Combined Effect of Salt Stress and Nitrogen Level on the Primary Metabolism of Two Contrasting Hydroponically Grown Cichorium spinosum L. Ecotypes

Stamnagathi (Cichorium spinosum L.) is an indigenous plant species well-known for its health-promoting properties. Salinity is a long-term issue with devastating consequences on land and farmers. Nitrogen (N) constitutes a crucial element for plant growth and development (chlorophyll, primary metabolites, etc.). Thus, it is of paramount importance to investigate the impact of salinity and N supply on plants’ metabolism. Within this context, a study was conducted aiming to assess the impact of salinity and N stress on the primary metabolism of two contrasting ecotypes of stamnagathi (montane and seaside). Both ecotypes were exposed to three different salinity levels (0.3 mM—non-saline treatment, 20 mM—medium, and 40 mM—high salinity level) combined with two different total-N supply levels: a low-N at 4 mM and a high-N at 16 mM, respectively. The differences between the two ecotypes revealed the variable responses of the plant under the applied treatments. Fluctuations were observed at the level of TCA cycle intermediates (fumarate, malate, and succinate) of the montane ecotype, while the seaside ecotype was not affected. In addition, the results showed that proline (Pro) levels increased in both ecotypes grown under a low N-supply and high salt stress, while other osmoprotectant metabolites such as γ-aminobutyric acid (GABA) exhibited variable responses under the different N supply levels. Fatty acids such as α-linolenate and linoleate also displayed variable fluctuations following plant treatments. The carbohydrate content of the plants, as indicated by the levels of glucose, fructose, α,α-trehalose, and myo-inositol, was significantly affected by the applied treatments. These findings suggest that the different adaptation mechanisms among the two contrasting ecotypes could be strongly correlated with the observed changes in their primary metabolism. This study also suggests that the seaside ecotype may have developed unique adaptation mechanisms to cope with high N supply and salinity stress, making it a promising candidate for future breeding programs aimed at developing stress tolerant varieties of C. spinosum L.

GC/EI/MS and 1H NMR Metabolomics Reveal the Effect of an Olive Tree Endophytic Bacillus sp. Lipopeptide Extract on the Metabolism of Colletotrichum acutatum

The transition to the Green Deal era requires the discovery of alternative sources of bioactivity and an in-depth understanding of their toxicity to target and non-target organisms. Endophytes have recently emerged as a source of bioactivity of high potential for applications in plant protection, used either per se as biological control agents or their metabolites as bioactive compounds. The olive tree endophytic isolate Bacillus sp. PTA13 produces an array of bioactive lipopeptides (LPs), which additionally exhibit reduced phytotoxicity, features that make them candidates for further research focusing on olive tree plant protection. Here, GC/EI/MS and ¹H NMR metabolomics were employed to study the toxicity of a Bacillus sp. PTA13 LP extract on the olive tree pathogen Colletotrichum acutatum, which causes the devastating disease olive anthracnose. The discovery of resistant isolates of the pathogen to the applied fungicides makes the research on the development of improved sources of bioactivity of paramount importance. Analyses revealed that the applied extract affects the metabolism of the fungus by interfering with the biosynthesis of various metabolites and its energy production. LPs had a great impact on the aromatic amino acid metabolism, the energy equilibrium of the fungus and its fatty acid content. Additionally, the applied LPs affected the levels of pathogenesis-related metabolites, a finding that supports their potential for further research as plant protection agents.

Genetic and Metabolite Variability among Commercial Varieties and Advanced Lines of Vicia faba L

Vicia faba L. (faba bean) is one of the most promising pulse crops due to its nutritional value and high nitrogen fixation capacity. The aim of the present study was to compare the genetic diversity and the seed metabolite profiles of five genetic materials of faba bean. Specifically, three newly developed advanced lines (KK18, KK14 and KK10) and two commercial cultivars (POLIKARPI and TANAGRA), were evaluated for this purpose. Genetic diversity among populations was assessed by SCoT molecular markers. Through UPGMA dendrogram, genetic distances between populations were estimated. Untargeted metabolomics analysis of the seeds was performed employing GC/EI/MS. The cultivar POLYKARPI exhibited the highest polymorphism. All varieties showed a higher within-cultivars and advanced lines variability than between. POLYKARPI and KK14 had the lowest genetic distances, while KK18 and TANAGRA presented the highest ones. The advanced line KK18 displayed the best nutritional profile, the highest concentration of desirable metabolites (lactic acid and trehalose), the lowest concentration of anti-nutritional factors (oxalic acid) and the lowest concentration of saturated fatty acids (palmitic and stearic acid). According to the results of the present study, KK18 line is a very promising material for further exploration and utilization in breeding programs.

Combined Transcriptomic and Metabolomic Analysis Reveals Insights into Resistance of Arabidopsis bam3 Mutant against the Phytopathogenic Fungus Fusarium oxysporum

The wilt-inducing strains of Fusarium oxysporum are responsible for severe damage to many economically important plant species. The most cost-effective and environmentally safe method for the management of Fusarium wilt is the use of resistant cultivars when they are available. In the present study, the Arabidopsis genotype with disruptions in the β-amylase 3 (BAM3) gene, which encodes the major hydrolytic enzyme that degrades starch to maltose, had significantly lower susceptibility to Fusarium oxysporum f. sp. raphani (For) compared to wild-type (wt) plants. It showed the lowest disease severity and contained reduced quantities of fungal DNA in the plant vascular tissues when analyzed with real-time PCR. Through metabolomic analysis using gas chromatography (GC)-mass spectrometry (MS) and gene-expression analysis by reverse-transcription quantitative PCR (RT-qPCR), we observed that defense responses of Arabidopsis bam3 mutants are associated with starch-degradation enzymes, the corresponding modification of the carbohydrate balance, and alterations in sugar (glucose, sucrose, trehalose, and myo-inositol) and auxin metabolism.

