Metabolomics as an Emerging Tool for the Study of Plant-Pathogen Interactions

Mapping and Omics Integration: Towards Precise Rice Disease Resistance Breeding

Rice (Oryza sativa), as a staple crop feeding a significant portion of the global population, particularly in Asian countries, faces constant threats from various diseases jeopardizing global food security. A precise understanding of disease resistance mechanisms is crucial for developing resilient rice varieties. Traditional genetic mapping methods, such as QTL mapping, provide valuable insights into the genetic basis of diseases. However, the complex nature of rice diseases demands a holistic approach to gain an accurate knowledge of it. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, enable a comprehensive analysis of biological molecules, uncovering intricate molecular interactions within the rice plant. The integration of various mapping techniques using multi-omics data has revolutionized our understanding of rice disease resistance. By overlaying genetic maps with high-throughput omics datasets, researchers can pinpoint specific genes, proteins, or metabolites associated with disease resistance. This integration enhances the precision of disease-related biomarkers with a better understanding of their functional roles in disease resistance. The improvement of rice breeding for disease resistance through this integration represents a significant stride in agricultural science because a better understanding of the molecular intricacies and interactions underlying disease resistance architecture leads to a more precise and efficient development of resilient and productive rice varieties. In this review, we explore how the integration of mapping and omics data can result in a transformative impact on rice breeding for enhancing disease resistance.

Untargeted metabolomics reveals PTI-associated metabolites

Plants employ a multilayered immune system to combat pathogens. In one layer, recognition of Pathogen- or Microbe-Associated Molecular Patterns or elicitors, triggers a cascade that leads to defence against the pathogen and Pattern Triggered Immunity. Secondary or specialised metabolites (SMs) are expected to play a role, because they are potentially anti-fungal compounds. Tomato (Solanum lycopersicum) plants inoculated with Alternaria solani s.l. show symptoms of infection after inoculation. Plants inoculated with Alternaria alternata remain symptomless. We hypothesised that pattern-triggered induction of resistance related metabolites in tomato contributes to the resistance against A. alternata. We compared the metabolomic profile (metabolome) of tomato after treatments with A. alternata, A. solani and the fungal elicitor chitin, and identified SMs involved in early defence of tomato plants. We revealed differential metabolome fingerprints. The composition of A. alternata and chitin induced metabolomes show larger overlap with each other than with the A. solani induced metabolome. We identify 65 metabolites possibly associated with PTI in tomato plants, including NAD and trigonelline. We confirm that trigonelline inhibits fungal growth in vitro at physiological concentrations. Thus, a true pattern-triggered, chemical defence is mounted against A. alternata, which contains anti-fungal compounds that could be interesting for crop protection strategies.

Metabolomics approach to understand molecular mechanisms involved in fungal pathogen-citrus pathosystems

Citrus is a crucial crop with a significant economic impact globally. However, postharvest decay caused by fungal pathogens poses a considerable threat, leading to substantial financial losses. Penicillium digitatum, Penicillium italicum, Geotrichum citri-aurantii and Phyllosticta citricarpa are the main fungal pathogens, causing green mold, blue mold, sour rot and citrus black spot diseases, respectively. The use of chemical fungicides as a control strategy in citrus raises concerns about food and environmental safety. Therefore, understanding the molecular basis of host-pathogen interactions is essential to find safer alternatives. This review highlights the potential of the metabolomics approach in the search for bioactive compounds involved in the pathogen-citrus interaction, and how the integration of metabolomics and genomics contributes to the understanding of secondary metabolites associated with fungal virulence and the fungal infection mechanisms. Our goal is to provide a pipeline combining metabolomics and genomics that can effectively guide researchers to perform studies aiming to contribute to the understanding of the fundamental chemical and biochemical aspects of pathogen-host interactions, in order to effectively develop new alternatives for fungal diseases in citrus cultivation. We intend to inspire the scientific community to question unexplored biological systems, and to employ diverse analytical approaches and metabolomics techniques to address outstanding questions about the non-studied pathosystems from a chemical biology perspective.

Rice-Magnaporthe oryzae interactions in resistant and susceptible rice cultivars under panicle blast infection based on defense-related enzyme activities and metabolomics

Rice blast, caused by rice blast fungus (Magnaporthe oryzae), is a global threat to food security, with up to 50% yield losses. Panicle blast is a severe form of rice blast, and disease responses vary between cultivars with different genotypes. Reactive oxygen species (ROS)-mediated signaling reactions and the phenylpropanoid pathway are important defense mechanisms involved in recognizing and resisting against fungal infection. To understand rice-M. oryzae interactions in resistant and susceptible cultivars, we determined dynamic changes in the activities of five defense-related enzymes in resistant cultivar jingsui 18 and susceptible cultivar jinyuan 899 infected with M. oryzae from 4 to 25 days after infection. We then performed untargeted metabolomics analyses to profile the metabolomes of the cultivars under infected and non-infected conditions. Dynamic changes in the activities of five defense-related enzymes were closely related to panicle blast resistance in rice. Metabolome data analysis identified 634 differentially accumulated metabolites (DAMs) between resistant and susceptible cultivars following infection, potentially explaining differences in disease response between varieties. The most enriched DAMs were associated with lipids and lipid-like molecules, phenylpropanoids and polyketides, organoheterocyclic compounds, organic acids and derivatives, and lignans, neolignans, and related compounds. Multiple metabolic pathways are involved in resistance to panicle blast in rice, including biosynthesis of other secondary metabolites, amino acid metabolism, lipid metabolism, phenylpropanoid biosynthesis, arachidonic acid metabolism, arginine biosynthesis, tyrosine metabolism, tryptophan metabolism, tyrosine and tryptophan biosynthesis, lysine biosynthesis, and oxidative phosphorylation.

The endophytic fungal community plays a crucial role in the resistance of host plants to necrotic bacterial pathogens

Konjac species (Amorphophallus spp.) are the only plant species in the world that are rich in a large amount of konjac glucomannan (KGM). These plants are widely cultivated as cash crops in tropical and subtropical countries in Asia, including China. Pectobacterium carotovorum subsp. carotovorum (Pcc) is one of the most destructive bacterial pathogens of konjac. Here, we analyzed the interactions between Pcc and susceptible and resistant konjac species from multiple perspectives. At the transcriptional and metabolic levels, the susceptible species A. konjac and resistant species A. muelleri exhibit similar molecular responses, activating plant hormone signaling pathways and metabolizing defense compounds such as phenylpropanoids and flavonoids to resist infection. Interestingly, we found that Pcc stress can lead to rapid recombination of endophytic microbial communities within a very short period (96 h). Under conditions of bacterial pathogen infection, the relative abundance of most bacterial communities in konjac tissue decreased sharply compared with that in healthy plants, while the relative abundance of some beneficial fungal communities increased significantly. The relative abundance of Cladosporium increased significantly in both kinds of infected konjac compared to that in healthy plants, and the relative abundance in resistant A. muelleri plants was greater than that in susceptible A. konjac plants. Among the isolated cultivable microorganisms, all three strains of Cladosporium strongly inhibited Pcc growth. Our results further elucidate the potential mechanism underlying konjac resistance to Pcc infection, highlighting the important role of endophytic microbial communities in resisting bacterial pathogen infections, especially the more direct role of fungal communities in inhibiting pathogen growth.

Harnessing root exudates for plant microbiome engineering and stress resistance in plants

A wide range of abiotic and biotic stresses adversely affect plant's growth and production. Under stress, one of the main responses of plants is the modulation of exudates excreted in the rhizosphere, which consequently leads to alterations in the resident microbiota. Thus, the exudates discharged into the rhizospheric environment play a preponderant role in the association and formation of plant-microbe interactions. In this review, we aimed to provide a synthesis of the latest and most pertinent literature on the diverse biochemical and structural compositions of plant root exudates. Also, this work investigates into their multifaceted role in microbial nutrition and intricate signaling processes within the rhizosphere, which includes quorum-sensing molecules. Specifically, it explores the contributions of low molecular weight compounds, such as carbohydrates, phenolics, organic acids, amino acids, and secondary metabolites, as well as the significance of high molecular weight compounds, including proteins and polysaccharides. It also discusses the state-of-the-art omics strategies that unveil the vital role of root exudates in plant-microbiome interactions, including defense against pathogens like nematodes and fungi. We propose multiple challenges and perspectives, including exploiting plant root exudates for host-mediated microbiome engineering. In this discourse, root exudates and their derived interactions with the rhizospheric microbiota should receive greater attention due to their positive influence on plant health and stress mitigation.

