The 'prime-ome': towards a holistic approach to priming

Fluorescence detection of pyrene-stained Bacillus subtilis LPM1 rhizobacteria from colonized patterns of tomato roots

A series of water soluble 8-alcoxypyrene-1,3,6-trisulfonic sodium salts bearing different alcoxy lateral chains and functional end groups was synthesized and the molecular structure was corroborated by nuclear magnetic resonance spectroscopy. The photophysical properties in water analyzed by UV-Vis and static and dynamic fluorescence revealed that all of the pigments emit in the blue region at a maximal wavelength of 436 nm and with fluorescence lifetimes in the range of ns. Among them, sodium 8-((10-carboxydecyl) oxy) pyrene-1,3,6-trisulfonate M1 exhibits a high fluorescence quantum yield (φ = 80%) and a good interaction with B. subtilis LPM1 rhizobacteria; this has been demonstrated through in vitro staining assays. Tomato plants (Solanum lycopersicon cv. Micro-Tom) increased the release of root exudates, mainly malic and fumaric acids, after 12 h of treatment with benzothiadiazole (BTH) as a foliar elicitor. However, the chemotaxis analysis demonstrated that malic acid is the most powerful chemoattractant of the rhizobacteria Bacillus subtilis LPM1: in agar plates, a major growth (60 mm) was found for a concentration of 100 mM, while in capillary tubes, the earliest response was at 30 min with 3.3 × 108 CFU mL-1. The confocal microscopic analysis carried out on the tomato roots of the pyrene stained B. subtilis LPM1 revealed that this bacterium mainly colonizes the epidermal zones, i.e. the junctions to primary roots, lateral roots and root hairs, meaning that these root hair sections are the highest colonisable sites involved in the biosynthesis of exudates. This fluorescent pyrene marker M1 represents a valuable tool to evaluate B. subtilis-plant interactions in an easy and quick test in both in vitro and in vivo tomato crops.

Plant chromatin, metabolism and development - an intricate crosstalk

Chromatin structure influences DNA accessibility and underlying gene expression. Disturbances of chromatin structure often result in pleiotropic developmental phenotypes. Interactions between chromatin modifications and development have been the main focus of epigenetic studies. Recent years brought major advance in uncovering and understanding connections between chromatin organisation in the nucleus and metabolic processes that take place in the cytoplasm or other cellular compartments. Products of primary metabolism and cell redox states influence chromatin-modifying complexes, and chromatin modifiers in turn affect expression of metabolic genes. Current evidence indicates that complex interaction loops between these biological system layers exist. Applying interdisciplinary and holistic approaches will decipher causality and molecular mechanisms of the dynamic crosstalk between chromatin structure, metabolism and plant growth and development.

Distinctive in-planta acclimation responses to basal growth and acute heat stress were induced in Arabidopsis by cattle manure biochar

In-planta mechanisms of biochar (BC)-mediated improved growth were evaluated by examining oxidative stress, metabolic, and hormonal changes of Arabidopsis wild-type plants under basal or acute heat stress (-HS/ + HS) conditions with or without BC (+ BC/-BC). The oxidative stress was evaluated by using Arabidopsis expressing redox-sensitive green fluorescent protein in the plastids (pla-roGFP2). Fresh biomass and inflorescence height were greater in + BC(‒HS) plants than in the -BC(‒HS) plants, despite similar leaf nutrient levels, photosystem II (PSII) maximal efficiencies and similar oxidative poise. Endogenous levels of jasmonic and abscisic acids were higher in the + BC(‒HS) treatment, suggesting their role in growth improvement. HS in ‒BC plants caused reductions in inflorescence height and PSII maximum quantum yield, as well as significant oxidative stress symptoms manifested by increased lipid peroxidation, greater chloroplast redox poise (oxidized form of roGFP), increased expression of DNAJ heat shock proteins and Zn-finger genes, and reduced expression of glutathione-S-transferase gene in addition to higher abscisic acid and salicylic acid levels. Oxidative stress symptoms were significantly reduced by BC. Results suggest that growth improvements by BC occurring under basal and HS conditions are induced by acclimation mechanisms to 'microstresses' associated with basal growth and to oxidative stress of HS, respectively.

