Comparative Metabolic Phenotyping of Tomato (Solanum lycopersicum) for the Identification of Metabolic Signatures in Cultivars Differing in Resistance to Ralstonia solanacearum

Identification of antioxidant and flavour marker compounds in Kalosi-Enrekang Arabica brewed coffee processed using different postharvest treatment methods

This research aims to predict the presence of marker compounds that differentiate tubruk brew from coffee beans with different postharvest processing. This research also aims to predict compounds correlating with antioxidant activity and sensory flavour attributes. This research used Kalosi-Enrekang Arabica coffee beans, which were processed with three different postharvest processing (honey, full-washed and natural), roasted at medium level, and brewed using the tubruk method. Each brew was analyzed for chemical profiles using LC-MS and GC-MS, antioxidant analysis using the DPPH IC50 and FRAP methods, and sensory analysis for flavour using the QDA and SCAA methods for cupping scores. OPLS-DA analysis revealed the presence of marker compounds from each brew, and the dried fruit flavour attribute was to be an inter-process marker. After that, OPLS analysis showed marker compounds that correlate to antioxidant activity and flavour attributes. Rhaponticin is thought to be one of the marker compounds in natural coffee brews and is one of the compounds that correlates to the antioxidant activity of the DPPH method (IC50); prunin is thought to be one of the marker compounds for full-washed coffee brews and is one of the compounds that correlates to the activity antioxidants of FRAP method. Triacetin, which is thought to be a marker compound in natural brewed coffee, correlates with fruity flavour. 3-acetylpyridine, as a marker in honey-brewed coffee, correlates with nutty flavour. Even though there are differences in dominant flavours, the cupping score shows the brew is categorized as a specialty. This research shows that different post-harvest processing processes influence the compound profile, antioxidant activity and flavour attributes of Tubruk brewed coffee.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-024-05948-8.

Ralstonia solanacearum pandemic lineage strain UW551 overcomes inhibitory xylem chemistry to break tomato bacterial wilt resistance

Plant-pathogenic Ralstonia strains cause bacterial wilt disease by colonizing xylem vessels of many crops, including tomato. Host resistance is the best control for bacterial wilt, but resistance mechanisms of the widely used Hawaii 7996 tomato breeding line (H7996) are unknown. Using growth in ex vivo xylem sap as a proxy for host xylem, we found that Ralstonia strain GMI1000 grows in sap from both healthy plants and Ralstonia-infected susceptible plants. However, sap from Ralstonia-infected H7996 plants inhibited Ralstonia growth, suggesting that in response to Ralstonia infection, resistant plants increase inhibitors in their xylem sap. Consistent with this, reciprocal grafting and defence gene expression experiments indicated that H7996 wilt resistance acts in both above- and belowground plant parts. Concerningly, H7996 resistance is broken by Ralstonia strain UW551 of the pandemic lineage that threatens highland tropical agriculture. Unlike other Ralstonia, UW551 grew well in sap from Ralstonia-infected H7996 plants. Moreover, other Ralstonia strains could grow in sap from H7996 plants previously infected by UW551. Thus, UW551 overcomes H7996 resistance in part by detoxifying inhibitors in xylem sap. Testing a panel of xylem sap compounds identified by metabolomics revealed that no single chemical differentially inhibits Ralstonia strains that cannot infect H7996. However, sap from Ralstonia-infected H7996 contained more phenolic compounds, which are known to be involved in plant antimicrobial defence. Culturing UW551 in this sap reduced total phenolic levels, indicating that the resistance-breaking Ralstonia strain degrades these chemical defences. Together, these results suggest that H7996 tomato wilt resistance depends in part on inducible phenolic compounds in xylem sap.

Ralstonia solanacearum Suppresses Tomato Root Growth by Downregulation of a Wall-Associated Receptor Kinase

The root architecture of a range of host plants is altered in response to Ralstonia solanacearum infection. This work aimed to identify host genes involved in root development during R. solanacearum infection. A deficient mutant of the type III secretion system regulator hrpB was created in R. solanacearum GMI1000. The hrpB mutant was impaired in virulence but showed a similar suppressive effect as wild-type GMI1000 on tomato root development. Based on comparative transcriptome analysis, 209 genes were found that showed the same changed expression pattern in GMI1000 and hrpB mutant infected roots relative to uninoculated roots. Among them, the wall-associated receptor kinase WAKL20 was substantially downregulated in GMI1000 and hrpB mutant infected roots. Knockdown of WAKL20 led to a shorter primary root length and fewer lateral roots in tomato as well as in Nicotiana benthamiana. The WAKL20 is a pivotal target suppressed by R. solanacearum to shape the altered root development during infection.

