Mass spectrometry as a quantitative tool in plant metabolomics

Widely targeted metabolomics reveals the phytoconstituent changes in Platostoma palustre leaves and stems at different growth stages

Platostoma palustre (Blume) A. J. Paton is an important edible and medicinal plant. To gain a comprehensive and clear understanding of the variation patterns of metabolites in P. palustre, we employed the UPLC-MS platform along with widely targeted metabolomics techniques to analyze the metabolites in the stems and leaves of P. palustre at different stages. Our results revealed a total of 1228 detected metabolites, including 241 phenolic acids, 203 flavonoids, 152 lipids, 128 terpenes, 106 amino acids, 79 organic acids, 74 saccharides, 66 alkaloids, 44 lignans, etc. As the growth time increased, the differential metabolites (DAMs) mainly enriched in P. palustre leaves were terpenoids, phenolic acids, and lipids, while the DAMs primarily enriched in stems were terpenoids. Compared to stems, there were more differential flavonoids in leaves, and saccharides and flavonoids were significantly enriched in leaves during the S1 and S2 stages. Additionally, we identified 13, 10, and 23 potential markers in leaf, stem, and leaf vs. stem comparison groups. KEGG enrichment analysis revealed that arginine biosynthesis was the common differential metabolic pathway in different growth stages and tissues. Overall, this study comprehensively analyzed the metabolic profile information of P. palustre, serving as a solid foundation for its further development and utilization.

SCALiR: A Web Application for Automating Absolute Quantification of Mass Spectrometry-Based Metabolomics Data

Quantitative liquid chromatography-mass spectrometry (LC-MS)-based metabolomics is becoming an important approach for studying complex biological systems but presents several technical challenges that limit its widespread use. Computing metabolite concentrations using standard curves generated from standard mixtures of known concentrations is a labor-intensive process that is often performed manually. Currently, there are few options for open-source software tools that can automatically calculate metabolite concentrations. Herein, we introduce SCALiR (standard curve application for determining linear ranges), a new web-based software tool specifically built for this task, which allows users to automatically transform LC-MS signals into absolute quantitative data (https://www.lewisresearchgroup.org/software). SCALiR uses an algorithm that automatically finds the equation of the line of best fit for each standard curve and uses this equation to calculate compound concentrations from the LC-MS signal. Using a standard mix containing 77 metabolites, we show a close correlation between the concentrations calculated by SCALiR and the expected concentrations of each compound (R2 = 0.99 for a y = x curve fitting). Moreover, we demonstrate that SCALiR reproducibly calculates concentrations of midrange standards across ten analytical batches (average coefficient of variation 0.091). SCALiR can be used to calculate metabolite concentrations either using external calibration curves or by using internal standards to correct for matrix effects. This open-source and vendor agnostic software offers users several advantages in that (1) it requires only 10 s of analysis time to compute concentrations of >75 compounds, (2) it facilitates automation of quantitative workflows, and (3) it performs deterministic evaluations of compound quantification limits. SCALiR therefore provides the metabolomics community with a simple and rapid tool that enables rigorous and reproducible quantitative metabolomics studies.

Spatiotemporal metabolic responses to water deficit stress in distinct leaf cell-types of poplar

The impact of water-deficit (WD) stress on plant metabolism has been predominantly studied at the whole tissue level. However, plant tissues are made of several distinct cell types with unique and differentiated functions, which limits whole tissue 'omics'-based studies to determine only an averaged molecular signature arising from multiple cell types. Advancements in spatial omics technologies provide an opportunity to understand the molecular mechanisms underlying plant responses to WD stress at distinct cell-type levels. Here, we studied the spatiotemporal metabolic responses of two poplar (Populus tremula× P. alba) leaf cell types -palisade and vascular cells- to WD stress using matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI). We identified unique WD stress-mediated metabolic shifts in each leaf cell type when exposed to early and prolonged WD stresses and recovery from stress. During water-limited conditions, flavonoids and phenolic metabolites were exclusively accumulated in leaf palisade cells. However, vascular cells mainly accumulated sugars and fatty acids during stress and recovery conditions, respectively, highlighting the functional divergence of leaf cell types in response to WD stress. By comparing our MALDI-MSI metabolic data with whole leaf tissue gas chromatography-mass spectrometry (GC-MS)-based metabolic profile, we identified only a few metabolites including monosaccharides, hexose phosphates, and palmitic acid that showed a similar accumulation trend at both cell-type and whole leaf tissue levels. Overall, this work highlights the potential of the MSI approach to complement the whole tissue-based metabolomics techniques and provides a novel spatiotemporal understanding of plant metabolic responses to WD stress. This will help engineer specific metabolic pathways at a cellular level in strategic perennial trees like poplars to help withstand future aberrations in environmental conditions and to increase bioenergy sustainability.

Linking the use of reclaimed water to indicators of crop stress by metabolomic and transcriptomic analyses. A tool to compare water irrigation quality

The occurrence of contaminants of emerging concern (CECs) or heavy metals in reclaimed water used for agricultural irrigation may affect crop morphology and physiology. Here, we analyzed lettuce (Lactuca sativa) grown in outdoor lysimeters and irrigated with either tap water, used as a control, or reclaimed water: CAS-reclaimed water, an effluent from a conventional activated sludge system (CAS) followed by chlorination and sand filtration, or MBR-reclaimed water, an effluent from a membrane biological reactor (MBR). Chemical analyses identified seven CECs in the reclaimed waters, but only two of them were detected in lettuce (carbamazepine and azithromycin). Metabolomic and transcriptomic analyses revealed that irrigation with reclaimed water increased the concentrations of several crop metabolites (5-oxoproline, leucine, isoleucine, and fumarate) and of transcripts codifying for the plant stress-related genes Heat-Shock Protein 70 (HSP70) and Manganese Superoxide Dismutase (MnSOD). In both cases, MBR-water elicited the strongest response in lettuce, perhaps related to its comparatively high sodium adsorption ratio (4.5), rather than to its content in CECs or heavy metals. Our study indicates that crop metabolomic and transcriptomic profiles depend on the composition of irrigating water and that they could be used for testing the impact of water quality in agriculture.

Identification of Stress-Responsive Metabolites in Plants Using an Untargeted Metabolomics Approach

Stress can affect different groups of plant metabolites and multiple signaling pathways. Untargeted metabolomics enables the collection of whole-spectrum data for the entire metabolite content present in plant tissues at that point in time. We present a thorough approach for large-scale, untargeted metabolomics of plant tissues using reverse-phase liquid chromatography connected to high-resolution mass spectrometry (LC-MS) of dilute methanolic extract. MZmine is a specialized computer software that automates the alignment and baseline modification of all derived mass peaks across all samples, resulting in precise information on the relative abundance of hundreds of metabolites reflected by thousands of mass signals. Further processing with statistic and bioinformatic techniques will provide a comprehensive perspective of the variations and connections among groups of samples.

