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Metabolites
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Metabolomics in Agriculture
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Metabolomics in Agriculture

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

Deadline for manuscript submissions: closed (30 March 2019) | Viewed by 33309

Special Issue Editors

Prof. Dr. Ian Dubery

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Guest Editor
Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
Interests: plant metabolomics; plant-microbe interactions; plant stress responses; secondary metabolites
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Lizelle A. Piater

E-Mail Website
Guest Editor
Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
Interests: plant innate immunity; plant biochemistry; plant–pathogen interactions
Special Issues, Collections and Topics in MDPI journals
Dr. Fidele Tugizimana

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Guest Editor
1. Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
2. International R&D Division, Omnia Group, Ltd., Johannesburg 2021, South Africa
Interests: metabolomics; chemometrics; metabolic pathways; mass spectrometry; metabolite identification; biochemistry; computational metabolomics; big data analytics; cellular immunity and defences; plant-environment interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

During the last decade, metabolomics has developed from an emerging field to becoming an essential aspect in almost every study of plant biology. As such, small molecules (primary and secondary metabolites, with molecular masses ≤1500 Da) constitute the end products of gene expression and define the phenotype of a cell or tissue under defined physiological conditions at a biochemical level. As a post-genomic approach, metabolomics has proven to be a powerful and indispensable tool to interrogate cellular biochemistry, investigating metabolism and its reciprocal crosstalk with cellular signalling and regulation. The recent resurgence of interest in metabolism and increasing awareness about the physiological insights that can be obtained by measuring the total small-molecule complement of a biological system, have made metabolomics a central pillar in systems biology approaches. Metabolite profile patterns can thus provide a holistic signature of the physiological state under study as well as deeper knowledge of specific biochemical processes.

This Special Issue is devoted to “Metabolomics in Agriculture” and topics that will be covered include (not exclusively):  Studies on metabolomic analyses of host responses to biotic stresses, such as pathogen infection and insect attacks; adaptation mechanisms to abiotic stresses such as drought, heat and salt and mitigation effects of bio-stimulants thereon, as well as optimization and development of crop traits to enhance diet and health.

Prof. Ian A. Dubery
Prof. Lizelle A. Piater
Dr. Fidele Tugizimana
Guest Editors

Manuscript Submission Information

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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

  • agricultural biotechnology
  • metabolomics
  • metabolic networks
  • stress adaptation

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Published Papers (7 papers)