Lipopolysaccharides from Ralstonia solanacearum induce a broad metabolomic response in Solanum lycopersicum

Ralstonia solanacearum, one of the most destructive crop pathogens worldwide, causes bacterial wilt disease in a wide range of host plants. The major component of the outer membrane of Gram-negative bacteria, lipopolysaccharides (LPS), has been shown to function as elicitors of plant defense leading to the activation of signaling and defense pathways in several plant species. LPS from a R. solanacearum strain virulent on tomato (LPSR. sol.), were purified, chemically characterized, and structurally elucidated. The lipid A moiety consisted of tetra- to hexa-acylated bis-phosphorylated disaccharide backbone, also decorated by aminoarabinose residues in minor species, while the O-polysaccharide chain consisted of either linear tetrasaccharide or branched pentasaccharide repeating units containing α-L-rhamnose, N-acetyl-β-D-glucosamine, and β-L-xylose. These properties might be associated with the evasion of host surveillance, aiding the establishment of the infection. Using untargeted metabolomics, the effect of LPSR. sol. elicitation on the metabolome of Solanum lycopersicum leaves was investigated across three incubation time intervals with the application of UHPLC-MS for metabolic profiling. The results revealed the production of oxylipins, e.g., trihydroxy octadecenoic acid and trihydroxy octadecadienoic acid, as well as several hydroxycinnamic acid amide derivatives, e.g., coumaroyl tyramine and feruloyl tyramine, as phytochemicals that exhibit a positive correlation to LPSR. sol. treatment. Although the chemical properties of these metabolite classes have been studied, the functional roles of these compounds have not been fully elucidated. Overall, the results suggest that the features of the LPSR. sol. chemotype aid in limiting or attenuating the full deployment of small molecular host defenses and contribute to the understanding of the perturbation and reprogramming of host metabolism during biotic immune responses.

Metabolite profiling of susceptible and resistant wheat (Triticum aestivum) cultivars responding to Puccinia striiformis f. sp. tritici infection

BACKGROUND

Puccinia striiformis f. sp. tritici (Pst) is an economically devasting disease that is prominent in cereal crops such as wheat (Triticum aestivum). The fungal pathogen can cause approximately 30-70% losses in crop productivity and yields. Pst has become difficult to manage due to its ease of transmission through wind dispersal over long distances, and intercontinental dispersal has been previously reported. The ease of transmission has resulted in further destruction because of new and more virulent strains infecting crops previously resistant to a different strain.

RESULTS

In this study, a liquid chromatography-mass spectrometry-based untargeted metabolomics approach, in combination with multivariate data analytical tools, was used to elucidate the mechanistic nature of the defence systems of a Pst-resistant and a susceptible wheat cultivar infected with P. striiformis. We also investigated the time-dependant metabolic reconfiguration of infected plants over a four-week period. The untargeted metabolomic analysis revealed a time-course metabolic reprogramming involving phenylpropanoids (majority flavonoids), amino acids, lipids, benzoic acids, TCA cycle intermediates and benzoxazinoids responding to Pst infection. Interestingly, the results do not show a linear course for the decrease and increase (up-/down-regulation) of said classes of metabolites, but rather the up- or down-regulation of specific metabolites in response to the pathogen infection. The resistant Koonap cultivar had an abundance of phenolic compounds such as rutin, isoorintin-7-O-glucoside and luteolin-6-C-hexoside-O-hexoside. These compounds showed a decrease over time in control Koonap plants compared to an increase in Pst-infected plants. These metabolites were down-regulated in the susceptible Gariep cultivar, which could serve as biomarkers for plant responses to biotic stress and resistance against Pst.

CONCLUSIONS

Overall, an LC-MS-based metabolomics approach allowed for the metabolic profiling and analysis of the impact of plant-pathogen interactions on the overall plant metabolome and provided a real-time snapshot of the differential significant metabolic perturbations occurring in wheat plants responding to the Pst pathogen. The Pst-resistant Koonap cultivar showed a rapid accumulation of defence metabolites in response to pathogen infection compared to the susceptible Gariep cultivar. These findings provide insight into the mechanistic biochemical nature of plant-microbe interactions and the prospects of metabolic engineering for improved plant tolerance and resistance to biotic stresses.