Comparative metabolomic study of fungal foliar endophytes and their long-lived host Astrocaryum sciophilum: a model for exploring the chemodiversity of host-microbe interactions

Introduction

In contrast to the dynamics observed in plant/pathogen interactions, endophytic fungi have the capacity to establish enduring associations within their hosts, leading to the development of a mutually beneficial relationship that relies on specialized chemical interactions. Research indicates that the presence of endophytic fungi has the ability to significantly modify the chemical makeup of the host organism. Our hypothesis proposes the existence of a reciprocal exchange of chemical signals between plants and fungi, facilitated by specialized chemical processes that could potentially manifest within the tissues of the host. This research aimed to precisely quantify the portion of the cumulative fungal endophytic community's metabolome detectable within host leaves, and tentatively evaluate its relevance to the host-endophyte interplay. The understory palm Astrocaryum sciophilum (Miq.) Pulle was used as a interesting host plant because of its notable resilience and prolonged life cycle, in a tropical ecosystem.

Method

Using advanced metabolome characterization, including UHPLC-HRMS/MS and molecular networking, the study explored enriched metabolomes of both host leaves and 15 endophytic fungi. The intention was to capture a metabolomic "snapshot" of both host and endophytic community, to achieve a thorough and detailed analysis.

Results and discussion

This approach yielded an extended MS-based molecular network, integrating diverse metadata for identifying host- and endophyte-derived metabolites. The exploration of such data (>24000 features in positive ionization mode) enabled effective metabolome comparison, yielding insights into cultivable endophyte chemodiversity and occurrence of common metabolites between the holobiont and its fungal communities. Surprisingly, a minor subset of features overlapped between host leaf and fungal samples despite significant plant metabolome enrichment. This indicated that fungal metabolic signatures produced in vitro remain sparingly detectable in the leaf. Several classes of primary metabolites were possibly shared. Specific fungal metabolites and/or compounds of their chemical classes were only occasionally discernible in the leaf, highlighting endophytes partial contribution to the overall holobiont metabolome. To our knowledge, the metabolomic study of a plant host and its microbiome has rarely been performed in such a comprehensive manner. The general analytical strategy proposed in this paper seems well-adapted for any study in the field of microbial- or microbiome-related MS and can be applied to most host-microbe interactions.

Physiological Effects of Microbial Biocontrol Agents in the Maize Phyllosphere

In a world with constant population growth, and in the context of climate change, the need to supply the demand of safe crops has stimulated an interest in ecological products that can increase agricultural productivity. This implies the use of beneficial organisms and natural products to improve crop performance and control pests and diseases, replacing chemical compounds that can affect the environment and human health. Microbial biological control agents (MBCAs) interact with pathogens directly or by inducing a physiological state of resistance in the plant. This involves several mechanisms, like interference with phytohormone pathways and priming defensive compounds. In Argentina, one of the world's main maize exporters, yield is restricted by several limitations, including foliar diseases such as common rust and northern corn leaf blight (NCLB). Here, we discuss the impact of pathogen infection on important food crops and MBCA interactions with the plant's immune system, and its biochemical indicators such as phytohormones, reactive oxygen species, phenolic compounds and lytic enzymes, focused mainly on the maize-NCLB pathosystem. MBCA could be integrated into disease management as a mechanism to improve the plant's inducible defences against foliar diseases. However, there is still much to elucidate regarding plant responses when exposed to hemibiotrophic pathogens.

Metabolomics of early blight (Alternaria solani) susceptible tomato (Solanum lycopersicum) unfolds key biomarker metabolites and involved metabolic pathways

Tomato (Solanum lycopersicum) is among the most important commercial horticultural crops worldwide. The crop quality and production is largely hampered due to the fungal pathogen Alternaria solani causing necrotrophic foliage early blight disease. Crop plants usually respond to the biotic challenges with altered metabolic composition and physiological perturbations. We have deciphered altered metabolite composition, modulated metabolic pathways and identified metabolite biomarkers in A. solani-challenged susceptible tomato variety Kashi Aman using Liquid Chromatography-Mass Spectrometry (LC-MS) based metabolomics. Alteration in the metabolite feature composition of pathogen-challenged (m/z 9405) and non-challenged (m/z 9667) plant leaves including 8487 infection-exclusive and 8742 non-infection exclusive features was observed. Functional annotation revealed putatively annotated metabolites and pathway mapping indicated their enrichment in metabolic pathways, biosynthesis of secondary metabolites, ubiquinone and terpenoid-quinones, brassinosteroids, steroids, terpenoids, phenylpropanoids, carotenoids, oxy/sphingolipids and metabolism of biotin and porphyrin. PCA, multivariate PLS-DA and OPLS-DA analysis showed sample discrimination. Significantly up regulated 481 and down regulated 548 metabolite features were identified based on the fold change (threshold ≥ 2.0). OPLS-DA model based on variable importance in projection (VIP scores) and FC threshold (> 2.0) revealed 41 up regulated discriminant metabolite features annotated as sphingosine, fecosterol, melatonin, serotonin, glucose 6-phosphate, zeatin, dihydrozeatin and zeatin-β-D-glucoside. Similarly, 23 down regulated discriminant metabolites included histidinol, 4-aminobutyraldehyde, propanoate, tyramine and linalool. Melatonin and serotonin in the leaves were the two indoleamines being reported for the first time in tomato in response to the early blight pathogen. Receiver operating characteristic (ROC)-based biomarker analysis identified apigenin-7-glucoside, uridine, adenosyl-homocysteine, cGMP, tyrosine, pantothenic acid, riboflavin (as up regulated) and adenosine, homocyctine and azmaline (as down regulated) biomarkers. These results could aid in the development of metabolite-quantitative trait loci (mQTL). Furthermore, stress-induced biosynthetic pathways may be the potential targets for modifications through breeding programs or genetic engineering for improving crop performance in the fields.

Non-Targeted Spectranomics for the Early Detection of Xylella fastidiosa Infection in Asymptomatic Olive Trees, cv. Cellina di Nardò

Olive quick decline syndrome (OQDS) is a disease that has been seriously affecting olive trees in southern Italy since around 2009. During the disease, caused by Xylella fastidiosa subsp. pauca sequence type ST53 (Xf), the flow of water and nutrients within the trees is significantly compromised. Initially, infected trees may not show any symptoms, making early detection challenging. In this study, young artificially infected plants of the susceptible cultivar Cellina di Nardò were grown in a controlled environment and co-inoculated with additional xylem-inhabiting fungi. Asymptomatic leaves of olive plants at an early stage of infection were collected and analyzed using nuclear magnetic resonance (NMR), hyperspectral reflectance (HSR), and chemometrics. The application of a spectranomic approach contributed to shedding light on the relationship between the presence of specific hydrosoluble metabolites and the optical properties of both asymptomatic Xf-infected and non-infected olive leaves. Significant correlations between wavebands located in the range of 530-560 nm and 1380-1470 nm, and the following metabolites were found to be indicative of Xf infection: malic acid, fructose, sucrose, oleuropein derivatives, and formic acid. This information is the key to the development of HSR-based sensors capable of early detection of Xf infections in olive trees.

Profiling and Localization of Stilbene Phytoalexins Revealed by MALDI-MSI during the Grapevine-Botrytis cinerea Interaction

Stilbene phytoalexins are among the most accumulated compounds during grapevine-pathogen interactions. However, their steady-state accumulation level and spatial distribution within the tissues to counteract Botrytis cinerea infection remain to be explored. In this work, matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) was used to determine the spatial distribution of different phytoalexins in grapevine leaves upon infection with B. cinerea. Ultraperformance liquid chromatography-fluorescence (UPLC-FL) was also employed to monitor the accumulation pattern of these phytoalexins. This study showed that stilbene compounds accumulate in areas close to the pathogen infection sites. It was also revealed that the accumulation patterns of the stilbene phytoalexins can vary from one time point postinfection to another with specific accumulation patterns within each time point. To the best of our knowledge, this is the first time that the separate localization of grapevine stilbene phytoalexins has been revealed following B. cinerea infection.

