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Plant Metabolomics II

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A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Plant Metabolism".

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 28586

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Dr. Sandor Gonda

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Department of Botany, University of Debrecen, 4032 Debrecen, Hungary
Interests: phytochemistry; metabolomics; endophytes; plant-fungal interactions; glucosinolates
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Metabolomics has become a widely recognized approach to studying biological phenomena in biological, environmental, and other samples. This approach aims at gathering an abundance of data on several hundreds of compounds, and subsequent data-mining to find explanations to the phenomena of interest.

This Special Issue is devoted to publishing research papers that use the metabolomics approach on plants or extracts thereof, as well as review papers on plant metabolomics-related topics.

Therefore, we invite manuscripts on different aspects of plant biology and plant natural product chemistry that use the metabolomic approach, including but not limited to agricultural applications, plant–pathogen interactions, endophytes, quality control, and chemotaxonomy. Papers on plant-specific sample preparation, metabolite databases, or other technical improvements are also welcome. The main methods used should be LC-MS, NMR, GC-MS, or other techniques, with suitable quality control measures taken, followed by data-mining for the phenomena of interest, and putative identification of the analytes of interest. Papers on medicinal plants, functional foods, spices, and otherwise economically important plants, and manuscripts that utilize fortification of data by using a wide array of authentic standards are especially welcome.

Research papers not utilizing the above techniques, those with no or improper annotations (putative identification) of analytes, those without proper identification of the plant material, and those without any quality control assessment will not be considered.

The Special Issue is open for submission now. A proper extension may be granted. Please kindly let us know in advance if you plan to make a submission. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the Special Issue website.

Dr. Sandor Gonda
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

Plant metabolomics
Phytochemical analysis
Phytochemistry
Bioactive compounds
Natural products
medicinal plants

Published Papers (9 papers)

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Research

18 pages, 5730 KiB

Open AccessArticle

Supervised Statistical Learning Prediction of Soybean Varieties and Cultivation Sites Using Rapid UPLC-MS Separation, Method Validation, and Targeted Metabolomic Analysis of 31 Phenolic Compounds in the Leaves

by Chan-Su Rha, Eun Kyu Jang, Yong Deog Hong and Won Seok Park

Metabolites 2021, 11(12), 884; https://doi.org/10.3390/metabo11120884 - 17 Dec 2021

Cited by 2 | Viewed by 2524

Abstract

Soybean (Glycine max; SB) leaf (SL) is an abundant non-conventional edible resource that possesses value-adding bioactive compounds. We predicted the attributes of SB based on the metabolomes of an SL using targeted metabolomics. The SB was planted in two cities, and SLs were regularly obtained from the SB plant. Nine flavonol glycosides were purified from SLs, and a validated simultaneous quantification method was used to establish rapid separation by ultrahigh-performance liquid chromatography-mass detection. Changes in 31 targeted compounds were monitored, and the compounds were discriminated by various supervised machine learning (ML) models. Isoflavones, quercetin derivatives, and flavonol derivatives were discriminators for cultivation days, varieties, and cultivation sites, respectively, using the combined criteria of supervised ML models. The neural model exhibited higher prediction power of the factors with high fitness and low misclassification rates while other models showed lower. We propose that a set of phytochemicals of SL is a useful predictor for discriminating characteristics of edible plants. Full article

(This article belongs to the Special Issue Plant Metabolomics II)

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26 pages, 5833 KiB

Open AccessArticle

A Global Metabolic Map Defines the Effects of a Si-Based Biostimulant on Tomato Plants under Normal and Saline Conditions

by Kekeletso H. Chele, Paul Steenkamp, Lizelle A. Piater, Ian A. Dubery, Johan Huyser and Fidele Tugizimana

Metabolites 2021, 11(12), 820; https://doi.org/10.3390/metabo11120820 - 30 Nov 2021

Cited by 6 | Viewed by 2638

Abstract

The ongoing unpredictability of climate changes is exponentially exerting a negative impact on crop production, further aggravating detrimental abiotic stress effects. Several research studies have been focused on the genetic modification of crop plants to achieve more crop resilience against such stress factors; however, there has been a paradigm shift in modern agriculture focusing on more organic, eco-friendly and long-lasting systems to improve crop yield. As such, extensive research into the use of microbial and nonmicrobial biostimulants has been at the core of agricultural studies to improve crop growth and development, as well as to attain tolerance against several biotic and abiotic stresses. However, the molecular mechanisms underlying the biostimulant activity remain enigmatic. Thus, this study is a liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics approach to unravel the hypothetical biochemical framework underlying effects of a nonmicrobial biostimulant (a silicon-based formulation) on tomato plants (Solanum lycopersium) under salinity stress conditions. This metabolomics study postulates that Si-based biostimulants could alleviate salinity stress in tomato plants through modulation of the primary metabolism involving changes in the tricarboxylic acid cycle, fatty acid and numerous amino acid biosynthesis pathways, with further reprogramming of several secondary metabolism pathways such as the phenylpropanoid pathway, flavonoid biosynthesis pathways including flavone and flavanol biosynthesis. Thus, the postulated hypothetical framework, describing biostimulant-induced metabolic events in tomato plants, provides actionable knowledge necessary for industries and farmers to, confidently and innovatively, explore, design, and fully implement Si-based formulations and strategies into agronomic practices for sustainable agriculture and food production. Full article

