Special Issue "Metabolomics in Agriculture Volume 2"

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

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 14422

Special Issue Editors

Prof. Dr. Ian Dubery
E-Mail Website
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
E-Mail Website
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 in plant biology. 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 the biochemical level. As a post-genomic approach, metabolomics has proven to be a powerful and indispensable tool for interrogating cellular biochemistry and investigating metabolism and its reciprocal crosstalk with cellular signaling 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 the topics that will be covered include (not exclusively) studies on the metabolomic analyses of host responses to biotic stresses such as pathogen infection and insect attacks; mechanisms of adaptation to abiotic stresses such as drought, heat and salt and the mitigating effects of bio-stimulants; and the optimization and development of crop traits to enhance diet and health.

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

Manuscript Submission Information

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Keywords

  • Agricultural biotechnology
  • Metabolomics
  • Metabolic networks
  • Biotic – and abiotic stress
  • Stress adaptation

Published Papers (11 papers)

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Research

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Article
Hordatines and Associated Precursors Dominate Metabolite Profiles of Barley (Hordeum vulgare L.) Seedlings: A Metabolomics Study of Five Cultivars
Metabolites 2022, 12(4), 310; https://doi.org/10.3390/metabo12040310 - 31 Mar 2022
Viewed by 420
Abstract
In the process of enhancing crop potential, metabolomics offers a unique opportunity to biochemically describe plant metabolism and to elucidate metabolite profiles that govern specific phenotypic characteristics. In this study we report an untargeted metabolomic profiling of shoots and roots of barley seedlings [...] Read more.
In the process of enhancing crop potential, metabolomics offers a unique opportunity to biochemically describe plant metabolism and to elucidate metabolite profiles that govern specific phenotypic characteristics. In this study we report an untargeted metabolomic profiling of shoots and roots of barley seedlings performed to reveal the chemical makeup therein at an early growth stage. The study was conducted on five cultivars of barley: ‘Overture’, ‘Cristalia’, ‘Deveron’, ‘LE7′ and ‘Genie’. Seedlings were grown for 16 days post germination under identical controlled conditions, and methanolic extracts were analysed on an ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC–HRMS) system. In addition, an unsupervised pattern identification technique, principal component analysis (PCA), was performed to process the generated multidimensional data. Following annotation of specific metabolites, several classes were revealed, among which phenolic acids represented the largest group in extracts from both shoot and root tissues. Interestingly, hordatines, barley-specific metabolites, were not found in the root tissue. In addition, metabolomic profiling revealed metabolites potentially associated with the plants’ natural protection system against potential pathogens. The study sheds light on the chemical composition of barley at a young developmental stage and the information gathered could be useful in plant research and biomarker-based breeding programs. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture Volume 2)
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Article
Metabolomic Characterisation of Discriminatory Metabolites Involved in Halo Blight Disease in Oat Cultivars Caused by Pseudomonas syringae pv. coronafaciens
Metabolites 2022, 12(3), 248; https://doi.org/10.3390/metabo12030248 - 16 Mar 2022
Viewed by 528
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture Volume 2)
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Article
Comparative Metabolite Profiling of Wheat Cultivars (Triticum aestivum) Reveals Signatory Markers for Resistance and Susceptibility to Stripe Rust and Aluminium (Al3+) Toxicity
Metabolites 2022, 12(2), 98; https://doi.org/10.3390/metabo12020098 - 20 Jan 2022
Viewed by 870
Abstract
Plants continuously produce essential metabolites that regulate their growth and development. The enrichment of specific metabolites determines plant interactions with the immediate environment, and some metabolites become critical in defence responses against biotic and abiotic stresses. Here, an untargeted UHPLC-qTOF-MS approach was employed [...] Read more.
