Ian Dubery - Academia.edu (original) (raw)
Papers by Ian Dubery
Suid-Afrikaanse Tydskrif vir Natuurwetenskap en Tegnologie, 2014
Metabolites
The rhizosphere microbiome is a major determinant of plant health. Plant-beneficial or plant grow... more The rhizosphere microbiome is a major determinant of plant health. Plant-beneficial or plant growth-promoting rhizobacteria (PGPR) influence plant growth, plant development and adaptive responses, such as induced resistance/priming. These new eco-friendly choices have highlighted volatile organic compounds (biogenic VOCs) as a potentially inexpensive, effective and efficient substitute for the use of agrochemicals. Secreted bacterial VOCs are low molecular weight lipophilic compounds with a low boiling point and high vapor pressures. As such, they can act as short- or long-distance signals in the rhizosphere, affecting competing microorganisms and impacting plant health. In this study, secreted VOCs from four PGPR strains (Pseudomonas koreensis (N19), Ps. fluorescens (N04), Lysinibacillus sphaericus (T19) and Paenibacillus alvei (T22)) were profiled by solid-phase micro-extraction gas chromatography mass spectrometry (SPME–GC–MS) combined with a multivariate data analysis. Metabolom...
<p>Models are based on the UHPLC-qTOF-MS (positive mode) data sets of Arabidopsis cell–and ... more <p>Models are based on the UHPLC-qTOF-MS (positive mode) data sets of Arabidopsis cell–and medium extracts comparing control <i>versus</i> samples treated with LPS for 24 h. Numbers 1–3 indicate selected variables with <i>m/z</i> and Rt indicated. The equivalent plots for the data obtained in negative mode is presented in Fig E in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0163572#pone.0163572.s002" target="_blank">S2 File</a>.</p
Membranes
Plants recognise bacterial microbe-associated molecular patterns (MAMPs) from the environment via... more Plants recognise bacterial microbe-associated molecular patterns (MAMPs) from the environment via plasma membrane (PM)-localised pattern recognition receptor(s) (PRRs). Lipopolysaccharides (LPSs) are known as MAMPs from gram-negative bacteria that are most likely recognised by PRRs and trigger defence responses in plants. The Arabidopsis PRR(s) and/or co-receptor(s) complex for LPS and the associated defence signalling remains elusive. As such, proteomic identification of LPS receptors and/or co-receptor complexes will help to elucidate the molecular mechanisms that underly LPS perception and defence signalling in plants. The Arabidopsis LPS-binding protein (LBP) and bactericidal/permeability-increasing protein (BPI)-related-2 (LBR2) have been shown to recognise LPS and trigger defence responses while brassinosteroid insensitive 1 (BRI1)-associated receptor kinase 1 (BAK1) acts as a co-receptor for several PRRs. In this study, Arabidopsis wild type (WT) and T-DNA knock out mutants (...
<p>The fungal derived MAMP, ergosterol, induced an intra-cellular metabolic reprogramming t... more <p>The fungal derived MAMP, ergosterol, induced an intra-cellular metabolic reprogramming that involves terpenoid and phenylpropanoid pathways and their branches, indicated on this diagram. IPP, isopentenyl diphosphate DMAPP, dimethylallyl diphosphate; GGPP, geranylgeranyl diphosphate; FPP, farnesyl diphosphate; H/M CA, hydroxylated/methoxylated cinnamic acids. Metabolites shown in blue have been tentatively identified in this study (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087846#pone-0087846-t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087846#pone.0087846.s004" target="_blank">Table S1</a>).</p
Metabolites, 2022
In the process of enhancing crop potential, metabolomics offers a unique opportunity to biochemic... 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 phenoli...
Metabolites, 2022
The metabolome is the underlying biochemical layer of the phenotype and offers a functional reado... 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-inocul...
Metabolites, 2021
The first step in crop introduction—or breeding programmes—requires cultivar identification and c... 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 ch...