Solanum dulcamara L. Berries: A Convenient Model System to Study Redox Processes in Relation to Fruit Ripening

The present study provides, for the first time, a physicochemical and biochemical characterization of the redox processes associated with the ripening of Solanum dulcamara L. (bittersweet) berries. Electron Paramagnetic Resonance Spectroscopy (EPRS) and Imaging (EPRI) measurements of reactive oxygen species (ROS) were performed in parallel with the tissue-specific metabolic profiling of major antioxidants and assessment of antioxidant enzymes activity. Fruit transition from the mature green (MG) to ripe red (RR) stage involved changes in the qualitative and quantitative content of antioxidants and the associated cellular oxidation and peroxidation processes. The skin of bittersweet berries, which was the major source of antioxidants, exhibited the highest antioxidant potential against DPPH radicals and nitroxyl spin probe 3CP. The efficient enzymatic antioxidant system played a critical protective role against the deleterious effects of progressive oxidative stress during ripening. Here, we present the EPRI methodology to assess the redox status of fruits and to discriminate between the redox states of different tissues. Interestingly, the intracellular reoxidation of cell-permeable nitroxide probe 3CP was observed for the first time in fruits or any other plant tissue, and its intensity is herein proposed as a reliable indicator of oxidative stress during ripening. The described noninvasive EPRI technique has the potential to have broader application in the study of redox processes associated with the development, senescence, and postharvest storage of fruits, as well as other circumstances in which oxidative stress is implicated.

Induced defense strategies of plants against Ralstonia solanacearum

Plants respond to Ralstonia solanacearum infestation through two layers of immune system (PTI and ETI). This process involves the production of plant-induced resistance. Strategies for inducing resistance in plants include the formation of tyloses, gels, and callose and changes in the content of cell wall components such as cellulose, hemicellulose, pectin, lignin, and suberin in response to pathogen infestation. When R. solanacearum secrete cell wall degrading enzymes, plants also sense the status of cell wall fragments through the cell wall integrity (CWI) system, which activates deep-seated defense responses. In addition, plants also fight against R. solanacearum infestation by regulating the distribution of metabolic networks to increase the production of resistant metabolites and reduce the production of metabolites that are easily exploited by R. solanacearum. We review the strategies used by plants to induce resistance in response to R. solanacearum infestation. In particular, we highlight the importance of plant-induced physical and chemical defenses as well as cell wall defenses in the fight against R. solanacearum.

Transcriptome and metabolome response of eggplant against Ralstonia solanacearum infection

Bacterial wilt is a soil-borne disease that represents ubiquitous threat to Solanaceae crops. The whole-root transcriptomes and metabolomes of bacterial wilt-resistant eggplant were studied to understand the response of eggplant to bacterial wilt. A total of 2,896 differentially expressed genes and 63 differences in metabolites were identified after inoculation with Ralstonia solanacearum. Further analysis showed that the biosynthesis pathways for phytohormones, phenylpropanoids, and flavonoids were altered in eggplant after inoculation with R. solanacearum. The results of metabolomes also showed that phytohormones played a key role in eggplant response to bacterial wilt. Integrated analyses of the transcriptomic and metabolic datasets indicated that jasmonic acid (JA) content and gene involved in the JA signaling pathway increased in response to bacterial wilt. These findings remarkably improve our understanding of the mechanisms of induced defense response in eggplant and will provide insights intothe development of disease-resistant varieties of eggplant.

Detection of Markers in Green Beans and Roasted Beans of Kalosi-Enrekang Arabica Coffee with Different Postharvest Processing Using LC-MS/MS

Our study is aimed at evaluating the effect of postharvest processing (natural, honey, and fully washed) on the compounds profile in green beans and roasted beans of Kalosi-Enrekang Arabica coffee and determining the marker compounds for each process. These beans were extracted using boiling water, and the extract was analyzed using LC-MS/MS. The results of this work confirmed the significant impact of postharvest processing on compounds in the coffee beans, and each process has a marker compound. Green beans by natural processing have 3 marker compounds, honey processing has 6 marker compounds, and fully washed processing has 2 marker compounds. Meanwhile, roasted beans by natural processing have 4 marker compounds, honey processing has 5 marker compounds, and fully washed processing has 7 marker compounds. In addition, our research identified caffeoyl tyrosine in green beans from natural and honey processing, which was previously only identified in Robusta coffee. These marker compounds can differentiate postharvest processing (natural, honey, and fully washed). These results can also help understand the effect of postharvest processing on the chemical composition of green and roasted beans.

Metabolomic evaluation of PGPR defence priming in wheat (Triticum aestivum L.) cultivars infected with Puccinia striiformis f. sp. tritici (stripe rust)