Metabolomic and Genomic Approach to Study Defense Induction by Nesidiocoris tenuis against Tuta absoluta and Tetranychus urticae in Tomato Plants

The phytophagy of the predator Nesidiocoris tenuis (Hemiptera: Miridae) can trigger defense responses in tomato plants against pests, such as two spotted spider mite Tetranychus urticae (Acari: Tetranychidae) and South American leaf miner Tuta absoluta (Lepidoptera: Gelechiidae). The expression of genes governing Jasmonic Acid (JA) biosynthesis pathway and fluctuations in the levels of underlying metabolites have been rarely studied in mirid-infested plants. In the present study, fifteen 3rd instar nymphs of N.tenuis were caged on each top and lower leaf of tomato plants for 4 d to induce plant defense; after this period the predators were removed. With regard to T. absoluta, oviposition preference; larval period; and pupal weight were significantly reduced in N. tenuis-punctured plants. T. urticae adults exhibited a significantly higher escape tendency and reduced survival on punctured plants. Metabolomics confirmed such observations revealing substantial differences between N. tenuis-punctured and unpunctured (control) plants. Metabolites directly associated with the activation of the JA defense pathway, such as the precursor α-linolenic acid, had increased concentrations. The expression of the defense-related genes PI-II, MYC2, VSP2, and HEL was increased in the top leaves and only VSP2 and MBP2 in the lower leaves; interestingly, in the middle (unpunctured) leaves VSP2, HEL, and MBP2 were also upregulated, indicating systemic signaling. Collectively, phytophagy of N. tenuis caused adverse effects on T. absoluta and T. urticae, whereas the multi-omics approach (phenomics, metabolomics, and genomics) offered valuable insights into the nature of the plant defense responses and provided useful evidence for future applications in integrated pest management, plausibly resulting in the reduction in the required pesticide volumes.

A Metabolomic Approach to Assess the Toxicity of the Olive Tree Endophyte Bacillus sp. PTA13 Lipopeptides to the Aquatic Macrophyte Lemna minor L

Pesticides represent a major human input into the ecosystem, posing a serious risk to non-target organisms. Therefore, there is pressure toward the reduction in their use and the discovery of alternative sources of bioactivity. Endophytic microorganisms represent a source of bioactivity, whose potential for plant protection has been recently established. In this context, an olive tree endophytic Bacillus sp. was isolated, exhibiting superior antifungal activity, mainly attributed to its major surfactin, iturin, and fengycin and the minor gageotetrin and bacilotetrin groups of lipopeptides (LP). Based on the potential of LP and the lack of information on their toxicity to aquatic organisms, we have investigated the toxicity of an LP extract to the model macrophyte Lemna minor L. The extract exhibited low phytotoxicity (EC₅₀ = 419 μg·mL^-1), and for the investigation of its effect on the plant, GC/EI/MS metabolomics was applied following exposure to sub-lethal doses (EC₂₅ and EC₅₀). Results revealed a general disturbance of plants' biosynthetic capacity in response to LP treatments, with substantial effect on the amino acid pool and the defense mechanism regulated by jasmonate. There are no previous reports on the phytotoxicity of LP to L. minor, with evidence supporting their improved toxicological profile and potential in plant protection.

Discovering the Next-Generation Plant Protection Products: A Proof-of-Concept via the Isolation and Bioactivity Assessment of the Olive Tree Endophyte Bacillus sp. PTA13 Lipopeptides

Endophytic microorganisms (EMs) have recently attracted interest for applications in plant protection, mainly due to their bioactive compound-producing capacity. Therefore, we underwent the task of isolating olive tree EMs and investigating their bioactivity against the devastating pathogen Colletotrichum acutatum. Several EMs were isolated; however, the Bacillus sp. PTA13 isolate exhibited the highest toxicity to the phytopathogen. Bacteria of the genus Bacillus exhibit superior bioactive metabolite-producing capacity, with the lipopeptides (LPs) of surfactin, iturin, and fengycin groups being the most studied. A total LP extract and several fractions were obtained, and their bioactivity was assessed against C. acutatum strains. LPs of the major surfactin, iturin, and fengycin groups and the minor gageotetrin and bacilotetrin groups were annotated. The results confirmed the bioactivity of the major LPs, with fengycins being the most fungitoxic. Interestingly, the minor LP fraction exhibited selective toxicity to the fungicide-resistant C. acutatum isolate, an observation that highlights the significance of our approach to comprehensively mine the total LP extract. This work represents a proof of concept of the exploitation of EMs in customized olive tree plant protection and aligns well with strategies that focus on the sustainability and safety of food production via the development of next-generation plant protection products.

Do pesticides promote or hinder sustainability in agriculture? The challenge of sustainable use of pesticides in modern agriculture

Sustainable agriculture aims to meet the food needs of the growing world population while ensuring minimal impact on the environment and humans as well as productivity. Although pesticides represent the backbone of the agri-food sector in its endeavor to secure food production their application is perceived by many as an obstacle towards the achievement of sustainability; the main concerns are linked with their adverse effects on human health and the environment. Τhis review aims to present the status of chemical plant protection and provide insights into the use of pesticides within the context of sustainable agriculture. It mainly focuses on the strengthened legislation frameworks, which especially in the European Union and the United States of America ensure the placement in the market of pesticides with acceptable toxicological and environmental profiles without compromising crop production. Furthermore, the implementation of Integrated Pest Management principles plays a key role in the sustainable use of pesticides. The stringent regulatory requirements have resulted in the dramatic increase of the associated effort and costs in pesticide research and development (R&D) of improved products. Nevertheless, the investment of leading agrochemical companies in the R&D of new pesticides remains high. All the above set the ground for the sustainable use of pesticides in crop production while their successful application remains a challenge.

Untargeted metabolomics as a hypothesis-generation tool in plant protection product discovery: Highlighting the potential of trehalose and glycerol metabolism of fungal conidiospores as novel targets

INTRODUCTION

The production of high quality and safe food represents a main priority for the agri-food sector in the effort to sustain the exponentially growing human population. Nonetheless, there are major challenges that require the discovery of new, alternative, and improved plant protection products (PPPs). Focusing on fungal plant pathogens, the dissection of mechanisms that are essential for their survival provides insights that could be exploited towards the achievement of the aforementioned aim. In this context, the germination of fungal spores, which are essential structures for their dispersal, survival, and pathogenesis, represents a target of high potential for PPPs. To the best of our knowledge, no PPPs that target the germination of fungal spores currently exist.