(This article belongs to the Special Issue Plant Metabolomics II)

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15 pages, 2573 KiB

Open AccessArticle

Metabolomics and Molecular Networking to Characterize the Chemical Space of Four Momordica Plant Species

by Anza-Tshilidzi Ramabulana, Daniel Petras, Ntakadzeni E. Madala and Fidele Tugizimana

Metabolites 2021, 11(11), 763; https://doi.org/10.3390/metabo11110763 - 08 Nov 2021

Cited by 24 | Viewed by 5097

Abstract

Momordica plant species (Cucurbitaceae), have been used for centuries in traditional medicine and for nutritional purposes. Plants from this family are thus claimed to be phytochemically rich, representing an inexhaustible source of natural products. However, the chemical space of these Momordica species has not yet been fully decoded, and due to the inherent complexity of plant metabolomes, the characterization of the Momordica phytochemistry remains challenging. Thus, in this study we propose the use of molecular networking to unravel the molecular families within the metabolomes of four Momordica species (M. cardiospermoides, M. balsamina, M. charantia and M. foetida) and highlight the relevance of molecular networking in exploring the chemotaxonomy of these plants. In silico annotation tools (Network Annotation Propagation and DEREPLICATOR) and an unsupervised substructure identification tool (MS2LDA) were also explored to complement the classical molecular networking output and integration using MolNetEnhancer within GNPS. This allowed for the visualisation of chemical classes and the variety of substructures within the molecular families. The use of computational tools in this study highlighted various classes of metabolites, such as a wide range of flavonoids, terpenoids and lipids. Herein, these species are revealed to be phytochemically rich plants consisting of many biologically active metabolites differentially distributed within the different species, with the metabolome of M. cardiospermoides dereplicated in this paper for the first time. Full article

(This article belongs to the Special Issue Plant Metabolomics II)

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17 pages, 2701 KiB

Open AccessArticle

Nontargeted Metabolomics as a Screening Tool for Estimating Bioactive Metabolites in the Extracts of 50 Indigenous Korean Plants

by Se Rin Choi, Mee Youn Lee, Seung A Kim, Jieun Oh, Da Won Hyun, Sarah Lee, Byoung-Hee Lee, Jae Youl Cho and Choong Hwan Lee

Metabolites 2021, 11(9), 585; https://doi.org/10.3390/metabo11090585 - 30 Aug 2021

Cited by 3 | Viewed by 2705

Abstract

Many indigenous Korean plants have been used in medicinal preparations and health-promoting foods. These plant species contain beneficial metabolites with various bioactivities, such as antioxidant and anti-inflammatory activities. Herein, we suggest a new screening strategy using metabolomics to explore the bioactive compounds in 50 Korean plants. Secondary metabolites were analyzed using UHPLC-LTQ-Orbitrap-MS/MS. The plant extracts were subjected to antioxidant and anti-inflammatory assays. We identified metabolites that contributed to bioactivities according to the results of bioassays and multivariate analyses. Using Pearson’s correlation, phenolics (e.g., casuarictin, 3-O-methylellagic acid) showed positive correlation with antioxidant activity, while biflavonoids (e.g., amentoflavone, rosbustaflavone) were correlated with nitric oxide (NO) inhibition activity. To compensate for the limitation of this new strategy, we further validated these by investigating three parts (branches, fruits, leaves) of Platycladus orientalis which showed high activities on both bioassays. Unlike the above observation, we identified significantly different metabolites from different parts, which was not the results of bioassays. In these validation steps, interestingly, biflavonoids (e.g., robustaflavone, sciadopitysin) contributed to both activities in P. orientalis. The findings of this work suggest that new strategy could be more beneficial in the identification of bioactive plant species as well as that of their corresponding bioactive compounds that impart the bioactivity. Full article

(This article belongs to the Special Issue Plant Metabolomics II)

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15 pages, 2189 KiB

Open AccessArticle

Characterization of Phytoestrogens in Medicago sativa L. and Grazing Beef Cattle

by Jessica M. Wyse, Sajid Latif, Saliya Gurusinghe, Erica D. Berntsen, Leslie A. Weston and Cyril P. Stephen

