage to crops plays an increasingly important role for the food security of many developing countries. Ethylenediurea (EDU) could be a tool to assess ozone damage to vegetation on field scale, but its physiological mode of action remains unclear. This study investigated mechanisms underlying the ozone-protection effect of EDU in controlled chamber experiments. Ozone sensitive and tolerant rice genotypes were exposed to ozone (108 ppb, 7 hr day^-1 ) and control conditions. EDU alleviated ozone effects on plant morphology, foliar symptoms, lipid peroxidation, and photosynthetic parameters in sensitive genotypes. Transcriptome profiling by RNA sequencing revealed that thousands of genes responded to ozone in a sensitive variety, but almost none responded to EDU. Significant interactions between ozone and EDU application occurred mostly in ozone responsive genes, in which up-regulation was mitigated by EDU application. Further experiments documented ozone degrading properties of EDU, as well as EDU deposits on leaf surfaces possibly related to surface protection. EDU application did not mitigate the reaction of plants to other abiotic stresses, including iron toxicity, zinc deficiency, and salinity. This study provided evidence that EDU is a surface protectant that specifically mitigates ozone stress without interfering directly with the plants' stress response systems.

Novel Arsenic Markers for Discriminating Wild and Cultivated Cordyceps

Ophiocordyceps sinensis has been utilized in China and adjacent countries for thousands of years as a rare functional food to promote health and treat diverse chronic diseases. In recent years, adulterants are usually identified in the processed products of wild O. sinensis. However, the effective adulteration examination has to be additionally performed except their routine test, and accordingly is time- and money-consuming. Recently, arsenic determination has become a necessary test for confirming whether the concentrations of inorganic arsenic are over the O. sinensis limit. In this work, the contents of total arsenic and As species in cultivated O. sinensis, Cordyceps militaris, and other edible fungi were determined by ICP-MS and HPLC-ICP-MS. The results suggest that the As speciation exhibits a species-specific behavior, and accompanies the effect of the As background. The proportions of unknown organic As and contents of total As may be considered as sensitive markers for discriminating wild O. sinensis. This result provides a novel clue for discriminating wild and artificially cultivated mushrooms/their products, with emphasis on arsenic markers for authenticating wild O. sinensis.

Closing the global ozone yield gap: Quantification and cobenefits for multistress tolerance

Increasing both crop productivity and the tolerance of crops to abiotic and biotic stresses is a major challenge for global food security in our rapidly changing climate. For the first time, we show how the spatial variation and severity of tropospheric ozone effects on yield compare with effects of other stresses on a global scale, and discuss mitigating actions against the negative effects of ozone. We show that the sensitivity to ozone declines in the order soybean > wheat > maize > rice, with genotypic variation in response being most pronounced for soybean and rice. Based on stomatal uptake, we estimate that ozone (mean of 2010-2012) reduces global yield annually by 12.4%, 7.1%, 4.4% and 6.1% for soybean, wheat, rice and maize, respectively (the "ozone yield gaps"), adding up to 227 Tg of lost yield. Our modelling shows that the highest ozone-induced production losses for soybean are in North and South America whilst for wheat they are in India and China, for rice in parts of India, Bangladesh, China and Indonesia, and for maize in China and the United States. Crucially, we also show that the same areas are often also at risk of high losses from pests and diseases, heat stress and to a lesser extent aridity and nutrient stress. In a solution-focussed analysis of these results, we provide a crop ideotype with tolerance of multiple stresses (including ozone) and describe how ozone effects could be included in crop breeding programmes. We also discuss altered crop management approaches that could be applied to reduce ozone impacts in the shorter term. Given the severity of ozone effects on staple food crops in areas of the world that are also challenged by other stresses, we recommend increased attention to the benefits that could be gained from addressing the ozone yield gap.

Understanding and improving global crop response to ozone pollution

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.

