Metabolomic approach reveals the biochemical mechanisms underlying drought stress tolerance in thyme

Physiological and proteomic changes of Castanopsis fissa in response to drought stress

Castanopsis fissa is a native, broadleaf tree species in Guangdong with characteristics of barrenness and fast growth and is often used as a pioneer species for vegetation restoration with excellent ecological benefits. To explore the response of C.fissa to drought, this study investigated the drought tolerance mechanism of C.fissa using physiological and proteomic assessments. Using a potted continuous drought experimental method with normal water supply as a control, we measured photosynthetic parameters, antioxidant enzyme activities, and osmoregulatory substances of C. fissa in response to drought stress for 1 to 4 weeks, respectively. In addition, we used TMT quantitative proteomics to identify differentially expressed proteins (DEPs) between the drought-stress-treated C. fissa leaves and the control leaves. With the extension of drought stress time, the photosynthetic indexes and peroxidase (POD) activity of C. fissa leaves showed a decreasing trend. The malondialdehyde (MDA) content; superoxide Dismutase (SOD) and catalase (CAT) activities; and proline (Pro), soluble sugar (SS) and soluble protein (SP) contents showed an overall increasing trend, all of which reached significant differences at 4 w of stress. We identified 177 and 529 DEPs in the 2 and 4 weeks drought-stress leaves, respectively, in reference to the control leaves. These DEPs were closely related to physiological metabolic processes such as photosynthesis, energy and carbohydrate metabolism, stress response and defense, transcriptional regulation, and signal ion transduction. Drought stress mainly affects photosynthesis, carbohydrate metabolism, and protein synthesis and degradation in C. fissa leaves. At 2 weeks of stress, the expression of carbon metabolism, pyruvate metabolism and ribosome-related proteins was significantly changed, however, and at 4 weeks of stress, protein processing in the endoplasmic reticulum and spliceosome-related proteins were significantly increased in plant leaves. To alleviate the effect of water unavailability, the drought-stressed C.fissa leaves increased its oxidative protective enzyme system to eliminate excess reactive oxygen species (ROS) and also increased its Pro and SP contents to maintain the intracellular osmotic potential balance.

The Enzyme Lysine Malonylation of Calvin Cycle and Gluconeogenesis Regulated Glycometabolism in Nostoc flagelliforme to Adapt to Drought Stress

Lysine malonylation (Kmal) is an evolutionarily conserved post-translational modification (PTM) that has been demonstrated to be involved in cellular and organismal metabolism. However, the role that Kmal plays in response to drought stress of the terrestrial cyanobacteria N. flagelliforme is still unknown. In this study, we performed the first proteomic analysis of Kmal in N. flagelliforme under different drought stresses using LC-MS/MS. In total, 421 malonylated lysine residues were found in 236 different proteins. GO and KEGG enrichment analysis indicated that these malonylated proteins were highly enriched in several metabolic pathways, including carbon metabolism and photosynthesis. Decreased malonylation levels were found to hinder the reception and transmission of light energy and CO₂ fixation, which led to a decrease in photosynthetic activity. Kmal was also shown to inhibit the flux of the TCA cycle and activate the gluconeogenesis pathway in response to drought stress. Furthermore, malonylated antioxidant enzymes and antioxidants were synergistically involved in reactive oxygen species (ROS) scavenging. Malonylation was involved in lipid degradation and amino acid biosynthesis as part of drought stress adaptation. This work represents the first comprehensive investigation of the role of malonylation in dehydrated N. flagelliforme, providing an important resource for understanding the drought tolerance mechanism of this organism.

On the Future Perspectives of Some Medicinal Plants within Lamiaceae Botanic Family Regarding Their Comprehensive Properties and Resistance against Biotic and Abiotic Stresses

Lamiaceae is one of the largest botanical families, encompassing over 6000 species that include a variety of aromatic and medicinal spices. The current study is focused on three plants within this botanical family: basil (Ocimum basilicum L.), thyme (Thymus vulgaris L.), and summer savory (Satureja hortensis L.). These three species contain primary and secondary metabolites such as phenolic and flavonoid compounds, fatty acids, antioxidants, and essential oils and have traditionally been used for flavoring, food preservation, and medicinal purposes. The goal of this study is to provide an overview of the nutraceutical, therapeutic, antioxidant, and antibacterial key features of these three aromatics to explore new breeding challenges and opportunities for varietal development. In this context, a literature search has been performed to describe the phytochemical profile of both primary and secondary metabolites and their pharmacological uses, as well as to further explore accession availability in the medicine industry and also to emphasize their bioactive roles in plant ecology and biotic and abiotic stress adaptability. The aim of this review is to explore future perspectives on the development of new, highly valuable basil, summer savory, and thyme cultivars. The findings of the current review emphasize the importance of identifying the key compounds and genes involved in stress resistance that can also provide valuable insights for further improvement of these important medicinal plants.