An Integrated Multi-Omics and Artificial Intelligence Framework for Advance Plant Phenotyping in Horticulture

This review discusses the transformative potential of integrating multi-omics data and artificial intelligence (AI) in advancing horticultural research, specifically plant phenotyping. The traditional methods of plant phenotyping, while valuable, are limited in their ability to capture the complexity of plant biology. The advent of (meta-)genomics, (meta-)transcriptomics, proteomics, and metabolomics has provided an opportunity for a more comprehensive analysis. AI and machine learning (ML) techniques can effectively handle the complexity and volume of multi-omics data, providing meaningful interpretations and predictions. Reflecting the multidisciplinary nature of this area of research, in this review, readers will find a collection of state-of-the-art solutions that are key to the integration of multi-omics data and AI for phenotyping experiments in horticulture, including experimental design considerations with several technical and non-technical challenges, which are discussed along with potential solutions. The future prospects of this integration include precision horticulture, predictive breeding, improved disease and stress response management, sustainable crop management, and exploration of plant biodiversity. The integration of multi-omics and AI holds immense promise for revolutionizing horticultural research and applications, heralding a new era in plant phenotyping.

Metabolomics Insight into the Variety-Mediated Responses to Aspergillus carbonarius Infection in Grapevine Berries

Limited knowledge regarding the susceptibility of grape varieties to ochratoxin A (OTA)-producing fungi is available to date. This study aimed to investigate the susceptibility of different grape varieties to Aspergillus carbonarius concerning OTA contamination and modulation at the metabolome level. Six grape varieties were selected, sampled at early veraison and ripening, artificially inoculated with A. carbonarius, and incubated at two temperature regimes. Significant differences were observed across cultivars, with Barbera showing the highest incidence of moldy berries (around 30%), while Malvasia and Ortrugo showed the lowest incidence (about 2%). OTA contamination was the lowest in Ortrugo and Malvasia, and the highest in Croatina, although it was not significantly different from Barbera, Merlot, and Sauvignon Blanc. Fungal development and mycotoxin production changed with grape variety; the sugar content in berries could also have played a role. Unsupervised multivariate statistical analysis from metabolomic fingerprints highlighted cultivar-specific responses, although a more generalized response was observed by supervised OPLS-DA modeling. An accumulation of nitrogen-containing compounds (alkaloids and glucosinolates), phenylpropanoids, and terpenoids, in addition to phytoalexins, was observed in all samples. A broader modulation of the metabolome was observed in white grapes, which were less contaminated by OTA. Jasmonates and oxylipins were identified as critical upstream modulators in metabolomic profiles. A direct correlation between the plant defense machinery and OTA was not observed, but the information was acquired and can contribute to optimizing preventive actions.

Metabolomic Reconfiguration in Primed Barley (Hordeum vulgare) Plants in Response to Pyrenophora teres f. teres Infection

Necrotrophic fungi affect a wide range of plants and cause significant crop losses. For the activation of multi-layered innate immune defences, plants can be primed or pre-conditioned to rapidly and more efficiently counteract this pathogen. Untargeted and targeted metabolomics analyses were applied to elucidate the biochemical processes involved in the response of 3,5-dichloroanthranilic acid (3,5-DCAA) primed barley plants to Pyrenophora teres f. teres (Ptt). A susceptible barley cultivar ('Hessekwa') at the third leaf growth stage was treated with 3,5-DCAA 24 h prior to infection using a Ptt conidia suspension. The infection was monitored over 2, 4, and 6 days post-inoculation. For untargeted studies, ultra-high performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-MS) was used to analyse methanolic plant extracts. Acquired data were processed to generate the data matrices utilised in chemometric modelling and multi-dimensional data mining. For targeted studies, selected metabolites from the amino acids, phenolic acids, and alkaloids classes were quantified using multiple reaction monitoring (MRM) mass spectrometry. 3,5-DCAA was effective as a priming agent in delaying the onset and intensity of symptoms but could not prevent the progression of the disease. Unsupervised learning methods revealed clear differences between the sample extracts from the control plants and the infected plants. Both orthogonal projection to latent structure-discriminant analysis (OPLS-DA) and 'shared and unique structures' (SUS) plots allowed for the extraction of potential markers of the primed and naïve plant responses to Ptt. These include classes of organic acids, fatty acids, amino acids, phenolic acids, and derivatives and flavonoids. Among these, 5-oxo-proline and citric acid were notable as priming response-related metabolites. Metabolites from the tricarboxylic acid pathway were only discriminant in the primed plant infected with Ptt. Furthermore, the quantification of targeted metabolites revealed that hydroxycinnamic acids were significantly more prominent in the primed infected plants, especially at 2 d.p.i. Our research advances efforts to better understand regulated and reprogrammed metabolic responses that constitute defence priming in barley against Ptt.

Morphological, physiological and metabolomic analysis to unravel the adaptive relationship between root growth of ephemeral plants and different soil habitats

To gain insights into the adaptive characteristics of ephemeral plants and enrich their potential for resource exploitation, the adaptive changes in two highly dominant species (Malcolmia scorpioides and Isatis violascens) to soil habitats (aeolian soil, AS; grey desert soil, GS) were investigated from the aspects of root morphology, physiology, and metabolism in this study. The results revealed that changes in root morphology and enzyme activity were affected by soil habitat. Total root length (TRL), root volume (RV) and root surface area (RSA) were higher in GS than in AS. The levels of proline (Pro), glutathione (GSH), soluble sugar (SS), and lysine (Lys) were higher in GS than in AS. Untargeted LC-MS metabolomics indicates that root metabolites of both species differed among the two soil habitats. Root responses to different soil habitats mainly affected some metabolic pathways. A total of 780 metabolites were identified, common differential metabolites (DMs) in both species included amino acids, fatty acids, organic acids, carbohydrates, benzene and derivatives, and flavonoids, which were mainly involved in carbohydrate metabolism, amino acid metabolism, flavonoid biosynthesis and fatty acid metabolism, and their abundance varied among different habitats and species. Some key DMs were significantly related to root morphology and enzyme activity, and indole, malonate, quercetin, uridine, tetrahydroharmine, and gluconolactone were important metabolites associated with root growth. Therefore, the response changes in root growth and metabolite of ephemeral plants in response to soil habitats reflect their ecological adaptation, and lay a foundation for the exploitation of plant resources in various habitats.

Novel nanotechnological approaches for managing Phytophthora diseases of plants

Members of the Phytophthora genus are soil-dwelling pathogens responsible for diseases of several important plants. Among these, Phytophthora infestans causes late blight of potatoes, which was responsible for the Irish potato famine during the mid-19th century. Various strategies have been applied to control Phytophthora, including integrated management programs (IMPs) and quarantine, but without successful full management of the disease. Thus, there is a need to search for alternative tools. Here, we discuss the emerging role of nanomaterials in the detection and treatment of Phytophthora species, including slow delivery of agrochemicals (microbicides and pesticides). We propose integrating these tools into an IMP, which could lead to a reduction in pesticide use and provide more effective and sustainable control of Phytophthora pathogens.

CRISPR/Cas, Multiomics, and RNA Interference in Virus Disease Management

Plant viruses infect a wide range of commercially important crop plants and cause significant crop production losses worldwide. Numerous alterations in plant physiology related to the reprogramming of gene expression may result from viral infections. Although conventional integrated pest management-based strategies have been effective in reducing the impact of several viral diseases, continued emergence of new viruses and strains, expanding host ranges, and emergence of resistance-breaking strains necessitate a sustained effort toward the development and application of new approaches for virus management that would complement existing tactics. RNA interference-based techniques, and more recently, clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing technologies have paved the way for precise targeting of viral transcripts and manipulation of viral genomes and host factors. In-depth knowledge of the molecular mechanisms underlying the development of disease would further expand the applicability of these recent methods. Advances in next-generation/high-throughput sequencing have made possible more intensive studies into host-virus interactions. Utilizing the omics data and its application has the potential to expedite fast-tracking traditional plant breeding methods, as well as applying modern molecular tools for trait enhancement, including virus resistance. Here, we summarize the recent developments in the CRISPR/Cas system, transcriptomics, endogenous RNA interference, and exogenous application of dsRNA in virus disease management.