Plants continuously produce essential metabolites that regulate their growth and development. The enrichment of specific metabolites determines plant interactions with the immediate environment, and some metabolites become critical in defence responses against biotic and abiotic stresses. Here, an untargeted UHPLC-qTOF-MS approach was employed to profile metabolites of wheat cultivars resistant or susceptible to the pathogen Puccinia striiformis f. sp. tritici (Pst) and Aluminium (Al3+) toxicity. Multivariate statistical analysis (MVDA) tools, viz. principal component analysis (PCA) and hierarchical cluster analysis (HiCA) were used to qualify the correlation between the identified metabolites and the designated traits. A total of 100 metabolites were identified from primary and secondary metabolisms, including phenolic compounds, such as flavonoid glycosides and hydroxycinnamic acid (HCA) derivatives, fatty acids, amino acids, and organic acids. All metabolites were significantly variable among the five wheat cultivars. The Pst susceptible cultivars demonstrated elevated concentrations of HCAs compared to their resistant counterparts. In contrast, ‘Koonap’ displayed higher levels of flavonoid glycosides, which could point to its resistant phenotype to Pst and Al3+ toxicity. The data provides an insight into the metabolomic profiles and thus the genetic background of Pst- and Al3+-resistant and susceptible wheat varieties. This study demonstrates the prospects of applied metabolomics for chemotaxonomic classification, phenotyping, and potential use in plant breeding and crop improvement. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture Volume 2)
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Communication
Metabolomics Differences of Glycine max QTLs Resistant to Soybean Looper
Metabolites 2021, 11(10), 710; https://doi.org/10.3390/metabo11100710 - 19 Oct 2021
Viewed by 783
Abstract
Quantitative trait loci (QTLs) E and M are major soybean alleles that confer resistance to leaf-chewing insects, and are particularly effective in combination. Flavonoids and/or isoflavonoids are classes of plant secondary metabolites that previous studies agree are the causative agents of resistance of [...] Read more.
Quantitative trait loci (QTLs) E and M are major soybean alleles that confer resistance to leaf-chewing insects, and are particularly effective in combination. Flavonoids and/or isoflavonoids are classes of plant secondary metabolites that previous studies agree are the causative agents of resistance of these QTLs. However, all previous studies have compared soybean genotypes that are of dissimilar genetic backgrounds, leaving it questionable what metabolites are a result of the QTL rather than the genetic background. Here, we conducted a non-targeted mass spectrometry approach without liquid chromatography to identify differences in metabolite levels among QTLs E, M, and both (EM) that were introgressed into the background of the susceptible variety Benning. Our results found that E and M mainly confer low-level, global differences in distinct sets of metabolites. The isoflavonoid daidzein was the only metabolite that demonstrated major increases, specifically in insect-treated M and EM. Interestingly, M confers increased daidzein levels in response to insect, whereas E restores M’s depleted daidzein levels in the absence of insect. Since daidzein levels do not parallel levels of resistance, our data suggest a novel mechanism that the QTLs confer resistance to insects by mediating changes in hundreds of metabolites, which would be difficult for the insect to evolve tolerance. Collective global metabolite differences conferred by E and M might explain the increased resistance of EM. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture Volume 2)
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Article
Metabolomics Reveals Heterogeneity in the Chemical Composition of Green and White Spears of Asparagus (A. officinalis)
Metabolites 2021, 11(10), 708; https://doi.org/10.3390/metabo11100708 - 16 Oct 2021
Cited by 1 | Viewed by 1159
Abstract
Green and white asparagus are quite different crops but can be harvested from the same plant. They have distinct morphological differences due to their mode of cultivation and they are characterised by having contrasting appearance and flavour. Significant chemical differences are therefore expected. [...] Read more.
Green and white asparagus are quite different crops but can be harvested from the same plant. They have distinct morphological differences due to their mode of cultivation and they are characterised by having contrasting appearance and flavour. Significant chemical differences are therefore expected. Spears from three varieties of both green and white forms, harvested in two consecutive seasons were analysed using headspace GC-MS and LC-MS with an untargeted metabolomic workflow. Mainly C5 and C8 alcohols and aldehydes, and phenolic compounds were more abundant in green spears, whereas benzenoids, monoterpenes, unsaturated aldehydes and steroidal saponins were more abundant in white ones. Previously reported key asparagus volatiles and non-volatiles were detected at similar or not significantly different levels in the two asparagus types. Spatial metabolomics revealed also that many volatiles with known positive aroma attributes were significantly more abundant in the upper parts of the spears and showed a decreasing trend towards the base. These findings provide valuable insights into the metabolome of raw asparagus, the contrasts between green and white spears as well as the different chemical distributions along the stem. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture Volume 2)
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Article
A Metabolomics Approach and Chemometric Tools for Differentiation of Barley Cultivars and Biomarker Discovery
Metabolites 2021, 11(9), 578; https://doi.org/10.3390/metabo11090578 - 26 Aug 2021
Cited by 3 | Viewed by 1125
Abstract
One of the ultimate goals of plant breeding is the development of new crop cultivars capable of withstanding increasing environmental stresses, to sustain the constantly growing population and economic demands. Investigating the chemical composition of the above and underground tissues of cultivars is [...] Read more.
