Integrative functional genomics of salt acclimatization in the model legume Lotus japonicus

Beneficial or detrimental? How nickel application alters the ionome of soybean plants

The use of nickel (Ni) in agriculture may represent one of the most significant cases of plant hormesis ever reported, as plants exhibit both positive and negative responses depending on the level of exposure to this element. For a more comprehensive understanding of this effect, the next step is to conduct studies on the dynamics of pre-existing chemical elements in the system (ionomic profile), especially when introducing Ni as a novel nutrient for the plants. This micronutrient is of particular interest to the fertilization of leguminous plants, such as the soybean, due to its additional effects on the biological nitrogen fixation process. This study thus evaluated the influence of five doses of Ni (0.0, 0.5, 1.0, 3.0, and 9.0 mg of Ni kg-1) on the ionomic profile of soybean genotypes using modern quantification techniques. The results revealed that the addition of Ni reduced the concentration of cationic micronutrients manganese (Mn), iron (Fe), zinc (Zn), and copper (Cu), while it increased the concentration of macronutrients nitrogen (N) and magnesium (Mg). The application of Ni also resulted in a reduction of the potentially toxic element aluminum (Al). Correlations were also observed for these elements, indicating that Ni could be a controlling agent in elemental absorption and translocation. The ionome of the leaf tissues exhibited the most significant alterations, followed by the grains, nodules, and roots. Exogenous agronomic doses of Ni proved beneficial for the growth and production of soybean plants, although a genotypic effect was observed. The treatment with 9.0 mg of Ni kg-1, resulted in a new ionomic profile related to toxicity, demonstrating suboptimal plant development. Thus, the application of Ni in appropriate doses had a significant impact on the ionomic profile of soybeans, improving plant development and implying resistance to potentially toxic elements such as Al.

Global omics study of Tetraselmis chuii reveals time-related metabolic adaptations upon oxidative stress

Microalgae species encounter oxidative stress in their natural environments, prompting the development of species-specific adaptation mechanisms. Understanding these mechanisms can offer valuable insights for biotechnological applications in microalgal metabolic manipulation. In this study, we investigated the response of Tetraselmis chuii, an industrially important microalga, to H2O2-induced oxidative stress. Exposure to 0.5-mM H2O2 resulted in reduced cell viability, and higher concentrations led to a drastic decline. After 1 h of exposure to H2O2, photosynthetic capacity (Qy) was negatively impacted, and this reduction intensified after 6 h of continuous stress. Global multi-omics analysis revealed that T. chuii rapidly responded to H2O2-induced oxidative stress within the first hour, causing significant changes in both transcriptomic and metabolomic profiles. Among the cellular functions negatively affected were carbon and energy flow, with photosynthesis-related PSBQ having a 2.4-fold downregulation, pyruvate kinase decreased by 1.5-fold, and urea content reduced by threefold. Prolonged exposure to H2O2 incurred a high energy cost, leading to unsuccessful attempts to enhance carbon metabolism, as depicted, for example, by the upregulation of photosystems-related PETC and PETJ by more than twofold. These findings indicate that T. chuii quickly responds to oxidative stress, but extended exposure can have detrimental effects on its cellular functions. KEY POINTS: • 0.5-mM H2O2-induced oxidative stress strongly affects T. chuii • Distinct short- and long-term adaptation mechanisms are induced • Major metabolic adaptations occur within the first hour of exposure.

Visualizing plant salt stress with a NaCl-responsive fluorescent probe

Salt stress is an adverse environmental condition that harms plant growth and development. The development of salt stress probes is critical for tracking the growth dynamics of plants, molecular breeding or screening of growth regulators. The sodium chloride (NaCl)-responsive fluorescent probe Aza-CyBz is designed based on the tenet that NaCl induces formation of ordered aggregates, and the sensitive fluorescence response can enable the visualization of plant salt stress in root tip tissues and live plants. Herein, we describe a detailed three-step route for synthesis of Aza-CyBz and applications to monitoring salt stress in Arabidopsis thaliana. The procedures for operating fluorescence imaging under various stresses are also listed to eliminate interference from the oxidative mechanism of salt stress. Compared with conventional invasive approaches such as inductively coupled plasma emission spectrometry and flame photometer, our protocol can real-time monitor salt stress experienced by plants, which demands simple pretreatment procedure and staining technique. Due to near infrared fluorescence, this method provides direct visual observation of salt stress at both tissue and live plant levels, which is superior to conventional noninvasive approaches. The preparation of probe Aza-CyBz takes ~2 d, and the imaging experiments for assessing salt stress experienced by plants, including the preparation of stressed plant samples takes ~9-11 d for root tip tissues and ~23 d for live plants. Notably, acquisition and analysis visual images of salt stress in plants can be completed within 2 h and they require only a basic knowledge of spectroscopy and chemistry.

Halotolerant Citrobacter sp. remediates salinity stress and promotes the growth of Vigna radiata (L) by secreting extracellular polymeric substances (EPS) and biofilm formation: a novel active cell for microbial desalination cell (MDC)

To address soil salinization and its impact on crop production, microbial desalination cells (MDCs) offer a promising solution. These bioelectrochemical systems integrate desalination and wastewater treatment through microbial activity. A halotolerant beneficial bacterial strain called Citrobacter sp. strain KUT (CKUT) was isolated from India's salt desert Run of Kutch, Gujrat, highlighting its potential application in combating soil salinization. CKUT exhibits high salt tolerance and has the ability to produce extracellular polymeric substances (EPS) at a concentration of 0.04 mg/ml. It forms biofilm that enable it to withstand up to 10% NaCl concentration. Additionally, CKUT shows promise in remediating salinity levels, reducing it from 4.5 to 2.7 gL-1. These characteristics are driven by biofilm formation and EPS production. In an experiment where V. radiata L. seedlings were inoculated with CKUT, the treated plants exhibited enhanced chlorophyll content, growth, and overall plant characteristics compared to seedlings treated with sodium chloride (NaCl). These improvements included increased shoot length (150 mm), root length (40 mm), and biomass. This indicates that CKUT treatment has the potential to enhance the suitability of V. radiata and other crops for cultivation in saline lands, effectively addressing the issue of soil salinization. Furthermore, integrating CKUT into microbial desalination cells (MDCs) offers an opportunity for freshwater production from seawater, contributing to sustainable agriculture by promoting improved crop growth and increased yield in areas prone to salinity. HIGHLIGHTS : • Soil salinization reduces crop yield, including Vigna radiata L. • Citrobacter sp. strain KUT (CKUT) is a halotolerant bacterium isolated from the salt desert Run of Kutch, Gujarat, which can tolerate high salt concentrations. • CKUT mitigates salinity by producing extracellular polymeric substances (EPS) and forming biofilms. • CKUT treatment demonstrated increased plant growth, biomass, and chlorophyll content under salinity stress, showcasing its potential in microbial desalination cell (MDC) for enhancing crop yield in salinized soils.

Canonical transcriptional gene silencing may contribute to long-term heat response and recovery through MOM1

Plant canonical transcriptional gene silencing (TGS) is involved in epigenetic mechanisms that mediate genomic imprinting and the suppression of transposable elements (TEs). It has been recognised that long-term heat disrupts epigenetic silencing, with the ensuing activation of TEs. However, the physiological involvement of the TGS machinery under prolonged high temperatures has not yet been established. Here, we performed non-lethal extended periodic heat stress and recovery treatments on Arabidopsis thaliana lines mutated on key TGS factors, analysing transcriptomic changes of coding-protein genes and TEs. Plants bearing MET1, DRM2 and CMT3, and MOM1 mutated alleles showed novel transcriptional properties compatible with functionalities concerning the induction/repression of partially shared or private heat-triggered transcriptome networks. Certain observations supported the idea that some responses are based on thermal de-silencing. TEs transcriptional activation uncovered the interaction with specific epigenetic layers, which may play dedicated suppressing roles under determinate physiological conditions such as heat. Furthermore, physiological experimentation suggested that MOM1 is required to resume growth after stress. Our data thus provide initial evidence that at least one canonical TGS factor may contribute to plant acclimation and recovery from non-lethal long-term heat despite the stress-induced epigenetic disturbance.