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25 pages, 3074 KiB  
Article
Unravelling the Metabolic Reconfiguration of the Post-Challenge Primed State in Sorghum bicolor Responding to Colletotrichum sublineolum Infection
by Fidele Tugizimana, Paul A. Steenkamp, Lizelle A. Piater, Nico Labuschagne and Ian A. Dubery
Metabolites 2019, 9(10), 194; https://doi.org/10.3390/metabo9100194 - 20 Sep 2019
Cited by 27 | Viewed by 4589
Abstract
Priming is a natural phenomenon that pre-conditions plants for enhanced defence against a wide range of pathogens. It represents a complementary strategy, or sustainable alternative that can provide protection against disease. However, a comprehensive functional and mechanistic understanding of the various layers of [...] Read more.
Priming is a natural phenomenon that pre-conditions plants for enhanced defence against a wide range of pathogens. It represents a complementary strategy, or sustainable alternative that can provide protection against disease. However, a comprehensive functional and mechanistic understanding of the various layers of priming events is still limited. A non-targeted metabolomics approach was used to investigate metabolic changes in plant growth-promoting rhizobacteria (PGPR)-primed Sorghum bicolor seedlings infected with the anthracnose-causing fungal pathogen, Colletotrichum sublineolum, with a focus on the post-challenge primed state phase. At the 4-leaf growth stage, the plants were treated with a strain of Paenibacillus alvei at 108 cfu mL−1. Following a 24 h PGPR application, the plants were inoculated with a C. sublineolum spore suspension (106 spores mL−1), and the infection monitored over time: 1, 3, 5, 7 and 9 days post-inoculation. Non-infected plants served as negative controls. Intracellular metabolites from both inoculated and non-inoculated plants were extracted with 80% methanol-water. The extracts were chromatographically and spectrometrically analysed on an ultra-high performance liquid chromatography (UHPLC) system coupled to high-definition mass spectrometry. The acquired multidimensional data were processed to create data matrices for chemometric modelling. The computed models indicated time-related metabolic perturbations that reflect primed responses to the fungal infection. Evaluation of orthogonal projection to latent structure-discriminant analysis (OPLS-DA) loading shared and unique structures (SUS)-plots uncovered the differential stronger defence responses against the fungal infection observed in primed plants. These involved enhanced levels of amino acids (tyrosine, tryptophan), phytohormones (jasmonic acid and salicylic acid conjugates, and zeatin), and defence-related components of the lipidome. Furthermore, other defence responses in both naïve and primed plants were characterised by a complex mobilisation of phenolic compounds and de novo biosynthesis of the flavones, apigenin and luteolin and the 3-deoxyanthocyanidin phytoalexins, apigeninidin and luteolinidin, as well as some related conjugates. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture)
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17 pages, 3244 KiB  
Article
Differential Metabolic Reprogramming in Paenibacillus alvei-Primed Sorghum bicolor Seedlings in Response to Fusarium pseudograminearum Infection
by René Carlson, Fidele Tugizimana, Paul A. Steenkamp, Ian A. Dubery and Nico Labuschagne
Metabolites 2019, 9(7), 150; https://doi.org/10.3390/metabo9070150 - 23 Jul 2019
Cited by 21 | Viewed by 4431
Abstract
Metabolic changes in sorghum seedlings in response to Paenibacillus alvei (NAS-6G6)-induced systemic resistance against Fusarium pseudograminearum crown rot were investigated by means of untargeted ultra-high performance liquid chromatography-high definition mass spectrometry (UHPLC-HDMS). Treatment of seedlings with the plant growth-promoting rhizobacterium P. alvei at [...] Read more.
Metabolic changes in sorghum seedlings in response to Paenibacillus alvei (NAS-6G6)-induced systemic resistance against Fusarium pseudograminearum crown rot were investigated by means of untargeted ultra-high performance liquid chromatography-high definition mass spectrometry (UHPLC-HDMS). Treatment of seedlings with the plant growth-promoting rhizobacterium P. alvei at a concentration of 1 × 108 colony forming units mL−1 prior to inoculation with F. pseudograminearum lowered crown rot disease severity significantly at the highest inoculum dose of 1 × 106 spores mL−1. Intracellular metabolites were subsequently methanol-extracted from treated and untreated sorghum roots, stems and leaves at 1, 4 and 7 days post inoculation (d.p.i.) with F. pseudograminearum. The extracts were analysed on an UHPLC-HDMS platform, and the data chemometrically processed to determine metabolic profiles and signatures related to priming and induced resistance. Significant treatment-related differences in primary and secondary metabolism post inoculation with F. pseudograminearum were observed between P. alvei-primed versus naïve S. bicolor seedlings. The differential metabolic reprogramming in primed plants comprised of a quicker and/or enhanced upregulation of amino acid-, phytohormone-, phenylpropanoid-, flavonoid- and lipid metabolites in response to inoculation with F. pseudograminearum. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture)
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13 pages, 1744 KiB  
Article
Effects of Water Availability in the Soil on Tropane Alkaloid Production in Cultivated Datura stramonium
by Abigail Moreno-Pedraza, Jennifer Gabriel, Hendrik Treutler, Robert Winkler and Fredd Vergara
Metabolites 2019, 9(7), 131; https://doi.org/10.3390/metabo9070131 - 3 Jul 2019
Cited by 13 | Viewed by 4598
Abstract
Background: different Solanaceae and Erythroxylaceae species produce tropane alkaloids. These alkaloids are the starting material in the production of different pharmaceuticals. The commercial demand for tropane alkaloids is covered by extracting them from cultivated plants. Datura stramonium is cultivated under greenhouse conditions as [...] Read more.