Early and Late Transcriptomic and Metabolomic Responses of Rhododendron 'Xiaotaohong' Petals to Infection with Alternaria sp

In recent years, petal blight disease caused by pathogens has become increasingly epidemic in Rhododendron. Breeding disease-resistant rhododendron is considered to be a more environmentally friendly strategy than is the use of chemical reagents. In this study, we aimed to investigate the response mechanisms of rhododendron varieties to petal blight, using transcriptomics and metabolomics analyses. Specifically, we monitored changes in gene expression and metabolite accumulation in Rhododendron 'Xiaotaohong' petals infected with the Alternaria sp. strain (MR-9). The infection of MR-9 led to the development of petal blight and induced significant changes in gene transcription. Differentially expressed genes (DEGs) were predominantly enriched in the plant-pathogen interaction pathway. These DEGs were involved in carrying out stress responses, with genes associated with H2O2 production being up-regulated during the early and late stages of infection. Correspondingly, H2O2 accumulation was detected in the vicinity of the blight lesions. In addition, defense-related genes, including PR and FRK, exhibited significant up-regulated expression during the infection by MR-9. In the late stage of the infection, we also observed significant changes in differentially abundant metabolites (DAMs), including flavonoids, alkaloids, phenols, and terpenes. Notably, the levels of euscaphic acid, ganoderol A, (-)-cinchonidine, and theophylline in infected petals were 21.8, 8.5, 4.5, and 4.3 times higher, respectively, compared to the control. Our results suggest that H2O2, defense-related genes, and DAM accumulation are involved in the complex response mechanisms of Rhododendron 'Xiaotaohong' petals to MR-9 infection. These insights provide a deeper understanding of the pathogenesis of petal blight disease and may have practical implications for developing disease-resistant rhododendron varieties.

Secondary metabolites related to the resistance of Psidium spp. against the nematode Meloidogyneenterolobii

The guava tree (Psidium guajava) is a tropical species native to South America and is recognized as the 11th most economically important fruit tree in Brazil. However, the presence of the nematode Meloidogyne enterolobii and the fungus Fusarium solani in the roots of guava plants leads to the development of root galls, causing significant damage. In contrast, the species P. guineense and P. cattleianum have been identified as resistant and immune to the nematode, respectively. In this study, the researchers aimed to compare the metabolomic profiles of infected and uninfected roots of P. guajava, P. cattleianum, and P. guineense using mass spectrometry coupled with liquid chromatography (LC-MS). The goal was to identify secondary metabolites that could potentially be utilized as biochemical resources for nematode control. The findings of the study demonstrated that the plant metabolism of all three species undergoes alterations in response to the phytopathogen inoculation. By employing molecular networks, the researchers identified that the secondary metabolites affected by the infection, whether produced or suppressed, are primarily of a polar chemical nature. Further analysis of the database confirmed the polar nature of the regulated substances after infection, specifically hydrolysable tannins and lignans in P. guineense and P. cattleianum. Interestingly, a group of non-polar substances belonging to the terpene class was also identified in the resistant and immune species. This suggests that these terpenes may act as inhibitors of M. enterolobii, working as repellents or as molecules that can reduce oxidative stress during the infection process, thus enhancing the guava resistance to the nematode. Overall, this study provides valuable insights into the metabolic alterations occurring in different Psidium spp. in response to M. enterolobii infection. The identification of specific secondary metabolites, particularly terpenes, opens up new possibilities for developing effective strategies to control the nematode and enhance guava resistance.

Genome engineering of disease susceptibility genes for enhancing resistance in plants

Introgression of disease resistance genes (R-genes) to fight against an array of phytopathogens takes several years using conventional breeding approaches. Pathogens develop mechanism(s) to escape plants immune system by evolving new strains/races, thus making them susceptible to disease. Conversely, disruption of host susceptibility factors (or S-genes) provides opportunities for resistance breeding in crops. S-genes are often exploited by phytopathogens to promote their growth and infection. Therefore, identification and targeting of disease susceptibility genes (S-genes) are gaining more attention for the acquisition of resistance in plants. Genome engineering of S-genes results in targeted, transgene-free gene modification through CRISPR-Cas-mediated technology and has been reported in several agriculturally important crops. In this review, we discuss the defense mechanism in plants against phytopathogens, tug of war between R-genes and S-genes, in silico techniques for identification of host-target (S-) genes and pathogen effector molecule(s), CRISPR-Cas-mediated S-gene engineering, its applications, challenges, and future prospects.

Integrated transcriptome and metabolome analysis unveil the response mechanism in wild rice (Zizania latifolia griseb.) against sheath rot infection

Sheath rot disease (SRD) is one of the most devastating diseases of Manchurian wild rice (MWR) (Zizania latifolia Griseb). Pilot experiments in our laboratory have shown that an MWR cultivar "Zhejiao NO.7"exhibits signs of SRD tolerance. To explore the responses of Zhejiao No. 7 to SRD infection, we used a combined transcriptome and metabolome analysis approach. A total of 136 differentially accumulated metabolites (DAMs, 114 up- and 22 down-accumulated in FA compared to CK) were detected. These up-accumulated metabolites were enriched in tryptophan metabolism, amino acid biosynthesis, flavonoids, and phytohormone signaling. Transcriptome sequencing results showed the differential expression of 11,280 genes (DEGs, 5,933 up-, and 5,347 downregulated in FA compared to CK). The genes expressed in tryptophan metabolism, amino acid biosynthesis, phytohormone biosynthesis and signaling, and reactive oxygen species homeostasis confirmed the metabolite results. In addition, genes related to the cell wall, carbohydrate metabolism, and plant-pathogen interaction (especially hypersensitive response) showed changes in expression in response to SRD infection. These results provide a basis for understanding the response mechanisms in MWR to FA attack that can be used for breeding SRD-tolerant MWR.

Can Metabolomic Approaches Become a Tool for Improving Early Plant Disease Detection and Diagnosis with Modern Remote Sensing Methods? A Review

The various areas of ultra-sensitive remote sensing research equipment development have provided new ways for assessing crop states. However, even the most promising areas of research, such as hyperspectral remote sensing or Raman spectrometry, have not yet led to stable results. In this review, the main methods for early plant disease detection are discussed. The best proven existing techniques for data acquisition are described. It is discussed how they can be applied to new areas of knowledge. The role of metabolomic approaches in the application of modern methods for early plant disease detection and diagnosis is reviewed. A further direction for experimental methodological development is indicated. The ways to increase the efficiency of modern early plant disease detection remote sensing methods through metabolomic data usage are shown. This article provides an overview of modern sensors and technologies for assessing the biochemical state of crops as well as the ways to apply them in synergy with existing data acquisition and analysis technologies for early plant disease detection.

Integrative Analysis of Metabolomic and Transcriptomic Data Reveals the Mechanism of Color Formation in Corms of Pinellia ternata

Pinellia ternata (Thunb.) Breit. (P. ternata) is a very important plant that is commonly used in traditional Chinese medicine. Its corms can be used as medicine and function to alleviate cough, headache, and phlegm. The epidermis of P. ternata corms is often light yellow to yellow in color; however, within the range of P. ternata found in JingZhou City in Hubei Province, China, there is a form of P. ternata in which the epidermis of the corm is red. We found that the total flavonoid content of red P. ternata corms is significantly higher than that of yellow P. ternata corms. The objective of this study was to understand the molecular mechanisms behind the difference in epidermal color between the two forms of P. ternata. The results showed that a high content of anthocyanidin was responsible for the red epidermal color in P. ternata, and 15 metabolites, including cyanidin-3-O-rutinoside-5-O-glucoside, cyanidin-3-O-glucoside, and cyanidin-3-O-rutinoside, were screened as potential color markers in P. ternata through metabolomic analysis. Based on an analysis of the transcriptome, seven genes, including PtCHS1, PtCHS2, PtCHI1, PtDFR5, PtANS, PtUPD-GT2, and PtUPD-GT3, were found to have important effects on the biosynthesis of anthocyanins in the P. ternata corm epidermis. Furthermore, two transcription factors (TFs), bHLH1 and bHLH2, may have regulatory functions in the biosynthesis of anthocyanins in red P. ternata corms. Using an integrative analysis of the metabolomic and transcriptomic data, we identified five genes, PtCHI, PtDFR2, PtUPD-GT1, PtUPD-GT2, and PtUPD-GT3, that may play important roles in the presence of the red epidermis color in P. ternata corms.

