A common metabolomic signature is observed upon inoculation of rice roots with various rhizobacteria

Differentiation of Ayahuasca Samples According to Preparation Mode and Botanical Varieties Using Metabolomics

Ayahuasca is a brew traditionally prepared with a mixture of Psychotria viridis leaves and Banisteriopsis caapi vine and has demonstrated therapeutic properties for depression. Knowledge of the brew composition is important to improve the therapeutic potential and decrease side effects if ayahuasca becomes an option for refractory depression treatment. Ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) was applied to analyze 126 ayahuasca samples collected from different ayahuasqueiro groups and geographic origins. We were able to observe a differentiation in the metabolite composition of ayahuasca samples prepared by diverse ayahuasqueiro groups. These samples presented different antioxidant effects based on FRAP and ORAC assays. Exploratory statistical analysis demonstrated a trend of separating the samples according to the religious group. The most important identified compounds for differentiation of the brew prepared by distinct religious groups are glycosylated and/or phenolic compounds. The comparison based on the mode of ayahuasca preparation presented more variability than the comparison based on the botanical variety of B. caapi used. We conclude that ayahuasca samples prepared with "caupuri" or "tucunacá" separately exhibited differences in the analysis of L-glutamate and the metabolism of arginine and proline. This suggests that a possible variation in this pathway could explain the occurrence of swollen stem nodes in "caupuri," one of the B. caapi varieties.

Physiological and transcriptomic analysis reveals the coating of microcapsules embedded with bacteria can enhance wheat salt tolerance

Salt stress is one of the most important abiotic stress factors limiting crop production. Therefore, improving the stress resistance of seeds is very important for crop growth. Our previous studies have shown that using microcapsules encapsulating bacteria (Pontibacter actiniarum DSM 19842) as seed coating for wheat can alleviate salt stress. In this study, the genes and pathways involved in the response of wheat to salt stress were researched further. The results showed that compared with the control, the coating can improve osmotic stress and decrease oxidative damage by increasing the content of proline (29.1%), the activity of superoxide dismutase (SOD) (94.2%), peroxidase (POD) (45.7%) and catalase (CAT) (3.3%), reducing the content of hydrogen peroxide (H2O2) (39.8%) and malondialdehyde (MDA) (45.9%). In addition, ribonucleic acid (RNA) sequencing data showed that 7628 differentially expressed genes (DEGs) were identified, and 4426 DEGs up-regulated, 3202 down-regulated in the coated treatment. Many DEGs related to antioxidant enzymes were up-regulated, indicating that coating can promote the expression of antioxidant enzyme-related genes and alleviate oxidative damage under salt stress. The differential gene expression analysis demonstrated up-regulation of 27 genes and down-regulation of 20 genes. Transcription factor families, mostly belonging to bHLH, MYB, B3, NAC, and WRKY. Overall, this seed coating can promote the development of sustainable agriculture in saline soil.

Metabolomics analysis of the effects of chelerythrine on Ustilaginoidea virens

Rice false smut (RFS) caused by Ustilaginoidea virens is widely distributed in major rice-producing regions. Previous studies have shown that treating RFS with chelerythrine can decrease the germination of fungus spores by 86.7% and induce fungal cell apoptosis. In the present study, the effects of chelerythrine on the metabolism of U. virens explored using metabolomics and analyses of differentially accumulated metabolites and altered metabolic pathways. The top 15 metabolites in random forest analysis were significantly different between groups. In positive ion mode, purine, phenylalanine metabolism, phenylalanine, tyrosine, tryptophan biosynthesis, pyrimidine metabolism, and nitrogen metabolism were dominant. Alanine, aspartate, glutamate metabolism, and phenylalanine metabolism were enriched in negative ion mode. Differentially expressed genes and altered metabolic pathways of U. virens were effected by chelerythrine. The findings support future research on the prevention and treatment of RFS by chelerythrine and provide a theoretical basis for targeted drug delivery.

Tea-Derived Polyphenols Enhance Drought Resistance of Tea Plants (Camellia sinensis) by Alleviating Jasmonate-Isoleucine Pathway and Flavonoid Metabolism Flow

Extreme drought weather has occurred frequently in recent years, resulting in serious yield loss in tea plantations. The study of drought in tea plantations is becoming more and more intensive, but there are fewer studies on drought-resistant measures applied in actual production. Therefore, in this study, we investigated the effect of exogenous tea polyphenols on the drought resistance of tea plant by pouring 100 mg·L-1 of exogenous tea polyphenols into the root under drought. The exogenous tea polyphenols were able to promote the closure of stomata and reduce water loss from leaves under drought stress. Drought-induced malondialdehyde (MDA) accumulation in tea leaves and roots was also significantly reduced by exogenous tea polyphenols. Combined transcriptomic and metabolomic analyses showed that exogenous tea polyphenols regulated the abnormal responses of photosynthetic and energy metabolism in leaves under drought conditions and alleviated sphingolipid metabolism, arginine metabolism, and glutathione metabolism in the root system, which enhanced the drought resistance of tea seedlings. Exogenous tea polyphenols induced jasmonic acid-isoleucine (JA-ILE) accumulation in the root system, and the jasmonic acid-isoleucine synthetase gene (TEA028623), jasmonic acid ZIM structural domain proteins (JAMs) synthesis genes (novel.22237, TEA001821), and the transcription factor MYC2 (TEA014288, TEA005840) were significantly up-regulated. Meanwhile, the flavonoid metabolic flow was significantly altered in the root; for example, the content of EGCG, ECG, and EGC was significantly increased. Thus, exogenous tea polyphenols enhance the drought resistance of tea plants through multiple pathways.