Seed 'primeomics': plants memorize their germination under stress

Seed priming is a pre-germination treatment administered through various chemical, physical and biological agents, which induce mild stress during the early phases of germination. Priming facilitates synchronized seed germination, better seedling establishment, improved plant growth and enhanced yield, especially in stressful environments. In parallel, the phenomenon of 'stress memory' in which exposure to a sub-lethal stress leads to better responses to future or recurring lethal stresses has gained widespread attention in recent years. The versatility and realistic yield gains associated with seed priming and its connection with stress memory make a critical examination useful for the design of robust approaches for maximizing future yield gains. Herein, a literature review identified selenium, salicylic acid, poly-ethylene glycol, CaCl₂ and thiourea as the seed priming agents (SPRs) for which the most studies have been carried out. The average priming duration for SPRs generally ranged from 2 to 48 h, i.e. during phase I/II of germination. The major signalling events for regulating early seed germination, including the DOG1 (delay of germination 1)-abscisic acid (ABA)-heme regulatory module, ABA-gibberellic acid antagonism and nucleus-organelle communication are detailed. We propose that both seed priming and stress memory invoke a 'bet-hedging' strategy in plants, wherein their growth under optimal conditions is compromised in exchange for better growth under stressful conditions. The molecular basis of stress memory is explained at the level of chromatin reorganization, alternative transcript splicing, metabolite accumulation and autophagy. This provides a useful framework to study similar mechanisms operating during seed priming. In addition, we highlight the potential for merging findings on seed priming with those of stress memory, with the dual benefit of advancing fundamental research and boosting crop productivity. Finally, a roadmap for future work, entailing identification of SPR-responsive varieties and the development of dual/multiple-benefit SPRs, is proposed for enhancing SPR-mediated agricultural productivity worldwide.

Transgenerational Effects of Salt Stress Imposed to Rapeseed (Brassica napus var. oleifera Del.) Plants Involve Greater Phenolic Content and Antioxidant Activity in the Edible Sprouts Obtained from Offspring Seeds

Previous research has demonstrated that rapeseed sprouts obtained under salinity demonstrate greater phenolic content and antioxidant activity compared to those sprouted with distilled water. This work aimed to test the hypothesis that these effects of salinity may persist into the next generation, so that offspring seeds of plants grown under salt stress may give edible sprouts with increased phenolic content and antioxidant activity. Plants of one rapeseed cultivar were grown in pots with 0, 100 and 200 mM NaCl, isolated from each other at flowering to prevent cross-pollination. Offspring seeds harvested from each salinity treatment were then sprouted with distilled water. We performed the extraction of free and bound phenolic fractions of sprouts and, in each fraction (methanolic extract), we determined the total polyphenols (P), flavonoids, (F), and tannins (T) with Folin-Ciocalteu reagent, the phenolic acids (PAs) by ultra-high-performance liquid chromatographs (UHPLC) analysis, and the antioxidant activity with three tests (2,2-diphenyl-1-picrylhydrazyl-hydrate, DPPH; ferric reducing antioxidant power, FRAP; 2,2'-azino-bis[3-ethylbenzothiazoline-6-sulfonic acid] diammonium salt, ABTS). Individual seed weight was slightly decreased by salinity, whereas germination performance was improved, with a lower mean germination time for salted treatments. No significant differences were observed among treatments for P, F and T, except for bound P, while, in most cases, single PAs (as free, bound and total fractions) and antioxidant activity were significantly increased in salted treatments. Our results open new perspectives for the elicitation of secondary metabolites in the offspring seeds by growing parental plants under stressing conditions, imposed on purpose or naturally occurring.

Comparative Analysis of the Apple Root Transcriptome as Affected by Rootstock Genotype and Brassicaceae Seed Meal Soil Amendment: Implications for Plant Health

Brassicaceae seed meal (SM) soil amendment has been utilized as an effective strategy to control the biological complex of organisms, which includes oomycetes, fungi, and parasitic nematodes, that incites the phenomenon termed apple replant disease. Soil-borne disease control attained in response to Brassicaceae SM amendment is reliant on multiple chemical and biological attributes, including specific SM-generated modifications to the soil/rhizosphere microbiome. In this study, we conducted a comparative analyses of apple root gene expression as influenced by rootstock genotype combined with a seed meal (SM) soil amendment. Apple replant disease (ARD) susceptible (M.26) and tolerant (G.210) rootstocks cultivated in SM-amended soil exhibited differential gene expression relative to corresponding non-treated control (NTC) orchard soil. The temporal dynamics of gene expression indicated that the SM-amended soil system altered the trajectory of the root transcriptome in a genotype-specific manner. In both genotypes, the expression of genes related to plant defense and hormone signaling were altered in SM-amended soil, suggesting SM-responsive phytohormone regulation. Altered gene expression was temporally associated with changes in rhizosphere microbiome density and composition in the SM-treated soil. Gene expression analysis across the two rootstocks cultivated in the pathogen-infested NTC soil showed genotype-specific responses indicative of different defensive strategies. These results are consistent with previously described resistance mechanisms of ARD “tolerant” rootstock cultivars and also add to our understanding of the multiple mechanisms by which SM soil amendment and the resulting rhizosphere microbiome affect apple rootstock physiology. Future studies which assess transcriptomic and metagenomic data in parallel will be important for illuminating important connections between specific rhizosphere microbiota, gene-regulation, and plant health.