Untargeted Metabolomics of Alternaria solani-Challenged Wild Tomato Species Solanum cheesmaniae Revealed Key Metabolite Biomarkers and Insight into Altered Metabolic Pathways

Untargeted metabolomics of moderately resistant wild tomato species Solanum cheesmaniae revealed an altered metabolite profile in plant leaves in response to Alternaria solani pathogen. Leaf metabolites were significantly differentiated in non-stressed versus stressed plants. The samples were discriminated not only by the presence/absence of specific metabolites as distinguished markers of infection, but also on the basis of their relative abundance as important concluding factors. Annotation of metabolite features using the Arabidopsis thaliana (KEGG) database revealed 3371 compounds with KEGG identifiers belonging to biosynthetic pathways including secondary metabolites, cofactors, steroids, brassinosteroids, terpernoids, and fatty acids. Annotation using the Solanum lycopersicum database in PLANTCYC PMN revealed significantly upregulated (541) and downregulated (485) features distributed in metabolite classes that appeared to play a crucial role in defense, infection prevention, signaling, plant growth, and plant homeostasis to survive under stress conditions. The orthogonal partial least squares discriminant analysis (OPLS-DA), comprising a significant fold change (≥2.0) with VIP score (≥1.0), showed 34 upregulated biomarker metabolites including 5-phosphoribosylamine, kaur-16-en-18-oic acid, pantothenate, and O-acetyl-L-homoserine, along with 41 downregulated biomarkers. Downregulated metabolite biomarkers were mapped with pathways specifically known for plant defense, suggesting their prominent role in pathogen resistance. These results hold promise for identifying key biomarker metabolites that contribute to disease resistive metabolic traits/biosynthetic routes. This approach can assist in mQTL development for the stress breeding program in tomato against pathogen interactions.

Metabolic profiles of Sri Lankan cassava mosaic virus-infected and healthy cassava (Manihot esculenta Crantz) cultivars with tolerance and susceptibility phenotypes

BACKGROUND

Cassava mosaic disease (CMD) of cassava (Manihot esculenta Crantz) has expanded across many continents. Sri Lankan cassava mosaic virus (SLCMV; family Geminiviridae), which is the predominant cause of CMD in Thailand, has caused agricultural and economic damage in many Southeast Asia countries such as Vietnam, Loas, and Cambodia. The recent SLCMV epidemic in Thailand was commonly found in cassava plantations. Current understanding of plant-virus interactions for SLCMV and cassava is limited. Accordingly, this study explored the metabolic profiles of SLCMV-infected and healthy groups of tolerant (TME3 and KU50) and susceptible (R11) cultivars of cassava. Findings from the study may help to improve cassava breeding, particularly when combined with future transcriptomic and proteomic research.

RESULTS

SLCMV-infected and healthy leaves were subjected to metabolite extraction followed by ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS/MS). The resulting data were analyzed using Compound Discoverer software, the mzCloud, mzVault, and ChemSpider databases, and published literature. Of the 85 differential compounds (SLCMV-infected vs healthy groups), 54 were differential compounds in all three cultivars. These compounds were analyzed using principal component analysis (PCA), hierarchical clustering dendrogram analysis, heatmap analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation. Chlorogenic acid, DL-carnitine, neochlorogenic acid, (E)-aconitic acid, and ascorbyl glucoside were differentially expressed only in TME3 and KU50, with chlorogenic acid, (E)-aconitic acid, and neochlorogenic acid being downregulated in both SLCMV-infected TME3 and KU50, DL-carnitine being upregulated in both SLCMV-infected TME3 and KU50, and ascorbyl glucoside being downregulated in SLCMV-infected TME3 but upregulated in SLCMV-infected KU50. Furthermore, 7-hydroxycoumarine was differentially expressed only in TME3 and R11, while quercitrin, guanine, N-acetylornithine, uridine, vorinostat, sucrose, and lotaustralin were differentially expressed only in KU50 and R11.

CONCLUSIONS

Metabolic profiling of three cassava landrace cultivars (TME3, KU50, and R11) was performed after SLCMV infection and the profiles were compared with those of healthy samples. Certain differential compounds (SLCMV-infected vs healthy groups) in different cultivars of cassava may be involved in plant-virus interactions and could underlie the tolerance and susceptible responses in this important crop.

Decoding Metabolic Reprogramming in Plants under Pathogen Attacks, a Comprehensive Review of Emerging Metabolomics Technologies to Maximize Their Applications

In their environment, plants interact with a multitude of living organisms and have to cope with a large variety of aggressions of biotic or abiotic origin. What has been known for several decades is that the extraordinary variety of chemical compounds the plants are capable of synthesizing may be estimated in the range of hundreds of thousands, but only a fraction has been fully characterized to be implicated in defense responses. Despite the vast importance of these metabolites for plants and also for human health, our knowledge about their biosynthetic pathways and functions is still fragmentary. Recent progress has been made particularly for the phenylpropanoids and oxylipids metabolism, which is more emphasized in this review. With an increasing interest in monitoring plant metabolic reprogramming, the development of advanced analysis methods should now follow. This review capitalizes on the advanced technologies used in metabolome mapping in planta, including different metabolomics approaches, imaging, flux analysis, and interpretation using bioinformatics tools. Advantages and limitations with regards to the application of each technique towards monitoring which metabolite class or type are highlighted, with special emphasis on the necessary future developments to better mirror such intricate metabolic interactions in planta.

The use of evolutionary analyses to predict functionally relevant traits in filamentous plant pathogens

Identifying traits involved in plant-pathogen interactions is one of the major objectives in molecular plant pathology. Evolutionary analyses may assist in the identification of genes encoding traits that are involved in virulence and local adaptation, including adaptation to agricultural intervention strategies. In the past decades, the number of available genome sequences of fungal plant pathogens has rapidly increased, providing a rich source for the discovery of functionally important genes as well as inference of species histories. Positive selection in the form of diversifying or directional selection leaves particular signatures in genome alignments and can be identified with statistical genetics methods. This review summarises the concepts and approaches used in evolutionary genomics and lists major discoveries related to plant-pathogen adaptative evolution. We underline the significant contribution of evolutionary genomics in discovering virulence-related traits and the study of plant-pathogen ecology and adaptive evolution.

Metabolic Profiling Identifies Changes in the Winter Wheat Grains Following Fusarium Treatment at Two Locations in Croatia

Fusarium head blight (FHB) is one of the most dangerous diseases of winter wheat, resulting in reduced grain yield and quality, and production of mycotoxins by the Fusarium fungi. In the present study, changes in the grain metabolomics of winter wheat samples infected with Fusarium spp. and corresponding non-infected samples from two locations in Croatia were investigated by GC-MS. A Mann-Whitney test revealed that 24 metabolites detected were significantly separated between Fusarium-inoculated and non-infected samples during the variety by treatment interactions. The results confirmed that in grains of six FHB-resistant varieties, ten metabolites were identified as possible resistance-related metabolites. These metabolites included heptadecanoic acid, 9-(Z)-hexadecenoic acid, sophorose, and secolaganin in grains of FHB-resistant varieties at the Osijek location, as well as 2-methylaminomethyltartronic acid, maleamic acid, 4-hydroxyphenylacetonitrile, 1,4-lactonearabinonic acid, secolaganin, and alanine in grains of FHB-resistant varieties at the Tovarnik location. Moreover, on the PCA bi-plot, FHB-susceptible wheat varieties were closer to glycyl proline, decanoic acid, and lactic acid dimer that could have affected other metabolites, and thus, suppressed resistance to FHB. Although defense reactions were genetically conditioned and variety specific, resulting metabolomics changes may give insight into defense-related pathways that could be manipulated to engineer plants with improved resistance to the pathogen.

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.

Investigating the Resistance Mechanism of Wheat Varieties to Fusarium Head Blight Using Comparative Metabolomics

Fusarium head blight (FHB) is primarily caused by Fusarium graminearum and severely reduces wheat yield, causing mycotoxin contamination in grains and derived products. F. graminearum-secreted chemical toxins stably accumulate in plant cells, disturbing host metabolic homeostasis. We determined the potential mechanisms underlying FHB resistance and susceptibility in wheat. Three representative wheat varieties (Sumai 3, Yangmai 158, and Annong 8455) were inoculated with F. graminearum and their metabolite changes were assessed and compared. In total, 365 differentiated metabolites were successfully identified. Amino acids and derivatives, carbohydrates, flavonoids, hydroxycinnamate derivatives, lipids, and nucleotides constituted the major changes in response to fungal infection. Changes in defense-associated metabolites, such as flavonoids and hydroxycinnamate derivatives, were dynamic and differed among the varieties. Nucleotide and amino acid metabolism and the tricarboxylic acid cycle were more active in the highly and moderately resistant varieties than in the highly susceptible variety. We demonstrated that two plant-derived metabolites, phenylalanine and malate, significantly suppressed F. graminearum growth. The genes encoding the biosynthetic enzymes for these two metabolites were upregulated in wheat spike during F. graminearum infection. Thus, our findings uncovered the metabolic basis of resistance and susceptibility of wheat to F. graminearum and provided insights into engineering metabolic pathways to enhance FHB resistance in wheat.