Cross-Platform Comparison of Amino Acid Metabolic Profiling in Three Model Organisms Used in Environmental Metabolomics

Environmental metabolomics is a promising approach to study pollutant impacts to target organisms in both terrestrial and aquatic environments. To this end, both nuclear magnetic resonance (NMR)- and mass spectrometry (MS)-based methods are used to profile amino acids in different environmental metabolomic studies. However, these two methods have not been compared directly which is an important consideration for broader comparisons in the environmental metabolomics field. We compared the quantification of 18 amino acids in the tissue extracts of Daphnia magna, a common model organism used in both ecotoxicology and ecology, using both 1H NMR spectroscopy and liquid chromatography with tandem MS (LC-MS/MS). 1H NMR quantification of amino acids agreed with the LC-MS/MS quantification for 17 of 18 amino acids measured. We also tested both quantitative methods in a D. magna sub-lethal exposure study to copper and lithium. Again, both NMR and LC-MS/MS measurements showed agreement. We extended our analyses with extracts from the earthworm Eisenia fetida and the plant model Nicotiana tabacum. The concentrations of amino acids by both 1H NMR and LC-MS/MS, agreed and demonstrated the robustness of both techniques for quantitative metabolomics. These findings demonstrate the compatibility of these two analytical platforms for amino acid profiling in environmentally relevant model organisms and emphasizes that data from either method is robust for comparisons across studies to further build the knowledge base related to pollutant exposure impacts and toxic responses of diverse environmental organisms.

Metabolomic Analysis of Key Metabolites and Their Pathways Revealed the Response of Alfalfa (Medicago sativa L.) Root Exudates to rac-GR24 under Drought Stress

The rac-GR24, an artificial analog of strigolactone, is known for its roles in inhibiting branches, and previous studies have reported that it has a certain mechanism to relieve abiotic stress, but the underlying metabolic mechanisms of mitigation for drought-induced remain unclear. Therefore, the objectives of this study were to identify associated metabolic pathways that are regulated by rac-GR24 in alfalfa (Medicago sativa L.) and to determine the metabolic mechanisms of rac-GR24 that are involved in drought-induced root exudate. The alfalfa seedling WL-712 was treated with 5% PEG to simulate drought, and rac-GR24 at a concentration of 0.1 µM was sprayed. After three days of treatment, root secretions within 24 h were collected. Osmotic adjustment substances and antioxidant enzyme activities were measured as physiological indicators, while LS/MS was performed to identify metabolites regulated by rac-GR24 of root exudate under drought. The results demonstrated that rac-GR24 treatment could alleviate the negative effects from drought-induced on alfalfa root, as manifested by increased osmotic adjustment substance content, cell membrane stability, and antioxidant enzyme activities. Among the 14 differential metabolites, five metabolites were uniquely downregulated in plants in rac-GR24 treatment. In addition, rac-GR24 could relieve drought-induced adverse effects on alfalfa through metabolic reprogramming in the pathways of the TCA cycle, pentose phosphate, tyrosine metabolism, and the purine pathway. This study indicated that rac-GR24 could improve the drought resistance of alfalfa by influencing the components of root exudates.

Metabolomic Approach to Study the 'Purple Queen' Pomegranate Cultivar Response to Alternative Culture Media and Phenological Stages

The increasingly evident threat of depletion of world peat bogs is encouraging the search for and study of alternative agricultural substrates that can fully or partially replace peat, guaranteeing food supply (quality and quantity). On the other hand, the identification of the potential for the reuse of waste from relevant economic activities has increased in recent years, mainly motivated by the change to a sustainable circular economy, as is the case of port sediments. Taking into account that significant volumes of dredged port sediments are generated annually so that ports can maintain their economic activity, it is necessary to find objective, sustainable and safe reuse alternatives. In this sense, the objective of this study was to study the response of the "Purple Queen" pomegranate when grown with dredged port sediment. For this, the fruit production (kg), number of fruits (fruits tree-1), fruit weight (g), and seed yield (%) aiming to verify the correct tree development were evaluated. In addition, a 1H-NMR foliar metabolomic study for the three most relevant phenological phases was performed (flowering, fruit development, and post-harvest) to identify metabolic changes in trees. In total, 29 metabolites were identified; among them, 11 were amino acids, 6 organic acids, 5 sugars, and 7 secondary metabolites. The good agronomical development of the trees and fruits indicated the potential for using the dredged sediment as an agricultural substrate. On the other hand, the results revealed that the greatest variability in the metabolomic study occurred between the phenological phases and a lower variability is explained by the substrates used.

Fingerprinting based on gas chromatography-Orbitrap high-resolution mass spectrometry and chemometrics to reveal geographical origin, processing, and volatile markers for thyme authentication

Thyme is an aromatic herb traditionally used for food purposes due to its organoleptic characteristics and medicinal properties, which is highly susceptible to food fraud. In this study, GC-HRMS-based fingerprinting was applied for the first time to determine the geographical traceability of thyme based on different origins (Spain, Poland, and Morocco), as well as to assess its processing by comparing sterilized vs. non-sterilized thyme. Unsupervised chemometric methods (PCA and HCA) revealed a predominant influence of the geographical origin on thyme fingerprints rather than processing effects. Supervised PLS-DA and OPLS-DA were used for discrimination purposes, revealing high predictive ability for further samples (100%), and allowing the identification of differential compounds (markers). A total of 24 markers were putatively identified (13 metabolites were confirmed) belonging to different classes: monoterpenoids, diterpenoids, sesquiterpenoids, alkenylbenzenes, and other miscellaneous compounds. This study outlines the potential of combining untargeted analysis by GC-HRMS with chemometrics for thyme authenticity and traceability.