OBJECTIVES

Within this context, we have mined for changes in the metabolite profiles of the model fungus Aspergillus nidulans FGSC A4 conidiospores during germination, in an effort to discover key metabolites and reactions that could potentially become targets of PPPs.

METHODS

Untargeted GC/EI-TOF/MS metabolomics and multivariate analyses were employed to monitor time-resolved changes in the metabolomes of germinating A. nidulans conidiospores.

RESULTS

Analyses revealed that trehalose hydrolysis plays a pivotal role in conidiospore germination and highlighted the osmoregulating role of the sugar alcohols, glycerol, and mannitol.

CONCLUSION

The ineffectiveness to introduce active ingredients that exhibit new mode(s)-of-action as fungicides, dictates the urge for the discovery of PPPs, which could be exploited to combat major plant protection issues. Based on the crucial role of trehalose hydrolysis in conidiospore dormancy breakage, and the subsequent involvement of glycerol in their germination, it is plausible to suggest their biosynthesis pathways as potential novel targets for the next-generation antifungal PPPs. Our study confirmed the applicability of untargeted metabolomics as a hypothesis-generation tool in PPPs' research and discovery.

An integrated approach to improve plant protection against olive anthracnose caused by the Colletotrichum acutatum species complex

The olive tree (Olea europaea L.) is the most important oil-producing crop of the Mediterranean basin. However, although plant protection measures are regularly applied, disease outbreaks represent an obstacle towards the further development of the sector. Therefore, there is an urge for the improvement of plant protection strategies based on information acquired by the implementation of advanced methodologies. Recently, heavy fungal infections of olive fruits have been recorded in major olive-producing areas of Greece causing devastating yield losses. Thus, initially, we have undertaken the task to identify their causal agent(s) and assess their pathogenicity and sensitivity to fungicides. The disease was identified as the olive anthracnose, and although Colletotrichum gloeosporioides and Colletotrichum acutatum species complexes are the two major causes, the obtained results confirmed that in Southern Greece the latter is the main causal agent. The obtained isolates were grouped into eight morphotypes based on their phenotypes, which differ in their sensitivities to fungicides and pathogenicity. The triazoles difenoconazole and tebuconazole were more toxic than the strobilurins being tested. Furthermore, a GC/EI/MS metabolomics model was developed for the robust chemotaxonomy of the isolates and the dissection of differences between their endo-metabolomes, which could explain the obtained phenotypes. The corresponding metabolites-biomarkers for the discrimination between morphotypes were discovered, with the most important ones being the amino acids L-tyrosine, L-phenylalanine, and L-proline, the disaccharide α,α-trehalose, and the phytotoxic pathogenesis-related metabolite hydroxyphenylacetate. These metabolites play important roles in fungal metabolism, pathogenesis, and stress responses. The study adds critical information that could be further exploited to combat olive anthracnose through its monitoring and the design of improved, customized plant protection strategies. Also, results suggest the necessity for the comprehensive mapping of the C. acutatum species complex morphotypes in order to avoid issues such as the development of fungicide-resistant genotypes.

1H NMR metabolic profiling dataset of spiny chicory (Cichorium spinosum L.) exposed to abiotic stresses

The data presented here were derived by ¹H NMR metabolic profiling of stamnagathi (Cichorium spinosum L.) plants following treatments with different isosmotic salt solutions; eight saline nutrient solutions with two different levels of total molar concentrations, which were obtained by adding different amounts of NaCl, KCl, Na₂SO₄ or CaCl₂ to the replenishment nutrient solution, were applied. The ¹H NMR metabolite profiles of stamnagathi plants’, which are included in this article, were recorded 56 days after transplanting. Since stamnagathi is a niche product combining unique taste and superior phytonutrient content (e.g. vitamins C and K1, lutein, β-carotene, tocopherols, phenolic acids, fatty acids, minerals, and glutathione), the dataset could serve as a reference for future metabolomics studies related to the investigation of the effects of the four salinity sources on the plant's metabolism. Also, the dataset could be a valuable resource for the discovery of validated biomarkers of the plant's tolerance to salinity stress and responses to new plant protection products (e.g. bioelicitors). The dataset support the research article “Salinity source alters mineral composition and metabolism of Cichorium spinosum” authored by Ntatsi et al., (2017) [1].

Cannabinomics: Application of Metabolomics in Cannabis (Cannabis sativa L.) Research and Development

Cannabis (Cannabis sativa L.) is a complex, polymorphic plant species, which produces a vast array of bioactive metabolites, the two major chemical groups being cannabinoids and terpenoids. Nonetheless, the psychoactive cannabinoid tetrahydrocannabinol (Δ 9 -THC) and the non-psychoactive cannabidiol (CBD), are the two major cannabinoids that have monopolized the research interest. Currently, more than 600 Cannabis varieties are commercially available, providing access to a multitude of potent extracts with complex compositions, whose genetics are largely inconclusive. Recently introduced legislation on Cannabis cultivation in many countries represents a great opportunity, but at the same time, a great challenge for Cannabis research and development (R&D) toward applications in the pharmaceutical, food, cosmetics, and agrochemical industries. Based on its versatility and unique capabilities in the deconvolution of the metabolite composition of complex matrices, metabolomics represents an ideal bioanalytical tool that could greatly assist and accelerate Cannabis R&D. Among others, Cannabis metabolomics or cannabinomics can be applied in the taxonomy of Cannabis varieties in chemovars, the research on the discovery and assessment of new Cannabis-based sources of bioactivity in medicine, the development of new food products, and the optimization of its cultivation, aiming for improvements in yield and potency. Although Cannabis research is still in its infancy, it is highly foreseen that the employment of advanced metabolomics will provide insights that could assist the sector to face the aforementioned challenges. Within this context, here, the current state-of-the-art and conceptual aspects of cannabinomics are presented.