Untargeted metabolomics reveal rhizosphere metabolites mechanisms on continuous ramie cropping

Ramie is an important fiber feed dual-purpose crop in China and plays an important role in the national economy. However, ramie yield and quality can be reduced after many years of continuous cultivation. Currently, relatively little research has been conducted on rhizosphere metabolites and their pathways in continuous ramie cropping. Therefore, a healthy group (CK) and obstacle groups (XZQG, JZ, DJY, and GXD) with 8 years of continuous cultivation were selected for the study. LC-MS and GC-MS untargeted metabolomics were used to explore and analyze ramie rhizosphere metabolites and pathways. The results revealed that significant differences in the agronomic traits of ramie occurred after 8 years of continuous cultivation, with dwarfed plants and decreased yields in the obstacle groups. Metabolomic analysis identified 49 and 19 rhizosphere metabolites, including lipids, organic acids, phenols, and amino acids. In addition, four differential metabolic pathways (phenylpropanoid biosynthesis, fatty acid metabolism, amino acid metabolism, and ascorbate and aldarate metabolism) were elucidated. It was also clarified that sinapic acid, jasmonic acid, glutamine, and inositol might be the main metabolites affecting ramie continuous-cropping obstacle groups, and they were significantly correlated with ramie agronomic traits and physiological indicators. This provided important insights into the mechanisms affecting continuous ramie cropping. Accordingly, it is expected that the increase or decrease of sinapic acid, jasmonic acid, glutamine, and inositol in the soil will alleviate obstacles to continuous ramie cropping and promote the healthy development of the ramie industry in the future.

Primary and Secondary Metabolites in Lotus japonicus

Lotus japonicus is a leguminous model plant used to gain insight into plant physiology, stress response, and especially symbiotic plant-microbe interactions, such as root nodule symbiosis or arbuscular mycorrhiza. Responses to changing environmental conditions, stress, microbes, or insect pests are generally accompanied by changes in primary and secondary metabolism to account for physiological needs or to produce defensive or signaling compounds. Here we provide an overview of the primary and secondary metabolites identified in L. japonicus to date. Identification of the metabolites is mainly based on mass spectral tags (MSTs) obtained by gas chromatography linked with tandem mass spectrometry (GC-MS/MS) or liquid chromatography-MS/MS (LC-MS/MS). These MSTs contain retention index and mass spectral information, which are compared to databases with MSTs of authentic standards. More than 600 metabolites are grouped into compound classes such as polyphenols, carbohydrates, organic acids and phosphates, lipids, amino acids, nitrogenous compounds, phytohormones, and additional defense compounds. Their physiological effects are briefly discussed, and the detection methods are explained. This review of the exisiting literature on L. japonicus metabolites provides a valuable basis for future metabolomics studies.

Transcriptional Expression of Nitrogen Metabolism Genes and Primary Metabolic Variations in Rice Affected by Different Water Status

The era of climate change strongly requires higher efficiency of energies, such as light, water, nutrients, etc., during crop production. Rice is the world's greatest water-consuming plant, and, thus, water-saving practices such as alternative wetting and drying (AWD) are widely recommended worldwide. However the AWD still has concerns such as lower tillering, shallow rooting, and an unexpected water deficit. The AWD is a possibility to not only save water consumption but also utilize various nitrogen forms from the soil. The current study tried to investigate the transcriptional expression of genes in relation to the acquisition-transportation-assimilation process of nitrogen using qRT-PCR at the tillering and heading stages and to profile tissue-specific primary metabolites. We employed two water supply systems, continuous flooding (CF) and alternative wetting and drying (AWD), during rice growth (seeding to heading). The AWD system is effective at acquiring soil nitrate; however, nitrogen assimilation was predominant in the root during the shift from the vegetative to the reproductive stage. In addition, as a result of the greater amino acids in the shoot, the AWD was likely to rearrange amino acid pools to produce proteins in accordance with phase transition. Accordingly, it is suggested that the AWD 1) actively acquired nitrate from soil and 2) resulted in an abundance of amino acid pools, which are considered a rearrangement under limited N availability. Based on the current study, further steps are necessary to evaluate form-dependent N metabolism and root development under the AWD condition and a possible practice in the rice production system.

Overexpression of LjPLT3 Enhances Salt Tolerance in Lotus japonicus

Intracellular polyols are used as osmoprotectants by many plants under environmental stress. However, few studies have shown the role of polyol transporters in the tolerance of plants to abiotic stresses. Here, we describe the expression characteristics and potential functions of Lotus japonicus polyol transporter LjPLT3 under salt stress. Using LjPLT3 promoter-reporter gene plants showed that LjPLT3 was expressed in the vascular tissue of L. japonicus leaf, stem, root, and nodule. The expression was also induced by NaCl treatment. Overexpression of LjPLT3 in L. japonicus modified the growth rate and saline tolerance of the transgenic plants. The OELjPLT3 seedlings displayed reduced plant height under both nitrogen-sufficient and symbiotic nitrogen fixation conditions when 4 weeks old. The nodule number of OELjPLT3 plants was reduced by 6.7–27.4% when 4 weeks old. After exposure to a NaCl treatment in Petri dishes for 10 days, OELjPLT3 seedlings had a higher chlorophyll concentration, fresh weight, and survival rate than those in the wild type. For symbiotic nitrogen fixation conditions, the decrease in nitrogenase activity of OELjPLT3 plants was slower than that of the wild type after salt treatment. Compared to the wild type, both the accumulation of small organic molecules and the activity of antioxidant enzymes were higher under salt stress. Considering the concentration of lower reactive oxygen species (ROS) in transgenic lines, we speculate that overexpression of LjPLT3 in L. japonicus might improve the ROS scavenging system to alleviate the oxidative damage caused by salt stress, thereby increasing plant salinity tolerance. Our results will direct the breeding of forage legumes in saline land and also provide an opportunity for the improvement of poor and saline soils.

Wheat genotypes with higher yield sensitivity to drought overproduced proline and lost minor biomass under severer water stress

To clarify the differences in growth and yield responses to drought stress among genotypes contrasting in environmental background, dryland and irrigated genotypes, as well as the underlying biochemical mechanism would provide valuable information for developing superior dryland cultivars. Pot experiments for the whole life cycle in fifteen genotypes and comparative metabolomics analysis for seedlings between two drought tolerant (DT) dryland genotypes and two drought sensitive (DS) irrigated ones were carried out. The DT dryland genotypes suffered heavy biomass loss during severer drought but showed minor yield loss ultimately, while the DS irrigated ones showed minor biomass loss but greater yield loss. Additionally, the superior DT dryland genotypes showed better yield performance under both drought stress and well-watered conditions, indicating their possessing both drought tolerance and high yield potential traits. Suffering severer drought stress, seedling leaves of the DS irrigated genotypes increased some amino acids and organic acids to maintain cell metabolism and accumulate more biomass. Proline in particular was overproduced, which might cause toxicity to cell systems and lead to enormous yield loss ultimately. In contrast, DT dryland genotypes increased the beneficial amino acid and phenolic acids to enhance cell self-protection for alleviating drought damage and efficiently minimized yield loss ultimately.

Reprogramming of Plant Central Metabolism in Response to Abiotic Stresses: A Metabolomics View

Abiotic stresses rewire plant central metabolism to maintain metabolic and energy homeostasis. Metabolites involved in the plant central metabolic network serve as a hub for regulating carbon and energy metabolism under various stress conditions. In this review, we introduce recent metabolomics techniques used to investigate the dynamics of metabolic responses to abiotic stresses and analyze the trend of publications in this field. We provide an updated overview of the changing patterns in central metabolic pathways related to the metabolic responses to common stresses, including flooding, drought, cold, heat, and salinity. We extensively review the common and unique metabolic changes in central metabolism in response to major abiotic stresses. Finally, we discuss the challenges and some emerging insights in the future application of metabolomics to study plant responses to abiotic stresses.