Impact of key parameters involved with plant-microbe interaction in context to global climate change

Anthropogenic activities have a critical influence on climate change that directly or indirectly impacts plant and microbial diversity on our planet. Due to climate change, there is an increase in the intensity and frequency of extreme environmental events such as temperature rise, drought, and precipitation. The increase in greenhouse gas emissions such as CO2, CH4, NOx, water vapor, increase in global temperature, and change in rainfall patterns have impacted soil–plant-microbe interactions, which poses a serious threat to food security. Microbes in the soil play an essential role in plants’ resilience to abiotic and biotic stressors. The soil microbial communities are sensitive and responsive to these stressors. Therefore, a systemic approach to climate adaptation will be needed which acknowledges the multidimensional nature of plant-microbe-environment interactions. In the last two scores of years, there has been an enhancement in the understanding of plant’s response to microbes at physiological, biochemical, and molecular levels due to the availability of techniques and tools. This review highlights some of the critical factors influencing plant-microbe interactions under stress. The association and response of microbe and plants as a result of several stresses such as temperature, salinity, metal toxicity, and greenhouse gases are also depicted. New tools to study the molecular complexity of these interactions, such as genomic and sequencing approaches, which provide researchers greater accuracy, reproducibility, and flexibility for exploring plant-microbe–environment interactions under a changing climate, are also discussed in the review, which will be helpful in the development of resistant crops/plants in present and future.

Manufactured Nano-Objects Confer Viral Protection against Cucurbit Chlorotic Yellows Virus (CCYV) Infecting Nicotiana benthamiana

Nanotechnology has emerged as a new tool to combat phytopathogens in agricultural crops. Cucurbit chlorotic yellows virus (CCYV) mainly infects Solanaceae crops and causes significant crop losses. Nanomaterials (NMs) may have efficacy against plant viruses, but the mechanisms underlying complex nanomaterials-plant-virus interactions remain elusive. We challenged Nicotiana benthamiana plants with GFP-tagged CCYV and observed morphological, physiological, and molecular changes in response to 21-d foliar exposure to nanoscale Fe and Zn and C₆₀ fullerenes at 100 mg/L concentration for 21 days. We observed that in response to C₆₀ (100 mg/L) treatment, plants displayed a normal phenotype while the viral infection was not seen until 5 days post-inoculation. On the contrary, Fe and Zn were unable to suppress viral progression. The mRNA transcriptional analysis for GFP and viral coat protein revealed that the transcripts of both genes were 5-fold reduced in response to C₆₀ treatment. Evaluation of the chloroplast ultrastructure showed that NMs treatment maintained the normal chloroplast structure in the plants as compared to untreated plants. C₆₀ upregulated the defense-related phytohormones (abscisic acid and salicylic acid) by 42–43%. Our results demonstrate the protective function of carbon-based NMs, with suppression of CCYV symptoms via inhibition of viral replication and systemic movement.

Elemental Profiles of Wild Thymus L. Plants Growing in Different Soil and Climate Conditions

Plants of the genus Thymus L. are traditionally used in medicine and cooking due to the presence of biologically active compounds in them that have fungicidal, antibacterial and other medicinal properties and original taste qualities. Genetic features and growing conditions cause the elemental composition, responsibly of the synthesised medicinal compounds. However, information on the contents and distributions of elements in the organs of Thymus L. is very limited. This study was to set and compare the elements in organs of wild thyme for different soil and climatic conditions. Two species of wild Thymus L. from Mongolian steppe and on the coast of Lake Baikal were collected during flowering. Twenty-four elements, including Si, in soils, roots, stems, leaves and flowers were simultaneously determined by atomic emission spectrometry. Elemental profiles of two species of wild Thymus L. are described. It is assumed that Si is a necessary element of the plant. The predominance of the genetic resistance of plants over the influence of soil and climatic conditions is shown.

Physiology and metabonomics reveal differences in drought resistance among soybean varieties

BACKGROUND

The soybean is an important food crop worldwide. Drought during the first pod stage significantly affects soybean yield, and understanding the metabolomic and physiological changes in soybeans under drought stress is crucial. This study identified the differential metabolites in initial pod stage soybean leaves under polyethylene glycol-simulated drought stress, using ultra performance liquid chromatography and tandem mass spectrometry, and the physiological indexes related to drought resistance.

RESULTS

Physiologically, drought resistance also generates enzyme and antioxidant activity; levels of superoxide dismutase, peroxidase, and catalase first increased and subsequently decreased, while those of soluble sugar, soluble protein, malondialdehyde, and proline content increased in both varieties. The contents of CAT, proline and soluble sugar in Heinong 44 (HN44) were higher than those in Heinong 65 (HN65), and the contents of MDA were lower than those in HN65. In metabolomics, the OPLS-DA model was used to screen different metabolites. KEGG analysis showed that the two varieties resisted drought through different ways. Amino acid metabolism and lipid metabolism play a key role in drought resistance of the two varieties, respectively. TCA cycle was one of the core pathways of drought resistance in two varieties. Changes in the content of L-Asparagine and citric acid may be one of the reasons for the difference in drought resistance between the two varieties.

CONCLUSIONS

We think that the reasons of drought resistance among soybean varieties are as follows: the main metabolic pathways are different under drought stress; the contents of metabolites in these metabolic pathways are different; some physiological indexes are different, such as MDA, CAT, proline content and so on. Our study enhances the understanding of the metabolomic soybean drought stress response and provides a reference for soybean drought resistance breeding.