The yeast (Saccharomyces cerevisiae) YCF1 vacuole transporter: Evidence on its implication into the yeast resistance to flusilazole as revealed by GC/EI/MS metabolomics

The development of plant protection product (PPPs)-resistant populations of plant pathogens, pests, and weeds, represents a major challenge that the crop protection sector is facing. Focusing on plant pathogenic fungi, the increased efflux of the active ingredients (a.i.) from the cytoplasm is highly correlated to elevated resistance levels to the applied fungicides. Such mechanism is regulated by ATP-binding cassette transporters (ABC transporters), and although it has been investigated for the past two decades, the latest developments in "omics" technologies could provide new insights with potential applications in crop protection. Within this context, and based on results from preliminary experiments, we have undertaken the task of mining the involvement of the ABC transporter YCF1, which is located in the vacuole membrane, in the fungicide resistance development, applying a functional genomics approach and using yeast (Saccharomyces cerevisiae) as the model organism. Among the fungicides being assessed, flusilazole, which belongs to the azole group of dimethylation inhibitors (DMIs), was discovered as a possible substrate of the YCF1. GC/EI/MS metabolomics analysis revealed the effect of the fungicide's toxicity and that of genotype on yeast's metabolism, confirming the role of this transporter. Fluctuations in the activity of various yeast biosynthetic pathways associated with stress responses were recorded, and corresponding metabolites-biomarkers of flusilazole toxicity were discovered. The metabolites α,α-trehalose, glycerol, myo-inositol-1-phosphate, GABA, l-glutamine, l-tryptophan, l-phenylalanine, l-tyrosine, and phosphate, were the major identified biomarkers of toxicity. Among these, are metabolites that play important roles in fungal metabolism (e.g., cell responses to osmotic stress) or serve as signaling molecules. To the best of our knowledge, this is the first report on the implication of YCF1 in fungal resistance to PPPs. Additionally, the results of GC/EI/MS yeast metabolomics confirmed the robustness of the method and its applicability in the high-throughput study of fungal resistance to fungicides.

Metabolomics reveals differential mechanisms of toxicity of hyperbranched poly(ethyleneimine)-derived nanoparticles to the soil-borne fungus Verticillium dahliae Kleb

There is a consensus on the urge for the discovery and assessment of alternative, improved sources of bioactivity that could be developed as plant protection products (PPPs), in order to combat issues that the agrochemical sector is facing. Based on the recent advances in nanotechnology, nanoparticles seem to have a great potential towards the development of the next generation nano-PPPs used as active ingredients (a.i.) per se or as nanocarriers in their formulation. Nonetheless, information on their mode(s)-of-action (MoA) and mechanisms of toxicity is yet largely unknown, representing a bottleneck in their further assessment and development. Therefore, we have undertaken the task to assess the fungitoxicity of hyperbranched poly(ethyleneimine) (HPEI), quaternized hyperbranched poly(ethyleneimine) (QPEI), and guanidinylated hyperbranched poly(ethyleneimine) (GPEI) nanoparticles to the soil-born plant pathogenic fungus Verticillium dahliae Kleb, and dissect their effects on its metabolism applying GC/EI/MS metabolomics. Results revealed that functionalization of HPEI nanoparticles with guanidinium end groups (GPEI) increases their toxicity to V. dahliae, while functionalization with quaternary ammonium end groups (QPEI) decreases it. The treatments with the nanoparticles affected the chemical homeostasis of the fungus, altering substantially its amino acid pool, energy production, and fatty acid content, causing additionally oxidative and osmotic stresses. To the best of our knowledge, this is the first report on the comparative toxicity of HPEI, QPEI, and GPEI to filamentous fungi applying metabolomics. The findings could be exploited in the study of the quantitative structure-activity relationship (QSAR) of HPEI-derived nanoparticles and their further development as nano-PPPs.

Yeast (Saccharomyces cerevisiae) GC/EI/MS metabolomics dataset

Gas chromatography-electron impact-mass spectrometry (GC/EI/MS) global profiling of the endo-metabolome of wild and genetically engineered yeast (Saccharomyces cerevisiae) strains was performed. The strains were treated or not with sub-lethal doses of the fungicide flusilazole, in order to mine the involvement of the ABC transporter YCF1, which is located in the yeast vacuole membrane, in its resistance to fungicides. Raw GC/EI/MS total ion chromatograms (*.cdf format) of the yeast endo-metabolome were recoded, which are included in this article. Since yeast is a model organism, the dataset could serve as a reference for yeast metabolomics studies related to the investigation of the effects of bioactive ingredients on its metabolism. The dataset support the research article "Karamanou D. and Aliferis K.A, 2019. The yeast (Saccharomyces cerevisiae) YCF1 vacuole transporter: evidence on its implication into the yeast resistance to flusilazole as revealed by GC/EI/MS metabolomics. Pest. Biochem. Physiol. doi: https://doi.org/10.1016/j.pestbp.2019.09.013". 10.1016/j.pestbp.2019.09.013.

Assessment of the effects of metribuzin, glyphosate, and their mixtures on the metabolism of the model plant Lemna minor L. applying metabolomics

Chemical plant protection products (PPPs) is a major group of xenobiotics that are being released in the environment. Although the effects of individual active ingredients (a.i.) on organisms have been studied, information on those of mixtures, is fragmented. Aquatic environments are being polluted by PPPs, posing serious risks for the environment, human, and other organisms. Based on the potential of the model aquatic plant Lemna minor L. in the assessment of PPPs-caused stresses, we have undertaken the task of developing a metabolomics approach for the study of the effects of metribuzin and glyphosate, and their mixtures. Bioassays revealed that metribuzin exhibit higher toxicity than glyphosate and metabolomics highlighted corresponding changes in its metabolome. Treatments had a substantial impact on plants' amino acid pool, resulting in elevated levels of the majority of the identified amino acids. Results indicate that the increased proteolytic activity is a common effect of the a.i. and their mixtures. Additionally, the activation of salicylate-signaling pathways was recorded as a response to the toxicity caused by mixtures. Among the identified metabolites that were discovered as biomarkers were γ-aminobutyric acid (GABA), salicylate, caffeate, α,α-trehalose, and squalene, which play multiple roles in plants' metabolism such as, signaling, antioxidant, and structure protection. No reports exist on the combined effects of PPPs on Lemna and results confirm the applicability of Lemna metabolomics in the study of the combined effects of herbicides and its potential in the monitoring of the environmental health of aquatic environments based on fluctuations of the plant's metabolism.