Biology, 2022
Plant growth-promoting rhizobacteria (PGPR) are beneficial microorganisms colonising the rhizosph... more Plant growth-promoting rhizobacteria (PGPR) are beneficial microorganisms colonising the rhizosphere. PGPR are involved in plant growth promotion and plant priming against biotic and abiotic stresses. Plant–microbe interactions occur through chemical communications in the rhizosphere and a tripartite interaction mechanism between plants, pathogenic microbes and plant-beneficial microbes has been defined. However, comprehensive information on the rhizosphere communications between plants and microbes, the tripartite interactions and the biochemical implications of these interactions on the plant metabolome is minimal and not yet widely available nor well understood. Furthermore, the mechanistic nature of PGPR effects on induced systemic resistance (ISR) and priming in plants at the molecular and metabolic levels is yet to be fully elucidated. As such, research investigating chemical communication in the rhizosphere is currently underway. Over the past decades, metabolomics approaches...
UHPLC-MS spectra showing MS/MS fragmentation patterns for biomarkers 5â 7. (TIFF 574 kb)
UHPLC-MS spectra showing MS/MS fragmentation patterns for biomarkers 1â 4. (TIFF 615 kb)
Structures of annotated biomarkers: (1) caffeoylputrescine glycoside, (2) cis-5-caffeoylquinic ac... more Structures of annotated biomarkers: (1) caffeoylputrescine glycoside, (2) cis-5-caffeoylquinic acid, (3) feruloylglycoside, (4) azelaic acid glycoside, (5) feruloyl-3-methyltyramine glycoside, (6) feruloyl-3-methyltyramine conjugate and (7) feruloyl-3-methyltyramine. (TIFF 25 kb)
UHPLC-MS (ESI negative) base peak intensity (BPI) chromatograms of hexanoic acid-treated Nicotian... more UHPLC-MS (ESI negative) base peak intensity (BPI) chromatograms of hexanoic acid-treated Nicotiana tabacum cell extracts at 24 h (a), 12 h (b), 6 h (c) and 0 h (d) post-treatment. The most intense peaks at a specific retention time (Rt) are indicated with m/z values. (TIFF 299 kb)
RATIONALE: Caffeoylquinic acid (CQA) derivatives are a group of structurally diverse phytochemica... more RATIONALE: Caffeoylquinic acid (CQA) derivatives are a group of structurally diverse phytochemicals that have attracted attention due to their many health benefits. The structural diversity of these molecules is due in part to the presence of regio-and geometrical isomerism. This structural diversity hampers the accurate annotation of these molecules in plant extracts. Mass spectrometry (MS) is successfully used to differentiate between the different regioisomers of the CQA derivatives; however, the accurate discrimination of the geometrical isomers of these molecules has proven to be an elusive task. METHODS: UV-irradiated methanolic solutions of diCQA were analysed using an UHPLC-QTOF-MS method in negative ionisation mode. An in-source collision induced dissociation (ISCID) method was optimized by varying both the capillary and cone voltages to achieve differential fragmentation patterns between UV-generated geometrical isomers of the diCQAs during MS analyses. RESULTS: Changes in...
Metabolites, 2021
One of the ultimate goals of plant breeding is the development of new crop cultivars capable of w... 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 lear...
Catalysts, 2022
The biocatalytic conversion of sclareol to ambradiol, a valuable component in the fragrance indus... more The biocatalytic conversion of sclareol to ambradiol, a valuable component in the fragrance industry, using whole-cell biotransformation by the dimorphic yeast Hyphozyma roseoniger, was investigated using metabolomics tools. An integrated approach was used to identify and quantify the participating intermediates in this bioconversion using both nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography coupled to mass spectrometry (LC–MS). This study entailed growth stage-dependent analysis of H. roseoniger suspensions grown in batch culture over a 14-day period, beginning with a three-day induction period using 20 mg/200 mL sclareol, followed by a further 1 g/200 mL sclareol dose to enable ambradiol production. The progress of the bioconversion and the resulting dynamic changes to the metabolome were monitored using NMR analysis and semi-targeted LC–MS metabolomics. This outlined the molecular conversions occurring within the matrix and no novel intermediates participa...
