Adaptation of the metabolomics profile of rice after Pyricularia oryzae infection

Organs-specific metabolomics and anticholinesterase activity suggests a trade-off between metabolites for therapeutic advantages of Trillium govanianum Wall. ex D. Don

Trillium govanianum is traditionally used to treat innumerable alignments like sexual disorders, cancer, inflammation etc. Mainly rhizomes of T. govanianum have been explored for phytochemical profiling but comprehensive metabolomics of other parts has not been yet deeply investigated. Thus, current study was aimed for organs-specific (roots, rhizomes, rhizomatous buds, stems, leaves, and fruits) phytochemical profiling of T. govanianum via metabolomics approach. Targeted (steroidal saponins and free sugars) and non-targeted metabolomics were performed by UPLC-PDA/ELSD & UHPLC-Q-TOF-IMS. Among steroidal compounds, 20-hydroxyecdysone, pennogenin-3-O-β-chacotrioside, dioscin were found predominantly in all samples while diosgenin was identified only in rhizomes. Further, four free sugars viz. 2-deoxyribose (116.24 ± 1.26 mg/g: leaves), fructose (454.76 ± 12.14 mg/g: rhizomes), glucose (243.21 ± 7.53 mg/g: fruits), and galactose (69.06 ± 2.14 mg/g: fruits) were found significant in respective parts of T. govanianum. Elemental analysis of targeted samples was determined by atomic absorption spectrophotometer. Heavy metals (Cd, Hg, Pd, As) were absent while micro- (Mn, Na, Zn, Cu) and macro- (Ca, Fe, Mg, K) elements were found in all samples. Furthermore, UHPLC-Q-TOF-IMS had identified 103 metabolites based on their mass fragmentation patterns and 839 were tentatively predicted using METLIN database. The multivariate statistical analysis showed organs specific clustering and variance of metabolites. Apart from this, extracts were evaluated for in vitro anticholinesterase activity, and found potentials inhibitors with IC50 values 2.02 ± 0.15 to 27.65 ± 0.89 mg/mL and 3.58 ± 0.12 to 16.81 ± 2.48 mg/mL of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzyme, respectively. Thus, comprehensive metabolomics and anti-cholinesterase activity of different parts of T. govanianum would lay the foundation for improving medicinal importance and health benefits of T. govanianum.

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.

Recent Advances in the Specialized Metabolites Mediating Resistance to Insect Pests and Pathogens in Tea Plants (Camellia sinensis)

Tea is the second most popular nonalcoholic beverage consumed in the world, made from the buds and young leaves of the tea plants (Camellia sinensis). Tea trees, perennial evergreen plants, contain abundant specialized metabolites and suffer from severe herbivore and pathogen attacks in nature. Thus, there has been considerable attention focusing on investigating the precise function of specialized metabolites in plant resistance against pests and diseases. In this review, firstly, the responses of specialized metabolites (including phytohormones, volatile compounds, flavonoids, caffeine, and L-theanine) to different attacks by pests and pathogens were compared. Secondly, research progress on the defensive functions and action modes of specialized metabolites, along with the intrinsic molecular mechanisms in tea plants, was summarized. Finally, the critical questions about specialized metabolites were proposed for better future research on phytohormone-dependent biosynthesis, the characteristics of defense responses to different stresses, and molecular mechanisms. This review provides an update on the biological functions of specialized metabolites of tea plants in defense against two pests and two pathogens.

Comparative Metabolomic Profiling of Compatible and Incompatible Interactions Between Potato and Phytophthora infestans

Late blight is one of the main biological stresses limiting the potato yield; however, the biochemical mechanisms underlying the infection process of Phytophthora infestans remain unrevealed. In this study, the late blight-resistant potato cultivar Ziyun No.1 (R) and the susceptible cultivar Favorita (S) were inoculated with P. infestans. Untargeted metabolomics was used to study the changes of metabolites in the compatible and incompatible interactions of the two cultivars and the pathogen at 0, 48, and 96 h postinoculation (hpi). A total of 819 metabolites were identified, and the metabolic differences mainly emerged after 48 hpi. There were 198 and 115 differentially expressed metabolites (DEMs) in the compatible and incompatible interactions. These included 147 and 100 upregulated metabolites during the compatible and incompatible interactions, respectively. Among them, 73 metabolites were identified as the P. infestans-responsive DEMs. Furthermore, the comparisons between the two cultivars identified 57 resistance-related metabolites. Resistant potato cultivar had higher levels of salicylic acid and several upstream phenylpropanoid biosynthesis metabolites, triterpenoids, and hydroxycinnamic acids and their derivatives, such as sakuranetin, ferulic acid, ganoderic acid Mi, lucidenic acid D2, and caffeoylmalic acid. These metabolites play crucial roles in cell wall thickening and have antibacterial and antifungal activities. This study reports the time-course metabolomic responses of potatoes to P. infestans. The findings reveal the responses involved in the compatible and incompatible interactions of potatoes and P. infestans.