Direct introduction MALDI FTICR MS based on dried droplet deposition applied to non-targeted metabolomics on Pisum Sativum root exudates

Non-targeted metabolomic approaches based on direct introduction (DI) through a soft ionization source are nowadays used for large-scale analysis and wide cover-up of metabolites in complex matrices. When coupled with ultra-high-resolution Fourier-Transform ion cyclotron resonance (FTICR MS), DI is generally performed through electrospray (ESI), which, despite the great analytical throughput, can suffer of matrix effects due to residual salts or charge competitors. In alternative, matrix assisted laser desorption ionization (MALDI) coupled with FTICR MS offers relatively high salt tolerance but it is mainly used for imaging of small molecule within biological tissues. In this study, we report a systematic evaluation on the performance of direct introduction ESI and MALDI coupled with FTICR MS applied to the analysis of root exudates (RE), a complex mixture of metabolites released from plant root tips and containing a relatively high salt concentration. Classic dried droplet deposition followed by screening of best matrices and ratio allowed the selection of high ranked conditions for non-targeted metabolomics on RE. Optimization of MALDI parameters led to improved reproducibility and precision. A RE desalted sample was used for comparison on ionization efficiency of the two sources and ion enhancement at high salinity was highlighted in MALDI by spiking desalted solution with inorganic salts. Application of a true lyophilized RE sample exhibited the complementarity of the two sources and the ability of MALDI in the detection of undisclosed metabolites suffering of matrix effects in ESI mode.

A metabolomic platform to identify and quantify polyphenols in coffee and related species using liquid chromatography mass spectrometry

INTRODUCTION

Products of plant secondary metabolism, such as phenolic compounds, flavonoids, alkaloids, and hormones, play an important role in plant growth, development, stress resistance. The plant family Rubiaceae is extremely diverse and abundant in Central America and contains several economically important genera, e.g. Coffea and other medicinal plants. These are known for the production of bioactive polyphenols (e.g. caffeine and quinine), which have had major impacts on human society. The overall goal of this study was to develop a high-throughput workflow to identify and quantify plant polyphenols.

METHODS

First, a method was optimized to extract over 40 families of phytochemicals. Then, a high-throughput metabolomic platform has been developed to identify and quantify 184 polyphenols in 15 min.

RESULTS

The current metabolomics study of secondary metabolites was conducted on leaves from one commercial coffee variety and two wild species that also belong to the Rubiaceae family. Global profiling was performed using liquid chromatography high-resolution time-of-flight mass spectrometry. Features whose abundance was significantly different between coffee species were discriminated using statistical analysis and annotated using spectral databases. The identified features were validated by commercially available standards using our newly developed liquid chromatography tandem mass spectrometry method.

DISCUSSION

Caffeine, trigonelline and theobromine were highly abundant in coffee leaves, as expected. Interestingly, wild Rubiaceae leaves had a higher diversity of phytochemicals in comparison to commercial coffee: defense-related molecules, such as phenylpropanoids (e.g., cinnamic acid), the terpenoid gibberellic acid, and the monolignol sinapaldehyde were found more abundantly in wild Rubiaceae leaves.

Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectives

Plants are natural experts in organic synthesis, being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges. Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry, statistics, and biochemistry. Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites. Metabolomics is usually performed by targeting either a specific cell, a specific tissue, or the entire organism. Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics, in which metabolomics, despite at an earlier developmental stage than genomics, transcriptomics, and proteomics, offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype. Here, we summarize the state of the art of metabolite detection and identification, and illustrate these techniques with four case study applications: (i) comparing metabolite composition within and between species, (ii) assessing spatio-temporal metabolic changes during plant development, (iii) mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses, and (iv) assessing the performance of metabolomics as a means of functional gene identification , metabolic pathway elucidation, and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations. In addition, we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets, including those from genomics, transcriptomics, proteomics, epigenomics, phenomics, microbiomes, and ion-omics studies. Finally, we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.

Unveiling Chemical Interactions Between Plants and Fungi Using Metabolomics Approaches

Metabolomics has been extensively used in clinical studies in the search for new biomarkers of human diseases. However, this approach has also been highlighted in agriculture and biological sciences, once metabolomics studies have been assisting researchers to deduce new chemical mechanisms involved in biological interactions that occur between microorganisms and plants. In this sense, the knowledge of the biological role of each metabolite (virulence factors, signaling compounds, antimicrobial metabolites, among others) and the affected biochemical pathways during the interaction contribute to a better understand of different ecological relationships established in nature. The current chapter addresses five different applications of the metabolomics approach in fungal-plant interactions research: (1) Discovery of biomarkers in pathogen-host interactions, (2) plant diseases diagnosis, (3) chemotaxonomy, (4) plant defense, and (5) plant resistance; using mass spectrometry and/or nuclear magnetic resonance spectroscopy, which are the techniques most used in metabolomics.

Effects of Poty-Potexvirus Synergism on Growth, Photosynthesis and Metabolite Status of Nicotiana benthamiana

Mixed virus infections threaten crop production because interactions between the host and the pathogen mix may lead to viral synergism. While individual infections by potato virus A (PVA), a potyvirus, and potato virus X (PVX), a potexvirus, can be mild, co-infection leads to synergistic enhancement of PVX and severe symptoms. We combined image-based phenotyping with metabolite analysis of single and mixed PVA and PVX infections and compared their effects on growth, photosynthesis, and metabolites in Nicotiana benthamiana. Viral synergism was evident in symptom severity and impaired growth in the plants. Indicative of stress, the co-infection increased leaf temperature and decreased photosynthetic parameters. In contrast, singly infected plants sustained photosynthetic activity. The host's metabolic response differed significantly between single and mixed infections. Over 200 metabolites were differentially regulated in the mixed infection: especially defense-related metabolites and aromatic and branched-chain amino acids increased compared to the control. Changes in the levels of methionine cycle intermediates and a low S-adenosylmethionine/S-adenosylhomocysteine ratio suggested a decline in the methylation potential in co-infected plants. The decreased ratio between reduced glutathione, an important scavenger of reactive oxygen species, and its oxidized form, indicated that severe oxidative stress developed during co-infection. Based on the results, infection-associated oxidative stress is successfully controlled in the single infections but not in the synergistic infection, where activated defense pathways are not sufficient to counter the impact of the infections on plant growth.

Fungal Secondary Metabolites and Small RNAs Enhance Pathogenicity during Plant-Fungal Pathogen Interactions

Fungal plant pathogens use proteinaceous effectors as well as newly identified secondary metabolites (SMs) and small non-coding RNA (sRNA) effectors to manipulate the host plant's defense system via diverse plant cell compartments, distinct organelles, and many host genes. However, most molecular studies of plant-fungal interactions have focused on secreted effector proteins without exploring the possibly equivalent functions performed by fungal (SMs) and sRNAs, which are collectively known as "non-proteinaceous effectors". Fungal SMs have been shown to be generated throughout the plant colonization process, particularly in the early biotrophic stages of infection. The fungal repertoire of non-proteinaceous effectors has been broadened by the discovery of fungal sRNAs that specifically target plant genes involved in resistance and defense responses. Many RNAs, particularly sRNAs involved in gene silencing, have been shown to transmit bidirectionally between fungal pathogens and their hosts. However, there are no clear functional approaches to study the role of these SM and sRNA effectors. Undoubtedly, fungal SM and sRNA effectors are now a treasured land to seek. Therefore, understanding the role of fungal SM and sRNA effectors may provide insights into the infection process and identification of the interacting host genes that are targeted by these effectors. This review discusses the role of fungal SMs and sRNAs during plant-fungal interactions. It will also focus on the translocation of sRNA effectors across kingdoms, the application of cross-kingdom RNA interference in managing plant diseases and the tools that can be used to predict and study these non-proteinaceous effectors.