Metabolomics-driven investigation of plant defense response against pest and pathogen attack

The advancement of metabolomics has assisted in the identification of various bewildering characteristics of the biological system. Metabolomics is a standard approach, facilitating crucial aspects of system biology with absolute quantification of metabolites using minimum samples, based on liquid/gas chromatography, mass spectrometry and nuclear magnetic resonance. The metabolome profiling has narrowed the wide gaps of missing information and has enhanced the understanding of a wide spectrum of plant-environment interactions by highlighting the complex pathways regulating biochemical reactions and cellular physiology under a particular set of conditions. This high throughput technique also plays a prominent role in combined analyses of plant metabolomics and other omics datasets. Plant metabolomics has opened a wide paradigm of opportunities for developing stress-tolerant plants, ensuring better food quality and quantity. However, despite advantageous methods and databases, the technique has a few limitations, such as ineffective 3D capturing of metabolites, low comprehensiveness, and lack of cell-based sampling. In the future, an expansion of plant-pathogen and plant-pest response towards the metabolite architecture is necessary to understand the intricacies of plant defence against invaders, elucidation of metabolic pathway operational during defence and developing a direct correlation between metabolites and biotic stresses. Our aim is to provide an overview of metabolomics and its utilities for the identification of biomarkers or key metabolites associated with biotic stress, devising improved diagnostic methods to efficiently assess pest and pathogen attack and generating improved crop varieties with the help of combined application of analytical and molecular tools.

Identification and profile of phenolamides with anthracnose resistance potential in tea (Camellia sinensis)

Tea anthracnose is a prevalent disease in China that can lead to reduced tea production and lower quality, yet there is currently a lack of effective means for controlling this disease. In this study, we identified 46 phenolamides (including 27 isomers) in different tissues and organs of tea plants based on a developed workflow, and the secondary mass spectra of all these compounds have been documented. It was revealed that tea plants predominantly accumulate protonated aliphatic phenolamides, rather than aromatic phenolamides. The profile of phenolamides indicate that their buildup in tea plants is specific to certain tissues and acyl-acceptors, and this distribution is associated with the extent of phenolamide acyl-modification. Additionally, it was observed that N-Feruloylputrescine (Fer-Put, a type of phenolamides) was responsive to the stimulated accumulation of the tea anthracnose pathogen. The findings of anti-anthracnose experiments in vitro and on tea leaf demonstrated that Fer-Put was capable of significantly inhibiting the growth of anthracnose pathogen colony, effectively prevented tea leaf disease. Furthermore, it was observed that Fer-Put treatment can enhance the antioxidant enzyme activity of tea leaves. TEA002780.1 and TEA013165.1 gene may be responsible for the biosynthesis of Fer-Put in the disease resistance process in tea plants. Through these studies, the types and distribution of phenolamides in tea plants have been elucidated, and Fer-Put's ability to resist anthracnose has been established, providing new insights into the resistance of tea anthracnose.

MarR Family Transcriptional Regulators and Their Roles in Plant-Interacting Bacteria

The relationship between plants and associated soil microorganisms plays a major role in ecosystem functioning. Plant-bacteria interactions involve complex signaling pathways regulating various processes required by bacteria to adapt to their fluctuating environment. The establishment and maintenance of these interactions rely on the ability of the bacteria to sense and respond to biotic and abiotic environmental signals. In this context, MarR family transcriptional regulators can use these signals for transcriptional regulation, which is required to establish adapted responses. MarR-like transcriptional regulators are essential for the regulation of the specialized functions involved in plant-bacteria interactions in response to a wide range of molecules associated with the plant host. The conversion of environmental signals into changes in bacterial physiology and behavior allows the bacteria to colonize the plant and ensure a successful interaction. This review focuses on the mechanisms of plant-signal perception by MarR-like regulators, namely how they (i) allow bacteria to cope with the rhizosphere and plant endosphere, (ii) regulate the beneficial functions of Plant-Growth-Promoting Bacteria and (iii) regulate the virulence of phytopathogenic bacteria.

An Untargeted Metabolomics Approach to Study the Variation between Wild and Cultivated Soybeans

The differential metabolite profiles of four wild and ten cultivated soybeans genotypes were explored using an untargeted metabolomics approach. Ground soybean seed samples were extracted with methanol and water, and metabolic features were obtained using ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-HRMS) in both positive and negative ion modes. The UHPLC-HRMS analysis of the two different extracts resulted in the putative identification of 98 metabolites belonging to several classes of phytochemicals, including isoflavones, organic acids, lipids, sugars, amino acids, saponins, and other compounds. The metabolic profile was significantly impacted by the polarity of the extraction solvent. Multivariate analysis showed a clear difference between wild and cultivated soybean cultivars. Unsupervised and supervised learning algorithms were applied to mine the generated data and to pinpoint metabolites differentiating wild and cultivated soybeans. The key identified metabolites differentiating wild and cultivated soybeans were isoflavonoids, free amino acids, and fatty acids. Catechin analogs, cynaroside, hydroxylated unsaturated fatty acid derivatives, amino acid, and uridine diphosphate-N-acetylglucosamine were upregulated in the methanol extract of wild soybeans. In contrast, isoflavonoids and other minor compounds were downregulated in the same soybean extract. This metabolic information will benefit breeders and biotechnology professionals to develop value-added soybeans with improved quality traits.