Multisite evaluation of phenotypic plasticity for specialized metabolites, some involved in carrot quality and disease resistance

Renewed consumer demand motivates the nutritional and sensory quality improvement of fruits and vegetables. Specialized metabolites being largely involved in nutritional and sensory quality of carrot, a better knowledge of their phenotypic variability is required. A metabolomic approach was used to evaluate phenotypic plasticity level of carrot commercial varieties, over three years and a wide range of cropping environments spread over several geographical areas in France. Seven groups of metabolites have been quantified by HPLC or GC methods: sugars, carotenoids, terpenes, phenolic compounds, phenylpropanoids and polyacetylenes. A large variation in root metabolic profiles was observed, in relation with environment, variety and variety by environment interaction effects in decreasing order of importance. Our results show a clear diversity structuration based on metabolite content. Polyacetylenes, β-pinene and α-carotene were identified mostly as relatively stable varietal markers, exhibiting static stability. Nevertheless, environment effect was substantial for a large part of carrot metabolic profile and various levels of phenotypic plasticity were observed depending on metabolites and varieties. A strong difference of environmental sensitivity between varieties was observed for several compounds, particularly myristicin, 6MM and D-germacrene, known to be involved in responses to biotic and abiotic stress. This work provides useful information about plasticity in the perspective of carrot breeding and production. A balance between constitutive content and environmental sensitivity for key metabolites should be reached for quality improvement in carrot and other vegetables.

Carbon-based nanomaterials suppress tobacco mosaic virus (TMV) infection and induce resistance in Nicotiana benthamiana

Although nanomaterials (NMs) may inhibit viral pathogens, the mechanisms governing plant-virus-nanomaterial interactions remain unknown. Nicotiana benthamiana plants were treated with nanoscale titanium dioxide (TiO2) and silver (Ag), C60 fullerenes, and carbon nanotubes (CNTs) at 100, 200 and 500 mg L-1 for a 21-day foliar exposure before inoculation with GFP-tagged tobacco mosaic virus (TMV). Plants treated with CNTs and C60 (200 mg L-1) exhibited normal phenotype and viral symptomology was not evident at 5 days post-infection. TiO2 and Ag failed to suppress viral infection. RT-qPCR analysis revealed that viral coat protein transcript abundance and GFP mRNA expression were reduced 74-81% upon CNTs and C60 treatment. TEM revealed that the chloroplast ultrastructure in carbon NM-treated plants was unaffected by TMV infection. Fluorescence measurement of CNTs and C60 (200 mg L-1) treated plants indicated photosynthesis equivalent to healthy controls. CNTs and C60 induced upregulation of the defense-related phytohormones abscisic acid and salicylic acid by 33-52%; the transcription of genes responsible for phytohormone biosynthesis was elevated by 94-104% in treated plants. Our findings demonstrate the protective role of carbon-based NMs, with suppression of TMV symptoms via hindered physical movement and viral replication. Given the lack of viral phytopathogen treatment options, this work represents a novel area of nano-enabled agriculture.

Metabolomics Intervention Towards Better Understanding of Plant Traits

The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decades, emphasis has been more on metabolome which plays a crucial role in defining the phenotype (trait) during crop improvement. The emergence of modern high throughput metabolome analyzing platforms have accelerated the discovery of a wide variety of biochemical types of metabolites and new pathways, also helped in improving the understanding of known existing pathways. Pinpointing the causal gene(s) and elucidation of metabolic pathways are very important for development of improved lines with high precision in crop breeding. Along with other-omics sciences, metabolomics studies have helped in characterization and annotation of a new gene(s) function. Hereby, we summarize several areas in the field of crop development where metabolomics studies have made its remarkable impact. We also assess the recent research on metabolomics, together with other omics, contributing toward genetic engineering to target traits and key pathway(s).

Advanced material modulation of nutritional and phytohormone status alleviates damage from soybean sudden death syndrome

Customized Cu3(PO4)2 and CuO nanosheets and commercial CuO nanoparticles were investigated for micronutrient delivery and suppression of soybean sudden death syndrome. An ab initio thermodynamics approach modelled how material morphology and matrix effects control the nutrient release. Infection reduced the biomass and photosynthesis by 70.3 and 60%, respectively; the foliar application of nanoscale Cu reversed this damage. Disease-induced changes in the antioxidant enzyme activity and fatty acid profile were also alleviated by Cu amendment. The transcription of two dozen defence- and health-related genes correlates a nanoscale Cu-enhanced innate disease response to reduced pathogenicity and increased growth. Cu-based nanosheets exhibited a greater disease suppression than that of CuO nanoparticles due to a greater leaf surface affinity and Cu dissolution, as determined computationally and experimentally. The findings highlight the importance and tunability of nanomaterial properties, such as morphology, composition and dissolution. The early seedling foliar application of nanoscale Cu to modulate nutrition and enhance immunity offers a great potential for sustainable agriculture.