The meristem-associated endosymbiont Methylorubrum extorquens DSM13060 reprograms development and stress responses of pine seedlings

Microbes living in plant tissues-endophytes-are mainly studied in crop plants where they typically colonize the root apoplast. Trees-a large carbon source with a high capacity for photosynthesis-provide a variety of niches for endophytic colonization. We have earlier identified a new type of plant-endophyte interaction in buds of adult Scots pine, where Methylorubrum species live inside the meristematic cells. The endosymbiont Methylorubrum extorquens DSM13060 significantly increases needle and root growth of pine seedlings without producing plant hormones, but by aggregating around host nuclei. Here, we studied gene expression and metabolites of the pine host induced by M. extorquens DSM13060 infection. Malic acid was produced by pine to potentially boost M. extorquens colonization and interaction. Based on gene expression, the endosymbiont activated the auxin- and ethylene (ET)-associated hormonal pathways through induction of CUL1 and HYL1, and suppressed salicylic and abscisic acid signaling of pine. Infection by the endosymbiont had an effect on pine meristem and leaf development through activation of GLP1-7 and ALE2, and suppressed flowering, root hair and lateral root formation by downregulation of AGL8, plantacyanin, GASA7, COW1 and RALFL34. Despite of systemic infection of pine seedlings by the endosymbiont, the pine genes CUL1, ETR2, ERF3, HYL, GLP1-7 and CYP71 were highly expressed in the shoot apical meristem, rarely in needles and not in stem or root tissues. Low expression of MERI5, CLH2, EULS3 and high quantities of ononitol suggest that endosymbiont promotes viability and protects pine seedlings against abiotic stress. Our results indicate that the endosymbiont positively affects host development and stress tolerance through mechanisms previously unknown for endophytic bacteria, manipulation of plant hormone signaling pathways, downregulation of senescence and cell death-associated genes and induction of ononitol biosynthesis.

The Response of Cowpea (Vigna unguiculata) Plants to Three Abiotic Stresses Applied with Increasing Intensity: Hypoxia, Salinity, and Water Deficit

Exposing plants to gradually increasing stress and to abiotic shock represents two different phenomena. The knowledge on plants’ responses following gradually increasing stress is limited, as many of the studies are focused on abiotic shock responses. We aimed to investigate how cowpea (Vigna unguiculata (L.) Walp.) plants respond to three common agricultural abiotic stresses: hypoxia (applied with the increasing time of exposure to nitrogen gas), salinity (gradually increasing NaCl concentration), and water deficit (gradual decrease in water supply). We hypothesized that the cowpea plants would increase in tolerance to these three abiotic stresses when their intensities rose in a stepwise manner. Following two weeks of treatments, leaf and whole-plant fresh weights declined, soluble sugar levels in leaves decreased, and lipid peroxidation of leaves and roots and the levels of leaf electrolyte leakage increased. Polyphenol oxidase activity in both roots and leaves exhibited a marked increase as compared to catalase and peroxidase. Leaf flavonoid content decreased considerably after hypoxia, while it increased under water deficit treatment. NO emission rates after 3 h in the hypoxically treated plants were similar to the controls, while the other two treatments resulted in lower values of NO production, and these levels further decreased with time. The degree of these changes was dependent on the type of treatment, and the observed effects were more substantial in leaves than in roots. In summary, the responses of cowpea plants to abiotic stress depend on the type and the degree of stress applied and the plant organs.

Omics Path to Increasing Productivity in Less-Studied Crops Under Changing Climate-Lentil a Case Study

Conventional breeding techniques for crop improvement have reached their full potential, and hence, alternative routes are required to ensure a sustained genetic gain in lentils. Although high-throughput omics technologies have been effectively employed in major crops, less-studied crops such as lentils have primarily relied on conventional breeding. Application of genomics and transcriptomics in lentils has resulted in linkage maps and identification of QTLs and candidate genes related to agronomically relevant traits and biotic and abiotic stress tolerance. Next-generation sequencing (NGS) complemented with high-throughput phenotyping (HTP) technologies is shown to provide new opportunities to identify genomic regions and marker-trait associations to increase lentil breeding efficiency. Recent introduction of image-based phenotyping has facilitated to discern lentil responses undergoing biotic and abiotic stresses. In lentil, proteomics has been performed using conventional methods such as 2-D gel electrophoresis, leading to the identification of seed-specific proteome. Metabolomic studies have led to identifying key metabolites that help differentiate genotypic responses to drought and salinity stresses. Independent analysis of differentially expressed genes from publicly available transcriptomic studies in lentils identified 329 common transcripts between heat and biotic stresses. Similarly, 19 metabolites were common across legumes, while 31 were common in genotypes exposed to drought and salinity stress. These common but differentially expressed genes/proteins/metabolites provide the starting point for developing high-yielding multi-stress-tolerant lentils. Finally, the review summarizes the current findings from omic studies in lentils and provides directions for integrating these findings into a systems approach to increase lentil productivity and enhance resilience to biotic and abiotic stresses under changing climate.

Stress-regulated elements in Lotus spp., as a possible starting point to understand signalling networks and stress adaptation in legumes

Although legumes are of primary economic importance for human and livestock consumption, the information regarding signalling networks during plant stress response in this group is very scarce. Lotus japonicus is a major experimental model within the Leguminosae family, whereas L. corniculatus and L. tenuis are frequent components of natural and agricultural ecosystems worldwide. These species display differences in their perception and response to diverse stresses, even at the genotype level, whereby they have been used in many studies aimed at achieving a better understanding of the plant stress-response mechanisms. However, we are far from the identification of key components of their stress-response signalling network, a previous step for implementing transgenic and editing tools to develop legume stress-resilient genotypes, with higher crop yield and quality. In this review we scope a body of literature, highlighting what is currently known on the stress-regulated signalling elements so far reported in Lotus spp. Our work includes a comprehensive review of transcription factors chaperones, redox signals and proteins of unknown function. In addition, we revised strigolactones and genes regulating phytochelatins and hormone metabolism, due to their involvement as intermediates in several physiological signalling networks. This work was intended for a broad readership in the fields of physiology, metabolism, plant nutrition, genetics and signal transduction. Our results suggest that Lotus species provide a valuable information platform for the study of specific protein-protein (PPI) interactions, as a starting point to unravel signalling networks underlying plant acclimatation to bacterial and abiotic stressors in legumes. Furthermore, some Lotus species may be a source of genes whose regulation improves stress tolerance and growth when introduced ectopically in other plant species.

Inoculation of barley with Trichoderma harzianum T-22 modifies lipids and metabolites to improve salt tolerance

Soil salinity has a serious impact on plant growth and agricultural yield. Inoculation of crop plants with fungal endophytes is a cost-effective way to improve salt tolerance. We used metabolomics to study how Trichoderma harzianum T-22 alleviates NaCl-induced stress in two barley (Hordeum vulgare L.) cultivars, Gairdner and Vlamingh, with contrasting salinity tolerance. GC-MS was used to analyse polar metabolites and LC-MS to analyse lipids in roots during the early stages of interaction with Trichoderma. Inoculation reversed the severe effects of salt on root length in sensitive cv. Gairdner and, to a lesser extent, improved root growth in more tolerance cv. Vlamingh. Biochemical changes showed a similar pattern in inoculated roots after salt treatment. Sugars increased in both cultivars, with ribulose, ribose, and rhamnose specifically increased by inoculation. Salt stress caused large changes in lipids in roots but inoculation with fungus greatly reduced the extent of these changes. Many of the metabolic changes in inoculated cv. Gairdner after salt treatment mirror the response of uninoculated cv. Vlamingh, but there are some metabolites that changed in both cultivars only after fungal inoculation. Further study is required to determine how these metabolic changes are induced by fungal inoculation.

Salt Stress Amelioration in Maize Plants through Phosphogypsum Application and Bacterial Inoculation

The use of phosphogypsum (PG) and plant growth-promoting rhizobacteria (PGPR) for agricultural purposes are good options to improve soil properties and increase crop yield. The objective of this study was to investigate the effect of different rates of PG (ton ha⁻¹; 0 (PG1), 3 (PG2), 6 (PG3), and 9 (PG4)) combined with PGPR inoculation (Azospirillum lipoferum (control, T1), A. lipoferum + Bacillus coagulans (T2), A. lipoferum + B. circulance (T3), and A. lipoferum + B. subtilis (T4)) on soil properties, plant physiology, antioxidant enzymes, nutrient uptake, and yield of maize plants (Zea mays L., cv. HSC 10) grown in salt-affected soil. Over two growing seasons, 2019 and 2020, field experiments were conducted as a split-plot design with triplicates. The results show that applying PG (9 ton ha⁻¹) and co-inoculation (A. lipoferum + B. circulance) treatment significantly increased chlorophyll and carotenoids content, antioxidant enzymes, microbial communities, soil enzymes activity, and nutrient contents, and showed inhibitory impacts on proline content and pH, as well as EC and ESP, thus improving the productivity of maize plant compared to the control treatment. It could be concluded that PG, along with microbial inoculation, may be an important approach for ameliorating the negative impacts of salinity on maize plants.