Herbaspirillum sp. ZXN111 Colonization Characters to Different Tea Cultivars and the Effects on Tea Metabolites Profiling on Zijuan (Camellia sinensis var. assamica)

Herbaspirillum sp. ZXN111 and its mutants (Δacc, Δtyrb, and Δacc-tyrb), which show PGP activity on Zijuan, were tested for tea plants' colonization characteristics and the strain-dependent response of tea metabolites. The results showed that strain ZXN111 could widely colonize in different tea cultivars of Zijuan, Yunkang-10, Longjin 43, and Shuchazao, but with significant colonization preference to Zijuan, which might be ascribed to anthocyanins' chemotaxis. After 9 weeks of co-cultivation, l-theanine and theobromine in Zijuan leaves that were inoculated with wild-type ZXN111 were decreased, while theobromine, caffeine, and l-theanine that were inoculated with mutant Δacc were increased; especially l-theanine increased much significantly. Metabolomics analysis showed that tea metabolite profiling of inoculant groups was clearly separated from the control; therein, the flavanols were downregulated in ZXN111 and Δacc groups, but the l-theanine of the Δacc group was significantly upregulated compared to control and ZXN111 groups. These results indicated that strain ZXN111, especially of mutant Δacc, improved Zijuan tea flavor.

Application of depolymerized chitosan in crop production: A review

Currently, chitosan (CHT) is well known for its uses, particularly in veterinary and agricultural fields. However, chitosan's uses suffer greatly due to its extremely solid crystalline structure, it is insoluble at pH levels above or equal to 7. This has sped up the process of derivatizing and depolymerizing it into low molecular weight chitosan (LMWCHT). As a result of its diverse physicochemical as well as biological features which include antibacterial activity, non-toxicity, and biodegradability, LMWCHT has evolved into new biomaterials with extremely complex functions. The most important physicochemical and biological property is antibacterial, which has some degree of industrialization today. CHT and LMWCHT have potential due to the antibacterial and plant resistance-inducing properties when applied in crop production. This study has highlighted the many advantages of chitosan derivatives as well as the most recent studies on low molecular weight chitosan applications in crop development.

PGPR: the treasure of multifarious beneficial microorganisms for nutrient mobilization, pest biocontrol and plant growth promotion in field crops

Plant growth-promoting rhizobacteria (PGPR) have multifarious beneficial activities for plant growth promotion; act as source of metabolites, enzymes, nutrient mobilization, biological control of pests, induction of disease resistance vis-a-vis bioremediation potentials by phytoextraction and detoxification of heavy metals, pollutants and pesticides. Agrochemicals and synthetic pesticides are currently being utilized widely in all major field crops, thereby adversely affecting human and animal health, and posing serious threats to the environments. Beneficial microorganisms like PGPR could potentially substitute and supplement the toxic chemicals and pesticides with promising application in organic farming leading to sustainable agriculture practices and bioremediation of heavy metal contaminated sites. Among field crops limited bio-formulations have been prepared till now by utilization of PGPR strains having plant growth promotion, metabolites, enzymes, nutrient mobilization and biocontrol activities. The present review contributes comprehensive description of PGPR applications in field crops including commercial, oilseeds, leguminous and cereal crops to further extend the utilization of these potent groups of beneficial microorganisms so that even higher level of crop productivity and quality produce of field crops could be achieved. PGPR and bacteria based commercialized bio-formulations available worldwide for its application in the field crops have been compiled in this review which can be a substitute for the harmful synthetic chemicals. The current knowledge gap and potential target areas for future research have also been projected.

Mutations in Rht-B1 Locus May Negatively Affect Frost Tolerance in Bread Wheat

The wheat semi-dwarfing genes Rht (Reduced height) are widely distributed among the contemporary wheat varieties. These genes also exert pleiotropic effects on plant tolerance towards various abiotic stressors. In this work, frost tolerance was studied in three near-isogenic lines of the facultative variety ‘April Bearded’ (AB), carrying the wild type allele Rht-B1a (tall phenotype), and the mutant alleles Rht-B1b (semi-dwarf) and Rht-B1c (dwarf), and was further compared with the tolerance of a typical winter type variety, ‘Mv Beres’. The level of freezing tolerance was decreasing in the order ‘Mv Beres’ > AB Rht-B1a > AB Rht-B1b > AB Rht-B1c. To explain the observed differences, cold acclimation-related processes were studied: the expression of six cold-related genes, the phenylpropanoid pathway, carbohydrates, amino acids, polyamines and compounds in the tricarboxylic acid cycle. To achieve this, a comprehensive approach was applied, involving targeted analyses and untargeted metabolomics screening with the help of gas chromatography/liquid chromatography—mass spectrometry setups. Several cold-related processes exhibited similar changes in these genotypes; indeed, the accumulation of eight putrescine and agmatine derivatives, 17 flavones and numerous oligosaccharides (max. degree of polymerization 18) was associated with the level of freezing tolerance in the ‘April Bearded’ lines. In summary, the mutant Rht alleles may further decrease the generally low frost tolerance of the Rht-B1a, and, based on the metabolomics study, the mechanisms of frost tolerance may differ for a typical winter variety and a facultative variety. Present results point to the complex nature of frost resistance.