Central Metabolic Responses to Ozone and Herbivory Affect Photosynthesis and Stomatal Closure

Plants have evolved adaptive mechanisms that allow them to tolerate a continuous range of abiotic and biotic stressors. Tropospheric ozone (O3), a global anthropogenic pollutant, directly affects living organisms and ecosystems, including plant-herbivore interactions. In this study, we investigate the stress responses of Brassica nigra (wild black mustard) exposed consecutively to O3 and the specialist herbivore Pieris brassicae Transcriptomics and metabolomics data were evaluated using multivariate, correlation, and network analyses for the O3 and herbivory responses. O3 stress symptoms resembled those of senescence and phosphate starvation, while a sequential shift from O3 to herbivory induced characteristic plant defense responses, including a decrease in central metabolism, induction of the jasmonic acid/ethylene pathways, and emission of volatiles. Omics network and pathway analyses predicted a link between glycerol and central energy metabolism that influences the osmotic stress response and stomatal closure. Further physiological measurements confirmed that while O3 stress inhibited photosynthesis and carbon assimilation, sequential herbivory counteracted the initial responses induced by O3, resulting in a phenotype similar to that observed after herbivory alone. This study clarifies the consequences of multiple stress interactions on a plant metabolic system and also illustrates how omics data can be integrated to generate new hypotheses in ecology and plant physiology.

Phylogenetic analysis and differential expression of EF1α genes in soybean during development, stress and phytohormone treatments

The EF1α is a multifunctional protein with additional unrelated activities to its primary function in translation. This protein is encoded by a multigene family and few studies are still available in plants. Expression of six EF1α genes in Glycine max was performed using RT-qPCR and RNA-seq data to advance in the function of each gene during plant development, stress conditions and phytohormone treatments. A phylogenetic classification in Phaseoleae tribe was used to identify the G. max EF1α genes (EF1α 1a1, 1a2, 1b, 2a, 2b and 3). Three EF1α types (1-3) were found in Phaseoleae revealing duplications in G. max types 1 and 2. EF1α genes were expressed in all studied tissues, however, specific amount of each transcript was detected. In plant development, all EF1α transcripts were generally more expressed in younger tissues, however, in unifoliolate leaves and cotyledons a higher expression occurred in older tissues. Five EF1α genes (except 2a) were up-regulated under stress in a response tissue/stress/cultivar-dependent. EF1α 3 was the most stress-induced gene linked to cultivar stress tolerance mainly in aerial tissues. Auxin, salicylate and ethylene induced differentially the EF1α expression. Overall, this study provides a consistent EF1α classification in Phaseoleae tribe to better understand their functional evolution. The RT-qPCR and RNA-seq EF1α expression profiles were consistent, both exhibiting expression diversification of each gene (spatio-temporal, stress and phytohormone stimuli). Our results point out the EF1α genes, especially EF1α 3, as candidate for developing a useful tool for future G. max breeding.

Expression Patterns of Genes Involved in Ascorbate-Glutathione Cycle in Aphid-Infested Maize (Zea mays L.) Seedlings

Reduced forms of ascorbate (AsA) and glutathione (GSH) are among the most important non-enzymatic foliar antioxidants in maize (Zea mays L.). The survey was aimed to evaluate impact of bird cherry-oat aphid (Rhopalosiphum padi L.) or grain aphid (Sitobion avenae F.) herbivory on expression of genes related to ascorbate-glutathione (AsA-GSH) cycle in seedlings of six maize varieties (Ambrozja, Nana, Tasty Sweet, Touran, Waza, Złota Karłowa), differing in resistance to the cereal aphids. Relative expression of sixteen maize genes encoding isoenzymes of ascorbate peroxidase (APX1, APX2, APX3, APX4, APX5, APX6, APX7), monodehydroascorbate reductase (MDHAR1, MDHAR2, MDHAR3, MDHAR4), dehydroascorbate reductase (DHAR1, DHAR2, DHAR3) and glutathione reductase (GR1, GR2) was quantified. Furthermore, effect of hemipterans’ attack on activity of APX, MDHAR, DHAR and GR enzymes, and the content of reduced and oxidized ascorbate and glutathione in maize plants were assessed. Seedling leaves of more resistant Z. mays varieties responded higher elevations in abundance of target transcripts. In addition, earlier and stronger aphid-triggered changes in activity of APX, MDHAR, DHAR and GR enzymes, and greater modulations in amount of the analyzed antioxidative metabolites were detected in foliar tissues of highly resistant Ambrozja genotype in relation to susceptible Tasty Sweet plants.