Plant-microbe interactions are a phenomenal display of symbiotic/parasitic relationships between living organisms. Plant growth-promoting rhizobacteria (PGPR) are some of the most widely investigated plant-beneficial microbes due to their capabilities in stimulating plant growth and development and conferring protection to plants against biotic and abiotic stresses. As such, PGPR-mediated plant priming/induced systemic resistance (ISR) has become a hot topic among researchers, particularly with prospects of applications in sustainable agriculture. The current study applies untargeted ultra-high performance liquid chromatography-high-definition mass spectrometry (UHPLC-HDMS) to investigate PGPR-based metabolic reconfigurations in the metabolome of primed wheat plants against Puccinia striiformis f. sp. tricti (Pst). A seed bio-priming approach was adopted, where seeds were coated with two PGPR strains namely Bacillus subtilis and Paenibacillus alvei (T22) and grown under controlled conditions in a glasshouse. The plants were infected with Pst one-week post-germination, followed by weekly harvesting of leaf material. Subsequent metabolite extraction was carried out for analysis on a UHPLC-HDMS system for data acquisition. The data was chemometrically processed to reveal the underlying trends and data structures as well as potential signatory biomarkers for priming against Pst. Results showed notable metabolic reprogramming in primary and secondary metabolism, where the amino acid and organic acid content of primed-control, primed-challenged and non-primed-challenged plants were differentially reprogrammed. Similar trends were observed from the secondary metabolism, in which primed plants (particularly primed-challenged) showed an up-regulation of phenolic compounds (flavonoids, hydroxycinnamic acids-HCAs- and HCA amides) compared to the non-primed plants. The metabolomics-based semi-quantitative and qualitative assessment of the plant metabolomes revealed a time-dependent metabolic reprogramming in primed-challenged and primed-unchallenged plants, indicating the metabolic adaptations of the plants to stripe rust infection over time.

Untargeted metabolite profiling to elucidate rhizosphere and leaf metabolome changes of wheat cultivars (Triticum aestivum L.) treated with the plant growth-promoting rhizobacteria Paenibacillus alvei (T22) and Bacillus subtilis

The rhizosphere is a highly complex and biochemically diverse environment that facilitates plant–microbe and microbe–microbe interactions, and this region is found between plant roots and the bulk soil. Several studies have reported plant root exudation and metabolite secretion by rhizosphere-inhabiting microbes, suggesting that these metabolites play a vital role in plant–microbe interactions. However, the biochemical constellation of the rhizosphere soil is yet to be fully elucidated and thus remains extremely elusive. In this regard, the effects of plant growth-promoting rhizobacteria (PGPR)–plant interactions on the rhizosphere chemistry and above ground tissues are not fully understood. The current study applies an untargeted metabolomics approach to profile the rhizosphere exo-metabolome of wheat cultivars generated from seed inoculated (bio-primed) with Paenibacillus (T22) and Bacillus subtilis strains and to elucidate the effects of PGPR treatment on the metabolism of above-ground tissues. Chemometrics and molecular networking tools were used to process, mine and interpret the acquired mass spectrometry (MS) data. Global metabolome profiling of the rhizosphere soil of PGPR-bio-primed plants revealed differential accumulation of compounds from several classes of metabolites including phenylpropanoids, organic acids, lipids, organoheterocyclic compounds, and benzenoids. Of these, some have been reported to function in plant–microbe interactions, chemotaxis, biocontrol, and plant growth promotion. Metabolic perturbations associated with the primary and secondary metabolism were observed from the profiled leaf tissue of PGPR-bio-primed plants, suggesting a distal metabolic reprograming induced by PGPR seed bio-priming. These observations gave insights into the hypothetical framework which suggests that PGPR seed bio-priming can induce metabolic changes in plants leading to induced systemic response for adaptation to biotic and abiotic stress. Thus, this study contributes knowledge to ongoing efforts to decipher the rhizosphere metabolome and mechanistic nature of biochemical plant–microbe interactions, which could lead to metabolome engineering strategies for improved plant growth, priming for defense and sustainable agriculture.

Cytotoxic evaluation and chemical investigation of tomatoes from plants (Solanum lycopersicum L.) grown in uncontaminated and experimentally contaminated soils

The aim of this study was to evaluate the cytotoxic activity and the chemical composition of the tomato extracts coming from, Pomodoro Giallo and San Marzano Cirio 3, and then to evaluate the potential changes when plants were grown in soils contaminated by cadmium, chromium and lead. Extracts were investigated by UHPLC-HRMS and UV–Vis. Cell viability (CellTiter-Glo Luminescent assay), enzyme aldehyde dehydrogenase activity (ALDEFLOUR Assay), cell cycle progression (Accuri C6 Flow Cytometer), apoptosis and necrosis (Annexin V-FITC assay) were evaluated on two gastric cancer (AGS and NCI-N87) and two colorectal cancer (HT-29 and HCT 116) cell lines. Different content of polyphenol and carotenoid constituents was observed. Extracts from uncontaminated soil induced cytotoxic activity towards all selected cancer cells, while extracts coming from contaminated soils showed the aberrant phenotype increased in colorectal cancer cells. Chloroform extracts exerted the highest cytotoxic activity. AGS and HT-29 were the most sensitive to cell cycle arrest and to apoptosis. No necrotic effect was observed in HCT 116. The contrasting effects on cancer cells were observed based on tomato variety, the extract polarity, heavy metal identity, and tested cell line. The investigation of potential adverse health effects due to Cd in the fruits should be explored.