Effects of Water Deficit and Heat Stress on Nicotiana langsdorffii Metabolomic Pattern Modified by Insertion of rolD Gene from Agrobacterium rhizogenes

Abiotic stresses are major factors that negatively affect plant growth and productivity. Plants have developed complex strategies to ensure their survival and reproduction under adverse conditions, activating mechanisms that involve changes at different metabolic levels. In order to select stress-resistant species, research has focused on molecular studies and genetic engineering, showing promising results. In this work, the insertion of the rolD gene from Agrobacterium rhizogenes into Nicotiana langsdorffii plants is investigated, in order to assess the potential of this genetic modification towards mitigating water and heat stresses. Different approaches were combined: a high-throughput metabolomics and ionomics study was performed, together with the determination of important plant phytohormones. The aim was to identify the influence of abiotic stresses on plants and to highlight the effects of the rolD genetic modification on plant stress response. The most relevant compounds for each kind of stress were identified, belonging mainly to the classes of lipids, acyl sugars, glycosides, and amino acid derivatives. Water stress (WS) determined a decrease of elements and secondary metabolites, while amino acids and their derivatives increased, proving to be key molecules in this type of stress. RolD plants exposed to high temperature stress (HS) presented higher dry weight levels than controls, as well as increased amounts of K and adenosine and lower levels of damage-associated metabolites, suggesting the increased resistance of rolD-modified plants toward HS.

Enantioselective effects of imazethapyr residues on Arabidopsis thaliana metabolic profile and phyllosphere microbial communities

Imazethapyr (IM) is a widely used acetolactate synthase-inhibiting chiral herbicide. It has long-term residuals that may be absorbed by the human body through the edible parts of plants, such as vegetable leaves or fruits. Here, we selected a model plant, Arabidopsis thaliana, to determine the effects of R-IM and S-IM on its leaf structure, photosynthetic efficiency, and metabolites, as well as the structures of microorganisms in the phyllosphere, after 7 days of exposure. Our results indicated enantiomeric differences in plant growth between R-IM and S-IM; 133 µg/kg R-IM showed heavier inhibition of photosynthetic efficiency and greater changes to subcellular structure than S-IM. R-IM and S-IM also had different effects on metabolism and leaf microorganisms. S-IM mainly increased lipid compounds and decreased amino acids, while R-IM increased sugar accumulation. The relative abundance of Moraxellaceae human pathogenic bacteria was increased by R-IM treatment, indicating that R-IM treatment may increase leaf surface pathogenic bacteria. Our research provides a new perspective for evaluating the harmfulness of pesticide residues in soil, phyllosphere microbiome changes via the regulation of plant metabolism, and induced pathogenic bacterial accumulation risks.

Chloride and amino acids are associated with K+-alleviated drought stress in tea (Camellia sinesis)

Drought is one of the main limiting factors affecting tea plant yield and quality. Previous studies have reported that K+ (potassium) application significantly alleviated drought-induced damage in tea plants. However, the intrinsic mechanisms underlying K+-alleviated drought stress are still obscure. In our study, two contrasting varieties, Taicha12 (drought tolerant) and Fuyun6 (drought sensitive), were used to investigate the intrinsic mechanisms behind K+-alleviated drought stress in tea plants. In the present study, we compared with the case of tea plants under drought: higher water and chlorophyll contents were found in drought-stressed tea plants with an external K+ supply, confirming the role of externally supplied K+ in mitigating drought stress. We also found that an adequate K+ supply promoted Cl- accumulation in the mesophyll of Taicha12 (drought tolerant) over that of in Fuyun6 (drought sensitive). Moreover, Gly, Cys, Lys and Arg were not detected in Fuyun6 under 'Drought' or 'Drought + K+' conditions. Results showed that an exogenous supply of Arg and Val significantly alleviated drought-induced damage in Fuyun6, suggesting their role in K+-alleviated drought stress in tea plants. Collectively, our results show that chloride and amino acids are important components associated with K+-alleviated drought stress in tea plants.

Variation in Terpene Profiles of Thymus vulgaris in Water Deficit Stress Response

Thyme (Thymus spp.) volatiles predominantly consisting of monoterpenes and sesquiterpenes, serve as antimicrobial, antiseptic and antioxidant in phytomedicine. They also play a key role in plants as secondary metabolites via their potential role against herbivores, attracting pollinators and abiotic stress tolerance. Plant volatiles are affected by different environmental factors including drought. Here, the effect of prolonged water deficit stress on volatile composition was studied on the sensitive and tolerant thyme plant cultivars (T. vulgaris Var. Wagner and T. vulgaris Var. Varico3, respectively). Volatile sampling along with morpho–physiological parameters such as soil moisture, water potential, shoot dry weight, photosynthetic rate and water content measurements were performed on one-month-old plants subsequent to water withholding at 4-day intervals until the plants wilted. The tolerant and sensitive plants had clearly different responses at physiological and volatile levels. The most stress-induced changes on the plants’ physiological traits occurred in the photosynthetic rates, where the tolerant plants maintained their photosynthesis similar to the control ones until the 8th day of the drought stress period. While the analysis of the volatile compounds (VOCs) of the sensitive thyme plants displayed the same pattern for almost all of them, in the tolerant plants, the comparison of the pattern of changes in the tolerant plants revealed that the changes could be classified into three separate groups. Our experimental and theoretical studies totally revealed that the most determinant compounds involved in drought stress adaptation included α-phellandrene, O-cymene, γ-terpinene and β-caryophyelene. Overall, it can be concluded that in the sensitive plants trade-off between growth and defense, the tolerant ones simultaneously activate their stress response mechanism and continue their growth.