Metabolome expression in Eucryphia cordifolia populations: Role of seasonality and ecological niche centrality hypothesis

The ecological niche centrality hypothesis states that population abundance is determined by the position in the ecological niche, expecting higher abundances towards the center of the niche and lower at the periphery. However, the variations in the conditions that favor the persistence of populations between the center and the periphery of the niche can be a surrogate of stress factors that are reflected in the production of metabolites in plants. In this study we tested if metabolomic similarity and diversity in populations of the tree species Eucryphia cordifolia Cav. vary according to their position with respect to the structure of the ecological niche. We hypothesize that populations growing near the centroid should exhibit lower metabolites diversity than plants growing at the periphery of the niche. The ecological niche of the species was modeled using correlative approaches and bioclimatic variables to define central and peripheral localities from which we chose four populations to obtain their metabolomic information using UHPLC-DAD-QTOF-MS. We observed that populations farther away from the centroid tend to have higher metabolome diversity, thus supporting our expectation of the niche centrality hypothesis. Nonetheless, the Shannon index showed a marked variation in metabolome diversity at the seasonal level, with summer and autumn being the periods with higher metabolite diversity compared to winter and spring. We conclude that both the environmental variation throughout the year in combination with the structure of the ecological niche are relevant to understand the variation in expression of metabolites in plants.

Peptaibiotics: Harnessing the potential of microbial secondary metabolites for mitigation of plant pathogens

Agricultural systems are in need of low-cost, safe antibiotics to protect crops from pests and diseases. Peptaibiotics, a family of linear, membrane-active, amphipathic polypeptides, have been shown to exhibit antibacterial, antifungal, and antiviral activity, and to be inducers of plant resistance against a wide range of phytopathogens. Peptaibiotics belong to the new generation of alternatives to agrochemicals, aligned with the United Nations Sustainable Development Goals and the One Health approach toward ensuring global food security and safety. Despite that, these fungi-derived, non-ribosomal peptides remain surprisingly understudied, especially in agriculture, where only a small number has been tested against a reduced number of phytopathogens. This lack of adoption stems from peptaibiotics' poor water solubility and the difficulty to synthesize and purify them in vitro, which compromises their delivery and inclusion in formulations. In this review, we offer a comprehensive analysis of peptaibiotics' classification, biosynthesis, relevance to plant protection, and mode of action against phytopathogens, along with the techniques enabling researchers to extract, purify, and elucidate their structure, and the databases holding such valuable data. It is also discussed how chemical synthesis and ionic liquids could increase their solubility, how genetic engineering and epigenetics could boost in vitro production, and how omics can reduce screenings' workload through in silico selection of the best candidates. These strategies could turn peptaibiotics into effective, ultra-specific, biodegradable tools for phytopathogen control.

Hepatoprotective effects of bioactive compounds from traditional herb Tulsi (Ocimum sanctum Linn) against galactosamine-induced hepatotoxicity in rats

Ocimum sanctum L. (Tulsi; Family: libiaceae), also known as "The Queen of herbs" or "Holy Basil," is an omnipresent, multipurpose plant that has been used in folk medicine of many countries as a remedy against several pathological conditions, including anticancer, antidiabetic, cardio-protective, antispasmodic, diaphoretic, and adaptogenic actions. This study aims to assess O. sanctum L.'s hepatoprotective potential against galactosamine-induced toxicity, as well as investigate bioactive compounds in each extract and identify serum metabolites. The extraction of O. sanctum L as per Ayurveda was simultaneously standardized and quantified for biochemical markers: rutin, ellagic acid, kaempferol, caffeic acid, quercetin, and epicatechin by HPTLC. Hepatotoxicity was induced albino adult rats by intra-peritoneal injection of galactosamine (400 mg/kg). The quantified hydroalcoholic and alcoholic extract of O. sanctum L (100 and 200 mg/kg body weight/day) were compared for evaluation of hepatoprotective potential, which were assessed in terms of reduction in histological damage, change in serum enzymes such as AST, ALT, ALP and increase TBARS. Twenty chemical constituents of serum metabolites of O. sanctum were identified and characterized based on matching recorded mass spectra by GC-MS with those obtained from the library-Wiley/NIST. We evaluated the hepatoprotective activity of various fractions of hydroalcoholic extracts based on the polarity and investigated the activity at each phase (hexane, chloroform, and ethyl acetate) in vitro to determine how they affected the toxicity of CCL4 (40 mM) toward Chang liver cells. The ethyl acetate fraction of the selected plants had a higher hepatoprotective activity than the other fractions, so it was used in vacuum liquid chromatography (VLC). The ethyl acetate fraction contains high amounts of rutin (0.34% w/w), ellagic acid (2.32% w/w), kaempferol (0.017% w/w), caffeic acid (0.005% w/w), quercetin (0.038% w/w), and epicatechin (0.057% w/w) which are responsible for hepatoprotection. In comparison to standard silymarin, isolated bioactive molecules displayed the most significant hepatoprotective activity in Chang liver cells treated to CCl4 toxicity. The significant high hepatoprotection provided by standard silymarin ranged from 77.6% at 100 μg/ml to 83.95% at 200 μg/ml, purified ellagic acid ranged from 70% at 100 μg/ml to 81.33% at 200 μg/ml, purified rutin ranged from 63.4% at 100 μg/ml to 76.34% at 200 μg/ml purified quercetin ranged from 54.33% at 100 μg/ml to 60.64% at 200 μg/ml, purified epicatechin ranged from 53.22% at 100 μg/ml to 65.6% at 200 μg/ml, and purified kaempferol ranged from 52.17% at 100 μg/ml to 60.34% at 200 μg/ml. These findings suggest that the bioactive compounds in O. sanctum L. have significant protective effects against galactosamine-induced hepatotoxicity.

SCALiR: a web application for automating absolute quantification of mass spectrometry-based metabolomics data

Metabolomics is an important approach for studying complex biological systems. Quantitative liquid chromatography-mass spectrometry (LC-MS)-based metabolomics is becoming a mainstream strategy but presents several technical challenges that limit its widespread use. Computing metabolite concentrations using standard curves generated from standard mixtures of known concentrations is a labor-intensive process which is often performed manually. Currently, there are few options for open-source software tools that can automatically calculate metabolite concentrations. Herein, we introduce SCALiR (Standard Curve Application for determining Linear Ranges), a new web-based software tool specifically built for this task, which allows users to automatically transform LC-MS signal data into absolute quantitative data (https://www.lewisresearchgroup.org/software). The algorithm used in SCALiR automatically finds the equation of the line of best fit for each standard curve and uses this equation to calculate compound concentrations from their LC-MS signal. Using a standard mix containing 77 metabolites, we found excellent correlation between the concentrations calculated by SCALiR and the expected concentrations of each compound (R2 = 0.99) and that SCALiR reproducibly calculated concentrations of mid-range standards across ten analytical batches (average coefficient of variation 0.091). SCALiR offers users several advantages, including that it (1) is open-source and vendor agnostic; (2) requires only 10 seconds of analysis time to compute concentrations of >75 compounds; (3) facilitates automation of quantitative workflows; and (4) performs deterministic evaluation of compound quantification limits. SCALiR provides the metabolomics community with a simple and rapid tool that enables rigorous and reproducible quantitative metabolomics studies.

Phytoestrogens as Biomarkers of Plant Raw Materials Used for Fish Feed Production

The intensive use of plant materials as a sustainable alternative for fish feed production, combined with their phytochemical content, which affects the growth and production characteristics of farmed fishes, necessitates their monitoring for the presence of raw materials of plant origin. This study reported herein concerns the development, validation and application of a workflow using high-performance liquid chromatography combined with tandem mass spectrometry (LC-MS/MS) for the quantification of 67 natural phytoestrogens in plant-derived raw materials that were used to produce fish feeds. Specifically, we verified the presence of 8 phytoestrogens in rapeseed meal samples, 20 in soybean meal samples, 12 in sunflower meal samples and only 1 in wheat meal samples in quantities enabling their efficient incorporation into clusters. Among the various constituents, the soybean phytoestrogens daidzein, genistein, daidzin, glycitin, apigenin, calycosin and coumestrol, as well as the sunflower neochlorogenic, caffeic and chlorogenic phenolic acids, displayed the highest correlations with their origin descriptions. A hierarchical cluster analysis of the studied samples, based on their phytoestrogen contents, led to the efficient clustering of raw materials. The accuracy and efficiency of this clustering were tested through the incorporation of additional samples of soybean meal, wheat meal and maize meal, which verified the utilization of the phytoestrogen content as a valuable biomarker for the discrimination of raw materials used for fish feed production.