Differential Metabolomics Reveals Pathogenesis of Pestalotiopsis kenyana Causing Leaf Spot Disease of Zanthoxylum schinifolium

Pepper leaf spot is a common disease of Zanthoxylum schinifolium. When it is serious, it directly affects the growth of Z. schinifolium, making the plant unable to blossom and bear fruit, which seriously restricts the development of the Z. schinifolium industry. Therefore, the pathogenic mechanism of leaf spots should be explored to provide a basis for a comprehensive understanding of the disease. Using liquid chromatography-mass spectrometry (LC-MS) technology combined with the data-dependent acquisition, the full spectrum analysis of pathogen mycelium samples was carried out. Partial least squares discriminant analysis (PLS-DA) was used to reveal the differences in metabolic patterns among different groups. Hierarchical clustering analysis (HCA) and PLS-DA were used to reveal the relationship between samples and metabolites, which reflected the metabolomics changes of Pestalotiopsis kenyana in the logarithmic growth phase of mycelia, the stable growth phase of mycelia, the massive spore stage, the induction culture conditions of PDA and Z. schinifolium leaves, and the possible pathogenic substances were selected for pathogenicity detection. PLS-DA had a strong predictive ability, indicating a clear analysis trend between different groups. The results of the metabolomics analysis showed that the differential metabolites of pathogenic bacteria were abundant at different stages and under different medium conditions, and the content of metabolites changed significantly. There were 3922 differential metabolites in nine groups under positive and negative ion modes, including lipids and lipid molecules, organic acids and their derivatives, organic heterocyclic compounds, organic oxygen compounds, carbohydrate polyketides, nucleosides, nucleotides, and analogs. The results of the pathogenicity test showed that the leaves treated with 3,5-dimethoxy benzoic acid, S-(5-adenosy)-l-homocysteine, 2-(1H-indol-3-yl) acetic acid, l-glutamic acid, and 2-(2-acetyl-3,5-dihydroxy phenyl) acetic acid showed different degrees of yellowish-brown lesions. This indicated that these substances may be related to the pathogenicity of P. kenyana, and the incidence was more serious when treated with 3,5-dimethoxybenzoic acid and S-(5-adenosy)- l -homocysteine. This study provides a basis for further analysis of differential metabolites and provides a theoretical reference for the prevention and treatment of Z. schinifolium leaf spot.

Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops

Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.

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

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

Metabolomic Analysis of Wheat Grains after Tilletia laevis Kühn Infection by Using Ultrahigh-Performance Liquid Chromatography–Q-Exactive Mass Spectrometry

Tilletia laevis causes common bunt disease in wheat, with severe losses of production yield and seed quality. Metabolomics studies provide detailed information about the biochemical changes at the cell and tissue level of the plants. Ultrahigh-performance liquid chromatography–Q-exactive mass spectrometry (UPLC-QE-MS) was used to examine the changes in wheat grains after T. laevis infection. PCA analysis suggested that T. laevis-infected and non-infected samples were scattered separately during the interaction. In total, 224 organic acids and their derivatives, 170 organoheterocyclic compounds, 128 lipids and lipid-like molecules, 85 organic nitrogen compounds, 64 benzenoids, 31 phenylpropanoids and polyketides, 21 nucleosides, nucleotides, their analogues, and 10 alkaloids and derivatives were altered in hyphal-infected grains. According to The Kyoto Encyclopedia of Genes and genomes analysis, the protein digestion and absorption, biosynthesis of amino acids, arginine and proline metabolism, vitamin digestion and absorption, and glycine, serine, and threonine metabolism pathways were activated in wheat crops after T. laevis infection.

Evolution of pathogenicity in obligate fungal pathogens and allied genera

Obligate fungal pathogens (ascomycetes and basidiomycetes) and oomycetes are known to cause diseases in cereal crop plants. They feed on living cells and most of them have learned to bypass the host immune machinery. This paper discusses some of the factors that are associated with pathogenicity drawing examples from ascomycetes, basidiomycetes and oomycetes, with respect to their manifestation in crop plants. The comparisons have revealed a striking similarity in the three groups suggesting convergent pathways that have arisen from three lineages independently leading to an obligate lifestyle. This review has been written with the intent, that new information on adaptation strategies of biotrophs, modifications in pathogenicity strategies and population dynamics will improve current strategies for breeding with stable resistance.

Multi-Omics Approaches to Improve Clubroot Resistance in Brassica with a Special Focus on Brassica oleracea L

Brassica oleracea is an agronomically important species of the Brassicaceae family, including several nutrient-rich vegetables grown and consumed across the continents. But its sustainability is heavily constrained by a range of destructive pathogens, among which, clubroot disease, caused by a biotrophic protist Plasmodiophora brassicae, has caused significant yield and economic losses worldwide, thereby threatening global food security. To counter the pathogen attack, it demands a better understanding of the complex phenomenon of Brassica-P. brassicae pathosystem at the physiological, biochemical, molecular, and cellular levels. In recent years, multiple omics technologies with high-throughput techniques have emerged as successful in elucidating the responses to biotic and abiotic stresses. In Brassica spp., omics technologies such as genomics, transcriptomics, ncRNAomics, proteomics, and metabolomics are well documented, allowing us to gain insights into the dynamic changes that transpired during host-pathogen interactions at a deeper level. So, it is critical that we must review the recent advances in omics approaches and discuss how the current knowledge in multi-omics technologies has been able to breed high-quality clubroot-resistant B. oleracea. This review highlights the recent advances made in utilizing various omics approaches to understand the host resistance mechanisms adopted by Brassica crops in response to the P. brassicae attack. Finally, we have discussed the bottlenecks and the way forward to overcome the persisting knowledge gaps in delivering solutions to breed clubroot-resistant Brassica crops in a holistic, targeted, and precise way.

Computational Metabolomics Tools Reveal Metabolic Reconfigurations Underlying the Effects of Biostimulant Seaweed Extracts on Maize Plants under Drought Stress Conditions

Drought is one of the major abiotic stresses causing severe damage and losses in economically important crops worldwide. Drought decreases the plant water status, leading to a disruptive metabolic reprogramming that negatively affects plant growth and yield. Seaweed extract-based biostimulants show potential as a sustainable strategy for improved crop health and stress resilience. However, cellular, biochemical, and molecular mechanisms governing the agronomically observed benefits of the seaweed extracts on plants are still poorly understood. In this study, a liquid chromatography–mass spectrometry-based untargeted metabolomics approach combined with computational metabolomics strategies was applied to unravel the molecular ‘stamps’ that define the effects of seaweed extracts on greenhouse-grown maize (Zea mays) under drought conditions. We applied mass spectral networking, substructure discovery, chemometrics, and metabolic pathway analyses to mine and interpret the generated mass spectral data. The results showed that the application of seaweed extracts induced alterations in the different pathways of primary and secondary metabolism, such as phenylpropanoid, flavonoid biosynthesis, fatty acid metabolism, and amino acids pathways. These metabolic changes involved increasing levels of phenylalanine, tryptophan, coumaroylquinic acid, and linolenic acid metabolites. These metabolic alterations are known to define some of the various biochemical and physiological events that lead to enhanced drought resistance traits. The latter include root growth, alleviation of oxidative stress, improved water, and nutrient uptake. Moreover, this study demonstrates the use of molecular networking in annotating maize metabolome. Furthermore, the results reveal that seaweed extract-based biostimulants induced a remodeling of maize metabolism, subsequently readjusting the plant towards stress alleviation, for example, by increasing the plant height and diameter through foliar application. Such insights add to ongoing efforts in elucidating the modes of action of biostimulants, such as seaweed extracts. Altogether, our study contributes to the fundamental scientific knowledge that is necessary for the development of a biostimulants industry aiming for a sustainable food security.

Metabolic Profiling of White and Green Radish Cultivars (Raphanus sativus)

Radish (Raphanus sativus) is a Brassica vegetable important for human nutrition and health because it is rich in diverse metabolites. Although previous studies have evaluated various metabolites, few studies have comprehensively profiled the primary and secondary metabolites in the roots of white- and green-colored radishes. Thus, this study aimed to provide information about the contents of metabolites beneficial for human health in both cultivars and to investigate the relationships between the various metabolites detected. In particular, among the 55 metabolites detected in radish roots, the levels of most amino acids and phenolic acids, vital to nutrition and health, were higher in green radish roots, while slightly higher levels of glucosinolates were observed in white radish roots—information which can be used to develop an effective strategy to promote vegetable consumption. Furthermore, glutamic acid, as a metabolic precursor of amino acids and chlorophylls, was positively correlated with other amino acids (cysteine, tryptophan, asparagine, alanine, serine, phenylalanine, valine, isoleucine, proline, leucine, beta-alanine, lysine, and GABA), and chlorophylls (chlorophyll a and chlorophyll b) detected in radish roots and phenylalanine, a metabolic precursor of phenolic compounds, were positively correlated with kaempferol, 4-hydroxybenzoate, and catechin. In addition, strong positive correlations between carbohydrates (sucrose and glucose) and phenolics were observed in this study, indicating that sucrose and glucose function as energy sources for phenolic compounds.