FTICR mass spectrometry-based multivariate analysis to explore distinctive metabolites and metabolic pathways: A comprehensive bioanalytical strategy toward time-course metabolic profiling of Thymus vulgaris plants responding to drought stress

In this research, metabolic profiling/pathways of Thymus vulgaris (thyme) plant were assessed during a water deficit stress using an FTICR mass spectrometry-based metabolomics strategy incorporating multivariate data analysis and bioinformatics techniques. Herein, differences of MS signals in specific time courses after water deficit stress and control cases without any timing period were distinguished significantly by common pattern recognition techniques, i.e., PCA, HCA-Heatmap, and PLS-DA. Subsequently, the results were compared with supervised Kohonen neural network (SKN) ones as a non-linear data visualization and capable mapping tool. The classification models showed excellent performance to predict the level of drought stress. By assessing variances contribution on the PCA-loadings of the MS data, the discriminant variables related to the most critical metabolites were identified and then confirmed by ANOVA. Indeed, FTICR MS-based multivariate analysis strategy could explore distinctive metabolites and metabolic pathways/profiles, grouped into three metabolism categories including amino acids, carbohydrates (i.e., galactose, glucose, fructose, sucrose, and mannose), and other metabolites (rosmarinic acid and citrate), to indicate biological mechanisms in response to drought stress for thyme. It was achieved and approved through the MS signals, genomics databases, and transcriptomics factors to interpret and predict the plant metabolic behavior. Eventually, a comprehensive pathway analysis was used to provide a pathway enrichment analysis and explore topological pathway characteristics dealing with the remarkable metabolites to demonstrate that galactose metabolism is the most significant pathway in the biological system of thyme.

New insights into the responses of soil microorganisms to polycyclic aromatic hydrocarbon stress by combining enzyme activity and sequencing analysis with metabolomics

Polycyclic aromatic hydrocarbons (PAHs), some of the most widespread organic contaminants, are highly toxic to soil microorganisms. Whether long-term polluted soils can still respond to the fresh input of pollutants is unknown. In this study, the soil enzyme activity, soil microbial community structure and function and microbial metabolism pathways were examined to systematically investigate the responses of soil microorganisms to fresh PAH stress. Microbial activity as determined by soil dehydrogenase and urease activity was inhibited upon microbe exposure to PAH stress. In addition, the soil microbial community and function were obviously shifted under PAH stress. Both microbial diversity and richness were decreased by PAH stress. Rhizobacter, Sphingobium, Mycobacterium, Massilia, Bacillus and Pseudarthrobacter were significantly affected by PAH stress and can be considered important indicators of PAH contamination in agricultural soils. Moreover, the majority of microbial metabolic function predicted to respond to PAH stress were affected adversely. Finally, soil metabolomics further revealed specific inhibition of soil metabolism pathways associated with fatty acids, carbohydrates and amino acids. Therefore, the soil metabolic composition distinctively changed, reflecting a change in the soil metabolism. In summary, fresh contaminant introduction into long-term polluted soils inhibited microbial activity and metabolism, which might profoundly affect the whole soil quality.

Combined impacts of prolonged drought and warming on plant size and foliar chemistry

BACKGROUND AND AIMS

Future shifts in precipitation regimes and temperature are expected to affect plant traits dramatically. To date, many studies have explored the effects of acute stresses, but few have investigated the consequences of prolonged shifts in climatic conditions on plant growth and chemistry.

METHODS

Plant size and metabolite profiles were assessed on naturally occurring Plantago lanceolata plants growing under different precipitation (ambient, 50 % less than ambient = drought) and temperature (ambient, +0.8, +2.4 and +4.0 °C above ambient) treatments at the Boston Area Climate Experiment (constructed in 2007).

KEY RESULTS

The analysis of primary and secondary metabolites revealed pronounced effects of drought, and a precipitation × temperature interaction. Strikingly, the effects of precipitation were minimal at the two lower temperatures but marked at the two higher temperatures. Compared with the ambient condition, plants in the drought plots had lower concentrations of foliar nitrogen, amino acids and most sugars, and higher concentrations of sorbitol, citrate and malate, common stress-induced metabolites. This pattern was especially evident at high temperatures. Moreover, drought-exposed plants showed lower concentrations of catalpol, an iridoid glycoside.

CONCLUSIONS

While the effect of warming on the metabolite profiles was less pronounced, differences were marked when combined with drought. Given the interactive effect of environmental variables on leaf chemistry, and the fact that woody and herbaceous plants seem to differ in their responses to temperature and precipitation, future studies should account for the direct and indirect effects of the community response to multifactorial field conditions.