β-Cyclocitral-Mediated Metabolic Changes Optimize Growth and Defense Responses in Solanum lycopersicum L

β-cyclocitral (βCC) is one of the significant oxidative products of β-carotene. It primes plants for multiple stress acclimation without compromising plant growth. Metabolic reorganization is necessary to maintain a balance between growth and defense. However, the βCC-mediated changes in a plant’s metabolic network are unknown. Here, we demonstrate how βCC-induced metabolic changes enable Solanum lycopersicum L. (tomato) plants to promote defense and maintain growth under stress. An analysis of early (0–240 min) and late (72 h) changes in the tomato metabolome after βCC-treatment using liquid chromatography and tandem mass spectrometry identified 57 compounds. A principal coordinate analysis suggested that βCC treatment significantly changes the metabolite profile. A variable importance in projection (VIP) analysis revealed 16 and 19 discriminant metabolites from early and late samples, respectively (VIP ≥ 1.0). Upregulated metabolites were mainly amino acids and phytophenols. Pathway enrichment analysis showed that βCC treatment influenced amino acid metabolism at early and later times; however, phenylpropanoid and isoquinoline biosynthesis were influenced only at the later time. A 66.6% similarity in the upregulated metabolites of βCC- and simulated-herbivory-treated plants confirmed βCC’s role against herbivores. We conclude that βCC steers a temporal separation in amino acids and defense metabolite accumulation that optimizes resource allocation to growth and defense.

Surface-Coated Acupuncture Needles as Solid-Phase Microextraction Probes for In Vivo Analysis of Bioactive Molecules in Living Plants by Mass Spectrometry

In this work, we report the coupling of solid-phase microextraction (SPME) enabled by surface-coated acupuncture needles with nano-electrospray mass spectrometry (nanoESI-MS) for the analysis of bioactive molecules in living plants. The needle tip was oxidized by a mixture of nitric acid and hydrogen peroxide solution and then subject to surface coating via carbonization of paraffin. A combination of oxidation and surface coating resulted in a thin coating of carbon film, whereby the significantly increased surface area promoted both analyte enrichment and ionization for MS analysis. The analytical performances were evaluated through the characterization of small molecules, peptides and proteins. Compared with conventional nanoESI, our new strategy of employing surface-coated needles had a high salt tolerance. The streamlined experimental workflow could be completed within one minute. The linear dynamic ranges for L-histidine and L-lysine, as two representatives, were over two orders of magnitude with a limit of detection (LOD) of 3.0~5.0 ng/mL. A mark is made on the needle at 2 mm from the tip, the needle is then kept in the sample for 30 s. In vivo sampling and identification of α-tomatine and organic acids from the stem of a living tomato plant were demonstrated as a practical application, while the physiological activities of the plant were not disrupted due to the minimally invasive sampling. We anticipate that the developed strategy may be of potential use for real-time clinical and other on-site analyses.

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.

Metabonomic profiling of clubroot-susceptible and clubroot-resistant radish and the assessment of disease-resistant metabolites

Plasmodiophora brassicae causes a serious threat to cruciferous plants including radish (Raphanus sativus L.). Knowledge on the pathogenic regularity and molecular mechanism of P. brassicae and radish is limited, especially on the metabolism level. In the present study, clubroot-susceptible and clubroot-resistant cultivars were inoculated with P. brassicae Race 4, root hairs initial infection of resting spores (10⁷ CFU/mL) at 24 h post-inoculation and root galls symptom arising at cortex splitting stage were identified on both cultivars. Root samples of cortex splitting stage of two cultivars were collected and used for untargeted metabonomic analysis. We demonstrated changes in metabolite regulation and pathways during the cortex splitting stage of diseased roots between clubroot-susceptible and clubroot-resistant cultivars using untargeted metabonomic analysis. We identified a larger number of differentially regulated metabolites and heavier metabolite profile changes in the susceptible cultivar than in the resistant counterpart. The metabolites that were differentially regulated in both cultivars were mostly lipids and lipid-like molecules. Significantly regulated metabolites and pathways according to the P value and variable important in projection score were identified. Moreover, four compounds, including ethyl α-D-thioglucopyranoside, imipenem, ginsenoside Rg1, and 6-gingerol, were selected, and their anti-P. brassicae ability and effects on seedling growth were verified on the susceptible cultivar. Except for ethyl α-D-thioglucopyranoside, the remaining could inhibit clubroot development of varing degree. The use of 5 mg/L ginsenoside Rg1 + 5 mg/L 6-gingerol resulted in the lowest disease incidence and disease index among all treatments and enhanced seedling growth. The regulation of pathways or metabolites of carbapenem and ginsenoside was further explored. The results provide a preliminary understanding of the interaction between radish and P. brassicae at the metabolism level, as well as the development of measures for preventing clubroot.

Effects of tetracycline, sulfonamide, fluoroquinolone, and lincosamide load in pig slurry on lettuce: Agricultural and human health implications

The application of pig slurry as fertilizer in agriculture provides nutrients, but it can also contain veterinary medicines, including antibiotic residues (ABs), which can have an ecotoxicological impact on agroecosystems. Furthermore, uptake, translocation, and accumulation of ABs in crops can mobilize them throughout the food chain. This greenhouse study aims to assess AB uptake from soil fertilized with pig slurry and its phenotypical effects on Lactuca sativa L. The plants were cropped in loamy clay soil dosed at 140 kg total N/ha and containing antibiotics (lincomycin, sulfadiazine, oxytetracycline, and enrofloxacin) at different concentration levels (0, 0.05, 0.5, 5, 50, and 500 mg/kg fresh weight, fw). Whereas sulfadiazine (11.8 ng/g fw) was detected in lettuce leaves at the intermediate doses (0.5 mg/kg), lincomycin and its transformation products (hydroxy/sulfate) were only detected at the 50 mg/kg fw dose. In addition, increased AB doses in the pig slurry resulted in decreased lettuce fresh weight and lipid and carbohydrate content and became lethal to lettuce at the highest AB concentrations (500 mg/kg fw). Nevertheless, even at higher doses, the AB content in lettuce following pig-slurry fertilization did not pose any direct significant human health risk (total hazard quotient<0.01). However, the promotion of antimicrobial resistance in humans due to the intake of these vegetables cannot be ruled out.