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.

Comparative Metabolite Profiling of Wheat Cultivars (Triticum aestivum) Reveals Signatory Markers for Resistance and Susceptibility to Stripe Rust and Aluminium (Al3+) Toxicity

Plants continuously produce essential metabolites that regulate their growth and development. The enrichment of specific metabolites determines plant interactions with the immediate environment, and some metabolites become critical in defence responses against biotic and abiotic stresses. Here, an untargeted UHPLC-qTOF-MS approach was employed to profile metabolites of wheat cultivars resistant or susceptible to the pathogen Puccinia striiformis f. sp. tritici (Pst) and Aluminium (Al³⁺) toxicity. Multivariate statistical analysis (MVDA) tools, viz. principal component analysis (PCA) and hierarchical cluster analysis (HiCA) were used to qualify the correlation between the identified metabolites and the designated traits. A total of 100 metabolites were identified from primary and secondary metabolisms, including phenolic compounds, such as flavonoid glycosides and hydroxycinnamic acid (HCA) derivatives, fatty acids, amino acids, and organic acids. All metabolites were significantly variable among the five wheat cultivars. The Pst susceptible cultivars demonstrated elevated concentrations of HCAs compared to their resistant counterparts. In contrast, ‘Koonap’ displayed higher levels of flavonoid glycosides, which could point to its resistant phenotype to Pst and Al³⁺ toxicity. The data provides an insight into the metabolomic profiles and thus the genetic background of Pst- and Al³⁺-resistant and susceptible wheat varieties. This study demonstrates the prospects of applied metabolomics for chemotaxonomic classification, phenotyping, and potential use in plant breeding and crop improvement.

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.

Altered metabolomic states elicited by Flg22 and FlgII-28 in Solanum lycopersicum: intracellular perturbations and metabolite defenses

BACKGROUND

Surveillance of potential pathogens is a key feature of plant innate immunity. For non-self-recognition plants rely on the perception of pathogen-derived molecules. Early post-perception events activate signaling cascades, leading to the synthesis of defense-related proteins and specialized metabolites, thereby providing a broad-spectrum antimicrobial coverage. This study was concerned with tracking changes in the tomato plant metabolome following perception of the flagellum-derived elicitors (Flg22 and FlgII-28).

RESULTS

Following an untargeted metabolomics workflow, the metabolic profiles of a Solanum lycopersicum cultivar were monitored over a time range of 16-32 h post-treatment. Liquid chromatography was used to resolve the complex mixture of metabolites and mass spectrometry for the detection of differences associated with the elicitor treatments. Stringent data processing and multivariate statistical tools were applied to the complex dataset to extract relevant metabolite features associated with the elicitor treatments. Following perception of Flg22 and FlgII-28, both elicitors triggered an oxidative burst, albeit with different kinetic responses. Signatory biomarkers were annotated from diverse metabolite classes which included amino acid derivatives, lipid species, steroidal glycoalkaloids, hydroxybenzoic acids, hydroxycinnamic acids and derivatives, as well as flavonoids.

CONCLUSIONS

An untargeted metabolomics approach adequately captured the subtle and nuanced perturbations associated with elicitor-linked plant defense responses. The shared and unique features characterizing the metabolite profiles suggest a divergence of signal transduction events following perception of Flg22 vs. FlgII-28, leading to a differential reorganization of downstream metabolic pathways.

Metabolomic Evaluation of Tissue-Specific Defense Responses in Tomato Plants Modulated by PGPR-Priming against Phytophthora capsici Infection

Plant growth-promoting rhizobacteria (PGPR) can stimulate disease suppression through the induction of an enhanced state of defense readiness. Here, untargeted ultra-high performance liquid chromatography–mass spectrometry (UHPLC–MS) and targeted ultra-high performance liquid chromatography coupled to triple-quadrupole mass spectrometry (UHPLC–QqQ-MS) were used to investigate metabolic reprogramming in tomato plant tissues in response to priming by Pseudomonas fluorescens N04 and Paenibacillus alvei T22 against Phytophthora capsici. Roots were treated with the two PGPR strains prior to stem inoculation with Ph. capsici. Metabolites were methanol-extracted from roots, stems and leaves at two–eight days post-inoculation. Targeted analysis by UHPLC–QqQ-MS allowed quantification of aromatic amino acids and phytohormones. For untargeted analysis, UHPLC–MS data were chemometrically processed to determine signatory biomarkers related to priming against Ph. capsici. The aromatic amino acid content was differentially reprogrammed in Ps. fluorescens and Pa. alvei primed plants responding to Ph. capsici. Furthermore, abscisic acid and methyl salicylic acid were found to be major signaling molecules in the tripartite interaction. LC–MS metabolomics analysis showed time-dependent metabolic changes in the primed-unchallenged vs. primed-challenged tissues. The annotated metabolites included phenylpropanoids, benzoic acids, glycoalkaloids, flavonoids, amino acids, organic acids, as well as oxygenated fatty acids. Tissue-specific reprogramming across diverse metabolic networks in roots, stems and leaves was also observed, which demonstrated that PGPR priming resulted in modulation of the defense response to Ph. capsici infection.