Investigating the physiological mechanisms underlying Salicornia ramosissima response to atmospheric CO2 enrichment under coexistence of prolonged soil flooding and saline excess

A 45-days long climatic chamber experiment was design to evaluate the effect of 400 and 700 ppm atmospheric CO₂ treatments with and without soil water logging in combination with 171 and 510 mM NaCl in the halophyte Salicornia ramosissima. In order to ascertain the possible synergetic impact of these factors associate to climatic change in this plant species physiological and growth responses. Our results indicated that elevated atmospheric CO₂ concentration improved plant physiological performance under suboptimal root-flooding and saline conditions plants. Thus, this positive impact was mainly ascribed to an enhancement of energy transport efficiency, as indicated the greater P_G, N and Sm values, and the maintaining of carbon assimilation capacity due to the higher net photosynthetic rate (A_N) and water use efficiency (_iWUE). This could contribute to reduce the risk of oxidative stress owing to the accumulation of reactive oxygen species (ROS). Moreover, plants grown at 700 ppm had a greater capacity to cope with flooding and salinity synergistic impact by a greater efficiency in the modulation in enzyme antioxidant machinery and by the accumulation of osmoprotective compounds and saturated fatty acids in its tissues. These responses indicate that atmospheric CO₂ enrichment would contribute to preserve the development of Salicornia ramosissima against the ongoing process of increment of soil stressful conditions linked with climatic change.

Effect of Thermal Stress on Tissue Ultrastructure and Metabolite Profiles During Initiation of Radiata Pine Somatic Embryogenesis

Climate change will inevitably lead to environmental variations, thus plant drought tolerance will be a determinant factor in the success of plantations and natural forestry recovery. Some metabolites, such as soluble carbohydrates and amino acids, have been described as being the key to both embryogenesis efficiency and abiotic stress response, contributing to phenotypic plasticity and the adaptive capacity of plants. For this reason, our main objectives were to evaluate if the temperature during embryonal mass initiation in radiata pine was critical to the success of somatic embryogenesis, to alter the morphological and ultrastructural organization of embryonal masses at cellular level and to modify the carbohydrate, protein, or amino acid contents. The first SE initiation experiments were carried out at moderate and high temperatures for periods of different durations prior to transfer to the control temperature of 23°C. Cultures initiated at moderate temperatures (30°C, 4 weeks and 40°C, 4 days) showed significantly lower initiation and proliferation rates than those at the control temperature or pulse treatment at high temperatures (50°C, 5 min). No significant differences were observed either for the percentage of embryogenic cell lines that produced somatic embryos, or for the number of somatic embryos per gram of embryonal mass. Based on the results from the first experiments, initiation was carried out at 40°C 4 h; 50°C, 30 min; and a pulse treatment of 60°C, 5 min. No significant differences were found for the initiation or number of established lines or for the maturation of somatic embryos. However, large morphological differences were observed in the mature somatic embryos. At the same time, changes observed at cellular level suggested that strong heat shock treatments may trigger the programmed cell death of embryogenic cells, leading to an early loss of embryogenic potential, and the formation of supernumerary suspensor cells. Finally, among all the differences observed in the metabolic profile, it is worth highlighting the accumulation of tyrosine and isoleucine, both amino acids involved in the synthesis of abiotic stress response-related secondary metabolites.

Time-Course Comparative Metabolite Profiling under Osmotic Stress in Tolerant and Sensitive Tibetan Hulless Barley

Tibetan hulless barley is widely grown in the extreme environmental conditions of the Qinghai-Tibet Plateau which is characterized by cold, high salinity, and drought. Osmotic stress always occurs simultaneously with drought and its tolerance is a vital part of drought tolerance. The diversity of metabolites leading to osmotic stress tolerance was characterized using widely-targeted metabolomics in tolerant (XL) and sensitive (D) accessions submitted to polyethylene glycol. XL regulated a more diverse set of metabolites than D, which may promote the establishment of a robust system to cope with the stress in XL. Compounds belonging to the group of flavonoids, amino acids, and glycerophospholipids constitute the core metabolome responsive to the stress, despite the tolerance levels. Moreover, 8 h appeared to be a critical time point for stress endurance involving a high accumulation of key metabolites from the class of nucleotide and its derivative which provide the ultimate energy source for the synthesis of functional carbohydrates, lipids, peptides, and secondary metabolites in XL. This intrinsic metabolic adjustment helped XL to efficiently alleviate the stress at the later stages. A total of 22 diverse compounds were constantly and exclusively regulated in XL, representing novel stress tolerance biomarkers which may help improving stress tolerance, especially drought, in hulless barley.

Metabolite profiling and molecular responses in a drought-tolerant savory, Satureja rechingeri exposed to water deficit

This study aimed to determine the response of Satureja rechingeri to water deficit by quantifying the expression of three targeted genes and four traditional reference genes using quantitative real-time PCR analysis (RT-qPCR). Drought stress was imposed by withholding water 4 months after planting. Profiling of volatile and non-volatile compounds using gas chromatography/mass spectrometry (GC/MS) and high-performance thin layer chromatography (HPTLC) showed an increasing-decreasing trend of major phenolic and terpenoid compounds such as rosmarinic and caffeic acids, carvacrole, thymol and p-Cymene. Drought stress also lead to significant increases in oil yield, soluble sugars and proline as well as significant reductions in leaf water potential (LWP), relative water content (RWC), and pigments. Metabolite profiling revealed the strategies savory employed to generate different biochemical phenotypes. RT-qPCR analysis showed that up-regulation of the three genes [1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR), 3-hydroxy-3-methylglutaryl-coenzyme. A reductase (HMGR) and rosmarinic acid synthase: 4-coumaroyl-CoA (RAS)] selected from the phenylpropanoid and terpenoid biosynthesis pathways were markedly enhanced at the transcript levels of the regulatory steps and directly increased the production of secondary metabolites, including phenolic and terpenoid compounds. Actin protein (ACT), elongation factor 1-α (EF1α), glyceraldehyde-3-phosphate dehydrogenase cytosolic (GAPC) and ubiquitin-conjugating enzyme (UBC) were used as traditional reference genes. UBC's suitability as the reference genes were verified in S. rechingeri. The study's results provide the foundation for gene expression analysis of savory and other species of Lamiaceae. Thus, the effective application of drought stress before harvesting can increase the quantity and quality of raw material.