One of the ultimate goals of plant breeding is the development of new crop cultivars capable of withstanding increasing environmental stresses, to sustain the constantly growing population and economic demands. Investigating the chemical composition of the above and underground tissues of cultivars is crucial for the understanding of common and specific traits thereof. Using an untargeted metabolomics approach together with appropriate chemometrics tools, the differential metabolite profiles of leaf and root extracts from five cultivars of barley (‘Erica’, ‘Elim’, ‘Hessekwa’, ‘S16’ and ‘Agulhas’) were explored and potential signatory biomarkers were revealed. The study was conducted on seedlings grown for 21 days under identical controlled conditions. An ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) was employed to analyse hydromethanolic leaf and root extracts of barley cultivars. Furthermore, unsupervised and supervised learning algorithms were applied to mine the generated data and to pinpoint cultivar-specific metabolites. Among all the classes of metabolites annotated, phenolic acids and derivatives formed the largest group and also represented the most discriminatory metabolites. In roots, saponarin, an important allelochemical differentially distributed across cultivars, was the only flavonoid annotated. The application of an untargeted metabolomics approach in phenotyping grain crops such as barley was demonstrated, and the metabolites responsible for differentiating between the selected cultivars were revealed. The study provides insights into the chemical architecture of barley, an agro-economically relevant cereal crop; and reiterates the importance of metabolomics tools in plant breeding practices for crop improvement. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture Volume 2)
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Article
Agronomic and Metabolomic Side-Effects of a Divergent Selection for Indol-3-Ylmethylglucosinolate Content in Kale (Brassica oleracea var. acephala)
Metabolites 2021, 11(6), 384; https://doi.org/10.3390/metabo11060384 - 14 Jun 2021
Cited by 3 | Viewed by 1688
Abstract
Brassica oleracea var. acephala (kale) is a cruciferous vegetable widely cultivated for its leaves and flower buds in Europe and a food of global interest as a “superfood”. Brassica crops accumulate phytochemicals called glucosinolates (GSLs) which play an important role in plant defense [...] Read more.
Brassica oleracea var. acephala (kale) is a cruciferous vegetable widely cultivated for its leaves and flower buds in Europe and a food of global interest as a “superfood”. Brassica crops accumulate phytochemicals called glucosinolates (GSLs) which play an important role in plant defense against biotic stresses. Studies carried out to date suggest that GSLs may have a role in the adaptation of plants to different environments, but direct evidence is lacking. We grew two kale populations divergently selected for high and low indol-3-ylmethylGSL (IM) content (H-IM and L-IM, respectively) in different environments and analyzed agronomic parameters, GSL profiles and metabolomic profile. We found a significant increase in fresh and dry foliar weight in H-IM kale populations compared to L-IM in addition to a greater accumulation of total GSLs, indole GSLs and, specifically, IM and 1-methoxyindol-3-ylmethylGSL (1MeOIM). Metabolomic analysis revealed a significant different concentration of 44 metabolites in H-IM kale populations compared to L-IM. According to tentative peak identification from MS interpretation, 80% were phenolics, including flavonoids (kaempferol, quercetin and anthocyanin derivates, including acyl flavonoids), chlorogenic acids (esters of hydroxycinnamic acids and quinic acid), hydroxycinnamic acids (ferulic acid and p-coumaric acid) and coumarins. H-IM kale populations could be more tolerant to diverse environmental conditions, possibly due to GSLs and the associated metabolites with predicted antioxidant potential. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture Volume 2)
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Article
A Comprehensive Targeted Metabolomics Assay for Crop Plant Sample Analysis
Metabolites 2021, 11(5), 303; https://doi.org/10.3390/metabo11050303 - 11 May 2021
Cited by 2 | Viewed by 1239
Abstract
Metabolomics plays an important role in various fields from health to agriculture. However, the comprehensive quantitative metabolomic analysis of plants and plant metabolites has not been widely performed. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS)-based plant metabolomics offers the sensitivity and breadth [...] Read more.