Elementomics combined with dd-SIMCA and K-NN to identify the geographical origin of rice samples from China, India, and Vietnam

The COVID-19 pandemic has impacted the food industry and consumers, with production gaps, shipping delays, and changes in supply and demand leading to an increased risk of food fraud. Rice has a high probability for adulteration by food fraudsters, being a staple commodity for more than half the global population, making the assessment of geographical origins of rice for authenticity important in terms of protecting businesses and consumers. In this study, we describe ICP-MS elemental profiling coupled with elementomic modelling to identify the geographical indications of Indian, Chinese, and Vietnamese rice. A PLS-DA model exhibited good discrimination (R² = 0.8393, Q² = 0.7673, accuracy = 1.0). Data-driven soft independent modelling of class analogy (dd-SIMCA) and K-nearest neighbours (K-NN) models have good sensitivity (98%) and specificity (100%).

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.

Nitrate mediated resistance against Fusarium infection in cucumber plants acts via photorespiration

Fusarium wilt is one of the major biotic factors limiting cucumber (Cucumis sativus L.) growth and yield. The outcomes of cucumber-Fusarium interactions can be influenced by the form of nitrogen nutrition (nitrate [NO₃^- ] or ammonium [NH₄⁺ ]); however, the physiological mechanisms of N-regulated cucumber disease resistance are still largely unclear. Here, we investigated the relationship between nitrogen forms and cucumber resistance to Fusarium infection. Our results showed that on Fusarium infection, NO₃^- feeding decreased the levels of the fungal toxin, fusaric acid, leaf membrane oxidative, organelle damage and disease-associated loss in photosynthesis. Metabolomic analysis and gas-exchange measurements linked NO₃^- mediated plant defence with enhanced leaf photorespiration rates. Cucumber plants sprayed with the photorespiration inhibitor isoniazid were more susceptible to Fusarium and there was a negative correlation between photorespiration rate and leaf membrane injury. However, there were positive correlations between photorespiration rate, NO₃^- assimilation and the tricarboxylic acid (TCA) cycle. This provides a potential electron sink or the peroxisomal H₂ O₂ catalysed by glycolate oxidase. We suggest that the NO₃^- nutrition enhanced cucumber resistance against Fusarium infection was associated with photorespiration. Our findings provide a novel insight into a mechanism involving the interaction of photorespiration with nitrogen forms to drive wider defence.

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.

Application of UPLC-QTOF-MS Based Untargeted Metabolomics in Identification of Metabolites Induced in Pathogen-Infected Rice

Metabolomics is a useful tool for comparing metabolite changes in plants. Because of its high sensitivity, metabolomics combined with high-resolution mass spectrometry (HR-MS) is the most widely accepted metabolomics tools. In this study, we compared the metabolites of pathogen-infected rice (Oryza sativa) with control rice using an untargeted metabolomics approach. We profiled the mass features of two rice groups using a liquid chromatography quadrupole time-of-flight mass spectrometry (QTOF-MS) system. Twelve of the most differentially induced metabolites in infected rice were selected through multivariate data analysis and identified through a mass spectral database search. The role of these compounds in metabolic pathways was finally investigated using pathway analysis. Our study showed that the most frequently induced secondary metabolites are prostanoids, a subclass of eicosanoids, which are associated with plant defense metabolism against pathogen infection. Herein, we propose a new untargeted metabolomics approach for understanding plant defense system at the metabolic level.

Deciphering the Omics of Plant-Microbe Interaction: Perspectives and New Insights

Introduction

Plants do not grow in isolation, rather they are hosts to a variety of microbes in their natural environments. While, few thrive in the plants for their own benefit, others may have a direct impact on plants in a symbiotic manner. Unraveling plant-microbe interactions is a critical component in recognizing the positive and negative impacts of microbes on plants. Also, by affecting the environment around plants, microbes may indirectly influence plants. The progress in sequencing technologies in the genomics era and several omics tools has accelerated in biological science. Studying the complex nature of plant-microbe interactions can offer several strategies to increase the productivity of plants in an environmentally friendly manner by providing better insights. This review brings forward the recent works performed in building omics strategies that decipher the interactions between plant-microbiome. At the same time, it further explores other associated mutually beneficial aspects of plant-microbe interactions such as plant growth promotion, nitrogen fixation, stress suppressions in crops and bioremediation; as well as provides better insights on metabolic interactions between microbes and plants through omics approaches. It also aims to explore advances in the study of Arabidopsis as an important avenue to serve as a baseline tool to create models that help in scrutinizing various factors that contribute to the elaborate relationship between plants and microbes. Causal relationships between plants and microbes can be established through systematic gnotobiotic experimental studies to test hypotheses on biologically derived interactions.

Conclusion

This review will cover recent advances in the study of plant-microbe interactions keeping in view the advantages of these interactions in improving nutrient uptake and plant health.

High temperature-induced plant disease susceptibility: more than the sum of its parts

Higher temperatures associated with climate change often increase the severity of plant diseases. An understanding of how plants respond to pathogens during high temperature stress is required for crop improvement, but the molecular mechanisms underlying this response are largely unknown. Mechanistic research has primarily focused on plant responses during either single stresses or heat-induced loss of single gene resistance. Transcriptome analyses of plant responses to a single stress compared to combined-stresses reveal significant differences showing that single-stress response studies are inadequate for determining the mechanisms of high temperature-induced disease susceptibility. To combat plant disease in light of climate change, future research will require comprehensive study designs and analyses.