Plants, 2021
Plant growth-promoting rhizobacteria (PGPR) can stimulate disease suppression through the inducti... more Plant growth-promoting rhizobacteria (PGPR) can stimulate disease suppression through the induction of an enhanced state of defense readiness. Here, untargeted ultra-high performance liquid chromatography–mass spectrometry (UHPLC–MS) and targeted ultra-high performance liquid chromatography coupled to triple-quadrupole mass spectrometry (UHPLC–QqQ-MS) were used to investigate metabolic reprogramming in tomato plant tissues in response to priming by Pseudomonas fluorescens N04 and Paenibacillus alvei T22 against Phytophthora capsici. Roots were treated with the two PGPR strains prior to stem inoculation with Ph. capsici. Metabolites were methanol-extracted from roots, stems and leaves at two–eight days post-inoculation. Targeted analysis by UHPLC–QqQ-MS allowed quantification of aromatic amino acids and phytohormones. For untargeted analysis, UHPLC–MS data were chemometrically processed to determine signatory biomarkers related to priming against Ph. capsici. The aromatic amino acid ...
A new era of systems biology is disruptively emerging, holistically describing biochemical events... more A new era of systems biology is disruptively emerging, holistically describing biochemical events at both organismal and cellular level. In this new era, emerging ‘-omics’ technologies have brought about a paradigm shift in biological sciences and research. Metabolomics, the youngest of the omics trilogy and defined as the qualitative and quantitative investigation of the entire metabolome of a biological system, has positioned itself as an indispensable methodology to investigate global biochemistry phenomena at a cellular level. Metabolomics is a multidisciplinary research field, involving a convergence of biology, chemistry, chemometrics, statistics and computer science. Metabolomics accordingly can provide unprecedented in-depth explanations and insights of the mechanisms responsible for various physiological conditions, given the innovative developments in analytical technologies (integrating artificial intelligence and machine learning), advancement in chemometric and statisti...
Suid-Afrikaanse Tydskrif vir Natuurwetenskap en Tegnologie, 2014
Metabolites
The rhizosphere microbiome is a major determinant of plant health. Plant-beneficial or plant grow... more The rhizosphere microbiome is a major determinant of plant health. Plant-beneficial or plant growth-promoting rhizobacteria (PGPR) influence plant growth, plant development and adaptive responses, such as induced resistance/priming. These new eco-friendly choices have highlighted volatile organic compounds (biogenic VOCs) as a potentially inexpensive, effective and efficient substitute for the use of agrochemicals. Secreted bacterial VOCs are low molecular weight lipophilic compounds with a low boiling point and high vapor pressures. As such, they can act as short- or long-distance signals in the rhizosphere, affecting competing microorganisms and impacting plant health. In this study, secreted VOCs from four PGPR strains (Pseudomonas koreensis (N19), Ps. fluorescens (N04), Lysinibacillus sphaericus (T19) and Paenibacillus alvei (T22)) were profiled by solid-phase micro-extraction gas chromatography mass spectrometry (SPME–GC–MS) combined with a multivariate data analysis. Metabolom...