Original GC/EI/MS total ion chromatograms of Lemna (Lemna minor L.) treated or not with metribuzin, glyphosate, and their binary mixtures

The GC/EI/MS metabolite profiles of Lemna minor L. plants were recorded following treatments with sub-lethal concentrations of the herbicidal active ingredients (a.i.) metribuzin and glyphosate, and various of their binary mixtures. The raw GC/EI/MS total ion chromatograms (*.cdf format) of the Lemna's endo-metabolomes were recorded, which are included in this article. Since Lemna is a model organism in ecotoxicological studies, the dataset could serve as a reference for Lemna metabolomics studies related to the investigation of the effects of phytotoxic compounds and their mixtures on its metabolism. Also, the dataset could be a valuable resource for the discovery of validated biomarkers of the toxicity of mixtures. The dataset support the research article "Kostopoulou et al., Assessment of the effects of metribuzin, glyphosate, and their mixtures on the metabolism of the model plant Lemna minor L. applying metabolomics. "Chemosphere 239, 2020, 124582."

Fusarium graminearum1H NMR metabolomics

Raw ¹H NMR spectra of Fusarium graminearum hyphae can be found at the website of the pesticide metabolomics group (PMG) of the Agricultural University of Athens at the address: http://www.aua.gr/pesticide-metabolomicsgroup/Resources/Fusarium_graminearum_NMR_spectra.html, accession number PMG-01–17. The data set support the research article “Implication of Fusarium graminearum Primary Metabolism in its Resistance to Benzimidazole Fungicides as revealed by ¹H NMR Metabolomics” [1].

Implication of Fusarium graminearum primary metabolism in its resistance to benzimidazole fungicides as revealed by 1H NMR metabolomics

Fungal metabolomics is a field of high potential but yet largely unexploited. Focusing on plant-pathogenic fungi, no metabolomics studies exist on their resistance to fungicides, which represents a major issue that the agrochemical and agricultural sectors are facing. Fungal infections cause quantitative, but also qualitative yield losses, especially in the case of mycotoxin-producing species. The aim of the study was to correlate metabolic changes in Fusarium graminearum strains' metabolomes with their carbendazim-resistant level and discover corresponding metabolites-biomarkers, with primary focus on its primary metabolism. For this purpose, comparative ¹H NMR metabolomics was applied to a wild-type and four carbendazim-resistant Fusarium graminearum strains following or not exposure to the fungicide. Results showed an excellent discrimination between the strains based on their carbendazim-resistance following exposure to low concentration of the fungicide (2 mg L^-1). Both genotype and fungicide treatments had a major impact on fungal metabolism. Among the signatory metabolites, a positive correlation was discovered between the content of F. graminearum strains in amino acids of the aromatic and pyruvate families, l-glutamate, l-proline, l-serine, pyroglutamate, and succinate and their carbendazim-resistance level. In contrary, their content in l-glutamine and l-threonine, had a negative correlation. Many of these metabolites play important roles in fungal physiology and responses to stresses. This work represents a proof-of-concept of the applicability of ¹H NMR metabolomics for high-throughput screening of fungal mutations leading to fungicide resistance, and the study of its biochemical basis, focusing on the involvement of primary metabolism. Results could be further exploited in programs of resistance monitoring, genetic engineering, and crop protection for combating fungal resistance to fungicides.

Multiple nucleobase transporters contribute to boscalid sensitivity in Aspergillus nidulans

The development of fungicide-resistant fungal populations represents a major challenge for the agrochemical and agri-food sectors, which threatens food supply and security. The issue becomes complex for fungi that cause quantitative and qualitative losses due to mycotoxin biosynthesis. Nonetheless, currently, the molecular details underlying fungicide action and fungal resistance mechanisms are partially known. Here, we have investigated whether plasma membrane transporters contribute to specific fungicide uptake in the model fungus Aspergillus nidulans. Independent physiological tests and toxicity screening of selected fungicides provided evidence that the antifungal activity of Succinate Dehydrogenase Inhibitors (SDHIs) is associated with the expression of several nucleobase-related transporters. In particular, it was shown that a strain genetically inactivated in all seven nucleobase-related transporters is resistant to the fungicide boscalid, whereas none of the single null mutants exhibited significant resistance level. By constructing and testing isogenic strains that over-express each one of the seven transporters, we confirmed that five of them, namely, UapC, AzgA, FycB, CntA, and FurA, contribute to boscalid uptake. Additionally, by employing metabolomics we have examined the effect of boscalid on the metabolism of isogenic strains expressing or genetically lacking boscalid-related nucleobase transporters. The results confirmed the involvement of specific nucleobase transporters in fungicide uptake, leading to the discovery of corresponding metabolites-biomarkers. This work is the first report on the involvement of specific transporters in fungicide uptake and toxicity and their impact on fungal metabolism regulation and results might be further exploited towards the deeper understanding of fungal resistance to fungicides.

An integrated RNAseq-1H NMR metabolomics approach to understand soybean primary metabolism regulation in response to Rhizoctonia foliar blight disease

BACKGROUND

Rhizoctonia solani AG1-IA is a devastating phytopathogen causing Rhizoctonia foliar blight (RFB) of soybean worldwide with yield losses reaching 60%. Plant defense mechanisms are complex and information from different metabolic pathways is required to thoroughly understand plant defense regulation and function. Combining information from different "omics" levels such as transcriptomics, metabolomics, and proteomics is required to gain insights into plant metabolism and its regulation. As such, we studied fluctuations in soybean metabolism in response to R. solani infection at early and late disease stages using an integrated transcriptomics-metabolomics approach, focusing on the regulation of soybean primary metabolism and oxidative stress tolerance.