The Role of Hydroxycinnamic Acid Amide Pathway in Plant Immunity

The compounds involved in the hydroxycinnamic acid amide (HCAA) pathway are an important class of metabolites in plants. Extensive studies have reported that a variety of plant hydroxycinnamamides exhibit pivotal roles in plant-pathogen interactions, such as p-coumaroylagmatine and ferulic acid. The aim of this review is to discuss the emerging findings on the functions of hydroxycinnamic acid amides (HCAAs) accumulation associated with plant defenses against plant pathologies, antimicrobial activity of HCAAs, and the mechanism of HCAAs involved in plant immune responses (such as reactive oxygen species (ROS), cell wall response, plant defense hormones, and stomatal immunity). However, these advances have also revealed the complexity of HCAAs participation in plant defense reactions, and many mysteries remain to be revealed. This review provides an overview of the mechanistic and conceptual insights obtained so far and highlights areas for future exploration of phytochemical defense metabolites.

Metabolomics as an emerging tool to study plant-microbe interactions

In natural environments, interaction between plant roots and microorganisms are common. These interactions between microbial species and plants inhabited by them are being studied using various techniques. Metabolomics research based on mass spectrometric techniques is one of the crucial approaches that underpins system biology and relies on precision instrument analysis. In the last decade, this emerging field has received extensive attention. It provides a qualitative and quantitative approach for determining the mechanisms of symbiosis of bacteria and fungi with plants and also helps to elucidate the tolerance mechanisms of host plants against various abiotic stresses. However, this -omics application and its tools in plant-microbe interaction studies is still underutilized compared with genomic and transcriptomic methods. Therefore, it is crucial to bring this field forward to bear on the study of plant resistance and susceptibility. This review describes the current status of methods and progress in metabolomics applications for plant-microbe interaction studies discussing current challenges and future prospects.

Piriformospora indica recruits host-derived putrescine for growth promotion in plants

Growth promotion induced by the endosymbiont Piriformospora indica has been observed in various plants; however, except growth phytohormones, specific functional metabolites involved in P. indica-mediated growth promotion are unknown. Here, we used a gas chromatography-mass spectrometry-based untargeted metabolite analysis to identify tomato (Solanum lycopersicum) metabolites whose levels were altered during P. indica-mediated growth promotion. Metabolomic multivariate analysis revealed several primary metabolites with altered levels, with putrescine (Put) induced most significantly in roots during the interaction. Further, our results indicated that P. indica modulates the arginine decarboxylase (ADC)-mediated Put biosynthesis pathway via induction of SlADC1 in tomato. Piriformospora indica did not promote growth in Sladc1-(virus-induced gene silencing of SlADC1) lines of tomato and showed less colonization. Furthermore, using LC-MS/MS we showed that Put promoted growth by elevation of auxin (indole-3-acetic acid) and gibberellin (GA4 and GA7) levels in tomato. In Arabidopsis (Arabidopsis thaliana) adc knockout mutants, P. indica colonization also decreased and showed no plant growth promotion, and this response was rescued upon exogenous application of Put. Put is also important for hyphal growth of P. indica, indicating that it is co-adapted by both host and microbe. Taken together, we conclude that Put is an essential metabolite and its biosynthesis in plants is crucial for P. indica-mediated plant growth promotion and fungal growth.

Wheat Metabolite Interferences on Fluorescent Pseudomonas Physiology Modify Wheat Metabolome through an Ecological Feedback

Plant roots exude a wide variety of secondary metabolites able to attract and/or control a large diversity of microbial species. In return, among the root microbiota, some bacteria can promote plant development. Among these, Pseudomonas are known to produce a wide diversity of secondary metabolites that could have biological activity on the host plant and other soil microorganisms. We previously showed that wheat can interfere with Pseudomonas secondary metabolism production through its root metabolites. Interestingly, production of Pseudomonas bioactive metabolites, such as phloroglucinol, phenazines, pyrrolnitrin, or acyl homoserine lactones, are modified in the presence of wheat root extracts. A new cross metabolomic approach was then performed to evaluate if wheat metabolic interferences on Pseudomonas secondary metabolites production have consequences on wheat metabolome itself. Two different Pseudomonas strains were conditioned by wheat root extracts from two genotypes, leading to modification of bacterial secondary metabolites production. Bacterial cells were then inoculated on each wheat genotypes. Then, wheat root metabolomes were analyzed by untargeted metabolomic, and metabolites from the Adular genotype were characterized by molecular network. This allows us to evaluate if wheat differently recognizes the bacterial cells that have already been into contact with plants and highlights bioactive metabolites involved in wheat—Pseudomonas interaction.