Metabolomics and Network Pharmacology in the Exploration of the Multi-Targeted Therapeutic Approach of Traditional Medicinal Plants

Metabolomic is generally characterized as a comprehensive and the most copious analytical technique for the identification of targeted and untargeted metabolite diversity in a biological system. Recently, it has exponentially been used for phytochemical analysis and variability among plant metabolites, followed by chemometric analysis. Network pharmacology analysis is a computational technique used for the determination of multi-mechanistic and therapeutic evaluation of chemicals via interaction with the genomes involved in targeted or untargeted diseases. In considering the facts, the present review aims to explore the role of metabolomics and network pharmacology in the scientific validation of therapeutic claims as well as to evaluate the multi-targeted therapeutic approach of traditional Indian medicinal plants. The data was collected from different electronic scientific databases such as Google Scholar, Science Direct, ACS publication, PubMed, Springer, etc., using different keywords such as metabolomics, techniques used in metabolomics, chemometric analysis, a bioinformatic tool for drug discovery and development, network pharmacology, methodology and its role in biological evaluation of chemicals, etc. The screened articles were gathered and evaluated by different experts for their exclusion and inclusion in the final draft of the manuscript. The review findings suggest that metabolomics is one of the recent most precious and effective techniques for metabolite identification in the plant matrix. Various chemometric techniques are copiously used for metabolites discrimination analysis hence validating the unique characteristic of herbal medicines and their derived products concerning their authenticity. Network pharmacology remains the only option for the unique and effective analysis of hundreds of chemicals or metabolites via genomic interaction and thus validating the multi-mechanistic and therapeutic approach to explore the pharmacological aspects of herbal medicines for the management of the disease.

LC-qTOF-MS analysis of fish immune organs reveals the distribution of amino acids in response to metabolic adaptation of the survival phenotype in grouper against Vibrio infection

Epinephelus fuscoguttatus is economically crucial to various Southeast Asia countries where they are reared in fish farms to meet the demand for supply. However, a systemic infectious disease known as vibriosis has steadily and extensively affected the fish farming industry. The disease is caused by Vibrio spp., which are pathogenic gram-negative bacteria. This study focused on understanding the host's metabolic adaptation against Vibrio vulnificus infection, which features a survival phenotype, by profiling the metabolites in grouper fingerlings that survived the experimental infection. Mapping of the pathways is crucial to explain the roles of metabolites in fish immunity. A solvent extraction method was used on the grouper's immune organs (gills, liver and spleen) prior to Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry (LC-qTOF-MS) analysis. The metabolites identified in fingerlings that survived experimental infections were mostly amino acids (primary metabolites). Glutamine (0.44%), alanine (0.68%), phenylalanine (2.63%) and tyrosine (2.60%) were highly abundant in survived-infected gills. Aspartic acid (13.57%) and leucine (4.01%) were highly abundant in the livers of the survived-infected fish and lysine was highly abundant in both gills (2.94%) and liver (3.64%) of the survived-infected fish. Subsequent bioinformatics analysis revealed the involvement of the identified functional amino acids in various immune-related pathways. The current findings facilitate the comprehension of the metabolic adaptation of grouper fingerlings that exhibited a survival phenotype against Vibrio infection.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03269-1.

Metabolomics reveals primary response of wheat (Triticum aestivum) to irrigation with oilfield produced water

The reuse of oilfield produced water (PW) for agricultural irrigation has received increased attention for utility in drought-stricken regions. It was recently demonstrated that PW irrigation can affect physiological processes in food crops. However, metabolomic evaluations are important to further discern specific mechanisms of how PW may contribute as a plant-environmental stressor. Herein, the primary metabolic responses of wheat irrigated with PW and matching salinity controls were investigated. Non-targeted gas chromatography mass spectrometry (GC-MS) metabolomics was combined with multivariate analysis and revealed that PW irrigation altered the primary metabolic profiles of both wheat leaf and grain. Over 600 compounds (183 annotated metabolites) were detected that varied between controls (salinity control and tap water) and PW irrigated plants. While some of these changed metabolites are related to salinity stress, over half were found to be unique to PW. The primary metabolites exhibiting changes in abundance in leaf and grain tissues were amines/amino acids, organic acids, and saccharides. Metabolite pathway analysis revealed that amino acid metabolism, sugar metabolism, and nitrogen remobilization are all impacted by PW irrigation, independent of regular plant responses to salinity stress. These data, when combined with prior physiological studies, support a multi-faceted, physio-metabolic response of wheat to the unique stressor imposed by irrigation with PW.

The First Optimization Process from Cultivation to Flavonoid-Rich Extract from Moringa oleifera Lam. Leaves in Brazil

Flavonoids are significant antioxidant and anti-inflammatory agents and have multiple potential health applications. Moringa oleifera is globally recognized for its nutritional and pharmacological properties, correlated to the high flavonoid content in its leaves. However, the bioactive compounds found in plants may vary according to the cultivation, origin, season, and extraction process used, making it difficult to extract reliable raw material. Hence, this study aimed to standardize the best cultivation and harvest season in Brazil and the best extraction process conditions to obtain a flavonoid-rich extract from M. oleifera as a final product. Firstly, ultrasound-assisted extraction (UAE) was optimized to reach the highest flavonoid content by three-level factorial planning and response surface methodology (RSM). The optimal cultivation condition was mineral soil fertilizer in the drought season, and the optimized extraction was with 80% ethanol and 13.4 min of extraction time. The flavonoid-rich extract was safe and significantly decreased reactive oxygen species (ROS) and nitric oxide (NO) in LPS-treated RAW 264.7 cells. Lastly, the major flavonoids characterized by HPLC-ESI-QTRAP-MS/MS were compounds derived from apigenin, quercetin, and kaempferol glycosides. The results confirmed that it was possible to standardize the flavonoid-rich extract leading to a standardized and reliable raw material extracted from M. oleifera leaves.

LC-MS/MS metabolomics-facilitated identification of the active compounds responsible for anti-allergic activity of the ethanol extract of Xenostegia tridentata

In vivo and in vitro anti-allergic activities of ethanol extract of Xenostegia tridentata (L.) D.F. Austin & Staples were investigated using passive cutaneous anaphylaxis reaction assay and RBL-2H3 cell degranulation assay, respectively. The crude ethanol extract exhibited promising activities when compared with the known anti-allergic agents, namely dexamethasone and ketotifen fumarate. The ethyl acetate subfraction showed the highest anti-allergic activity among various sub-partitions and showed better activity than the crude extract, consistent with the high abundance of total phenolic and flavonoid contents in this subfraction. LC-MS/MS metabolomics analysis and bioassay-guided isolation were then used to identify chemical constituents responsible for the anti-allergic activity. The results showed that major components of the ethyl acetate subfraction consist of 3,5-dicaffeoylquinic acid, quercetin-3-O-rhamnoside, kaempferol-3-O-rhamnoside and luteolin-7-O-glucoside. The inhibitory activity of the isolated compounds against mast cell degranulation was validated, ensuring their important roles in the anti-allergic activity of the plant. Notably, besides showing the anti-allergic activity of X. tridentata, this work highlights the role of metabolomic analysis in identifying and selectively isolating active metabolites from plants.

1H-NMR-Based Metabolomic Study of Potato Cultivars, Markies and Fianna, Exposed to Different Water Regimes

This study investigated the effects of varying soil moisture conditions (through either flooding, drought, or provision of a moderate water supply) on the metabolomic profile of two potato cultivars, namely, Markies and Fianna. Representative tubers of the treated plants were collected 91 days after planting. The samples were freeze-dried, and ground to a fine powder in liquid nitrogen. The fine powder of the tuber samples was analyzed by nuclear magnetic resonance spectroscopy (NMR) to identify their metabolomic profiles. The NMR data was analyzed using principal component analysis and orthogonal partial least square-discriminant analysis to identify any variations between the treatments. In both models, plants exposed to drought clearly separated from the plants that received either excess or moderate water (control). The potato tubers that experienced drought and flood treatments had the highest quantities of aspartic acid, asparagine, and isoleucine. Furthermore, the potatoes exposed to either drought or flood had higher levels of valine and leucine (which are essential for plant defense and resistance against plant pathogens). Potato plants can respond metabolically to varying soil moisture stress.