Background: different Solanaceae and Erythroxylaceae species produce tropane alkaloids. These alkaloids are the starting material in the production of different pharmaceuticals. The commercial demand for tropane alkaloids is covered by extracting them from cultivated plants. Datura stramonium is cultivated under greenhouse conditions as a source of tropane alkaloids. Here we investigate the effect of different levels of water availability in the soil on the production of tropane alkaloids by D. stramonium. Methods: We tested four irrigation levels on the accumulation of tropane alkaloids. We analyzed the profile of tropane alkaloids using an untargeted liquid chromatography/mass spectrometry method. Results: Using a combination of informatics and manual interpretation of mass spectra, we generated several structure hypotheses for signals in D. stramonium extracts that we assign as putative tropane alkaloids. Quantitation of mass spectrometry signals for our structure hypotheses across different anatomical organs allowed us to identify patterns of tropane alkaloids associated with different levels of irrigation. Furthermore, we identified anatomic partitioning of tropane alkaloid isomers with pharmaceutical applications. Conclusions: Our results show that soil water availability is an effective method for maximizing the production of specific tropane alkaloids for industrial applications. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture)
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19 pages, 3847 KiB  
Article
Comparative Metabolomics of Early Development of the Parasitic Plants Phelipanche aegyptiaca and Triphysaria versicolor
by Kristen Clermont, Yaxin Wang, Siming Liu, Zhenzhen Yang, Claude W. dePamphilis, John I. Yoder, Eva Collakova and James H. Westwood
Metabolites 2019, 9(6), 114; https://doi.org/10.3390/metabo9060114 - 13 Jun 2019
Cited by 11 | Viewed by 4240
Abstract
Parasitic weeds of the family Orobanchaceae attach to the roots of host plants via haustoria capable of drawing nutrients from host vascular tissue. The connection of the haustorium to the host marks a shift in parasite metabolism from autotrophy to at least partial [...] Read more.
Parasitic weeds of the family Orobanchaceae attach to the roots of host plants via haustoria capable of drawing nutrients from host vascular tissue. The connection of the haustorium to the host marks a shift in parasite metabolism from autotrophy to at least partial heterotrophy, depending on the level of parasite dependence. Species within the family Orobanchaceae span the spectrum of host nutrient dependency, yet the diversity of parasitic plant metabolism remains poorly understood, particularly during the key metabolic shift surrounding haustorial attachment. Comparative profiling of major metabolites in the obligate holoparasite Phelipanche aegyptiaca and the facultative hemiparasite Triphysaria versicolor before and after attachment to the hosts revealed several metabolic shifts implicating remodeling of energy and amino acid metabolism. After attachment, both parasites showed metabolite profiles that were different from their respective hosts. In P. aegyptiaca, prominent changes in metabolite profiles were also associated with transitioning between different tissue types before and after attachment, with aspartate levels increasing significantly after the attachment. Based on the results from 15N labeling experiments, asparagine and/or aspartate-rich proteins were enriched in host-derived nitrogen in T. versicolor. These results point to the importance of aspartate and/or asparagine in the early stages of attachment in these plant parasites and provide a rationale for targeting aspartate-family amino acid biosynthesis for disrupting the growth of parasitic weeds. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture)
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16 pages, 2945 KiB  
Article
Deciphering the Resistance Mechanism of Tomato Plants Against Whitefly-Mediated Tomato Curly Stunt Virus Infection through Ultra-High-Performance Liquid Chromatography Coupled to Mass Spectrometry (UHPLC-MS)-Based Metabolomics Approaches
by Leandri T. Rossouw, Ntakadzeni E. Madala, Fidele Tugizimana, Paul A. Steenkamp, Lindy L. Esterhuizen and Ian A. Dubery
Metabolites 2019, 9(4), 60; https://doi.org/10.3390/metabo9040060 - 28 Mar 2019
Cited by 12 | Viewed by 4443
Abstract
Begomoviruses, such as the Tomato curly stunt virus (ToCSV), pose serious economic consequences due to severe crop losses. Therefore, the development and screening of possible resistance markers is imperative. While some tomato cultivars exhibit differential resistance to different begomovirus species, in most cases, [...] Read more.
Begomoviruses, such as the Tomato curly stunt virus (ToCSV), pose serious economic consequences due to severe crop losses. Therefore, the development and screening of possible resistance markers is imperative. While some tomato cultivars exhibit differential resistance to different begomovirus species, in most cases, the mechanism of resistance is not fully understood. In this study, the response of two near-isogenic lines of tomato (Solanum lycopersicum), differing in resistance against whitefly-mediated ToCSV infection were investigated using untargeted ultra-high-performance liquid chromatography coupled to mass spectrometry (UHPLC-MS)-based metabolomics. The responses of the two lines were deciphered using multivariate statistics models. Principal component analysis (PCA) scores plots from various time intervals revealed that the resistant line responded more rapidly with changes to the metabolome than the susceptible counterpart. Moreover, the metabolic reprogramming of chemically diverse metabolites that span a range of metabolic pathways was associated with the defence response. Biomarkers primarily included hydroxycinnamic acids conjugated to quinic acid, galactaric acid, and glucose. Minor constituents included benzenoids, flavonoids, and steroidal glycoalkaloids. Interestingly, when reduced to the level of metabolites, the phytochemistry of the infected plants’ responses was very similar. However, the resistant phenotype was strongly associated with the hydroxycinnamic acid derivatives deployed in response to infection. In addition, the resistant line was able to mount a stronger and quicker response. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture)