Metabolomics for Biomarker Discovery: Key Signatory Metabolic Profiles for the Identification and Discrimination of Oat Cultivars

The first step in crop introduction-or breeding programmes-requires cultivar identification and characterisation. Rapid identification methods would therefore greatly improve registration, breeding, seed, trade and inspection processes. Metabolomics has proven to be indispensable in interrogating cellular biochemistry and phenotyping. Furthermore, metabolic fingerprints are chemical maps that can provide detailed insights into the molecular composition of a biological system under consideration. Here, metabolomics was applied to unravel differential metabolic profiles of various oat (Avena sativa) cultivars (Magnifico, Dunnart, Pallinup, Overberg and SWK001) and to identify signatory biomarkers for cultivar identification. The respective cultivars were grown under controlled conditions up to the 3-week maturity stage, and leaves and roots were harvested for each cultivar. Metabolites were extracted using 80% methanol, and extracts were analysed on an ultra-high performance liquid chromatography (UHPLC) system coupled to a quadrupole time-of-flight (qTOF) high-definition mass spectrometer analytical platform. The generated data were processed and analysed using multivariate statistical methods. Principal component analysis (PCA) models were computed for both leaf and root data, with PCA score plots indicating cultivar-related clustering of the samples and pointing to underlying differential metabolic profiles of these cultivars. Further multivariate analyses were performed to profile differential signatory markers, which included carboxylic acids, amino acids, fatty acids, phenolic compounds (hydroxycinnamic and hydroxybenzoic acids, and associated derivatives) and flavonoids, among the respective cultivars. Based on the key signatory metabolic markers, the cultivars were successfully distinguished from one another in profiles derived from both leaves and roots. The study demonstrates that metabolomics can be used as a rapid phenotyping tool for cultivar differentiation.

Chemical Composition of Tomato Seed Flours, and Their Radical Scavenging, Anti-Inflammatory and Gut Microbiota Modulating Properties

In the current study, the chemical composition and total phenolic content of tomato seed flours, along with potential health beneficial properties, including free radical scavenging capacities, anti-inflammatory capacities, and gut microbiota profile modulation, were examined using two different batches. Eight compounds were identified in the tomato seed flour, including malic acid, 2-hydroxyadipic acid, salicylic acid, naringin, N-acetyl-tryptophan, quercetin-di-O-hexoside, kaempferol-di-O-hexoside, and azelaic acid. The total phenolic contents of tomato seed flour were 1.97-2.00 mg gallic acid equivalents/g. Oxygen radical absorbing capacities (ORAC), 2,2-diphenyl-1-picrylhydrazyl radical scavenging capacities (DPPH), and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) cation radical scavenging capacities (ABTS) were 86.32-88.57, 3.57-3.81, and 3.39-3.58 µmoles Trolox equivalents/g, respectively, on a per flour dry weight basis. The mRNA expression of the pro-inflammatory markers, interleukin-1 beta (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor alpha (TNF-α), were dose-dependently suppressed by tomato seed flour extracts. The extracts altered five of the eight bacterial phyla and genera evaluated. The results may provide some scientific support for the use of tomato seed flour as value-added food ingredients.

Concurrent Metabolic Profiling and Quantification of Aromatic Amino Acids and Phytohormones in Solanum lycopersicum Plants Responding to Phytophthora capsici

Pathogenic microorganisms account for large production losses in the agricultural sector. Phytophthora capsici is an oomycete that causes blight and fruit rot in important crops, especially those in the Solanaceae family. P. capsici infection is difficult to control due to genetic diversity, arising from sexual reproduction, and resistant spores that remain dormant in soil. In this study, the metabolomics of tomato plants responding to infection by P. capsici were investigated. Non-targeted metabolomics, based on liquid chromatography coupled to mass spectrometry (LC-MS), were used with multivariate data analyses to investigate time-dependent metabolic reprogramming in the roots, stems, and leaves of stem-infected plants, over an 8 day period. In addition, phytohormones and amino acids were determined using quantitative LC-MS. Methyl salicylate and 1-aminocyclopropane-1-carboxylate were detected as major signalling molecules in the defensive response to P. capsici. As aromatic amino acid precursors of secondary metabolic pathways, both phenylalanine and tryptophan showed a continuous increase over time in all tissues, whereas tyrosine peaked at day 4. Non-targeted metabolomic analysis revealed phenylpropanoids, benzoic acids, glycoalkaloids, flavonoids, amino acids, organic acids, and fatty acids as the major classes of reprogrammed metabolites. Correlation analysis showed that metabolites derived from the same pathway, or synthesised by different pathways, could either have a positive or negative correlation. Furthermore, roots, stems, and leaves showed contrasting time-dependent metabolic reprogramming, possibly related to the biotrophic vs. necrotrophic life-stages of the pathogen, and overlapping biotic and abiotic stress signaling. As such, the targeted and untargeted approaches complemented each other, to provide a detailed view of key time-dependent metabolic changes, occurring in both the asymptomatic and symptomatic stages of infection.