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.

Linking plant-root exudate changes to micropollutant exposure in aquatic plants (Lemna minor and Salvinia natans). A prospective metabolomic study

Recent findings indicate that plant-root exudates can stimulate plant-associated microorganisms to enhance the biodegradation of contaminants in constructed wetlands. To understand this process, we studied the root-exudation changes of two aquatic plants (Lemna minor and Salvinia natans) upon micropollutants exposure (10, 100 and 1000 μg/L mixes containing naproxen, diclofenac, carbamazepine, and benzotriazole). After a 2-day exposure, plant exudates were collected, extracted and non-target analysis was performed with a gas chromatography-high resolution Orbitrap mass-spectrometer. Plants didn't show morphological or growth differences between the control and spiked reactors, but exudation changes were observed in both plants at all concentration levels. Partial least squares discriminant analysis showed that, for Lemna minor, the increase of micropollutants exposure was linked to the reduction of sugar and fatty acid exudation. This may trigger changes in the microbial community living on complex carbon forms. Instead, in Salvinia natans, micropollutants exposure was linked to the release of long-chain compounds such as cuticular waxes and sesquiterpenoids, which might be related to stress signaling. These results demonstrate that plant micropollutant-exposure at environmentally relevant concentration levels triggers changes in root exudates. This may help to design new strategies to enhance micropollutants degradation in nature based solutions such as in constructed wetlands.

The state of the art in plant lipidomics

Lipids are a group of compounds with diverse structures that perform several important functions in plants. To unravel and better understand their in vivo functions, plant biologists have been using various lipidomic technologies including liquid-chromatography (LC)-mass spectrometry (MS). However, there are still significant challenges in LC-MS based plant lipidomics, which need to be addressed. In this review, we provide an overview of the key developments in LC-MS based lipidomic approaches to detect and identify plant lipids with emphasis on areas that can be further improved. Given that the cellular lipidome is estimated to contain hundreds of thousands of lipids,^1,2 many of the lipid structures remain to be discovered. Furthermore, the plant lipidome is considered to be significantly more complex compared to that of mammals. Recent technical developments in mass spectrometry have made the detection of novel lipids possible; hence, approaches that can be used for plant lipid discovery are also discussed.

Organic Electrochemical Transistors for In Vivo Bioelectronics

Organic electrochemical transistors (OECTs) are presently a focus of intense research and hold great potential in expanding the horizons of the bioelectronics industry. The notable characteristics of OECTs, including their electrolyte-gating, which offers intimate interfacing with biological environments, and aqueous stability, make them particularly suitable to be operated within a living organism (in vivo). Unlike the existing in vivo bioelectronic devices, mostly based on rigid metal electrodes, OECTs form a soft mechanical contact with the biological milieu and ensure a high signal-to-noise ratio because of their powerful amplification capability. Such features make OECTs particularly desirable for a wide range of in vivo applications, including electrophysiological recordings, neuron stimulation, and neurotransmitter detection, and regulation of plant processes in vivo. In this review, a systematic compilation of the in vivo applications is presented that are addressed by the OECT technology. First, the operating mechanisms, and the device design and materials design principles of OECTs are examined, and then multiple examples are provided from the literature while identifying the unique device properties that enable the application progress. Finally, one critically looks at the future of the OECT technology for in vivo bioelectronic applications.

Metabolomics analysis of dandelions from different geographical regions in China

INTRODUCTION

Dandelion (Taraxacum mongolicum Hand.-Mazz.) is a perennial herb with diverse pharmacological effects. The development and utilization of dandelion have attracted much attention.

OBJECTIVES

Our aims were to provide a reference basis for the identification of the origin of dandelions and to study the influence of their origin on their quality. Methods High-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry was used to analyze metabolites from dandelions from four different geographical regions in China, namely Gansu, Henan, Shanxi, and Jiangsu. Metabolite analysis was performed using orthogonal partial least-squares discriminant analysis, and to identify potential metabolic pathways, MBRole was used to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis.

RESULTS

Principal component analysis revealed that the chemical components of dandelions sampled from the four regions showed noticeable differences. Twenty-six, six, six, eight, eight, and fifteen differentially produced metabolites were identified upon comparison between Gansu and Jiangsu, Gansu and Shanxi, Gansu and Henan, Henan and Shanxi, Henan and Jiangsu, and Shanxi and Jiangsu, respectively. These differentially produced metabolites were mainly phenolic compounds. Further, KEGG pathway enrichment analysis showed that the main metabolic pathways involved were biosynthesis of phenylpropanoids and flavonoids.

CONCLUSION

The methods reported herein can be used to identify the origin of dandelions; moreover, our results can serve as a reference basis for future studies.

Effects of extraction parameters on lipid profiling of mosses using UPLC-ESI-QTOF-MS and multivariate data analysis

INTRODUCTION

Non-target lipid profiling by using ultra-performance liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-ESI-QTOF-MS) has been used extensively in the past decades in plant studies. However, the lipidomes of bryophytes have only been scarcely studied, although they are the second largest group in plant kingdom.

OBJECTIVES

We evaluated the effects of different cell disruption methods (no disruption, shake, ultrasound, and bead beating), and storage conditions (air-dried, freeze-dried, and fresh frozen) of five moss species (including Racomitrium lanuginosum B and D, Philonotis fontana, Sphagnum teres, and Hylocomium splendens).

METHODS

The lipid profiling results of each extraction parameter were analyzed by using multivariate data analysis including unsupervised principal component analysis and supervised orthogonal projections to latent structures discriminant analysis.

RESULTS

The results showed that extraction with bead beating resulted in the highest lipid content and the most detected features, but these were caused by the contamination from plastic tubes. Minor lipid metabolite changes were found in shaking and ultrasonication methods when compared with no disruption method. Significant amounts of phosphatidylcholine, diacylglyceryltrimethylhomoserine and their lyso lipids were observed in air-dried moss tissues, whereas diacylglycerol, triacylglycerol and ceramide were mostly exclusively detected when fresh frozen tissues were used for extraction.

CONCLUSION

We concluded that lipid extraction using fresh frozen samples with ultrasound assistance provide the most original lipid composition and gave a relatively high lipid content.

Study on changes in pigment composition during the blooming period of safflower based on plant metabolomics and semi-quantitative analysis

Red and yellow pigments are the major ingredients of safflower, often used to color food and cosmetics. Carthamin was the main component of red pigment and hydroxysafflor yellow A and anhydrosafflower yellow B were representative components of yellow pigment. Plant metabolomics and semi-quantitative analysis were used to analyze the changes of pigment composition during the blooming period, especially these characteristic components. Carthamin, hydroxysafflor yellow A, anhydrosafflower yellow B, and other components were screened out as differential metabolites based on plant metabolomics. Then semi-quantitative analysis was used to quantify these three representative components of pigments. Experimental results showed that the content of pigments has dynamic changes along with flowering, in the early blooming period, yellow pigment accumulated much and red pigment was low in content. In the middle period, the accumulation rate of the yellow pigment slowed down and content was stabilized. In the next step, the content of yellow pigments gradually decreased, and the content of red pigments gradually increased. Later, the level of yellow pigment decreased significantly, and the accumulation rate of red pigment increased significantly. Last, the appearance color of safflower was red, with yellow parts barely visible, and accumulation of red pigment was the highest and of the yellow pigment was the lowest in content.