The biological approaches of altering the growth and biochemical properties of medicinal plants under salinity stress

Due to their interesting properties for human health, medicinal plants are of worldwide interest, including Iran. More has yet to be investigated and analyzed on the use of methods affecting medicinal plant growth and biochemical properties under stress. The important question about medicinal plants is the purpose of their plantation, determining their growth conditions. The present review article is about the effects of salinity stress on the growth and production of secondary metabolites (SM) in medicinal plants. In stressful conditions including salinity, while the growth of medicinal plants decreases, the production of secondary metabolites (SM) may increase significantly affecting plant medicinal properties. SMs are self-protective substances that medicinal plants quickly accumulate to resist changes in the external environment. Although previous research has indicated the effects of salt stress on the growth and yield of medicinal plants, more has yet to be indicated on how the use of biological methods including plant growth regulators (PGR) and soil microbes (mycorrhizal fungi and plant growth-promoting rhizobacteria, PGPR) may affect the physiology of medicinal plants and the subsequent production of SM in salt stress conditions. The use of modern omics has become significantly important for the identification and characterization of new SM, transcriptomics, genomics, and proteomics of medicinal plants, as well as for the high production of plant-derived medicines. Accordingly, the possible biological mechanisms, which may affect such properties, have been presented. Future research perspectives for the production of medicinal plants in saline fields, using biological methods, have been suggested. KEY POINTS: • The important question about medicinal plants is the purpose of their plantation. • Secondary metabolites (SM) may significantly increase under salinity stress. • Biological methods, affecting the production of SM by stressed medicinal plants.

Molecular responses of legumes to abiotic stress: post-translational modifications of proteins and redox signaling

Legumes include several major crops that can fix atmospheric nitrogen in symbiotic root nodules, thus reducing the demand for nitrogen fertilizers and contributing to sustainable agriculture. Global change models predict increases in temperature and extreme weather conditions. This scenario might increase plant exposure to abiotic stresses and negatively affect crop production. Regulation of whole plant physiology and nitrogen fixation in legumes during abiotic stress is complex, and only a few mechanisms have been elucidated. Reactive oxygen species (ROS), reactive nitrogen species (RNS), and reactive sulfur species (RSS) are key players in the acclimation and stress tolerance mechanisms of plants. However, the specific redox-dependent signaling pathways are far from understood. One mechanism by which ROS, RNS, and RSS fulfil their signaling role is the post-translational modification (PTM) of proteins. Redox-based PTMs occur in the cysteine thiol group (oxidation, S-nitrosylation, S-glutathionylation, persulfidation), and also in methionine (oxidation), tyrosine (nitration), and lysine and arginine (carbonylation/glycation) residues. Unraveling PTM patterns under different types of stress and establishing the functional implications may give insight into the underlying mechanisms by which the plant and nodule respond to adverse conditions. Here, we review current knowledge on redox-based PTMs and their possible consequences in legume and nodule biology.

Expression dynamics of genes encoding nitrate and ammonium assimilation enzymes in rice genotypes exposed to reproductive stage salinity stress

Understanding the reproductive stage salinity stress tolerance is a key target for breeding stress tolerant rice genotypes. Nitrate and ammonium are equally important nitrogen forms utilized by rice. We evaluated nitrate and ammonium assimilation during reproductive stage in control and salinity (10dSm^-1 using NaCl) stressed rice plants. Osmotic stress tolerant rice genotype Shabhagidhan (SD) and high yielding yet osmotic and salinity stress sensitive genotype Pusa sugandh-5 (PS5) were evaluated. Salinity stress was given to plants during panicle emergence and flag leaves was collected after 1d, 3d 5d, 7d, 9d,12d and 15d after anthesis. Reproductive stage salinity stress resulted in decrease of membrane stability, relative water content and osmotic potential of rice plants. Reproductive stage salinity stress decreased the expression of nitrate reductase (OsNIA), nitrite reductase (OsNiR), Glutamine synthetase (OsGLN1.1, OsGLN1.2, OsGLN2) and glutamate synthase/GOGAT (OsFd-GOGAT, OsNADH-GOGAT) in flag leaves. In response to stress, SD showed better stress tolerance than PS5 in terms of higher yield stability. Variety SD showed higher leaf nitrate and ammonium content and maintained comparatively higher nitrate and ammonia metabolism enzyme activity than PS5. Salinity stress upregulated the activity of glutamate dehydrogenase enzyme and indirectly contributed to the higher proline content and maintenance of favourable osmotic potential in SD. Expression of GS2 which has role in photo respiratory ammonia assimilation was upregulated by salinity stress in PS5 in comparison to SD. Rice genotype showing better induction of nitrogen assimilatory genes will be more tolerant to reproductive stage salinity stress.

Untargeted LC-MS-based metabolomics revealed specific metabolic changes in cotyledons and roots of Ricinus communis during early seedling establishment under salt stress

Early seedling development is one of the most crucial period of the plant's life cycle, which is highly susceptible to adverse environmental conditions, especially those impose by salt stress. Castor plant (Ricinus communis) is a famous non-edible oilseed and salt-resistant crop worldwide. However, the specific metabolic responses in the cotyledons and roots of this species during seedling establishment under salt stress are still not clearly understood. In the present study, 16 d castor seedlings were treated with 150 mM NaCl for 6 d, and the metabolite profiling of cotyledons and roots was conducted using liquid chromatography (LC) combined with electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS). The Principal Component Analysis (PCA) results showed that the metabolites were great differed in cotyledons and roots under salt stress. There were 38 differential metabolites, mainly including fatty acid, nucleic acid and organic acids in the cotyledons, but only 19 differential metabolites, mainly including fatty acid and organic acids in the roots under such condition. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that flavone and flavonol biosynthesis, pantothenate and CoA biosynthesis, citrate cycle and carotenoid biosynthesis were the common metabolic pathways in response to salt stress in the two organs. Salt stress caused metabolite process alteration mainly on carbon and nitrogen metabolisms, and the carbon allocation from root to cotyledon was increased. Additionally, changes of amino acids and nucleic acids profiles were only found in the cotyledons, and the roots could enhance the activity of antioxidant enzyme systems to scavenge ROS under salinity. In conclusion, the present research provides an improved understanding on specific physiological changes in the cotyledons in castor early seedlings, and explores their interaction under salt stress.

Metabolomics, a Powerful Tool for Understanding Plant Abiotic Stress

Metabolomics is a technology that generates large amounts of data and contributes to obtaining wide and integral explanations of the biochemical state of a living organism. Plants are continuously affected by abiotic stresses such as water scarcity, high temperatures and high salinity, and metabolomics has the potential for elucidating the response-to-stress mechanisms and develop resistance strategies in affected cultivars. This review describes the characteristics of each of the stages of metabolomic studies in plants and the role of metabolomics in the characterization of the response of various plant species to abiotic stresses.

Identification and selection of reference genes for gene expression analysis by quantitative real-time PCR in Suaeda glauca's response to salinity

Quantitative real-time polymerase chain reaction (qPCR) using a stable reference gene is widely used for gene expression research. Suaeda glauca L. is a succulent halophyte and medicinal plant that is extensively used for phytoremediation and extraction of medicinal compounds. It thrives under high-salt conditions, which promote the accumulation of high-value secondary metabolites. However, a suitable reference gene has not been identified for gene expression standardization in S. glauca under saline conditions. Here, 10 candidate reference genes, ACT7, ACT11, CCD1, TUA5, UPL1, PP2A, DREB1D, V-H⁺-ATPase, MPK6, and PHT4;5, were selected from S. glauca transcriptome data. Five statistical algorithms (ΔCq, geNorm, NormFinder, BestKeeper, and RefFinder) were applied to determine the expression stabilities of these genes in 72 samples at different salt concentrations in different tissues. PP2A and TUA5 were the most stable reference genes in different tissues and salt treatments, whereas DREB1D was the least stable. The two reference genes were sufficient to normalize gene expression across all sample sets. The suitability of identified reference genes was validated with MYB and AP2 in germinating seeds of S. glauca exposed to different NaCl concentrations. Our study provides a foundational framework for standardizing qPCR analyses, enabling accurate gene expression profiling in S. glauca.