Metabolomics plays an important role in various fields from health to agriculture. However, the comprehensive quantitative metabolomic analysis of plants and plant metabolites has not been widely performed. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS)-based plant metabolomics offers the sensitivity and breadth of coverage for both phenotyping and disease diagnosis of plants. Here, we report a high-coverage and quantitative MS-based assay for plant metabolite analysis. The assay detects and quantifies 206 primary and secondary plant metabolites, including many key plant hormones. In total, it measures 28 amino acids and derivatives, 27 organic acids, 20 biogenic amines and derivatives, 40 acylcarnitines, 90 phospholipids and C-6 sugars. All the analysis methods in this assay are based on LC-MS/MS techniques using both positive and negative-mode multiple reaction monitoring (MRM). The recovery rates of spiked plant samples at three different concentration levels (low, medium and high) ranged from 80% to 120%, with satisfactory precision values of less than 20%. This targeted plant metabolomic assay has been successfully applied to the analysis of large numbers of pine and spruce needle samples, canola root samples, as well as cannabis samples. Moreover, the assay was specifically developed in a 96-well plate format, which enables automated, high-throughput sample analysis. This assay has already been used to analyze over 1500 crop plant samples in less than two months. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture Volume 2)
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Article
Metabolomics for Biomarker Discovery: Key Signatory Metabolic Profiles for the Identification and Discrimination of Oat Cultivars
Metabolites 2021, 11(3), 165; https://doi.org/10.3390/metabo11030165 - 12 Mar 2021
Cited by 3 | Viewed by 974
Abstract
The first step in crop introduction—or breeding programmes—requires cultivar identification and characterisation. Rapid identification methods would therefore greatly improve registration, breeding, seed, trade and inspection processes. Metabolomics has proven to be indispensable in interrogating cellular biochemistry and phenotyping. Furthermore, metabolic fingerprints are chemical [...] Read more.
The first step in crop introduction—or breeding programmes—requires cultivar identification and characterisation. Rapid identification methods would therefore greatly improve registration, breeding, seed, trade and inspection processes. Metabolomics has proven to be indispensable in interrogating cellular biochemistry and phenotyping. Furthermore, metabolic fingerprints are chemical maps that can provide detailed insights into the molecular composition of a biological system under consideration. Here, metabolomics was applied to unravel differential metabolic profiles of various oat (Avena sativa) cultivars (Magnifico, Dunnart, Pallinup, Overberg and SWK001) and to identify signatory biomarkers for cultivar identification. The respective cultivars were grown under controlled conditions up to the 3-week maturity stage, and leaves and roots were harvested for each cultivar. Metabolites were extracted using 80% methanol, and extracts were analysed on an ultra-high performance liquid chromatography (UHPLC) system coupled to a quadrupole time-of-flight (qTOF) high-definition mass spectrometer analytical platform. The generated data were processed and analysed using multivariate statistical methods. Principal component analysis (PCA) models were computed for both leaf and root data, with PCA score plots indicating cultivar-related clustering of the samples and pointing to underlying differential metabolic profiles of these cultivars. Further multivariate analyses were performed to profile differential signatory markers, which included carboxylic acids, amino acids, fatty acids, phenolic compounds (hydroxycinnamic and hydroxybenzoic acids, and associated derivatives) and flavonoids, among the respective cultivars. Based on the key signatory metabolic markers, the cultivars were successfully distinguished from one another in profiles derived from both leaves and roots. The study demonstrates that metabolomics can be used as a rapid phenotyping tool for cultivar differentiation. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture Volume 2)
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Article
An Ascophyllum nodosum-Derived Biostimulant Protects Model and Crop Plants from Oxidative Stress
Metabolites 2021, 11(1), 24; https://doi.org/10.3390/metabo11010024 - 31 Dec 2020
Cited by 5 | Viewed by 1732
Abstract
Abiotic stresses, which at the molecular level leads to oxidative damage, are major determinants of crop yield loss worldwide. Therefore, considerable efforts are directed towards developing strategies for their limitation and mitigation. Here the superoxide-inducing agent paraquat (PQ) was used to generate oxidative [...] Read more.
Abiotic stresses, which at the molecular level leads to oxidative damage, are major determinants of crop yield loss worldwide. Therefore, considerable efforts are directed towards developing strategies for their limitation and mitigation. Here the superoxide-inducing agent paraquat (PQ) was used to generate oxidative stress in the model species Arabidopsis thaliana and the crops tomato and pepper. Pre-treatment with the biostimulant SuperFifty (SF) effectively and universally suppressed PQ-induced leaf lesions, H2O2 build up, cell destruction and photosynthesis inhibition. To further investigate the stress responses and SF-induced protection at the molecular level, we investigated the metabolites by GC-MS metabolomics. PQ induced specific metabolic changes such as accumulation of free amino acids (AA) and stress metabolites. These changes were fully prevented by the SF pre-treatment. Moreover, the metabolic changes of the specific groups were tightly correlating with their phenotypic characteristics. Overall, this study presents physiological and metabolomics data which shows that SF protects against oxidative stress in all three plant species. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture Volume 2)
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Review