Improving Bambara Groundnut Production: Insight Into the Role of Omics and Beneficial Bacteria

With the rise in the world population, environmental hazards caused by chemical fertilizers, and a decrease in food supply due to global climate change, food security has become very pertinent. In addition, considerable parts of agriculture lands have been lost to urbanization. It has therefore been projected that at the present rate of population increase coupled with the other mentioned factors, available food will not be enough to feed the world. Hence, drastic approach is needed to improve agriculture output as well as human sustainability. Application of environmentally sustainable approach, such as the use of beneficial microbes, and improved breeding of underutilized legumes are one of the proposed sustainable ways of achieving food security. Microbiome-assisted breeding in underutilized legumes is an untapped area with great capabilities to improve food security. Furthermore, revolution in genomics adaptation to crop improvement has changed the approach from conventional breeding to more advanced genomic-assisted breeding on the host plant and its microbiome. The use of rhizobacteria is very important to improving crop yield, especially rhizobacteria from legumes like Bambara groundnut (BGN). BGN is an important legume in sub-Saharan Africa with high ability to tolerate drought and thrive well in marginalized soils. BGN and its interaction with various rhizobacteria in the soil could play a vital role in crop production and protection. This review focus on the importance of genomics application to BGN and its microbiome with the view of setting a potential blueprint for improved BGN breeding through integration of beneficial bacteria.

Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management

Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.

Soybean Metabolomics Based in Mass Spectrometry: Decoding the Plant's Signaling and Defense Responses under Biotic Stress

Metabolomics is an omics technology that is extremely valuable to analyze all small-molecule metabolites in organisms. Recent advances in analytical instrumentation, such as mass spectrometry combined with data processing tools, chemometrics, and spectral data libraries, allow plant metabolomics studies to play a fundamental role in the agriculture field and food security. Few studies are found in the literature using the metabolomics approach in soybean plants on biotic stress. In this review, we provide a new perspective highlighting the potential of metabolomics-based mass spectrometry for soybean in response to biotic stress. Furthermore, we highlight the response and adaptation mechanisms of soybean on biotic stress about primary and secondary metabolism. Consequently, we provide subsidies for further studies of the resistance and improvement of the crop.

Unfinished story of polyamines: Role of conjugation, transport and light-related regulation in the polyamine metabolism in plants

Polyamines play a fundamental role in the functioning of all cells. Their regulatory role in plant development, their function under stress conditions, and their metabolism have been well documented as regards both synthesis and catabolism in an increasing number of plant species. However, the majority of these studies concentrate on the levels of the most abundant polyamines, sometimes providing data on the enzyme activity or gene expression levels during polyamine synthesis, but generally making no mention of the fact that changes in the polyamine pool are very dynamic, and that other processes are also involved in the regulation of actual polyamine levels. Differences in the distribution of individual polyamines and their conjugation with other compounds were described some time ago, but these have been given little attention. In addition, the role of polyamine transporters in plants is only now being recognised. The present review highlights the importance of conjugated polyamines and also points out that investigations should not only deal with the polyamine metabolism itself, but should also cover other important questions, such as the relationship between light perception and the polyamine metabolism, or the involvement of polyamines in the circadian rhythm.

The Metabolic Response of Brachypodium Roots to the Interaction with Beneficial Bacteria Is Affected by the Plant Nutritional Status

The potential of plant growth promoting (PGP) bacteria in improving the performance of plants in suboptimal environments is increasingly acknowledged, but little information is available on the mechanisms underlying this interaction, particularly when plants are subjected to a combination of stresses. In this study, we investigated the effects of the inoculation with the PGP bacteria Azospirillum brasilense (Azospirillum) on the metabolism of the model cereal Brachypodium distachyon (Brachypodium) grown at low temperatures and supplied with insufficient phosphorus. Investigating polar metabolite and lipid fluctuations during early plant development, we found that the bacteria initially elicited a defense response in Brachypodium roots, while at later stages Azospirillum reduced the stress caused by phosphorus deficiency and improved root development of inoculated plants, particularly by stimulating the growth of branch roots. We propose that the interaction of the plant with Azospirillum was influenced by its nutritional status: bacteria were sensed as pathogens while plants were still phosphorus sufficient, but the interaction became increasingly beneficial for the plants as their phosphorus levels decreased. Our results provide new insights on the dynamics of the cereal-PGP bacteria interaction, and contribute to our understanding of the role of beneficial microorganisms in the growth of cereal crops in suboptimal environments.

Antagonistic Interaction between Auxin and SA Signaling Pathways Regulates Bacterial Infection through Lateral Root in Arabidopsis

Pathogen entry into host tissues is a critical and first step in infections. In plants, the lateral roots (LRs) are a potential entry and colonization site for pathogens. Here, using a GFP-labeled pathogenic bacterium Pseudomonas syringae pv. tomato strain DC3000 (Pto DC3000), we observe that virulent Pto DC3000 invades plants through emerged LRs in Arabidopsis. Pto DC3000 strongly induced LR formation, a process that was dependent on the AUXIN RESPONSE FACTOR7 (ARF7)/ARF19-LATERAL ORGAN BOUNDARIES-DOMAIN (LBD) regulatory module. We show that salicylic acid (SA) represses LR formation, and several mutants defective in SA signaling are also involved in Pto DC3000-induced LR development. Significantly, ARF7, a well-documented positive regulator of LR development, directly represses the transcription of PR1 and PR2 to promote LR development. This study indicates that ARF7-mediated auxin signaling antagonizes with SA signaling to control bacterial infection through the regulation of LR development.

Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health

Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.

Proteomics and Metabolomics Studies on the Biotic Stress Responses of Rice: an Update

Biotic stresses represent a serious threat to rice production to meet global food demand and thus pose a major challenge for scientists, who need to understand the intricate defense mechanisms. Proteomics and metabolomics studies have found global changes in proteins and metabolites during defense responses of rice exposed to biotic stressors, and also reported the production of specific secondary metabolites (SMs) in some cultivars that may vary depending on the type of biotic stress and the time at which the stress is imposed. The most common changes were seen in photosynthesis which is modified differently by rice plants to conserve energy, disrupt food supply for biotic stress agent, and initiate defense mechanisms or by biotic stressors to facilitate invasion and acquire nutrients, depending on their feeding style. Studies also provide evidence for the correlation between reactive oxygen species (ROS) and photorespiration and photosynthesis which can broaden our understanding on the balance of ROS production and scavenging in rice-pathogen interaction. Variation in the generation of phytohormones is also a key response exploited by rice and pathogens for their own benefit. Proteomics and metabolomics studies in resistant and susceptible rice cultivars upon pathogen attack have helped to identify the proteins and metabolites related to specific defense mechanisms, where choosing of an appropriate method to identify characterized or novel proteins and metabolites is essential, considering the outcomes of host-pathogen interactions. Despites the limitation in identifying the whole repertoire of responsive metabolites, some studies have shed light on functions of resistant-specific SMs. Lastly, we illustrate the potent metabolites responsible for resistance to different biotic stressors to provide valuable targets for further investigation and application.

Impact of root-associated strains of three Paraburkholderia species on primary and secondary metabolism of Brassica oleracea

Several root-colonizing bacterial species can simultaneously promote plant growth and induce systemic resistance. How these rhizobacteria modulate plant metabolism to accommodate the carbon and energy demand from these two competing processes is largely unknown. Here, we show that strains of three Paraburkholderia species, P. graminis PHS1 (Pbg), P. hospita mHSR1 (Pbh), and P. terricola mHS1 (Pbt), upon colonization of the roots of two Broccoli cultivars led to cultivar-dependent increases in biomass, changes in primary and secondary metabolism and induced resistance against the bacterial leaf pathogen Xanthomonas campestris. Strains that promoted growth led to greater accumulation of soluble sugars in the shoot and particularly fructose levels showed an increase of up to 280-fold relative to the non-treated control plants. Similarly, a number of secondary metabolites constituting chemical and structural defense, including flavonoids, hydroxycinnamates, stilbenoids, coumarins and lignins, showed greater accumulation while other resource-competing metabolite pathways were depleted. High soluble sugar generation, efficient sugar utilization, and suppression or remobilization of resource-competing metabolites potentially contributed to curb the tradeoff between the carbon and energy demanding processes induced by Paraburkholderia-Broccoli interaction. Collectively, our results provide a comprehensive and integrated view of the temporal changes in plant metabolome associated with rhizobacteria-mediated plant growth promotion and induced resistance.

A Cross-Metabolomic Approach Shows that Wheat Interferes with Fluorescent Pseudomonas Physiology through Its Root Metabolites

Roots contain a wide variety of secondary metabolites. Some of them are exudated in the rhizosphere, where they are able to attract and/or control a large diversity of microbial species. In return, the rhizomicrobiota can promote plant health and development. Some rhizobacteria belonging to the Pseudomonas genus are known to produce a wide diversity of secondary metabolites that can exert a biological activity on the host plant and on other soil microorganisms. Nevertheless, the impact of the host plant on the production of bioactive metabolites by Pseudomonas is still poorly understood. To characterize the impact of plants on the secondary metabolism of Pseudomonas, a cross-metabolomic approach has been developed. Five different fluorescent Pseudomonas strains were thus cultivated in the presence of a low concentration of wheat root extracts recovered from three wheat genotypes. Analysis of our metabolomic workflow revealed that the production of several Pseudomonas secondary metabolites was significantly modulated when bacteria were cultivated with root extracts, including metabolites involved in plant-beneficial properties.

A Metabolomic Landscape of Maize Plants Treated With a Microbial Biostimulant Under Well-Watered and Drought Conditions

Microbial plant biostimulants have been successfully applied to improve plant growth, stress resilience and productivity. However, the mechanisms of action of biostimulants are still enigmatic, which is the main bottleneck for the fully realization and implementation of biostimulants into the agricultural industry. Here, we report the elucidation of a global metabolic landscape of maize (Zea mays L) leaves in response to a microbial biostimulant, under well-watered and drought conditions. The study reveals that the increased pool of tricarboxylic acid (TCA) intermediates, alterations in amino acid levels and differential changes in phenolics and lipids are key metabolic signatures induced by the application of the microbial-based biostimulant. These reconfigurations of metabolism gravitate toward growth-promotion and defense preconditioning of the plant. Furthermore, the application of microbial biostimulant conferred enhanced drought resilience to maize plants via altering key metabolic pathways involved in drought resistance mechanisms such as the redox homeostasis, strengthening of the plant cell wall, osmoregulation, energy production and membrane remodeling. For the first time, we show key molecular events, metabolic reprogramming, activated by a microbial biostimulant for plant growth promotion and defense priming. Thus, these elucidated metabolomic insights contribute to ongoing efforts in decoding modes of action of biostimulants and generating fundamental scientific knowledgebase that is necessary for the development of the plant biostimulants industry, for sustainable food security.