Morpho-Physiological, Biochemical, and Genetic Responses to Salinity in Medicago truncatula

We used an integrated morpho-physiological, biochemical, and genetic approach to investigate the salt responses of four lines (TN1.11, TN6.18, JA17, and A10) of Medicago truncatula. Results showed that TN1.11 exhibited a high tolerance to salinity, compared with the other lines, recording a salinity induced an increase in soluble sugars and soluble proteins, a slight decrease in malondialdehyde (MDA) accumulation, and less reduction in plant biomass. TN6.18 was the most susceptible to salinity as it showed less plant weight, had elevated levels of MDA, and lower levels of soluble sugars and soluble proteins under salt stress. As transcription factors of the APETALA2/ethylene responsive factor (AP2/ERF) family play important roles in plant growth, development, and responses to biotic and abiotic stresses, we performed a functional characterization of MtERF1 gene. Real-time PCR analysis revealed that MtERF1 is mainly expressed in roots and is inducible by NaCl and low temperature. Additionally, under salt stress, a greater increase in the expression of MtERF1 was found in TN1.11 plants than that in TN6.18. Therefore, the MtERF1 pattern of expression may provide a useful marker for discriminating among lines of M. truncatula and can be used as a tool in breeding programs aiming at obtaining Medicago lines with improved salt tolerance.

A comparative metabolomics analysis of the halophyte Suaeda salsa and Salicornia europaea

Suaeda salsa and Salicornia europaea are both annual herbaceous species belonging to the Chenopodiaceae family, and often grow together through our observations in the Yellow River Delta Nature Reserve, and could be used as raw material to produce food and beverages in food industry due to its high nutritional value. In this study, we adopted widely targeted metabolomics to identify 822 and 694 metabolites in the leaves of S. salsa and S. europaea, respectively, to provide a basic data for the future development and utilization of these two species. We found that these two plants were rich in metabolic components with high medical value, such as flavonoids, alkaloids and coumarins. The high contents of branched chain amino acid in these two species may be an important factor for their adaptation to saline-alkali environments. In addition, the contents of glucosamine (FC = 7.70), maltose (FC = 9.34) and D-(+)-sucrose (FC = 7.19) increased significantly, and the contents of D-(+)-glucose, 2-propenyl (sinigrin) and fructose 1-phosphate were significantly increased in the leaves of S. salsa compared to S. europaea, indicating that some certain compounds in different plants have different sensitivity to salt stress. Our work provides new perspectives about important second metabolism pathways in salt tolerance between these two plants, which could be helpful for studying the tolerance mechanisms of wetland plants.

H2O2 priming promotes salt tolerance in maize by protecting chloroplasts ultrastructure and primary metabolites modulation

Hydrogen peroxide priming has emerged as a powerful strategy to trigger multiple responses involved in plant acclimation that reinforce tolerance to abiotic stresses, including salt stress. Thus, this study aimed to investigate the impact of foliar H₂O₂ priming on the physiological, biochemical, and ultrastructural traits related to photosynthesis of salt-stressed plants. Besides, we provided comparative leaf metabolomic profiles of Zea mays plants under such conditions. For this, H₂O or H₂O₂ pretreated plants were grown under saline conditions for 12-days. Salinity drastically affected photosynthetic parameters and structural chloroplasts integrity, also increased reactive oxygen species contents promoting disturbance in the plant metabolism when compared to non-saline conditions. Our results suggest that H₂O₂-pretreated plants improved photosynthetic performance avoiding salinity-induced energy excess and ultrastructural damage by preserving stacking thylakoids. It displayed modulation of some metabolites, as arabitol, glucose, asparagine, and tyrosine, which may contribute to the maintenance of osmotic balance and reduced oxidative stress. Hence, our study brings new insights into an understanding of plant acclimation to salinity by H₂O₂ priming based on photosynthesis maintenance and metabolite modulation.

Comprehensive identification of non-volatile bitter-tasting compounds in Zanthoxylum bungeanum Maxim. by untargeted metabolomics combined with sensory-guided fractionation technique

Zanthoxylum Bungeanum Maxim. is an important seasoning in Chinese cooking, but its bitter taste limits its use by some consumers. In this study, metabolomic analysis based on ultra-high-performance liquid chromatograph-tandem mass spectrometry (UPLC-MS) was used to screen out a vast number of potential non-volatile bitter compounds in Z. bungeanum. Results showed that there were 37 potential bitter compounds in Z. bungeanum, and possible mechanisms underlying its bitter taste were provided. Further, instrumental analyses combined with sensory evaluation were used to identify the key bitter compounds in Gou jiao, a wild variant of Z. Bungeanum with a strong bitter taste. Totally 15 key bitter compounds were identified, most of which have a low bitterness recognition threshold. This study is the first comprehensive identification of non-volatile bitter compounds in Z. bungeanum and provides a basis for future investigations into mitigating bitterness and uncovering how the interaction between different bitter compounds affects taste.

Comparative Transcriptome, Metabolome, and Ionome Analysis of Two Contrasting Common Bean Genotypes in Saline Conditions

Soil salinity is a major abiotic stress factor that limits agricultural productivity worldwide, and this problem is expected to grow in the future. Common bean is an important protein source in developing countries however highly susceptible to salt stress. To understand the underlying mechanism of salt stress responses, transcriptomics, metabolomics, and ion content analysis were performed on both salt-tolerant and susceptible common bean genotypes in saline conditions. Transcriptomics has demonstrated increased photosynthesis in saline conditions for tolerant genotype while the susceptible genotype acted in contrast. Transcriptome also displayed active carbon and amino-acid metabolism for the tolerant genotype. Analysis of metabolites with GC-MS demonstrated the boosted carbohydrate metabolism in the tolerant genotype with increased sugar content as well as better amino-acid metabolism. Accumulation of lysine, valine, and isoleucine in the roots of the susceptible genotype suggested a halted stress response. According to ion content comparison, the tolerant genotype managed to block accumulation of Na⁺ in the leaves while accumulating significantly less Na⁺ in the roots compared to susceptible genotype. K⁺ levels increased in the leaves of both genotype and the roots of the susceptible one but dropped in the roots of the tolerant genotype. Additionally, Zn⁺² and Mn⁺² levels were dropped in the tolerant roots, while Mo⁺² levels were significantly higher in all tissues in both control and saline conditions for tolerant genotype. The results of the presented study have demonstrated the differences in contrasting genotypes and thus provide valuable information on the pivotal molecular mechanisms underlying salt tolerance.

Molecular and physiological characterization of the monosaccharide transporters gene family in Medicago truncatula

Monosaccharide transporters (MSTs) represent key components of the carbon transport and partitioning mechanisms in plants, mediating the cell-to-cell and long-distance distribution of a wide variety of monosaccharides. In this study, we performed a thorough structural, molecular, and physiological characterization of the monosaccharide transporter gene family in the model legume Medicago truncatula. The complete set of MST family members was identified with a novel bioinformatic approach. Prolonged darkness was used as a test condition to identify the relevant transcriptomic and metabolic responses combining MST transcript profiling and metabolomic analysis. Our results suggest that MSTs play a pivotal role in the efficient partitioning and utilization of sugars, and possibly in the mechanisms of carbon remobilization in nodules upon photosynthate-limiting conditions, as nodules are forced to acquire a new role as a source of both C and N.