<p>Models are based on the UHPLC-qTOF-MS (positive mode) data sets of Arabidopsis cell–and ... more <p>Models are based on the UHPLC-qTOF-MS (positive mode) data sets of Arabidopsis cell–and medium extracts comparing control <i>versus</i> samples treated with LPS for 24 h. Numbers 1–3 indicate selected variables with <i>m/z</i> and Rt indicated. The equivalent plots for the data obtained in negative mode is presented in Fig E in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0163572#pone.0163572.s002" target="_blank">S2 File</a>.</p
Membranes
Plants recognise bacterial microbe-associated molecular patterns (MAMPs) from the environment via... more Plants recognise bacterial microbe-associated molecular patterns (MAMPs) from the environment via plasma membrane (PM)-localised pattern recognition receptor(s) (PRRs). Lipopolysaccharides (LPSs) are known as MAMPs from gram-negative bacteria that are most likely recognised by PRRs and trigger defence responses in plants. The Arabidopsis PRR(s) and/or co-receptor(s) complex for LPS and the associated defence signalling remains elusive. As such, proteomic identification of LPS receptors and/or co-receptor complexes will help to elucidate the molecular mechanisms that underly LPS perception and defence signalling in plants. The Arabidopsis LPS-binding protein (LBP) and bactericidal/permeability-increasing protein (BPI)-related-2 (LBR2) have been shown to recognise LPS and trigger defence responses while brassinosteroid insensitive 1 (BRI1)-associated receptor kinase 1 (BAK1) acts as a co-receptor for several PRRs. In this study, Arabidopsis wild type (WT) and T-DNA knock out mutants (...
<p>The fungal derived MAMP, ergosterol, induced an intra-cellular metabolic reprogramming t... more <p>The fungal derived MAMP, ergosterol, induced an intra-cellular metabolic reprogramming that involves terpenoid and phenylpropanoid pathways and their branches, indicated on this diagram. IPP, isopentenyl diphosphate DMAPP, dimethylallyl diphosphate; GGPP, geranylgeranyl diphosphate; FPP, farnesyl diphosphate; H/M CA, hydroxylated/methoxylated cinnamic acids. Metabolites shown in blue have been tentatively identified in this study (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087846#pone-0087846-t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087846#pone.0087846.s004" target="_blank">Table S1</a>).</p
Metabolites, 2022
In the process of enhancing crop potential, metabolomics offers a unique opportunity to biochemic... 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 phenoli...
Metabolites, 2022
The metabolome is the underlying biochemical layer of the phenotype and offers a functional reado... 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-inocul...
Metabolites, 2021
The first step in crop introduction—or breeding programmes—requires cultivar identification and c... 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 ch...
Biology, 2022
Plant growth-promoting rhizobacteria (PGPR) are beneficial microorganisms colonising the rhizosph... more Plant growth-promoting rhizobacteria (PGPR) are beneficial microorganisms colonising the rhizosphere. PGPR are involved in plant growth promotion and plant priming against biotic and abiotic stresses. Plant–microbe interactions occur through chemical communications in the rhizosphere and a tripartite interaction mechanism between plants, pathogenic microbes and plant-beneficial microbes has been defined. However, comprehensive information on the rhizosphere communications between plants and microbes, the tripartite interactions and the biochemical implications of these interactions on the plant metabolome is minimal and not yet widely available nor well understood. Furthermore, the mechanistic nature of PGPR effects on induced systemic resistance (ISR) and priming in plants at the molecular and metabolic levels is yet to be fully elucidated. As such, research investigating chemical communication in the rhizosphere is currently underway. Over the past decades, metabolomics approaches...
UHPLC-MS spectra showing MS/MS fragmentation patterns for biomarkers 5â 7. (TIFF 574 kb)
UHPLC-MS spectra showing MS/MS fragmentation patterns for biomarkers 1â 4. (TIFF 615 kb)
Structures of annotated biomarkers: (1) caffeoylputrescine glycoside, (2) cis-5-caffeoylquinic ac... more Structures of annotated biomarkers: (1) caffeoylputrescine glycoside, (2) cis-5-caffeoylquinic acid, (3) feruloylglycoside, (4) azelaic acid glycoside, (5) feruloyl-3-methyltyramine glycoside, (6) feruloyl-3-methyltyramine conjugate and (7) feruloyl-3-methyltyramine. (TIFF 25 kb)
UHPLC-MS (ESI negative) base peak intensity (BPI) chromatograms of hexanoic acid-treated Nicotian... more UHPLC-MS (ESI negative) base peak intensity (BPI) chromatograms of hexanoic acid-treated Nicotiana tabacum cell extracts at 24 h (a), 12 h (b), 6 h (c) and 0 h (d) post-treatment. The most intense peaks at a specific retention time (Rt) are indicated with m/z values. (TIFF 299 kb)
RATIONALE: Caffeoylquinic acid (CQA) derivatives are a group of structurally diverse phytochemica... more RATIONALE: Caffeoylquinic acid (CQA) derivatives are a group of structurally diverse phytochemicals that have attracted attention due to their many health benefits. The structural diversity of these molecules is due in part to the presence of regio-and geometrical isomerism. This structural diversity hampers the accurate annotation of these molecules in plant extracts. Mass spectrometry (MS) is successfully used to differentiate between the different regioisomers of the CQA derivatives; however, the accurate discrimination of the geometrical isomers of these molecules has proven to be an elusive task. METHODS: UV-irradiated methanolic solutions of diCQA were analysed using an UHPLC-QTOF-MS method in negative ionisation mode. An in-source collision induced dissociation (ISCID) method was optimized by varying both the capillary and cone voltages to achieve differential fragmentation patterns between UV-generated geometrical isomers of the diCQAs during MS analyses. RESULTS: Changes in...