In Planta Nanosensors: Understanding Biocorona Formation for Functional Design

Climate change and population growth are straining agricultural output. To counter these changes and meet the growing demand for food and energy, the monitoring and engineering of crops are becoming increasingly necessary. Nanoparticle-based sensors have emerged in recent years as new tools to advance agricultural practices. As these nanoparticle-based sensors enter and travel through the complex biofluids within plants, biomolecules including proteins, metabolites, lipids, and carbohydrates adsorb onto the nanoparticle surfaces, forming a coating known as the "bio-corona". Understanding these nanoparticle-biomolecule interactions that govern nanosensor function in plants will be essential to successfully develop and translate nanoparticle-based sensors into broader agricultural practice.

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

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

Identification of Key Metabolic Pathways and Biomarkers Underlying Flowering Time of Guar (Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis

Guar (Cyamopsis tetragonoloba (L.) Taub.) is an annual legume crop native to India and Pakistan. Seeds of the plant serve as a source of galactomannan polysaccharide (guar gum) used in the food industry as a stabilizer (E412) and as a gelling agent in oil and gas fracturing fluids. There were several attempts to introduce this crop to countries of more northern latitudes. However, guar is a plant of a short photoperiod, therefore, its introduction, for example, to Russia is complicated by a long day length during the growing season. Breeding of new guar varieties insensitive to photoperiod slowed down due to the lack of information on functional molecular markers, which, in turn, requires information on guar genome. Modern breeding strategies, e.g., genomic predictions, benefit from integration of multi-omics approaches such as transcriptome, proteome and metabolome assays. Here we present an attempt to use transcriptome-metabolome integration to understand the genetic determination of flowering time variation among guar plants that differ in their photoperiod sensitivity. This study was performed on nine early- and six delayed-flowering guar varieties with the goal to find a connection between 63 metabolites and 1,067 differentially expressed transcripts using Shiny GAM approach. For the key biomarker of flowering in guar myo-inositol we also evaluated the KEGG biochemical pathway maps available for Arabidopsis thaliana. We found that the phosphatidylinositol signaling pathway is initiated in guar plants that are ready for flowering through the activation of the phospholipase C (PLC) gene, resulting in an exponential increase in the amount of myo-inositol in its free form observed on GC-MS chromatograms. The signaling pathway is performed by suppression of myo-inositol phosphate kinases (phosphorylation) and alternative overexpression of phosphatases (dephosphorylation). Our study suggests that metabolome and transcriptome information taken together, provide valuable information about biomarkers that can be used as a tool for marker-assisted breeding, metabolomics and functional genomics of this important legume crop.

Genetic Improvement in Sunflower Breeding—Integrated Omics Approach

Foresight in climate change and the challenges ahead requires a systematic approach to sunflower breeding that will encompass all available technologies. There is a great scarcity of desirable genetic variation, which is in fact undiscovered because it has not been sufficiently researched as detection and designing favorable genetic variation largely depends on thorough genome sequencing through broad and deep resequencing. Basic exploration of genomes is insufficient to find insight about important physiological and molecular mechanisms unique to crops. That is why integrating information from genomics, epigenomics, transcriptomics, proteomics, metabolomics and phenomics enables a comprehensive understanding of the molecular mechanisms in the background of architecture of many important quantitative traits. Omics technologies offer novel possibilities for deciphering the complex pathways and molecular profiling through the level of systems biology and can provide important answers that can be utilized for more efficient breeding of sunflower. In this review, we present omics profiling approaches in order to address their possibilities and usefulness as a potential breeding tools in sunflower genetic improvement.

Metabolomics, a Powerful Tool for Understanding Plant Abiotic Stress

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

Mass spectrometry-based forest tree metabolomics

Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.

Diurnal in vivo xylem sap glucose and sucrose monitoring using implantable organic electrochemical transistor sensors

Bioelectronic devices that convert biochemical signals to electronic readout enable biosensing with high spatiotemporal resolution. These technologies have been primarily applied in biomedicine while in plants sensing is mainly based on invasive methods that require tissue sampling, hindering in-vivo detection and having poor spatiotemporal resolution. Here, we developed enzymatic biosensors based on organic electrochemical transistors (OECTs) for in-vivo and real-time monitoring of sugar fluctuations in the vascular tissue of trees. The glucose and sucrose OECT-biosensors were implanted into the vascular tissue of trees and were operated through a low-cost portable unit for 48hr. Our work consists a proof-of-concept study where implantable OECT-biosensors not only allow real-time monitoring of metabolites in plants but also reveal new insights into diurnal sugar homeostasis. We anticipate that this work will contribute to establishing bioelectronic technologies as powerful minimally invasive tools in plant science, agriculture and forestry.

Flavonoids and caffeoylquinic acids in Chrysanthemum morifolium Ramat flowers: A potentially rich source of bioactive compounds

Varieties of chrysanthemums are among the world's most valuable edible ornamental crops. However, the availability and relationship between the bio-chemicals of chrysanthemums and their morphological variations remain unclear. We developed liquid chromatography mass spectrometry to construct a spectral tag library to identify and quantify chemicals of 7 caffeoylquinic acids, 21 flavones and flavonols, 4 carotenoids, and 13 other compounds in 27 cultivars and representative tea of Chrysanthemum morifolium. A correlation analysis found that more acacetin 7-O-galactoside (23) resulted in lighter colored flowers and less acacetin (43) and kaempferol (44) was associated with yellow flowers. Hot-H₂O extraction of C. morifolium tea showed that most flavonoids and caffeoylquinic acids dissolved out at 30 min, with 20.977 and 8.958 mg/g GW indicated that C. morifolium, which is used in food and tea, is rich in flavonoids and carotenoids. The results improve our understanding of flavonoid biosynthesis and the mechanisms responsible for flower color.

Key metabolites associated with the onset of flowering of guar genotypes (Cyamopsis tetragonoloba (L.) Taub)

BACKGROUND

Guar (Cyamopsis tetragonoloba (L.) Taub.), a short-day plant, is an economically valuable legume crop. Seeds of guar serve as a source of galactomannan polysaccharide, known as guar gum, which is in demand in the gas and oil industries. The rapid and complete maturation of guar seeds depends on the flowering time of a particular genotype. It is known that flowering in guar is controlled by several gene systems. However, no information about the process and mechanisms that trigger flowering in guar on the molecular and biochemical levels was previously reported. The aim of the study was to investigate the metabolic landscape underlying transition to the flowering in guar using GC-MS-metabolomic analysis.

RESULTS

82 diverse guar genotypes (each in 8 replicates) from the VIR collection were grown under experimental conditions of high humidity and long photoperiod. In the stress environment some guar genotypes turned to flowering early (41 ± 1,8 days from the first true leaf appearance) while for others the serious delay of flowering (up to 95 ± 1,7 days) was observed. A total of 244 metabolites were detected by GC-MS analysis on the third true leaves stage of 82 guar genotypes. Among them some molecules were associated with the transition of the guar plants to flowering. Clear discrimination was observed in metabolomic profiles of two groups of «early flowering» and «delayed flowering» plants, with 65 metabolites having a significantly higher abundance in early flowering genotypes. Among them 7 key molecules were identified by S-plot, as potential biomarkers discriminating of «early flowering» and «delayed flowering» guar genotypes.