Identification of Alternative Mitochondrial Electron Transport Pathway Components in Chickpea Indicates a Differential Response to Salinity Stress between Cultivars

All plants contain an alternative electron transport pathway (AP) in their mitochondria, consisting of the alternative oxidase (AOX) and type 2 NAD(P)H dehydrogenase (ND) families, that are thought to play a role in controlling oxidative stress responses at the cellular level. These alternative electron transport components have been extensively studied in plants like Arabidopsis and stress inducible isoforms identified, but we know very little about them in the important crop plant chickpea. Here we identify AP components in chickpea (Cicer arietinum) and explore their response to stress at the transcript level. Based on sequence similarity with the functionally characterized proteins of Arabidopsis thaliana, five putative internal (matrix)-facing NAD(P)H dehydrogenases (CaNDA1-4 and CaNDC1) and four putative external (inter-membrane space)-facing NAD(P)H dehydrogenases (CaNDB1-4) were identified in chickpea. The corresponding activities were demonstrated for the first time in purified mitochondria of chickpea leaves and roots. Oxidation of matrix NADH generated from malate or glycine in the presence of the Complex I inhibitor rotenone was high compared to other plant species, as was oxidation of exogenous NAD(P)H. In leaf mitochondria, external NADH oxidation was stimulated by exogenous calcium and external NADPH oxidation was essentially calcium dependent. However, in roots these activities were low and largely calcium independent. A salinity experiment with six chickpea cultivars was used to identify salt-responsive alternative oxidase and NAD(P)H dehydrogenase gene transcripts in leaves from a three-point time series. An analysis of the Na:K ratio and Na content separated these cultivars into high and low Na accumulators. In the high Na accumulators, there was a significant up-regulation of CaAOX1, CaNDB2, CaNDB4, CaNDA3 and CaNDC1 in leaf tissue under long term stress, suggesting the formation of a stress-modified form of the mitochondrial electron transport chain (mETC) in leaves of these cultivars. In particular, stress-induced expression of the CaNDB2 gene showed a striking positive correlation with that of CaAOX1 across all genotypes and time points. The coordinated salinity-induced up-regulation of CaAOX1 and CaNDB2 suggests that the mitochondrial alternative pathway of respiration is an important facet of the stress response in chickpea, in high Na accumulators in particular, despite high capacities for both of these activities in leaf mitochondria of non-stressed chickpeas.

Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era

Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority. The rise of -omics approaches provides key strategies to promote effective research in the field, facilitating the investigations from reference models to an increasing number of species, tolerant and sensitive genotypes. Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now feasible, expanding the opportunities to clarify key molecular aspects involved in responses to abiotic stresses. To this aim, bioinformatics has become fundamental for data production, mining and integration, and necessary for extracting valuable information and for comparative efforts, paving the way to the modeling of the involved processes. We provide here an overview of bioinformatics resources for research on plant abiotic stresses, describing collections from -omics efforts in the field, ranging from raw data to complete databases or platforms, highlighting opportunities and still open challenges in abiotic stress research based on -omics technologies.

Comparative non-targeted metabolomic analysis reveals insights into the mechanism of rice yellowing

Yellowing of rice during storage is a highly concerned issue for managing rice quality whereas the yellowing mechanism is not clearly elucidated so far. Thus, the comparative untargeted metabolomic analysis was performed in this study. The results revealed that glycolysis pathway and tricarboxylic acid cycle (TCA) were significantly enhanced in yellowed rice, indicating the activated energy metabolism was trigged during the yellowing process. In addition, the increased aromatic compounds (4-hydroxycinnamic acid and benzoic acid) and their precursors (phenylalanine, tyrosine) suggested the activation of shikimate-phenylpropanoid biosynthesis in yellowed rice, which is an antioxidant defense related pathway. In particular, the pathways involved in the metabolism of glutamate and arginine also significantly altered in yellowed rice. Therefore, the enriched pathways of increased amino acids, sugars, sugar alcohols, and intermediates of the TCA cycle during yellowing process are proposed to be associated with the response of heat and dry induced by the yellowing process.

Stress and defense responses in plant secondary metabolites production

In the growth condition(s) of plants, numerous secondary metabolites (SMs) are produced by them to serve variety of cellular functions essential for physiological processes, and recent increasing evidences have implicated stress and defense response signaling in their production. The type and concentration(s) of secondary molecule(s) produced by a plant are determined by the species, genotype, physiology, developmental stage and environmental factors during growth. This suggests the physiological adaptive responses employed by various plant taxonomic groups in coping with the stress and defensive stimuli. The past recent decades had witnessed renewed interest to study abiotic factors that influence secondary metabolism during in vitro and in vivo growth of plants. Application of molecular biology tools and techniques are facilitating understanding the signaling processes and pathways involved in the SMs production at subcellular, cellular, organ and whole plant systems during in vivo and in vitro growth, with application in metabolic engineering of biosynthetic pathways intermediates.

Transcriptomic profiling and analysis of differentially expressed genes in asparagus bean (Vigna unguiculata ssp. sesquipedalis) under salt stress

Asparagus bean (Vigna unguiculata ssp. sesquipedalis) is a warm season legume which is widely distributed over subtropical regions and semiarid areas. It is mainly grown as a significant protein source in developing countries. Salinity, as one of the main abiotic stress factors, constrains the normal growth and yield of asparagus bean. This study used two cultivars (a salt-sensitive genotype and a salt-tolerant genotype) under salt stress vs. control to identify salt-stress-induced genes in asparagus bean using RNA sequencing. A total of 692,086,838 high-quality clean reads, assigned to 121,138 unigenes, were obtained from control and salt-treated libraries. Then, 216 root-derived DEGs (differentially expressed genes) and 127 leaf-derived DEGs were identified under salt stress between the two cultivars. Of these DEGs, thirteen were assigned to six transcription factors (TFs), including AP2/EREBP, CCHC(Zn), C2H2, WRKY, WD40-like and LIM. GO analysis indicated four DEGs might take effects on the "oxidation reduction", "transport" and "signal transduction" process. Moreover, expression of nine randomly-chosen DEGs was verified by quantitative real-time-PCR (qRT-PCR) analysis. Predicted function of the nine tested DEGs was mainly involved in the KEGG pathway of cation transport, response to osmotic stress, and phosphorelay signal transduction system. A salt-stress-related pathway of "SNARE interactions in vesicular transport" was concerned. As byproducts, 15, 321 microsatellite markers were found in all the unigenes, and 17 SNP linked to six salt-stress induced DEGs were revealed. These candidate genes provide novel insights for understanding the salt tolerance mechanism of asparagus bean in the future.

Metabolic alterations in conventional and genetically modified soybean plants with GmDREB2A;2 FL and GmDREB2A;2 CA transcription factors during water deficit

Water deficit is one of the main abiotic stress that affects plant growth and productivity. The GmDREB2A;2 (Glyma14g06080) gene is an important transcription factor involved in regulating the plants' responses under water deficit. In previous studies, soybean plants overexpressing full-length (GmDREB2A;2 FL) and constitutively active (GmDREB2A;2 CA) forms of the GmDREB2A;2 gene, presented higher tolerance to water deficit when compared with the conventional cultivar BRS 283. Therefore, identifying the changes in metabolite profile in these tolerant genotypes can contribute to the understanding of the metabolic pathways involved in the tolerance mechanism. In this work, the metabolic changes in roots and leaves of genetically modified (GM) soybean plants subjected to water deficit were elucidated by 1H-NMR spectroscopy. Three events were analyzed, one containing the gene in FL form (GmDREB2A;2 FL) and two presenting its CA form (GmDREB2A;2 CA-1 and GmDREB2A;2 CA-2) and compared with the conventional cultivar BRS 283. The results indicated different responses between leaves and roots for all genotypes. Most of these metabolic variations were related to carbohydrate and amino acid pathways. BRS 283 stood out with higher accumulation of amino acids in leaves under water deficit. The results also showed that the events GmDREB2A;2 FL and GmDREB2A;2 CA-1 presented higher concentrations of β-glucose and fructose in leaves, whereas BRS 283 accumulated more sucrose and pinitol. In roots, the GM events accumulated higher β-glucose, fructose, asparagine and phenylalanine, when compared with the conventional cultivar. These insights can add information on how the transcription factor (TF) DREB2A acts in soybean plants triggering and controlling a network of complex responses to drought.

Metabolomics in Plant Stress Physiology

Metabolomics is an essential technology for functional genomics and systems biology. It plays a key role in functional annotation of genes and understanding towards cellular and molecular, biotic and abiotic stress responses. Different analytical techniques are used to extend the coverage of a full metabolome. The commonly used techniques are NMR, CE-MS, LC-MS, and GC-MS. The choice of a suitable technique depends on the speed, sensitivity, and accuracy. This chapter provides insight into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics. It also describes the workflow of measuring metabolites in plants. Metabolomic studies in plant responses to stress are a key research topic in many laboratories worldwide. We summarize different approaches and provide a generic overview of stress responsive metabolite markers and processes compiled from a broad range of different studies. Graphical Abstract.