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Review
Biostimulants for Plant Growth and Mitigation of Abiotic Stresses: A Metabolomics Perspective
Metabolites 2020, 10(12), 505; https://doi.org/10.3390/metabo10120505 - 10 Dec 2020
Cited by 29 | Viewed by 2744
Abstract
Adverse environmental conditions due to climate change, combined with declining soil fertility, threaten food security. Modern agriculture is facing a pressing situation where novel strategies must be developed for sustainable food production and security. Biostimulants, conceptually defined as non-nutrient substances or microorganisms with [...] Read more.
Adverse environmental conditions due to climate change, combined with declining soil fertility, threaten food security. Modern agriculture is facing a pressing situation where novel strategies must be developed for sustainable food production and security. Biostimulants, conceptually defined as non-nutrient substances or microorganisms with the ability to promote plant growth and health, represent the potential to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and crop productivity. Current knowledge and phenotypic observations suggest that biostimulants potentially function in regulating and modifying physiological processes in plants to promote growth, alleviate stresses, and improve quality and yield. However, to successfully develop novel biostimulant-based formulations and programs, understanding biostimulant-plant interactions, at molecular, cellular and physiological levels, is a prerequisite. Metabolomics, a multidisciplinary omics science, offers unique opportunities to predictively decode the mode of action of biostimulants on crop plants, and identify signatory markers of biostimulant action. Thus, this review intends to highlight the current scientific efforts and knowledge gaps in biostimulant research and industry, in context of plant growth promotion and stress responses. The review firstly revisits models that have been elucidated to describe the molecular machinery employed by plants in coping with environmental stresses. Furthermore, current definitions, claims and applications of plant biostimulants are pointed out, also indicating the lack of biological basis to accurately postulate the mechanisms of action of plant biostimulants. The review articulates briefly key aspects in the metabolomics workflow and the (potential) applications of this multidisciplinary omics science in the biostimulant industry. Full article
(This article belongs to the Special Issue Metabolomics in Agriculture Volume 2)
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