Metabolites 2021, 11(8), 550; https://doi.org/10.3390/metabo11080550 - 20 Aug 2021

Cited by 9 | Viewed by 2657

Abstract

Phytoestrogens are plant-produced bioactive secondary metabolites known to play an integral role in plant defense that frequently accumulate in times of stress and/or microbial infection. Phytoestrogens typically belong to two distinct chemical classes; flavonoids (isoflavones) and non-flavonoids (lignans and coumestans). Upon consumption by livestock, high concentrations of phytoestrogens can cause long-term disruption in reproduction due to structural similarities with mammalian estrogens and their tendency to bind estrogen receptors. Wide variation in phytoestrogen concentration has been reported in pasture legumes and corresponding silage or hay. Lucerne is a common perennial pasture legume in temperate climates, but information on phytoestrogen production or accumulation in grazing livestock is currently limited. Therefore, metabolic profiling using UHPLC-MS-QToF was performed to identify and quantitate key phytoestrogens in both fresh and dried lucerne fodder from replicated field or controlled glasshouse environments. Phytoestrogens were also profiled in the blood plasma of Angus cattle grazing field-grown lucerne. Results revealed that phytoestrogens varied quantitatively and qualitatively among selected lucerne cultivars grown under glasshouse conditions. Fresh lucerne samples contained higher concentrations of coumestans and other phytoestrogenic isoflavones than did dried samples for all cultivars profiled, with several exceeding desirable threshold levels for grazing cattle. Coumestans and isoflavones profiled in plasma of Angus heifers grazing lucerne increased significantly over a 21-day sampling period following experimental initiation. Currently, threshold concentrations for phytoestrogens in plasma are unreported. However, total phytoestrogen concentration exceeded 300 mg·kg⁻¹ in fresh and 180 mg·kg⁻¹ in dried samples of selected cultivars, suggesting that certain genotypes may upregulate phytoestrogen production, while others may prove suitable sources of fodder for grazing livestock. Full article

(This article belongs to the Special Issue Plant Metabolomics II)

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19 pages, 4175 KiB

Open AccessArticle

Metabolite Profiling Reveals Distinct Modulation of Complex Metabolic Networks in Non-Pigmented, Black, and Red Rice (Oryza sativa L.) Cultivars

by Tae Jin Kim, So Yeon Kim, Young Jin Park, Sun-Hyung Lim, Sun-Hwa Ha, Sang Un Park, Bumkyu Lee and Jae Kwang Kim

Metabolites 2021, 11(6), 367; https://doi.org/10.3390/metabo11060367 - 09 Jun 2021

Cited by 19 | Viewed by 3338

Abstract

Comprehensive profiling of primary and secondary metabolites was performed to understand metabolic differences associated with color formation in pigmented rice (Oryza sativa L.). Overall, 110 metabolites from non-pigmented, black, and red rice cultivars were identified. Black and red rice contained high levels of flavonoids associated with plant color. Black rice also contained high levels of terpenoids (carotenoids, tocopherols, phytosterols, and monoterpenes). The non-pigmented rice contained relatively low levels of secondary metabolites. Multivariate and pathway analyses were performed to data-mine the metabolite profiles. Hierarchical clustering analysis of correlation coefficients revealed metabolite clusters based on nitrogen and carbon sources. These clusters suggested a negative correlation between nitrogen and carbon. Pathway analysis revealed that black rice was rich in carbon-based secondary metabolites, with relatively low levels of primary metabolites compared with other rice cultivars. These data highlight the complex interactions between nitrogen and carbon metabolism of primary and secondary metabolites in rice. For the first time, the relationships and metabolic differences in terpenoid content (monoterpenes, triterpenes, and tetraterpenes) of non-pigmented and pigmented rice cultivars were analyzed. These findings should greatly contribute to the understanding of pigmented rice metabolome and inform breeding programs for new rice cultivars. Full article

(This article belongs to the Special Issue Plant Metabolomics II)

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15 pages, 1835 KiB

Open AccessArticle

A Medicago truncatula Metabolite Atlas Enables the Visualization of Differential Accumulation of Metabolites in Root Tissues

by Clayton Kranawetter, Shuai Zeng, Trupti Joshi and Lloyd W. Sumner

Metabolites 2021, 11(4), 238; https://doi.org/10.3390/metabo11040238 - 13 Apr 2021