CONCLUSIONS

The metabolomic landscape accompanying transition to flowering in guar was firstly described. The results obtained can be used in subsequent genomic research for identifying metabolite-gene associations and revealing genes responsible for the onset of flowering and photoperiod sensitivity of guar. In addition, the detected key metabolites associated with flowering of guar can be employed as biomarkers allowing rapid screening of breeding material for the potentially early flowering genotypes.

Complexity of active medicinal ingredients in radix scutellariae with sodium hydrosulfite exposure

Both plants and animals are living things made up of similar cells as well as organelles, and their essence of life is the same. However, plants face more environmental stress than animals and generate excessive reactive oxygen species (ROS), a group of small molecules that can harm proteins, necessitating distinctive metabolic processes. Secondary metabolites in plants are a group of chemical components that can eliminate ROS and can also exhibit medicinal properties; therefore, herbal medicines are often closely linked to the ecological significance of secondary metabolites. Why plants contain so many, not few, active medicinal ingredients is unknown. The root of Scutellaria baicalensis, a popular herbal medicine, is rich in various flavonoids with diverse structural features. Sodium hydrosulfite (Na₂S₂O₄) can produce O˙^-₂ radicals and induce physical conditions under environmental stress. Using UHPLC-ESI-Q-TOF-MS/MS analysis, a total of 25 different compounds were identified in the roots of S. baicalensis between the Na₂S₂O₄ groups and suitable conditions. Based on the results of the t-test (P<0.05) performed for the groups and ions with values of VIP ≥ 2, the most significantly different chemical markers with Na₂S₂O₄ treatment were shikimic acid, citric acid, baicalin, wogonoside, baicalein, wogonin, 3,5,7,2',6'-pentahydroxyflavanone, 5,2',6'-trihydroxy-7,8-dimethoxy flavone, chrysin, eriodictyol, 5,8-dihydroxy-6,7 -dimethoxy flavone, skullcapflavone Ⅱ, and 5,7-dihydroxy-6,8,2',3'-tetrame thoxyflavone, and most of them were free flavonoids with many phenolic hydroxyl or methoxyl groups and characteristically high antioxidant activities. S. baicalensis roots modified their ability to eliminate ROS and maintained the equilibrium of ROS through the multitudinous biosynthesis and conversion of flavonoids, which is similar to the equilibrium established by an intricate buffer solution and perfectly explains the diversity and complexity of medicinal plant ingredients.

FUNCTIONAL METABOLOMICS DECIPHER BIOCHEMICAL FUNCTIONS AND ASSOCIATED MECHANISMS UNDERLIE SMALL-MOLECULE METABOLISM

Metabolism is the collection of biochemical reactions enabled by chemically diverse metabolites, which facilitate different physiological processes to exchange substances and synthesize energy in diverse living organisms. Metabolomics has emerged as a cutting-edge method to qualify and quantify the metabolites in different biological matrixes, and it has the extraordinary capacity to interrogate the biological significance that underlies metabolic modification and modulation. Liquid chromatography combined with mass spectrometry (LC/MS), as a robust platform for metabolomics analysis, has increased in popularity over the past 10 years due to its excellent sensitivity, throughput, and versatility. However, metabolomics investigation currently provides us with only phenotype data without revealing the biochemical functions and associated mechanisms. This limitation indeed weakens the core value of metabolomics data in a broad spectrum of the life sciences. In recent years, the scientific community has actively explored the functional features of metabolomics and translated this cutting-edge approach to be used to solve key multifaceted questions, such as disease pathogenesis, the therapeutic discovery of drugs, nutritional issues, agricultural problems, environmental toxicology, and microbial evolution. Here, we are the first to briefly review the history and applicable progression of LC/MS-based metabolomics, with an emphasis on the applications of metabolic phenotyping. Furthermore, we specifically highlight the next era of LC/MS-based metabolomics to target functional metabolomes, through which we can answer phenotype-related questions to elucidate biochemical functions and associated mechanisms implicated in dysregulated metabolism. Finally, we propose many strategies to enhance the research capacity of functional metabolomics by enabling the combination of contemporary omics technologies and cutting-edge biochemical techniques. The main purpose of this review is to improve the understanding of LC/MS-based metabolomics, extending beyond the conventional metabolic phenotype toward biochemical functions and associated mechanisms, to enhance research capability and to enlarge the applicable scope of functional metabolomics in small-molecule metabolism in different living organisms.

Evaluating Provitamin A Carotenoids and Polar Metabolite Compositions during the Ripening Stages of the Agung Semeru Banana (Musa paradisiaca L. AAB)

Banana cultivars that are rich in provitamin A carotenoids and other nutrients may offer a potential food source to help alleviate vitamin A deficiencies, particularly in developing countries. The local plantain type banana, Agung Semeru (Musa paradisiaca L.), was investigated, in order to analyse the changes in the compositions of the provitamin A carotenoids and metabolite compounds, including the amino acids, organic acids, and sugars, during the ripening stage as this banana is widely processed for food products in either the unripe, ripe, or overripe stages. The bananas that had reached the desired ripening stages were subjected to high-performance liquid chromatography (HPLC) analysis, and the results indicated that the total provitamin A carotenoid concentrations ranged between 4748.83 μg/100 g dry weight (dw) and 7330.40 μg/100 g dw, with the highest level of vitamin A activity at 457.33 ± 5.18 μg retinol activity equivalents (RAE)/100 g dw. Compared to the Cavendish variety, which is consumed worldwide, the Agung Semeru banana had vitamin A activity that was 40 to 90 times higher, dependent on the stage of ripening. The breakdown of the starch during the ripening stages resulted in an increase of its sugar compounds, such as sucrose, fructose, and glucose, as well as its dominant organic acids, such as malic acid, oxalic acid, and citric acid, which were observed using gas chromatography-mass spectrometry (GC-MS) during the ripening stages. The findings of this study show that the Agung Semeru banana is a promising fruit that could be widely produced as a nutritional and energy food resource, due to its high levels of vitamin A activity and sugars.

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

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

Caterpillars on a phytochemical landscape: The case of alfalfa and the Melissa blue butterfly

Modern metabolomic approaches that generate more comprehensive phytochemical profiles than were previously available are providing new opportunities for understanding plant-animal interactions. Specifically, we can characterize the phytochemical landscape by asking how a larger number of individual compounds affect herbivores and how compounds covary among plants. Here we use the recent colonization of alfalfa (Medicago sativa) by the Melissa blue butterfly (Lycaeides melissa) to investigate the effects of indivdiual compounds and suites of covarying phytochemicals on caterpillar performance. We find that survival, development time, and adult weight are all associated with variation in nutrition and toxicity, including biomolecules associated with plant cell function as well as putative anti-herbivore action. The plant-insect interface is complex, with clusters of covarying compounds in many cases encompassing divergent effects on different aspects of caterpillar performance. Individual compounds with the strongest associations are largely specialized metabolites, including alkaloids, phenolic glycosides, and saponins. The saponins are represented in our data by more than 25 individual compounds with beneficial and detrimental effects on L. melissa caterpillars, which highlights the value of metabolomic data as opposed to approaches that rely on total concentrations within broad defensive classes.