Multi-omic and physiologic approach to understand Lotus japonicus response upon exposure to 3,4 dimethylpyrazole phosphate nitrification inhibitor

Nitrogen fertilization is a major force in global greenhouse gases emissions and causes environmental contamination through nitrate leaching. The use of nitrification inhibitors has been proven successful to mitigate these effects. However, there is an increasing concern about the undesired effects that their potential persistence in the soil or accumulation in plants may provoke. In this study, we first exposed Lotus japonicus plants to high amounts of 3,4 dimethylpyrazole phosphate (DMPP) and 2-(N-3,4-dimethyl-1H-pyrazol-1-yl) succinic acid isomeric mixture (DMPSA) nitrification inhibitors. Exposure to doses higher than 1 mg·L^-1 provoked DMPP accumulation mostly in the aerial part, while DMPSA was only detected from 10 mg·L^-1 and nearly no translocation. To evaluate the effect that DMPP accumulation in leaves may provoke on plant performance we combined a transcriptome, proteome, and physiological analysis in plants treated with 10 mg/ L of DMPP. This treatment provoked changes in the expression of 229 genes and 59 proteins. Overall, we evidence that when DMPP accumulates in leaves it induces stress responses, notably provoking changes in cell redox balance, hormone signaling, protein synthesis and turnover and carbon and nitrogen metabolism.

Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes

Sustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on 'adaptive traits' that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping-genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated "omics-assisted" approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.

Multi-tissue integration of transcriptomic and specialized metabolite profiling provides tools for assessing the common bean (Phaseolus vulgaris) metabolome

Common bean (Phaseolus vulgaris L.) is an important legume species with a rich natural diversity of landraces that originated from the wild forms following multiple independent domestication events. After the publication of its genome, several resources for this relevant crop have been made available. A comprehensive characterization of specialized metabolism in P. vulgaris, however, is still lacking. In this study, we used a metabolomics approach based on liquid chromatography-mass spectrometry to dissect the chemical composition at a tissue-specific level in several accessions of common bean belonging to different gene pools. Using a combination of literature search, mass spectral interpretation, 13 C-labeling, and correlation analyses, we were able to assign chemical classes and/or putative structures for approximately 39% of all measured metabolites. Additionally, we integrated this information with transcriptomics data and phylogenetic inference from multiple legume species to reconstruct the possible metabolic pathways and identify sets of candidate genes involved in the biosynthesis of specialized metabolites. A particular focus was given to flavonoids, triterpenoid saponins and hydroxycinnamates, as they represent metabolites involved in important ecological interactions and they are also associated with several health-promoting benefits when integrated into the human diet. The data are presented here in the form of an accessible resource that we hope will set grounds for further studies on specialized metabolism in legumes.

Exogenous silicon alters organic acid production and enzymatic activity of TCA cycle in two NaCl stressed indica rice cultivars

The activities of TCA cycle enzymes viz., pyruvate dehydrogenase, citrate synthase, isocitrate dehydrogenase, succinate dehydrogenase and malate dehydrogenase as well as levels of different organic acids viz., pyruvic acid, citric acid, succinic acid and malic acid were studied in two rice cultivars viz. cv. Nonabokra and cv. MTU 1010 differing in salt tolerance grown under 25, 50 and 100 mM NaCl salinity levels. A contrasting response to salt stress on enzyme activities of TCA cycle and accumulation of organic acid was observed between two cultivars during twenty-one days period of study. Salinity caused enhanced organic acid production and increase in all five enzyme activities in cv. Nonabokra whereas in cv. MTU 1010 decrease in both organic acid production and enzymes activities were noted. Joint application of exogenous silicon along with NaCl, altered the organic acids levels and activities of enzymes in both cultivars of rice seedlings conferring tolerance against salt induced stress. Rice cv. MTU 1010 showed better response to exogenous silicon on parameters tested compared to cv. Nonabokra.

Genomic structure and expression of alternative oxidase genes in legumes

Mitochondria isolated from chickpea (Cicer arietinum) possess substantial alternative oxidase (AOX) activity, even in non-stressed plants, and one or two AOX protein bands were detected immunologically, depending on the organ. Four different AOX isoforms were identified in the chickpea genome: CaAOX1 and CaAOX2A, B and D. CaAOX2A was the most highly expressed form and was strongly expressed in photosynthetic tissues, whereas CaAOX2D was found in all organs examined. These results are very similar to those of previous studies with soybean and siratro. Searches of available databases showed that this pattern of AOX genes and their expression was common to at least 16 different legume species. The evolution of the legume AOX gene family is discussed, as is the in vivo impact of an inherently high AOX capacity in legumes on growth and responses to environmental stresses.

Ion-dependent metabolic responses of Vicia faba L. to salt stress

Salt-affected farmlands are increasingly burdened by chlorides, carbonates, and sulfates of sodium, calcium, and magnesium. Intriguingly, the underlying physiological processes are studied almost always under NaCl stress. Two faba bean cultivars were subjected to low- and high-salt treatments of NaCl, Na₂ SO₄ , and KCl. Assimilation rate and leaf water vapor conductance were reduced to approximately 25-30% without biomass reduction after 7 days salt stress, but this did not cause severe carbon shortage. The equimolar treatments of Na⁺ , K⁺ , and Cl^- showed comparable accumulation patterns in leaves and roots, except for SO₄^2- which did not accumulate. To gain a detailed understanding of the effects caused by the tested ion combinations, we performed nontargeted gas chromatography-mass spectrometry-based metabolite profiling. Metabolic responses to various salts were in part highly linearly correlated, but only a few metabolite responses were common to all salts and in both cultivars. At high salt concentrations, only myo-inositol, allantoin, and glycerophosphoglycerol were highly significantly increased in roots under all tested conditions. We discovered several metabolic responses that were preferentially associated with the presence of Na⁺ , K⁺ , or Cl^- . For example, increases of leaf proline and decreases of leaf fumaric acid and malic acid were apparently associated with Cl^- accumulation.

The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance

Solanum pimpinellifolium, a wild relative of cultivated tomato, offers a wealth of breeding potential for desirable traits such as tolerance to abiotic and biotic stresses. Here, we report the genome assembly and annotation of S. pimpinellifolium 'LA0480.' Moreover, we present phenotypic data from one field experiment that demonstrate a greater salinity tolerance for fruit- and yield-related traits in S. pimpinellifolium compared with cultivated tomato. The 'LA0480' genome assembly size (811 Mb) and the number of annotated genes (25,970) are within the range observed for other sequenced tomato species. We developed and utilized the Dragon Eukaryotic Analyses Platform (DEAP) to functionally annotate the 'LA0480' protein-coding genes. Additionally, we used DEAP to compare protein function between S. pimpinellifolium and cultivated tomato. Our data suggest enrichment in genes involved in biotic and abiotic stress responses. To understand the genomic basis for these differences in S. pimpinellifolium and S. lycopersicum, we analyzed 15 genes that have previously been shown to mediate salinity tolerance in plants. We show that S. pimpinellifolium has a higher copy number of the inositol-3-phosphate synthase and phosphatase genes, which are both key enzymes in the production of inositol and its derivatives. Moreover, our analysis indicates that changes occurring in the inositol phosphate pathway may contribute to the observed higher salinity tolerance in 'LA0480.' Altogether, our work provides essential resources to understand and unlock the genetic and breeding potential of S. pimpinellifolium, and to discover the genomic basis underlying its environmental robustness.

Integrating transcriptomic techniques and k-means clustering in metabolomics to identify markers of abiotic and biotic stress in Medicago truncatula

INTRODUCTION

Nitrogen-fixing legumes are invaluable crops, but are sensitive to physical and biological stresses. Whilst drought and infection from the soil-borne pathogen Fusarium oxysporum have been studied individually, their combined effects have not been widely investigated.

OBJECTIVES

We aimed to determine the effect of combined stress using methods usually associated with transcriptomics to detect metabolic differences between treatment groups that could not be identified by more traditional means, such as principal component analysis and partial least squares discriminant analysis.

METHODS

Liquid chromatography-high resolution mass spectrometry data from the root and leaves of model legume Medicago truncatula were analysed using Gaussian Process 2-Sample Test, k-means cluster analysis and temporal clustering by affinity propagation.