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12 pages, 2145 KiB  
Article
Metabolic Analysis of Four Cultivars of Liriope platyphylla
by Chang Ha Park, Abubaker Mohammed Awad Morgan, Byung Bae Park, Sook Young Lee, Sanghyun Lee, Jae Kwang Kim and Sang Un Park
Metabolites 2019, 9(3), 59; https://doi.org/10.3390/metabo9030059 - 26 Mar 2019
Cited by 13 | Viewed by 3963
Abstract
Liriope platyphylla (Liliaceae), a medical plant distributed mainly in China, Taiwan, and Korea, has been used traditionally for the treatment of cough, sputum, asthma, and neurodegenerative diseases. The present study involved the metabolic profiling of this plant and reports spicatoside A accumulation in [...] Read more.
Liriope platyphylla (Liliaceae), a medical plant distributed mainly in China, Taiwan, and Korea, has been used traditionally for the treatment of cough, sputum, asthma, and neurodegenerative diseases. The present study involved the metabolic profiling of this plant and reports spicatoside A accumulation in four different varieties of L. platyphylla (Cheongyangjaerae, Seongsoo, Cheongsim, and Liriope Tuber No. 1) using HPLC and gas chromatography time-of-flight mass spectrometry (GC–TOFMS). A total of 47 metabolites were detected in the different cultivars using GC–TOFMS-based metabolic profiling. The resulting data were subjected to principal component analysis (PCA) for determining the whole experimental variation, and the different cultivars were separated by score plots. Furthermore, hierarchical clustering, Pearson’s correlation, and partial least-squares discriminant analyses (PLS-DA) were subsequently performed to determine significant differences in the various metabolites of the cultivars. The HPLC data revealed that the presence of spicatoside A was detected in all four cultivars, with the amount of spicatoside A varying among them. Among the cultivars, Liriope Tuber No. 1 contained the highest amount of spicatoside A (1.83 ± 0.13 mg/g dry weight), followed by Cheongyangjaerae (1.25 ± 0.01 mg/g dry weight), Cheongsim (1.09 ± 0.04 mg/g dry weight), and Seongsoo (1.01 ± 0.02 mg/g dry weight). The identification of spicatoside A was confirmed by comparing the retention time of the sample with the retention time of the standard. Moreover, the Cheongsim cultivar contained higher levels of phenolic compounds—including vanillic acid, quinic acid, gallic acid, chlorogenic acid, caffeic acid, and benzoic acid—than those of the other two cultivars. On the other hand, the levels of amino acids were higher in the Seongsoo cultivar. Therefore, this study may help breeders produce new varieties with improved nutraceutical and nutritional qualities. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture)
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23 pages, 3995 KiB  
Article
Untargeted Metabolomics Reveal Defensome-Related Metabolic Reprogramming in Sorghum bicolor against Infection by Burkholderia andropogonis
by Charity R. Mareya, Fidele Tugizimana, Lizelle A. Piater, Ntakadzeni E. Madala, Paul A. Steenkamp and Ian A. Dubery
Metabolites 2019, 9(1), 8; https://doi.org/10.3390/metabo9010008 - 2 Jan 2019
Cited by 43 | Viewed by 5803
Abstract
Burkholderia andropogonis is the causal agent of bacterial leaf stripe, one of the three major bacterial diseases affecting Sorghum bicolor. However, the biochemical aspects of the pathophysiological host responses are not well understood. An untargeted metabolomics approach was designed to understand molecular [...] Read more.
Burkholderia andropogonis is the causal agent of bacterial leaf stripe, one of the three major bacterial diseases affecting Sorghum bicolor. However, the biochemical aspects of the pathophysiological host responses are not well understood. An untargeted metabolomics approach was designed to understand molecular mechanisms underlying S. bicolor–B. andropogonis interactions. At the 4-leaf stage, two sorghum cultivars (NS 5511 and NS 5655) differing in disease tolerance, were infected with B. andropogonis and the metabolic changes monitored over time. The NS 5511 cultivar displayed delayed signs of wilting and lesion progression compared to the NS 5655 cultivar, indicative of enhanced resistance. The metabolomics results identified statistically significant metabolites as biomarkers associated with the sorghum defence. These include the phytohormones salicylic acid, jasmonic acid, and zeatin. Moreover, metabolic reprogramming in an array of chemically diverse metabolites that span a wide range of metabolic pathways was associated with the defence response. Signatory biomarkers included aromatic amino acids, shikimic acid, metabolites from the phenylpropanoid and flavonoid pathways, as well as fatty acids. Enhanced synthesis and accumulation of apigenin and derivatives thereof was a prominent feature of the altered metabolomes. The analyses revealed an intricate and dynamic network of the sorghum defence arsenal towards B. andropogonis in establishing an enhanced defensive capacity in support of resistance and disease suppression. The results pave the way for future analysis of the biosynthesis of signatory biomarkers and regulation of relevant metabolic pathways in sorghum. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture)
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