RESULTS

Transcriptomics (RNAseq) and metabolomics (1H NMR) data were analyzed individually and by integration using bidirectional orthogonal projections to latent structures (O2PLS) to reveal possible links between the metabolome and transcriptome during early and late infection stages. O2PLS analysis detected 516 significant transcripts, double that reported in the univariate analysis, and more significant metabolites than detected in partial least squares discriminant analysis. Strong separation of treatments based on integration of the metabolomes and transcriptomes of the analyzed soybean leaves was revealed, similar trends as those seen in analyses done on individual datasets, validating the integration method being applied. Strong fluctuations of soybean primary metabolism occurred in glycolysis, the TCA cycle, photosynthesis and photosynthates in response to R. solani infection. Data were validated using quantitative real-time PCR on a set of specific markers as well as randomly selected genes. Significant increases in transcript and metabolite levels involved in redox reactions and ROS signaling, such as peroxidases, thiamine, tocopherol, proline, L-alanine and GABA were also recorded. Levels of ethanol increased 24 h post-infection in soybean leaves, and alcohol dehydrogenase (ADH) loss-of-function mutants of Arabidopsis thaliana had higher necrosis than wild type plants.

CONCLUSIONS

As a proof-of-concept, this study offers novel insights into the biological correlations and identification of candidate genes and metabolites that can be used in soybean breeding for resistance to R. solani AG1-IA infection. Additionally, these findings imply that alcohol and its associated gene product ADH may have important roles in plant resistance to R. solani AG1-IA causing foliar blight.

Alleviation of Drought Stress and Metabolic Changes in Timothy (Phleum pratense L.) Colonized with Bacillus subtilis B26

Drought is a major limiting factor of crop productivity worldwide and its incidence is predicted to increase under climate change. Drought adaptation of cool-season grasses is thus a major challenge to secure the agricultural productivity under current and future climate conditions. Endophytes are non-pathogenic plant-associated bacteria that can play an important role in conferring resistance and improving plant tolerance to drought. In this study, the effect of inoculation of the bacterial endophyte Bacillus subtilis strain B26 on growth, water status, photosynthetic activity and metabolism of timothy (Phleum pratense L.) subjected to drought stress was investigated under controlled conditions. Under both drought-stress and non-stressed conditions, strain B26 successfully colonized the internal tissues of timothy and had a positive impact on plant growth. Exposure of inoculated plant to a 8-week drought-stress led to significant increase in shoot and root biomass by 26.6 and 63.8%, and in photosynthesis and stomatal conductance by 55.2 and 214.9% respectively, compared to non-inoculated plants grown under similar conditions. There was a significant effect of the endophyte on plant metabolism; higher levels of several sugars, notably sucrose and fructans and an increase of key amino acids such as, asparagine, glutamic acid and glutamine were recorded in shoots and roots of colonized plants compared to non-colonized ones. The accumulation of the non-protein amino acid GABA in shoots of stressed plants and in roots of stressed and unstressed plants was increased in the presence of the endophyte. Taken together, our results indicate that B. subtilis B26 improves timothy growth under drought stress through the modification of osmolyte accumulation in roots and shoots. These results will contribute to the development of a microbial agent to improve the yield of grass species including forage crops and cereals exposed to environmental stresses.

Maple Bark Biochar Affects Rhizoctonia solani Metabolism and Increases Damping-Off Severity

Many studies have investigated the effect of biochar on plant yield, nutrient uptake, and soil microbial populations; however, little work has been done on its effect on soilborne plant diseases. To determine the effect of maple bark biochar on Rhizoctonia damping-off, 11 plant species were grown in a soilless potting substrate amended with different concentrations of biochar and inoculated or not with Rhizoctonia solani anastomosis group 4. Additionally, the effect of biochar amendment on R. solani growth and metabolism in vitro was evaluated. Increasing concentrations of maple bark biochar increased Rhizoctonia damping-off of all 11 plant species. Using multivariate analyses, we observed positive correlations between biochar amendments, disease severity and incidence, abundance of culturable bacterial communities, and physicochemical parameters. Additionally, biochar amendment significantly increased R. solani growth and hyphal extension in vitro, and altered its primary metabolism, notably the mannitol and tricarboxylic acid cycles and the glycolysis pathway. One or several organic compounds present in the biochar, as identified by gas chromatography-mass spectrometry analysis, may be metabolized by R. solani. Taken together, these results indicate that future studies on biochar should focus on the effect of its use as an amendment on soilborne plant pathogens before applying it to soils.

Metabolic responses of willow (Salix purpurea L.) leaves to mycorrhization as revealed by mass spectrometry and (1)H NMR spectroscopy metabolite profiling

The root system of most terrestrial plants form symbiotic interfaces with arbuscular mycorrhizal fungi (AMF), which are important for nutrient cycling and ecosystem sustainability. The elucidation of the undergoing changes in plants' metabolism during symbiosis is essential for understanding nutrient acquisition and for alleviation of soil stresses caused by environmental cues. Within this context, we have undertaken the task of recording the fluctuation of willow (Salix purpurea L.) leaf metabolome in response to AMF inoculation. The development of an advanced metabolomics/bioinformatics protocol employing mass spectrometry (MS) and (1)H NMR analyzers combined with the in-house-built metabolite library for willow (http://willowmetabolib.

RESEARCH

mcgill.ca/index.html) are key components of the research. Analyses revealed that AMF inoculation of willow causes up-regulation of various biosynthetic pathways, among others, those of flavonoid, isoflavonoid, phenylpropanoid, and the chlorophyll and porphyrin pathways, which have well-established roles in plant physiology and are related to resistance against environmental stresses. The recorded fluctuation in the willow leaf metabolism is very likely to provide AMF-inoculated willows with a significant advantage compared to non-inoculated ones when they are exposed to stresses such as, high levels of soil pollutants. The discovered biomarkers of willow response to AMF inoculation and corresponding pathways could be exploited in biomarker-assisted selection of willow cultivars with superior phytoremediation capacity or genetic engineering programs.