RESULTS

Metabolic differences were detected: we identified known stress markers, including changes in concentration for sucrose and citric acid, and showed that combined stress can exacerbate the effect of drought. Changes in roots were found to be smaller than those in leaves, but differences due to Fusarium infection were identified. The transfer of sucrose from leaves to roots can be seen in the time series using transcriptomic techniques with the metabolomics time series. Other metabolite concentrations that change as a result of treatment include phosphoric acid, malic acid and tetrahydroxychalcone.

CONCLUSIONS

Probing metabolomic data with transcriptomic tools provides new insights and could help to identify resilient plant varieties, thereby increasing future crop yield and improving food security.

Transcriptomic analysis of Aegilops tauschii during long-term salinity stress

Aegilops tauschii is the diploid progenitor of the bread wheat D-genome. It originated from Iran and is a source of abiotic stress tolerance genes. However, little is known about the molecular events of salinity tolerance in Ae. tauschii. This study investigates the leaf transcriptional changes associated with long-term salt stress. Total RNA extracted from leaf tissues of control and salt-treated samples was sequenced using the Illumina technology, and more than 98 million high-quality reads were assembled into 255,446 unigenes with an average length of 1398 bp and an N50 of 2269 bp. Functional annotation of the unigenes showed that 93,742 (36.69%) had at least a significant BLAST hit in the SwissProt database, while 174,079 (68.14%) showed significant similarity to proteins in the NCBI nr database. Differential expression analysis identified 4506 salt stress-responsive unigenes. Bioinformatic analysis of the differentially expressed unigenes (DEUs) revealed a number of biological processes and pathways involved in the establishment of ion homeostasis, signaling processes, carbohydrate metabolism, and post-translational modifications. Fine regulation of starch and sucrose content may be important features involved in salt tolerance in Ae. tauschii. Moreover, 82% of DEUs mapped to the D-subgenome, including known QTL for salt tolerance, and these DEUs showed similar salt stress responses in other accessions of Ae. tauschii. These results could provide fundamental insight into the regulatory process underlying salt tolerance in Ae. tauschii and wheat and facilitate identification of genes involved in their salt tolerance mechanisms.

Comparative assessment of chloroplast transcriptional responses highlights conserved and unique patterns across Triticeae members under salt stress

Chloroplast functional genomics, in particular understanding the chloroplast transcriptional response is of immense importance mainly due to its role in oxygenic photosynthesis. As a photosynthetic unit, its efficiency and transcriptional activity is directly regulated by reactive oxygen species during abiotic and biotic stress and subsequently affects carbon assimilation, and plant biomass. In crops, understanding photosynthesis is crucial for crop domestication by identifying the traits that could be exploited for crop improvement. Transcriptionally and translationally active chloroplast plays a key role by regulating the PSI and PSII photo-reaction centres, which ubiquitously affects the light harvesting. Using a comparative transcriptomics mapping approach, we identified differential regulation of key chloroplast genes during salt stress across Triticeae members with potential genes involved in photosynthesis and electron transport system such as CytB6f. Apart from differentially regulated genes involved in PSI and PSII, we found widespread evidence of intron splicing events, specifically uniquely spliced petB and petD in Triticum aestivum and high proportion of RNA editing in ndh genes across the Triticeae members during salt stress. We also highlight the role and differential regulation of ATP synthase as member of CF₀CF₁ and also revealed the effect of salt stress on the water-splitting complex under salt stress. It is worthwhile to mention that the observed conserved down-regulation of psbJ across the Triticeae is limiting the assembly of water-splitting complexes and thus making the BEP clade Triticeae members more vulnerable to high light during the salt stress. Comparative understanding of the chloroplast transcriptional dynamics and photosynthetic regulation will improve the approaches for improved crop domestication.

Rhizosphere Protists Change Metabolite Profiles in Zea mays

Plant growth and productivity depend on the interactions of the plant with the associated rhizosphere microbes. Rhizosphere protists play a significant role in this respect: considerable efforts have been made in the past to reveal the impact of protist-bacteria interactions on the remobilization of essential nutrients for plant uptake, or the grazing induced changes on plant-growth promoting bacteria and the root-architecture. However, the metabolic responses of plants to the presence of protists or to protist-bacteria interactions in the rhizosphere have not yet been analyzed. Here we studied in controlled laboratory experiments the impact of bacterivorous protists in the rhizosphere on maize plant growth parameters and the bacterial community composition. Beyond that we investigated the induction of plant biochemical responses by separately analyzing above- and below-ground metabolite profiles of maize plants incubated either with a soil bacterial inoculum or with a mixture of soil bacteria and bacterivorous protists. Significantly distinct leaf and root metabolite profiles were obtained from plants which grew in the presence of protists. These profiles showed decreased levels of a considerable number of metabolites typical for the plant stress reaction, such as polyols, a number of carbohydrates and metabolites connected to phenolic metabolism. We assume that this decrease in plant stress is connected to the grazing induced shifts in rhizosphere bacterial communities as shown by distinct T-RFLP community profiles. Protist grazing had a clear effect on the overall bacterial community composition, richness and evenness in our microcosms. Given the competition of plant resource allocation to either defense or growth, we propose that a reduction in plant stress levels caused directly or indirectly by protists may be an additional reason for corresponding positive effects on plant growth.

De novo transcriptome assembly and identification of salt-responsive genes in sugar beet M14

Sugar beet (Beta vulgaris) is an important crop of sugar production in the world. Previous studies reported that sugar beet monosomic addition line M14 obtained from the intercross between Beta vulgaris L. (cultivated species) and B. corolliflora Zoss (wild species) exhibited tolerance to salt (up to 0.5 M NaCl) stress. To estimate a broad spectrum of genes involved in the M14 salt tolerance will help elucidate the molecular mechanisms underlying salt stress. Comparative transcriptomics was performed to monitor genes differentially expressed in the leaf and root samples of the sugar beet M14 seedlings treated with 0, 200 and 400 mM NaCl, respectively. Digital gene expression revealed that 3856 unigenes in leaves and 7157 unigenes in roots were differentially expressed under salt stress. Enrichment analysis of the differentially expressed genes based on GO and KEGG databases showed that in both leaves and roots genes related to regulation of redox balance, signal transduction, and protein phosphorylation were differentially expressed. Comparison of gene expression in the leaf and root samples treated with 200 and 400 mM NaCl revealed different mechanisms for coping with salt stress. In addition, the expression levels of nine unigenes in the reactive oxygen species (ROS) scavenging system exhibited significant differences in the leaves and roots. Our transcriptomics results have provided new insights into the salt-stress responses in the leaves and roots of sugar beet.

Distinct Lotus japonicus Transcriptomic Responses to a Spectrum of Bacteria Ranging From Symbiotic to Pathogenic

Lotus japonicus is a well-studied nodulating legume and a model organism for the investigation of plant-microbe interactions. The majority of legume transcriptome studies have focused on interactions with compatible symbionts, whereas responses to non-adapted rhizobia and pathogenic bacteria have not been well-characterized. In this study, we first characterized the transcriptomic response of L. japonicus to its compatible symbiont, Mesorhizobium loti R7A, through RNA-seq analysis of various plant tissues. Early symbiotic signaling was largely Nod factor-dependent and enhanced within root hairs, and we observed large-scale transcriptional reprogramming in nodule primordia and mature nitrogen-fixing nodules. We then characterized root transcriptional responses to a spectrum of L. japonicus interacting bacteria ranging from semi-compatible symbionts to pathogens. M. loti R7A and the semi-compatible strain Sinorhizobium fredii HH103 showed remarkably similar responses, allowing us to identify a small number of genes potentially involved in differentiating between fully and semi-compatible symbionts. The incompatible symbiont Bradyrhizobium elkanii USDA61 induced a more attenuated response, but the weakest response was observed for the foliar pathogen Pseudomonas syringae pv. tomato DC3000, where the affected genes also responded to other tested bacteria, pointing to a small set of common bacterial response genes. In contrast, the root pathogen Ralstonia solanacearum JS763 induced a pronounced and distinct transcriptomic pathogen response, which we compared to the results of the other treatments. This comparative analysis did not support the concept that an early defense-like response is generally evoked by compatible rhizobia during establishment of symbiosis.