Metabolomic Insights Into Endophyte-Derived Bioactive Compounds

Among the various plant-associated microbiota, endophytes (the microbial communities inhabiting plant endosphere without causing disease symptoms) exhibit the most intimate and specific association with host plants. Endophytic microbes influence various aspects of plant responses (such as increasing availability of nutrients, tolerance against biotic and abiotic stresses, etc.) by modulating the primary and secondary metabolism of the host. Besides, endophytic microbes produce a diverse array of bioactive compounds, which have potential applications in the pharmaceutical, food, and cosmetic industries. Further, there is sufficient evidence for endophyte-derived plant metabolites, which could be pursued as alternative sources of commercially important plant metabolites. The field of bioprospecting, the discovery of novel chemistries, and endophyte-mediated production of plant metabolites have witnessed a boom with the advent of omics technologies (especially metabolomics) in endophyte research. The high throughput study of small metabolites at a particular timepoint or tissue forms the core of metabolomics. Being downstream to transcriptome and proteome, the metabolome provides the most direct reflection of the phenotype of an organism. The contribution of plant and microbial metabolomics for answering fundamental questions of plant-endophyte interaction, such as the effect of endophyte inoculation on plant metabolome, composition of metabolites on the impact of environmental stressors (biotic and abiotic), etc., have also been discussed.

Metabolomic Characterisation of Discriminatory Metabolites Involved in Halo Blight Disease in Oat Cultivars Caused by Pseudomonas syringae pv. coronafaciens

The metabolome is the underlying biochemical layer of the phenotype and offers a functional readout of the cellular mechanisms involved in a biological system. Since metabolites are considered end-products of regulatory processes at a cellular level, their levels are considered the definitive response of the biological system to genetic or environmental variations. The metabolome thus serves as a metabolic fingerprint of the biochemical events that occur in a biological system under specific conditions. In this study, an untargeted metabolomics approach was applied to elucidate biochemical processes implicated in oat plant responses to Pseudomonas syringae pv. coronafaciens (Ps-c) infection, and to identify signatory markers related to defence responses and disease resistance against halo blight. Metabolic changes in two oat cultivars (“Dunnart” and “SWK001”) responding to Ps-c, were examined at the three-leaf growth stage and metabolome changes monitored over a four-day post-inoculation period. Hydromethanolic extracts were analysed using an ultra-high-performance liquid chromatography (UHPLC) system coupled to a high-definition mass spectrometer (MS) analytical platform. The acquired multi-dimensional data were processed using multivariate statistical analysis and chemometric modelling. The validated chemometric models indicated time- and cultivar-related metabolic changes, defining the host response to the bacterial inoculation. Further multivariate analyses of the data were performed to profile differential signatory markers, putatively associated with the type of launched defence response. These included amino acids, phenolics, phenolic amides, fatty acids, flavonoids, alkaloids, terpenoids, lipids, saponins and plant hormones. Based on the results, metabolic alterations involved in oat defence responses to Ps-c were elucidated and key signatory metabolic markers defining the defence metabolome were identified. The study thus contributes toward a more holistic understanding of the oat metabolism under biotic stress.

Rhizosphere Tripartite Interactions and PGPR-Mediated Metabolic Reprogramming towards ISR and Plant Priming: A Metabolomics Review

Plant growth-promoting rhizobacteria (PGPR) are beneficial microorganisms colonising the rhizosphere. PGPR are involved in plant growth promotion and plant priming against biotic and abiotic stresses. Plant-microbe interactions occur through chemical communications in the rhizosphere and a tripartite interaction mechanism between plants, pathogenic microbes and plant-beneficial microbes has been defined. However, comprehensive information on the rhizosphere communications between plants and microbes, the tripartite interactions and the biochemical implications of these interactions on the plant metabolome is minimal and not yet widely available nor well understood. Furthermore, the mechanistic nature of PGPR effects on induced systemic resistance (ISR) and priming in plants at the molecular and metabolic levels is yet to be fully elucidated. As such, research investigating chemical communication in the rhizosphere is currently underway. Over the past decades, metabolomics approaches have been extensively used in describing the detailed metabolome of organisms and have allowed the understanding of metabolic reprogramming in plants due to tripartite interactions. Here, we review communication systems between plants and microorganisms in the rhizosphere that lead to plant growth stimulation and priming/induced resistance and the applications of metabolomics in understanding these complex tripartite interactions.

How do plants defend themselves against pathogens-Biochemical mechanisms and genetic interventions

In agro-ecosystem, plant pathogens hamper food quality, crop yield, and global food security. Manipulation of naturally occurring defense mechanisms in host plants is an effective and sustainable approach for plant disease management. Various natural compounds, ranging from cell wall components to metabolic enzymes have been reported to protect plants from infection by pathogens and hence provide specific resistance to hosts against pathogens, termed as induced resistance. It involves various biochemical components, that play an important role in molecular and cellular signaling events occurring either before (elicitation) or after pathogen infection. The induction of reactive oxygen species, activation of defensive machinery of plants comprising of enzymatic and non-enzymatic antioxidative components, secondary metabolites, pathogenesis-related protein expression (e.g. chitinases and glucanases), phytoalexin production, modification in cell wall composition, melatonin production, carotenoids accumulation, and altered activity of polyamines are major induced changes in host plants during pathogen infection. Hence, the altered concentration of biochemical components in host plants restricts disease development. Such biochemical or metabolic markers can be harnessed for the development of "pathogen-proof" plants. Effective utilization of the key metabolites-based metabolic markers can pave the path for candidate gene identification. This present review discusses the valuable information for understanding the biochemical response mechanism of plants to cope with pathogens and genomics-metabolomics-based sustainable development of pathogen proof cultivars along with knowledge gaps and future perspectives to enhance sustainable agricultural production.

Deploying Viruses against Phytobacteria: Potential Use of Phage Cocktails as a Multifaceted Approach to Combat Resistant Bacterial Plant Pathogens

Plants in nature are under the persistent intimidation of severe microbial diseases, threatening a sustainable food production system. Plant-bacterial pathogens are a major concern in the contemporary era, resulting in reduced plant growth and productivity. Plant antibiotics and chemical-based bactericides have been extensively used to evade plant bacterial diseases. To counteract this pressure, bacteria have evolved an array of resistance mechanisms, including innate and adaptive immune systems. The emergence of resistant bacteria and detrimental consequences of antimicrobial compounds on the environment and human health, accentuates the development of an alternative disease evacuation strategy. The phage cocktail therapy is a multidimensional approach effectively employed for the biocontrol of diverse resistant bacterial infections without affecting the fauna and flora. Phages engage a diverse set of counter defense strategies to undermine wide-ranging anti-phage defense mechanisms of bacterial pathogens. Microbial ecology, evolution, and dynamics of the interactions between phage and plant-bacterial pathogens lead to the engineering of robust phage cocktail therapeutics for the mitigation of devastating phytobacterial diseases. In this review, we highlight the concrete and fundamental determinants in the development and application of phage cocktails and their underlying mechanism, combating resistant plant-bacterial pathogens. Additionally, we provide recent advances in the use of phage cocktail therapy against phytobacteria for the biocontrol of devastating plant diseases.

Metabolomic Evaluation of Ralstonia solanacearum Cold Shock Protein Peptide (csp22)-Induced Responses in Solanum lycopersicum

Ralstonia solanacearum, the causal agent of bacterial wilt, is one of the most destructive bacterial plant pathogens. This is linked to its evolutionary adaptation to evade host surveillance during the infection process since many of the pathogen's associated molecular patterns escape recognition. However, a 22-amino acid sequence of R. solanacearum-derived cold shock protein (csp22) was discovered to elicit an immune response in the Solanaceae. Using untargeted metabolomics, the effects of csp22-elicitation on the metabolome of Solanum lycopersicum leaves were investigated. Additionally, the study set out to discover trends that may suggest that csp22 inoculation bestows enhanced resistance on tomato against bacterial wilt. Results revealed the redirection of metabolism toward the phenylpropanoid pathway and sub-branches thereof. Compared to the host response with live bacteria, csp22 induced a subset of the discriminant metabolites, but also metabolites not induced in response to R. solanacearum. Here, a spectrum of hydroxycinnamic acids (especially ferulic acid), their conjugates and derivatives predominated as signatory biomarkers. From a metabolomics perspective, the results support claims that csp22 pre-treatment of tomato plants elicits increased resistance to R. solanacearum infection and contribute to knowledge on plant immune systems operation at an integrative level. The functional significance of these specialized compounds may thus support a heightened state of defense that can be applied to ward off attacking pathogens or toward priming of defense against future infections.