Quantitation of Select Terpenes/Terpenoids and Nicotine Using Gas Chromatography-Mass Spectrometry with High-Temperature Headspace Sampling

Plants are the main sources of many high-value bioactive terpenoids used in the medical, fragrance, and food industries. Increasing demand for these bioactive plants and their derivative products (e.g., cannabis and extracts thereof) requires robust approaches to verify feedstock, identify product adulteration, and ensure product safety. Reported here are single-laboratory validation details for a robust testing method to quantitate select terpenes and terpenoids in dry plant materials and terpenoid-containing vaping liquids (e.g., a derivative product) using high-temperature headspace gas chromatography-mass spectrometry, with glycerol used as a headspace solvent. Validated method recoveries were 75-103%, with excellent repeatability (relative standard deviation (RSD) < 5%) and intermediate precision (RSD < 12%). The use of high-temperature headspace (180 °C) permitted terpene and terpenoid profiles to be monitored at temperatures consistent with vaping conditions.

HPLC-ESI-QqQ based standardization, mutagenic and genotoxic potential of methanol extract of Ziziphus mauritiana Lam leaves

BACKGROUND

The leaves of Ziziphus mauritiana Lam have been an integral part of the traditional system of medicine for the treatment of inflammation, wounds, fever, asthma and liver disorders. The leaves are utilised as an edible vegetable in rural parts of India and Indonesia. Despite its pharmacological significance, Ziziphus mauritiana Lam lacks scientific evidence on its mutagenic and genotoxic potential.

RATIONALE

The aim of the present work is to identify bioactive compounds present in the methanol extract of Ziziphus mauritiana Lam leaves (MEZ) using HPLC-ESI-QqQ and to evaluate its mutagenic and genotoxic potential.

METHODS

The phytochemical standardization of the MEZ was done using HPLC-ESI-QqQ. The mutagenic and genotoxic potential of MEZ was tested using bacterial reverse mutation (Ames test), chromosomal aberration, and micronucleus tests. The Ames test was performed in Salmonella typhimurium strains TA98, TA100, TA102, TA1535 and TA1537, and the genotoxic potential was tested in in-vitro using chromosome aberration assay with Chinese hamster ovary (CHO) cells and in-vivo micronucleus test using mouse bone marrow cells.

RESULTS

Fifteen phytochemical compounds were identified in HPLC-ESI- QqQ. It was observed from the Ames test that MEZ did not induce gene mutations in the S. typhimurium in the presence or absence of S9 activation. Similarly, no significant increase in the number of structural aberrations was observed in CHO cells with or without S9 activation. The oral administration of MEZ at a dose of up to 2000 mg/kg caused no significant increase in the number of micronucleated polychromatic erythrocytes or in the mean ratio of polychromatic to total erythrocytes.

CONCLUSION

The findings of the present study confirm that MEZ is not-mutagenic and non-genotoxic in the presence or absence of the exogenous metabolizing system.

Toward Development of Fluorescence-Quenching-Based Biosensors for Drought Stress in Plants

Abscisic acid (ABA) is a drought stress signaling molecule, and simple methods for detecting its levels could benefit agriculture. Here, we present proof-of-concept detection for ABA in aqueous solutions by the use of a mixture of Cyanine 5.5 (Cy5.5) fluorophore- and BHQ3 quencher-conjugated endogenous ABA receptor pyrabactin resistance 1 like proteins (PYL3). These dye-conjugated PYL3 protein form dimers in solutions without ABA and monomerize upon ABA binding. When they are in dimers, fluorescence of Cy5.5 is either nearly completely quenched by the BHQ3 or 20% quenched by another Cy5.5. Consequently, mixtures of equal amounts of the two protein conjugates were used to detect ABA in aqueous solution. As the ABA concentration increased from <1 μM to 1 mM, the intensity of fluorescence detected at around 680 nm from the mixture was more than doubled as a result of ABA-induced monomerization, which leads to halt of quenching and recovery of fluorescence of Cy5.5 in monomers. Kinetic modeling was used to simulate the fluorescence response from the mixture and the results generally agree with the experimentally observed trend. This work demonstrates that fluorescence measurements of a single dissociation reaction in one spectral region are adequate to assess the ABA concentration of a solution.

Experimental Design and Sample Preparation in Forest Tree Metabolomics

Appropriate experimental design and sample preparation are key steps in metabolomics experiments, highly influencing the biological interpretation of the results. The sample preparation workflow for plant metabolomics studies includes several steps before metabolite extraction and analysis. These include the optimization of laboratory procedures, which should be optimized for different plants and tissues. This is particularly the case for trees, whose tissues are complex matrices to work with due to the presence of several interferents, such as oleoresins, cellulose. A good experimental design, tree tissue harvest conditions, and sample preparation are crucial to ensure consistency and reproducibility of the metadata among datasets. In this review, we discuss the main challenges when setting up a forest tree metabolomics experiment for mass spectrometry (MS)-based analysis covering all technical aspects from the biological question formulation and experimental design to sample processing and metabolite extraction and data acquisition. We also highlight the importance of forest tree metadata standardization in metabolomics studies.

In silico annotation of discriminative markers of three Zanthoxylum species using molecular network derived annotation propagation

In liquid chromatography-mass spectrometry (LC-MS) metabolomics, data matrices with up to thousands of variables for each ion peak are subjected to multivariate analysis (MVA) to assess the homogeneity between samples. The large dimensions of LC/MS datasets hinder the identification of the discriminant or the metabolic markers. In the present study, the molecular network (MN) approach and two in silico annotation tools, network annotation propagation (NAP) and the hierarchical chemical classification method, ClassyFire, were used to annotate the metabolites of three Zanthoxylum species, Z. bungeanum, Z. schinifolium and Z. piperitum. The in silico annotation results of the MN nodes and the MVA variables were combined and visualized in loading plots. This approach helped intuitive detection of the variables that greatly contributed to the separation of the samples in the score plot as discriminant or metabolic markers, thereby allowing rapid annotation of two flavanone derivatives.

Metabolic responses to arbuscular mycorrhizal fungi are shifted in roots of contrasting soybean genotypes

Modern breeding programs have reduced genetic variability and might have caused a reduction in plant colonization by arbuscular mycorrhizal fungi (AM). In our previous studies, mycorrhizal colonization was affected in improved soybean genotypes, mainly arbuscule formation. Despite substantial knowledge of the symbiosis-related changes of the transcriptome and proteome, only sparse clues regarding metabolite alterations are available. Here, we evaluated metabolite changes between improved (I-1) and unimproved (UI-4) soybean genotypes and also compare their metabolic responses after AM root colonization. Soybean genotypes inoculated or not with AM were grown in a chamber under controlled light and temperature conditions. At 20 days after inoculation, we evaluated soluble metabolites of each genotype and treatment measured by GC-MS. In this analysis, when comparing non-AM roots between genotypes, I-1 had a lower amount of 31 and higher amount of only 4 metabolites than the UI-4 genotype. When comparing AM roots, I-1 had a lower amount of 36 and higher amount of 4 metabolites than UI-4 (different to those found altered in non-AM treated plants). Lastly, comparing the AM vs non-AM treatments, I-1 had increased levels of three and reduced levels of 24 metabolites, while UI-4 only had levels of 12 metabolites reduced by the effect of mycorrhizas. We found the major changes in sugars, polyols, amino acids, and carboxylic acids. In a targeted analysis, we found lower levels of isoflavonoids and alpha-tocopherol and higher levels of malondialdehyde in the I-1 genotype that can affect soybean-AM symbiosis. Our studies have the potential to support improving soybean with a greater capacity to be colonized and responsive to AM interaction.