Cited by 4 | Viewed by 2936

Abstract

Plant roots are composed of many differentiated tissue types, with each tissue exhibiting differential quantitative and qualitative accumulation of metabolites. The large-scale nontargeted metabolite profiles of these differentiated tissues are complex, which complicates the interpretation and development of hypotheses relative to the biological roles of differentially localized metabolites. Thus, we created a data visualization tool to aid in the visualization and understanding of differential metabolite accumulations in Medicago truncatula roots. This was achieved through the development of the Medicago truncatula Metabolite Atlas based upon an adaptation of the Arabidopsis Electronic Fluorescent Pictograph (eFP) Browser. Medicago truncatula roots were dissected into border cells, root cap, elongation zone, mature root, and root secretions. Each tissue was then analyzed by UHPLC-QTOF-MS and GC-Q-MS. Data were uploaded into a MySQL database and displayed in the Medicago truncatula Metabolite Atlas. The data revealed unique differential spatial localization of many metabolites, some of which are discussed here. Ultimately, the Medicago truncatula Metabolite Atlas compiles metabolite data into a singular, useful, and publicly available web-based tool that enables the visualization and understanding of differential metabolite accumulation and spatial localization. Full article

(This article belongs to the Special Issue Plant Metabolomics II)

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22 pages, 2993 KiB

Open AccessArticle

Effects of Long-Term Nitrogen Fertilization on the Formation of Metabolites Related to Tea Quality in Subtropical China

by Yuzhen Chen, Feng Wang, Zhidan Wu, Fuying Jiang, Wenquan Yu, Jie Yang, Jiaming Chen, Guotai Jian, Zhiming You and Lanting Zeng

Metabolites 2021, 11(3), 146; https://doi.org/10.3390/metabo11030146 - 02 Mar 2021

Cited by 20 | Viewed by 2524

Abstract

As a main agronomic intervention in tea cultivation, nitrogen (N) application is useful to improve tea yield and quality. However, the effects of N application on the formation of tea quality-related metabolites have not been fully studied, especially in long-term field trials. In this study, a 10-year field experiment was conducted to investigate the effect of long-term N application treatments on tea quality-related metabolites, their precursors, and related gene expression. Long-term N application up-regulated the expression of key genes for chlorophyll synthesis and promoted its synthesis, thus increasing tea yield. It also significantly increased the contents of total free amino acids, especially l-theanine, in fresh tea leaves, while decreasing the catechin content, which is conducive to enhancing tea liquor freshness. However, long-term N application significantly reduced the contents of benzyl alcohol and 2-phenylethanol in fresh tea leaves, and also reduced (E)-nerolidol and indole in withered leaves, which were not conducive to the formation of floral and fruity aroma compounds. In general, an appropriate amount of N fertilizer (225 kg/hm²) balanced tea yield and quality. These results not only provide essential information on how N application affects tea quality, but also provide detailed experimental data for field fertilization. Full article

(This article belongs to the Special Issue Plant Metabolomics II)

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15 pages, 20412 KiB

Open AccessArticle

Comparative Metabolomic Profiling of Citrullus spp. Fruits Provides Evidence for Metabolomic Divergence during Domestication

by Pingli Yuan, Nan He, Muhammad Jawad Umer, Shengjie Zhao, Weinan Diao, Hongju Zhu, Junling Dou, Mohamed Omar Kaseb, Hanhui Kuang, Xuqiang Lu and Wenge Liu

Metabolites 2021, 11(2), 78; https://doi.org/10.3390/metabo11020078 - 28 Jan 2021

Cited by 8 | Viewed by 2577

Abstract

Watermelon (Citrullus lanatus) is one of the most nutritional fruits that is widely distributed in the whole world. The nutritional compositions are mainly influenced by the genotype and environment. However, the metabolomics of different domestication status and different flesh colors watermelon types is not fully understood. In this study, we reported an extensive assessment of metabolomic divergence in the fruit flesh among Citrullus sp. and within Citrullus sp. We demonstrate that metabolic profiling was significantly different between the wild and cultivated watermelons, the apigenin 6-C-glucoside, luteolin 6-C-glucoside, chrysoeriol C-hexoside, naringenin C-hexoside, C-pentosyl-chrysoeriol O-hexoside, and sucrose are the main divergent metabolites. Correlation analysis results revealed that flavonoids were present in one tight metabolite cluster. The main divergent metabolites in different flesh-colored cultivated watermelon fruits are p-coumaric acid, 2,3-dihydroflavone, catechin, N-(3-indolylacetyl)-l-alanine, 3,4-dihydroxycinnamic acid, and pelargonidin o-hexoside. A total of 431 differentially accumulated metabolites were identified from pairwise comparative analyses. C. lanatus edible-seed watermelon (cultivars) and C. mucosospermus (wild) have similar fruit metabolic profiles and phenotypic traits, indicating that edible-seed watermelon may be a relative of wild species and a relatively primitive differentiation type of cultivated watermelon. Our data provide extensive knowledge for metabolomics-based watermelon improvement of Citrullus fruits meet their enhanced nutritive properties or upgraded germplasm utility values. Full article

(This article belongs to the Special Issue Plant Metabolomics II)

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