Identification of a small set of genes commonly regulated in rice roots in response to beneficial rhizobacteria

Rhizosphere bacteria, whether phytopathogenic or phytobeneficial, are thought to be perceived by the plant as a threat. Plant Growth-Promoting Rhizobacteria (PGPR), such as many strains of the Azospirillum genus known as the main phytostimulator of cereals, cooperate with host plants and favorably affect their growth and health. An earlier study of rice root transcriptome, undertaken with two rice cultivars and two Azospirillum strains, revealed a strain-dependent response during the rice-Azospirillum association and showed that only a few genes, including some implicated in plant defense, were commonly regulated in all tested conditions. Here, a set of genes was selected from previous studies and their expression was monitored by qRT-PCR in rice roots inoculated with ten PGPR strains isolated from various plants and belonging to various genera (Azospirillum, Herbaspirillum, Paraburkholderia). A common expression pattern was highlighted for four genes that are proposed to be markers of the rice-PGPR interaction: two genes involved in diterpenoid phytoalexin biosynthesis (OsDXS3 and OsDTC2) and one coding for an uncharacterized protein (Os02g0582900) were significantly induced by PGPR whereas one defense-related gene encoding a pathogenesis-related protein (PR1b, Os01g0382000) was significantly repressed. Interestingly, exposure to a rice bacterial pathogen also triggered the expression of OsDXS3 while the expression of Os02g0582900 and PR1b was down-regulated, suggesting that these genes might play a key role in rice-bacteria interactions. Integration of these results with previous data led us to propose that the jasmonic acid signaling pathway might be triggered in rice roots upon inoculation with PGPR.

Chitosan Induces Plant Hormones and Defenses in Tomato Root Exudates

In this work, we use electrophysiological and metabolomic tools to determine the role of chitosan as plant defense elicitor in soil for preventing or manage root pests and diseases sustainably. Root exudates include a wide variety of molecules that plants and root microbiota use to communicate in the rhizosphere. Tomato plants were treated with chitosan. Root exudates from tomato plants were analyzed at 3, 10, 20, and 30 days after planting (dap). We found, using high performance liquid chromatography (HPLC) and excitation emission matrix (EEM) fluorescence, that chitosan induces plant hormones, lipid signaling and defense compounds in tomato root exudates, including phenolics. High doses of chitosan induce membrane depolarization and affect membrane integrity. 1H-NMR showed the dynamic of exudation, detecting the largest number of signals in 20 dap root exudates. Root exudates from plants irrigated with chitosan inhibit ca. twofold growth kinetics of the tomato root parasitic fungus Fusarium oxysporum f. sp. radicis-lycopersici. and reduced ca. 1.5-fold egg hatching of the root-knot nematode Meloidogyne javanica.

Metabolomics analysis reveals differences in evolution between maize and rice

Metabolites are the intermediate and final products of metabolism, which play essential roles in plant growth, evolution and adaptation to changing climates. However, it is unclear how evolution contributes to metabolic variation in plants. Here, we investigated the metabolomics data from leaf and seed tissues in maize and rice. Using principal components analysis based on leaf metabolites but not seed metabolites, metabolomics data could be clearly separated for rice Indica and Japonica accessions, while two maize subgroups, temperate and tropical, showed more visible admixture. Rice and maize seed exhibited significant interspecific differences in metabolic variation, while within rice, leaf and seed displayed similar metabolic variations. Among 10 metabolic categories, flavonoids had higher variation in maize than rice, indicating flavonoids are a key constituent of interspecific metabolic divergence. Interestingly, metabolic regulation was also found to be reshaped dramatically from positive to negative correlations, indicative of the differential evolutionary processes in maize and rice. Moreover, perhaps due to this divergence significantly more metabolic interactions were identified in rice than maize. Furthermore, in rice, the leaf was found to harbor much more intense metabolic interactions than the seed. Our result suggests that metabolomes are valuable for tracking evolutionary history, thereby complementing and extending genomic insights concerning which features are responsible for interspecific differentiation in maize and rice.

Synergistic ameliorative effect of iron oxide nanoparticles and Bacillus subtilis S4 against arsenic toxicity in Cucurbita moschata: polyamines, antioxidants, and physiochemical studies

The present study was intended to assess the potential of iron oxide nanoparticles (IONPs) and Bacillus subtilis S4 in mitigation of arsenic (As) stress in Cucurbita moschata. Cucurbita moschata seedlings were subjected to As stress for 60 days. Reduced level of growth parameters including photosynthetic pigments, rate of photosynthesis and gas exchange characteristics was observed in seedlings subjected to As stress. However, IONPs and B. subtilis S4 improved growth attributes and proline contents in supplemented C. moschata seedlings. Bacillus subtilis S4 inoculated seedlings showed higher activity of peroxidase (POD) and superoxide dismutase (SOD) under As toxicity. Similarly, the co-application of IONPs and B. subtilis S4 further increased the activity of these antioxidative enzymes. The As stress alleviation in inoculated C. moschata seedlings is credited to reduced levels of hydrogen peroxide (H2O2), malondialdehyde (MDA) and electrolyte leakage (EL) in IONPs and B. subtilis S4-treated plants. Furthermore, synergism between plant growth promoting bacteria (PGPB) and IONPs enhanced the biosynthesis of stress mitigating polyamines including spermidine and putrescine in As-stressed seedlings. Current research reveals that synergistic application of IONPs and B. subtilis S4 is an effective sustainable and ecofriendly approach for alleviation of As stress in C. moschata seedlings.