Identification of signatory secondary metabolites during mycoparasitism of Rhizoctonia solani by Stachybotrys elegans

Stachybotrys elegans is able to parasitize the fungal plant pathogen Rhizoctonia solani AG-3 following a complex and intimate interaction, which, among others, includes the production of cell wall-degrading enzymes, intracellular colonization, and expression of pathogenic process encoding genes. However, information on the metabolome level is non-existent during mycoparasitism. Here, we performed a direct-infusion mass spectrometry (DIMS) metabolomics analysis using an LTQ Orbitrap analyzer in order to detect changes in the profiles of induced secondary metabolites of both partners during this mycoparasitic interaction 4 and 5 days following its establishment. The diketopiperazine(s) (DKPs) cyclo(S-Pro-S-Leu)/cyclo(S-Pro-S-Ile), ethyl 2-phenylacetate, and 3-nitro-4-hydroxybenzoic acid were detected as the primary response of Rhizoctonia 4 days following dual-culturing with Stachybotrys, whereas only the latter metabolite was up-regulated 1 day later. On the other hand, trichothecenes and atranones were mycoparasite-derived metabolites identified during mycoparasitism 4 and 5 days following dual-culturing. All the above secondary metabolites are known to exhibit bioactivity, including fungitoxicity, and represent key elements that determine the outcome of the interaction being studied. Results could be further exploited in programs for the evaluation of the bioactivity of these metabolites per se or their chemical analogs, and/or genetic engineering programs to obtain more efficient mycoparasite strains with improved efficacy and toxicological profiles.

A metabolic profiling strategy for the dissection of plant defense against fungal pathogens

Here we present a metabolic profiling strategy employing direct infusion Orbitrap mass spectrometry (MS) and gas chromatography-mass spectrometry (GC/MS) for the monitoring of soybean's (Glycine max L.) global metabolism regulation in response to Rhizoctonia solani infection in a time-course. Key elements in the approach are the construction of a comprehensive metabolite library for soybean, which accelerates the steps of metabolite identification and biological interpretation of results, and bioinformatics tools for the visualization and analysis of its metabolome. The study of metabolic networks revealed that infection results in the mobilization of carbohydrates, disturbance of the amino acid pool, and activation of isoflavonoid, α-linolenate, and phenylpropanoid biosynthetic pathways of the plant. Components of these pathways include phytoalexins, coumarins, flavonoids, signaling molecules, and hormones, many of which exhibit antioxidant properties and bioactivity helping the plant to counterattack the pathogen's invasion. Unraveling the biochemical mechanism operating during soybean-Rhizoctonia interaction, in addition to its significance towards the understanding of the plant's metabolism regulation under biotic stress, provides valuable insights with potential for applications in biotechnology, crop breeding, and agrochemical and food industries.

Characterization and transcriptional regulation of Stachybotrys elegans mitogen-activated-protein kinase gene smkA following mycoparasitism and starvation conditions

Mitogen-activated protein kinase (MAPK) signaling pathways play an important role in the development and conidiation of fungal pathogens on their hosts and the sensing of host-derived cues. Mycoparasitism is a fungus-fungus interaction comprising host-pathogen cross talk. Until now, only little information is available on the role of the MAPK signaling pathway during this interaction. Here, we report on the differential expression of a MAPK/ERK gene in the mycoparasite Stachybotrys elegans in response to direct parasitism of different vegetative structures of the plant pathogen Rhizoctonia solani (i.e., carbon-rich condition) and to nutrient starvation (i.e., carbon-poor condition). Western blot analysis against ERK1/2 highlighted an increase in their phosphorylated forms when S. elegans was grown under starvation condition compared to that detected in response to mycoparasitism. A higher abundance of phosphorylated ERK1/2 at the third day of interaction compared to that estimated under starvation condition was detected applying LC-MS/MS. At the transcriptional level, smkA, a YERK1 class member, was significantly induced in response to hyphal parasitism compared to parasitized sclerotia at 3, 4, and 5 days of interaction. However, under starvation condition, smkA levels were significantly induced after 7 days of growth. Southern blot analysis revealed that smkA is member of a small gene family. Collectively, these results suggest that smkA could be implicated in the mycoparasitic process in S. elegans as well as in stress-activated pathways. These results may be of wider significance in other fungus-fungus interactions.

Gas chromatography-mass spectrometry metabolite profiling of worker honey bee (Apis mellifera L.) hemolymph for the study of Nosema ceranae infection

Here, we are presenting a gas chromatography-mass spectrometry (GC/MS) approach for the study of infection of the worker honey bee (Apis mellifera L.) by the newly emerged obligate intracellular parasite Nosema ceranae based on metabolite profiling of hemolymph. Because of the severity of the disease, early detection is crucial for its efficient control. Results revealed that the parasite causes a general disturbance of the physiology of the honey bee affecting the mechanisms controlling the mobilization of energy reserves in infected individuals. The imposed nutritional and energetic stress to the host was depicted mainly in the decreased levels of the majority of carbohydrates and amino acids, including metabolites such as fructose, l-proline, and the cryoprotectants sorbitol and glycerol, which are implicated in various biochemical pathways. Interestingly, the level of glucose was detected at significantly higher levels in infected honey bees. Metabolomics analyses were in agreement with those of multiplex quantitative PCR analyses, indicating that it can be used as a complementary tool for the detection and the study of the physiology of the disease.

FT-ICR/MS and GC-EI/MS metabolomics networking unravels global potato sprout's responses to Rhizoctonia solani infection

The complexity of plant-pathogen interactions makes their dissection a challenging task for metabolomics studies. Here we are reporting on an integrated metabolomics networking approach combining gas chromatography/mass spectrometry (GC/MS) with Fourier transform ion cyclotron resonance/mass spectrometry (FT-ICR/MS) and bioinformatics analyses for the study of interactions in the potato sprout-Rhizoctonia solani pathosystem and the fluctuations in the global metabolome of sprouts. The developed bioanalytical and bioinformatics protocols provided a snapshot of the sprout's global metabolic network and its perturbations as a result of pathogen invasion. Mevalonic acid and deoxy-xylulose pathways were substantially up-regulated leading to the biosynthesis of sesquiterpene alkaloids such as the phytoalexins phytuberin, rishitin, and solavetivone, and steroidal alkaloids having solasodine and solanidine as their common aglycons. Additionally, the perturbation of the sprout's metabolism was depicted in fluctuations of the content of their amino acids pool and that of carboxylic and fatty acids. Components of the systemic acquired resistance (SAR) and hypersensitive reaction (HR) such as azelaic and oxalic acids were detected in increased levels in infected sprouts and strategies of the pathogen to overcome plant defense were proposed. Our metabolic approach has not only greatly expanded the multitude of metabolites previously reported in potato in response to pathogen invasion, but also enabled the identification of bioactive plant-derived metabolites providing valuable information that could be exploited in biotechnology, biomarker-assisted plant breeding, and crop protection for the development of new crop protection agents.