Metabolomics analysis reveals that elevated atmospheric CO2 alleviates drought stress in cucumber seedling leaves

Elevated atmospheric CO₂ alleviates moderate to severe drought stresses at physiological level in cucumber. To investigate the underlying metabolic mechanisms, cucumber seedlings were treated with two [CO₂] and three water treatments combinations, and their leaves were analyzed using a non-targeted metabolomics approach. The results showed that elevated [CO₂] changed 79 differential metabolites which were mainly associated with alanine, aspartate and glutamate metabolism; arginine and proline metabolism; TCA cycle; and glycerophospholipid metabolism under moderate drought stress. Moreover, elevated [CO₂] promoted the accumulation of secondary metabolites; including isoferulic acid, m-coumaric acid and salicyluric acid. Under severe drought stress, elevated [CO₂] changed 26 differential metabolites which mainly involved in alanine, aspartate and glutamate metabolism; pyruvate metabolism; arginine and proline metabolism; glyoxylate and dicarboxylate metabolism; cysteine and methionine metabolism; starch and sucrose metabolism; glycolysis or gluconeogenesis; and pyrimidine metabolism. In addition, elevated [CO₂] accumulated carbohydrates, 1,2,3-trihydroxybenzene, pyrocatechol, glutamate, and l-gulonolactone, to allow adaption to severe drought. In conclusion, the metabolites and metabolic pathways associated with the alleviation of drought stresses by elevated [CO₂] were different according to the level of drought stress. Our results may provide a theoretical basis for CO₂ fertilization and application of exogenous metabolites to enhance drought tolerance of cucumber.

NMR-based global metabolomics approach to decipher the metabolic effects of three plant growth regulators on strawberry maturation

Plant growth regulators (PGRs) are commonly used to regulate maturation in strawberry. Despite this, comprehensive assessments of the metabolomic effects of PGRs on strawberry maturation are lacking. In this study, a nuclear magnetic resonance-based approach, combined with multivariate and pathway analysis, was used to evaluate the regulatory effects of gibberellin, forchlorfenuron, and brassinolide, applied at two different maturation stages, on the expression of metabolites in strawberry. The results demonstrated that the PGRs differentially influenced metabolism, whether applied at the same or different maturation stages. Additionally, we also discovered that these different PGRs exhibited some similar metabolic trends when applied at the same growth period. Our findings validate the use of NMR-based metabolomics for identifying subtle changes in the expression of metabolites associated with PGR application.

Multiple nucleobase transporters contribute to boscalid sensitivity in Aspergillus nidulans

The development of fungicide-resistant fungal populations represents a major challenge for the agrochemical and agri-food sectors, which threatens food supply and security. The issue becomes complex for fungi that cause quantitative and qualitative losses due to mycotoxin biosynthesis. Nonetheless, currently, the molecular details underlying fungicide action and fungal resistance mechanisms are partially known. Here, we have investigated whether plasma membrane transporters contribute to specific fungicide uptake in the model fungus Aspergillus nidulans. Independent physiological tests and toxicity screening of selected fungicides provided evidence that the antifungal activity of Succinate Dehydrogenase Inhibitors (SDHIs) is associated with the expression of several nucleobase-related transporters. In particular, it was shown that a strain genetically inactivated in all seven nucleobase-related transporters is resistant to the fungicide boscalid, whereas none of the single null mutants exhibited significant resistance level. By constructing and testing isogenic strains that over-express each one of the seven transporters, we confirmed that five of them, namely, UapC, AzgA, FycB, CntA, and FurA, contribute to boscalid uptake. Additionally, by employing metabolomics we have examined the effect of boscalid on the metabolism of isogenic strains expressing or genetically lacking boscalid-related nucleobase transporters. The results confirmed the involvement of specific nucleobase transporters in fungicide uptake, leading to the discovery of corresponding metabolites-biomarkers. This work is the first report on the involvement of specific transporters in fungicide uptake and toxicity and their impact on fungal metabolism regulation and results might be further exploited towards the deeper understanding of fungal resistance to fungicides.

Comprehensive list of metabolites measured by DI-FTICR mass spectrometry in thyme plants with contrasting tolerance to drought

This article contains data related to the main research entitled "Metabolomic approach reveals the biochemical mechanisms underlying drought stress tolerance in Thyme" (Moradi et al., 2017) [1]. Two thyme populations with contrasting drought tolerance were subjected to long term water deficit. Leaf samples harvested at the end of stress period and bi-phasic extraction carried out to get polar and non-polar fractions. Extracted samples were analyzed through Direct Infusion FT-ICR mass spectrometry. Date files comprise of four separate tables for all the putatively identified metabolites and their intensities in watered and droughted plants. P-values beside each m/z values indicate significances of difference between peak intensities of stressed and control conditions.