Metabolic alterations provide insights into Stylosanthes roots responding to phosphorus deficiency

BACKGROUND

Phosphorus (P) deficiency is one of the major constraints limiting plant growth, especially in acid soils. Stylosanthes (stylo) is a pioneer tropical legume with excellent adaptability to low P stress, but its underlying mechanisms remain largely unknown.

RESULTS

In this study, the physiological, molecular and metabolic changes in stylo responding to phosphate (Pi) starvation were investigated. Under low P condition, the growth of stylo root was enhanced, which was attributed to the up-regulation of expansin genes participating in root growth. Metabolic profiling analysis showed that a total of 256 metabolites with differential accumulations were identified in stylo roots response to P deficiency, which mainly included flavonoids, sugars, nucleotides, amino acids, phenylpropanoids and phenylamides. P deficiency led to significant reduction in the accumulation of phosphorylated metabolites (e.g., P-containing sugars, nucleotides and cholines), suggesting that internal P utilization was enhanced in stylo roots subjected to low P stress. However, flavonoid metabolites, such as kaempferol, daidzein and their glycoside derivatives, were increased in P-deficient stylo roots. Furthermore, the qRT-PCR analysis showed that a set of genes involved in flavonoids synthesis were found to be up-regulated by Pi starvation in stylo roots. In addition, the abundances of phenolic acids and phenylamides were significantly increased in stylo roots during P deficiency. The increased accumulation of the metabolites in stylo roots, such as flavonoids, phenolic acids and phenylamides, might facilitate P solubilization and cooperate with beneficial microorganisms in rhizosphere, and thus contributing to P acquisition and utilization in stylo.

CONCLUSIONS

These results suggest that stylo plants cope with P deficiency by modulating root morphology, scavenging internal Pi from phosphorylated metabolites and increasing accumulation of flavonoids, phenolic acids and phenylamides. This study provides valuable insights into the complex responses and adaptive mechanisms of stylo roots to P deficiency.

Impact of Paraburkholderia phytofirmans PsJN on Grapevine Phenolic Metabolism

Phenolic compounds are implied in plant-microorganisms interaction and may be induced in response to plant growth-promoting rhizobacteria (PGPRs). Among PGPR, the beneficial bacterium Paraburkholderia phytofirmans PsJN was previously described to stimulate the growth of plants and to induce a better adaptation to both abiotic and biotic stresses. This study aimed to investigate the impact of PsJN on grapevine secondary metabolism. For this purpose, gene expression (qRT-PCR) and profiling of plant secondary metabolites (UHPLC-UV/DAD-MS QTOF) from both grapevine root and leaves were compared between non-bacterized and PsJN-bacterized grapevine plantlets. Our results showed that PsJN induced locally (roots) and systemically (leaves) an overexpression of PAL and STS and specifically in leaves the overexpression of all the genes implied in phenylpropanoid and flavonoid pathways. Moreover, the metabolomic approach revealed that relative amounts of 32 and 17 compounds in roots and leaves, respectively, were significantly modified by PsJN. Once identified to be accumulated in response to PsJN by the metabolomic approach, antifungal properties of purified molecules were validated in vitro for their antifungal effect on Botrytis cinerea spore germination. Taking together, our findings on the impact of PsJN on phenolic metabolism allowed us to identify a supplementary biocontrol mechanism developed by this PGPR to induce plant resistance against pathogens.

Inoculation of Lupinus albus with the nodule-endophyte Paenibacillus glycanilyticus LJ121 improves grain nutritional quality

Metabolic changes occurring in white lupine grain were investigated in response to Plant Growth Promoting Rhizobacteria (PGPR) root inoculation under field condition. We precisely targeted lipids and phenolics changes occurring in white lupine grain in response to Pseudomonas brenneri LJ215 and/or Paenibacillus glycanilyticus LJ121 inoculation. Lipids and phenolic composition were analyzed using an Ultra High-Performance Liquid Chromatography/Tandem Mass Spectrometry Methods. As compared to grain of un-inoculated control plant, Paenibacillus glycaniliticus inoculation highly increased the total lipids content (from 232.55 in seeds of un-inoculated control plant to 944.95 mg/kg) and the relative percentage of several fatty acid such as oleic acid (+20.95%) and linoleic acid (+14.28%) and decreased the relative percentage of glycerophospholipids (- 13.11%), sterol (- 0.2% and - 0.34% for stigmasterol and campesterol, respectively) and prenol (- 17.45%) class. Paenibacillus glycaniliticus inoculation did not affect total phenolic content, while it modulated content of individual phenolic compounds and induced the accumulation of "new" phenolics compounds such as kaempferol. Paenibacillus glycanilyticus LJ121 can be a useful bio-fertilizer to enhance nutritional quality of white lupine grain.