Metabolites, 2021
One of the ultimate goals of plant breeding is the development of new crop cultivars capable of w... 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 lear...
Catalysts, 2022
The biocatalytic conversion of sclareol to ambradiol, a valuable component in the fragrance indus... more The biocatalytic conversion of sclareol to ambradiol, a valuable component in the fragrance industry, using whole-cell biotransformation by the dimorphic yeast Hyphozyma roseoniger, was investigated using metabolomics tools. An integrated approach was used to identify and quantify the participating intermediates in this bioconversion using both nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography coupled to mass spectrometry (LC–MS). This study entailed growth stage-dependent analysis of H. roseoniger suspensions grown in batch culture over a 14-day period, beginning with a three-day induction period using 20 mg/200 mL sclareol, followed by a further 1 g/200 mL sclareol dose to enable ambradiol production. The progress of the bioconversion and the resulting dynamic changes to the metabolome were monitored using NMR analysis and semi-targeted LC–MS metabolomics. This outlined the molecular conversions occurring within the matrix and no novel intermediates participa...
Plants, 2021
Plant growth-promoting rhizobacteria (PGPR) can stimulate disease suppression through the inducti... more Plant growth-promoting rhizobacteria (PGPR) can stimulate disease suppression through the induction of an enhanced state of defense readiness. Here, untargeted ultra-high performance liquid chromatography–mass spectrometry (UHPLC–MS) and targeted ultra-high performance liquid chromatography coupled to triple-quadrupole mass spectrometry (UHPLC–QqQ-MS) were used to investigate metabolic reprogramming in tomato plant tissues in response to priming by Pseudomonas fluorescens N04 and Paenibacillus alvei T22 against Phytophthora capsici. Roots were treated with the two PGPR strains prior to stem inoculation with Ph. capsici. Metabolites were methanol-extracted from roots, stems and leaves at two–eight days post-inoculation. Targeted analysis by UHPLC–QqQ-MS allowed quantification of aromatic amino acids and phytohormones. For untargeted analysis, UHPLC–MS data were chemometrically processed to determine signatory biomarkers related to priming against Ph. capsici. The aromatic amino acid ...
A new era of systems biology is disruptively emerging, holistically describing biochemical events... more A new era of systems biology is disruptively emerging, holistically describing biochemical events at both organismal and cellular level. In this new era, emerging ‘-omics’ technologies have brought about a paradigm shift in biological sciences and research. Metabolomics, the youngest of the omics trilogy and defined as the qualitative and quantitative investigation of the entire metabolome of a biological system, has positioned itself as an indispensable methodology to investigate global biochemistry phenomena at a cellular level. Metabolomics is a multidisciplinary research field, involving a convergence of biology, chemistry, chemometrics, statistics and computer science. Metabolomics accordingly can provide unprecedented in-depth explanations and insights of the mechanisms responsible for various physiological conditions, given the innovative developments in analytical technologies (integrating artificial intelligence and machine learning), advancement in chemometric and statisti...