Application of Metabolomics Tools to Determine Possible Biomarker Metabolites Linked to Leaf Blackening in Protea

The postharvesting disorder leaf blackening is the main cause of product rejection in Protea during export. In this study, we report an investigation into metabolites associated with leaf blackening in Protea species. Methanol extracts of leaf and involucral bract tissue were analyzed by liquid chromatography hyphenated to photodiode array and high-resolution mass spectrometry (LC-PDA-HRMS), where 116 features were annotated. Analytical data obtained from 37 Protea species, selections, and hybrids were investigated using metabolomics tools, which showed that stems susceptible to leaf blackening cluster together and contained features identified as benzenetriol- and/or hydroquinone-derived metabolites. On the other hand, species, selections, and cultivars not prone to blackening were linked to metabolites with known protective properties against biotic and abiotic stressors. During the browning process, susceptible cultivars also produce these protective metabolites, yet at innately low levels, which may render these species and cultivars more vulnerable to blackening. Metabolites that were found to be correlated to the instigation of the browning process, all comprising benzenetriol- and hydroquinone-glycoside derivatives, are highlighted to provide preliminary insights to guide the development of new Protea cultivars not susceptible to leaf blackening.

Metabolomics: A Tool for Cultivar Phenotyping and Investigation of Grain Crops

The quality of plants is often enhanced for diverse purposes such as improved resistance to environmental pressures, better taste, and higher yields. Considering the world’s dependence on plants (nutrition, medicine, or biofuel), developing new cultivars with superior characteristics is of great importance. As part of the ‘omics’ approaches, metabolomics has been employed to investigate the large number of metabolites present in plant systems under well-defined environmental conditions. Recent advances in the metabolomics field have greatly expanded our understanding of plant metabolism, largely driven by potential application to agricultural systems. The current review presents the workflow for plant metabolome analyses, current knowledge, and future directions of such research as determinants of cultivar phenotypes. Furthermore, the value of metabolome analyses in contemporary crop science is illustrated. Here, metabolomics has provided valuable information in research on grain crops and identified significant biomarkers under different conditions and/or stressors. Moreover, the value of metabolomics has been redefined from simple biomarker identification to a tool for discovering active drivers involved in biological processes. We illustrate and conclude that the rapid advances in metabolomics are driving an explosion of information that will advance modern breeding approaches for grain crops and address problems associated with crop productivity and sustainable agriculture.

Metabolic Profiling of PGPR-Treated Tomato Plants Reveal Priming-Related Adaptations of Secondary Metabolites and Aromatic Amino Acids

Plant growth–promoting rhizobacteria (PGPR) are beneficial microbes in the rhizosphere that can directly or indirectly stimulate plant growth. In addition, some can prime plants for enhanced defense against a broad range of pathogens and insect herbivores. In this study, four PGPR strains (Pseudomonas fluorescens N04, P. koreensis N19, Paenibacillus alvei T19, and Lysinibacillus sphaericus T22) were used to induce priming in Solanum lycopersicum (cv. Moneymaker) plants. Plants were inoculated with each of the four PGPRs, and plant tissues (roots, stems, and leaves) were harvested at 24 h and 48 h post-inoculation. Methanol-extracted metabolites were analyzed by ultra-high performance liquid chromatography mass spectrometry (UHPLC-MS). Chemometric methods were applied to mine the data and characterize the differential metabolic profiles induced by the PGPR. The results revealed that all four strains induced defense-related metabolic reprogramming in the plants, characterized by dynamic changes to the metabolomes involving hydroxycinnamates, benzoates, flavonoids, and glycoalkaloids. In addition, targeted analysis of aromatic amino acids indicated differential quantitative increases or decreases over a two-day period in response to the four PGPR strains. The metabolic alterations point to an altered or preconditioned state that renders the plants primed for enhanced defense responses. The results contribute to ongoing efforts in investigating and unraveling the biochemical processes that define the PGPR priming phenomenon.