Metabolite composition and bioactivity of Rhizoctonia solani sclerotial exudates

Sclerotia are vegetative structures that play a major role in survival of fungi under adverse conditions. The sclerotia of the plant pathogen Rhizoctonia solani AG2-2 IIIB exude liquid brown droplets that were evaluated for their bioactivity and toxicity against microorganisms and plant species. Also, their metabolic composition was analyzed by integrating Fourier transform ion cyclotron resonance-mass spectrometry (FT-ICR/MS), gas chromatography-MS (GC/MS), and proton nuclear magnetic resonance ((1)H NMR) spectroscopy. The results showed that exudates are complex mixtures composed of phenolics (17.40%), carboxylic acids (12.79%), carbohydrates (6.08%), fatty acids (3.78%), and amino acids (3.47%). The presence of such metabolites contributed to their antifungal and phytotoxic activities. The biological interpretation of the results highly suggests that the exudates not only have multiple roles in fungal physiology but also are a potential bioactive source with moderate toxicity. Our findings show with certainty that the integration of different analytical platforms is a powerful approach for extracting the maximum and reliable information on the metabolic composition of complex biological samples.

Lemna minor L. as a model organism for ecotoxicological studies performing 1H NMR fingerprinting

A validated method applying (1)H NMR fingerprinting for the study of metabolic changes caused in Lemna minor L. by various phytotoxic substances is presented. (1)H NMR spectra of crude extracts from untreated and treated colonies with the herbicides glyphosate, mesotrione, norflurazon, paraquat and the phytotoxin pyrenophorol were subjected to multivariate analyses for detecting differences between groups of treatments. Partial least squares-discriminant analysis (PLS-DA) and hierarchical cluster analysis (HCA) were carried out in order to discriminate and classify treatments according to the observed changes in the metabolome of the plant. Although the compounds at the concentrations used did not cause macroscopically observable symptoms of phytotoxicity, characteristic metabolic changes were detectable by analyzing (1)H NMR spectra. Analyses results revealed that metabonomics applying (1)H NMR fingerprinting is a potential method for the investigation of toxicological effects of xenobiotics on L. minor, and possibly on other duckweed species, helping in the understanding of such interactions.

Comparative toxicity of the phytotoxins (8R,16R)-(-)-pyrenophorin and (5S,8R,13S,16R)-(-)-pyrenophorol on aquatic organisms

The acute toxicities of the fungal phytotoxins (8R,16R)-(-)-pyrenophorin and (5S,8R,13S,16R)-(-)-pyrenophorol on Vibrio fischeri, Oscillatoria perornata, Pseudokirchneriella subcapitata, Lemna minor and Artemia fransiscana were evaluated. (8R,16R)-(-)-pyrenophorin was more toxic than (5S,8R,13S,16R)-(-)-pyrenophorol to V. fischeri, O. perornata, L. minor and A. fransiscana. The highest acute toxicity of (8R,16R)-(-)-pyrenophorin was exhibited on V. fischeri (5 min median effective concentration of 3.57 M 10(-5)) whereas the corresponding value for (5S,8R,13S,16R)-(-)-pyrenophorol was 801 M 10(-5). P. subcapitata exhibited a lack of sensitivity (median inhibitory concentration of >10 M 10(-5)) to both phytotoxins.

Physiological and ultrastructural changes in "green islands" on Avena sterilis leaves caused by (8R,16R)-(-)-pyrenophorin

The biochemical and ultrastructural changes in "green islands" (GIs) on detached Avena sterilis leaves caused by the macrodiolide (8R,16R)-(-)-pyrenophorin in the dark were examined. In the absence of light, leaf segments retained their photosynthetic pigments for 96 h after treatment with (8R,16R)-(-)-pyrenophorin (70 muM), whereas in the untreated leaves complete senescence, loss of photosynthetic pigments and cell disorganization were observed 72 h after detachment. Proteolytic enzyme activity in treated tissues with pyrenophorin remained at low levels for 96 h after treatment and protein dissipation was lower in the treated than in the untreated. Although tissues in "GIs" seem macroscopically healthy, electron microscopy observations revealed structurally disorganized cells filled with granular, electron-dense material. Chloroplasts were severely damaged and contained a large number of plastoglobuli. Similar ultrastructural changes were also observed in A. sterilis tissues treated with the phytotoxin under illumination, indicating a mechanism operating both under illumination and in the dark.

Metabonomic strategy for the investigation of the mode of action of the phytotoxin (5S,8R,13S,16R)-(-)-pyrenophorol using 1H nuclear magnetic resonance fingerprinting

The biochemical mode of action of (5S,8R,13S,16R)-(-)-pyrenophorol isolated from a Drechslera avenae pathotype was investigated by using metabolic fingerprinting. (1)H NMR spectra of crude leaf extracts from untreated Avena sterilis seedlings and A. sterilis seedlings treated with pyrenophorol were compared with those obtained from treatments with the herbicides diuron, glyphosate, mesotrione, norflurazon, oxadiazon, and paraquat. Multivariate analysis was carried out to group treatments according to the mode of action of the phytotoxic substances applied. Analysis results revealed that none of the herbicide treatments fitted the pyrenophorol model and indicate that the effect of the phytotoxin on A. sterilis differs than those caused by glyphosate, mesotrione, norflurazon, oxadiazon, paraquat, and diuron, which inhibit 5-enolpyruvylshikimate-3-phosphate synthase, 4-hydroxyphenyl-pyruvate-dioxygenase, phytoene desaturase, protoporphyrinogen oxidase, photosystem I, and photosystem II, respectively. The method applied, combined with appropriate data preprocessing and analysis, was found to be rapid for the screening of phytotoxic substances for metabolic effects.