Metabolomic Profiling of the Host Response of Tomato (Solanum lycopersicum) Following Infection by Ralstonia solanacearum

Tomato (Solanum lycopersicum) is an important dietary source of bioactive phytochemicals and active breeding programs constantly produce new cultivars possessing superior and desirable traits. The phytopathogenic Ralstonia solanacearum, the causal agent of bacterial wilt, is a highly destructive bacterial disease with a high economic impact on tomato production. This study followed an untargeted metabolomic approach involving four tomato cultivars and aimed at the identification of secondary metabolites involved in plant defense after infection with R. solanacearum. Liquid chromatography coupled to mass spectrometry (LC-MS) in combination with multivariate data analysis and chemometric modelling were utilized for the identification of discriminant secondary metabolites. The total of 81 statistically selected features were annotated belonging to the metabolite classes of amino acids, organic acids, fatty acids, various derivatives of cinnamic acid and benzoic acids, flavonoids and steroidal glycoalkaloids. The results indicate that the phenylpropanoid pathway, represented by flavonoids and hydroxycinnamic acids, is of prime importance in the tomato defense response. The hydroxycinnamic acids esters of quinic acid, hexoses and glucaric acids were identified as signatory biomarkers, as well as the hydroxycinnamic acid amides to polyamines and tyramine. Interestingly, the rapid and differential accumulation of putrescine, dopamine, and tyramine derivatives, along with the presence of a newly documented metabolite, feruloyl serotonin, were documented in the infected plants. Metabolite concentration variability in the different cultivar tissues point to cultivar-specific variation in the speed and manner of resource redistribution between the host tissues. These metabolic phenotypes provide insights into the differential metabolic signatures underlying the defense metabolism of the four cultivars, defining their defensive capabilities to R. solanacearum.

The Pseudomonas syringae pv. tomato DC3000 PSPTO_0820 multidrug transporter is involved in resistance to plant antimicrobials and bacterial survival during tomato plant infection

Multidrug resistance efflux pumps protect bacterial cells against a wide spectrum of antimicrobial compounds. PSPTO_0820 is a predicted multidrug transporter from the phytopathogenic bacterium Pseudomonas syringae pv. tomato DC3000. Orthologs of this protein are conserved within many Pseudomonas species that interact with plants. To study the potential role of PSPTO_0820 in plant-bacteria interaction, a mutant in this gene was isolated and characterized. In addition, with the aim to find the outer membrane channel for this efflux system, a mutant in PSPTO_4977, a TolC-like gene, was also analyzed. Both mutants were more susceptible to trans-cinnamic and chlorogenic acids and to the flavonoid (+)-catechin, when added to the culture medium. The expression level of both genes increased in the presence of (+)-catechin and, in the case of PSPTO_0820, also in response to trans-cinnamic acid. PSPTO_0820 and PSPTO_4977 mutants were unable to colonize tomato at high population levels. This work evidences the involvement of these two proteins in the resistance to plant antimicrobials, supporting also the importance of chlorogenic acid, trans-cinnamic acid, and (+)-catechin in the tomato plant defense response against P. syringae pv. tomato DC3000 infection.

Deciphering the Resistance Mechanism of Tomato Plants Against Whitefly-Mediated Tomato Curly Stunt Virus Infection through Ultra-High-Performance Liquid Chromatography Coupled to Mass Spectrometry (UHPLC-MS)-Based Metabolomics Approaches

Begomoviruses, such as the Tomato curly stunt virus (ToCSV), pose serious economic consequences due to severe crop losses. Therefore, the development and screening of possible resistance markers is imperative. While some tomato cultivars exhibit differential resistance to different begomovirus species, in most cases, the mechanism of resistance is not fully understood. In this study, the response of two near-isogenic lines of tomato (Solanum lycopersicum), differing in resistance against whitefly-mediated ToCSV infection were investigated using untargeted ultra-high-performance liquid chromatography coupled to mass spectrometry (UHPLC-MS)-based metabolomics. The responses of the two lines were deciphered using multivariate statistics models. Principal component analysis (PCA) scores plots from various time intervals revealed that the resistant line responded more rapidly with changes to the metabolome than the susceptible counterpart. Moreover, the metabolic reprogramming of chemically diverse metabolites that span a range of metabolic pathways was associated with the defence response. Biomarkers primarily included hydroxycinnamic acids conjugated to quinic acid, galactaric acid, and glucose. Minor constituents included benzenoids, flavonoids, and steroidal glycoalkaloids. Interestingly, when reduced to the level of metabolites, the phytochemistry of the infected plants' responses was very similar. However, the resistant phenotype was strongly associated with the hydroxycinnamic acid derivatives deployed in response to infection. In addition, the resistant line was able to mount a stronger and quicker response.