Priming of seeds with INA and its transgenerational effect in common bean (Phaseolus vulgaris L.) plants

Priming is a mechanism of defense that prepares the plant's immune system for a faster and/or stronger activation of cellular defenses against future exposure to different types of stress. This enhanced resistance can be achieved by using inorganic and organic compounds which imitate the biological induction of systemic acquired resistance. INA (2,6 dichloro-isonicotinic acid) was the first synthetic compound created as a resistance inducer for plant-pathogen interactions. However, the use of INA to activate primed resistance in common bean, at the seed stage and during germination, remains experimentally unexplored. Here, we test the hypothesis that INA-seed treatment would induce resistance in common bean plants to Pseudomonas syringae pv. phaseolicola, and that the increased resistance is not accompanied by a tradeoff between plant defense and growth. Additionally, it was hypothesized that treating seeds with INA has a transgenerational priming effect. We provide evidence that seed treatment activates a primed state for disease resistance, in which low nucleosome enrichment and reduced histone activation marks during the priming phase, are associated with a defense-resistant phenotype, characterized by symptom appearance, pathogen accumulation, yield, and changes in gene expression. In addition, the priming status for induced resistance can be inherited to its offspring.

Priming Strategies for Benefiting Plant Performance under Toxic Trace Metal Exposure

Combating environmental stress related to the presence of toxic elements is one of the most important challenges in plant production. The majority of plant species suffer from developmental abnormalities caused by an exposure to toxic concentrations of metals and metalloids, mainly Al, As, Cd, Cu, Hg, Ni, Pb, and Zn. However, defense mechanisms are activated with diverse intensity and efficiency. Enhancement of defense potential can be achieved though exogenously applied treatments, resulting in a higher capability of surviving and developing under stress and become, at least temporarily, tolerant to stress factors. In this review, I present several already recognized as well as novel methods of the priming process called priming, resulting in the so-called “primed state” of the plant organism. Primed plants have a higher capability of surviving and developing under stress, and become, at least temporarily, tolerant to stress factors. In this review, several already recognized as well as novel methods of priming plants towards tolerance to metallic stress are discussed, with attention paid to similarities in priming mechanisms activated by the most versatile priming agents. This knowledge could contribute to the development of priming mixtures to counteract negative effects of multi-metallic and multi-abiotic stresses. Presentation of mechanisms is complemented with information on the genes regulated by priming towards metallic stress tolerance. Novel compounds and techniques that can be exploited in priming experiments are also summarized.

Biostimulants for Plant Growth and Mitigation of Abiotic Stresses: A Metabolomics Perspective

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.

Silicon: its ameliorative effect on plant defense against herbivory

Plants protect themselves against pest attack utilizing both direct and indirect modes of defense. The direct mode of defense includes morphological, biochemical, and molecular barriers that affect feeding, growth, and survival of herbivores whereas the indirect mode of defense includes release of a blend of volatiles that attract natural enemies of the pests. Both of these strategies adopted by plants are reinforced if the plants are supplied with one of the most abundant metalloids, silicon (Si). Plants absorb Si as silicic acid (Si(OH)4) and accumulate it as phytoliths, which strengthens their physical defense. This deposition of Si in plant tissue is up-regulated upon pest attack. Further, Si deposited in the apoplast, suppresses pest effector molecules. Additionally, Si up-regulates the expression of defense-related genes and proteins and their activity and enhances the accumulation of secondary metabolites, boosting induced molecular and biochemical defenses. Moreover, Si plays a crucial role in phytohormone-mediated direct and indirect defense mechanisms. It is also involved in the reduction of harmful effects of oxidative stress resulting from herbivory by accelerating the scavenging process. Despite increasing evidence of its multiple roles in defense against pests, the practical implications of Si for crop protection have received less attention. Here, we highlight recent developments in Si-mediated improved plant resistance against pests and its significance for future use in crop improvement.

Protein phosphorylation associated with drought priming-enhanced heat tolerance in a temperate grass species

Protein phosphorylation is known to play crucial roles in plant tolerance to individual stresses, but how protein phosphorylation is associated with cross-stress tolerance, particularly drought priming-enhanced heat tolerance is largely unknown. The objectives of the present study were to identify phosphorylated proteins and phosphorylation sites that were responsive to drought priming and to determine whether drought priming-enhanced heat tolerance in temperate grass species involves changes in protein phosphorylation. Comparative analysis of phosphoproteomic profiles was performed on leaves of tall fescue (Festuca arundinacea) exposed to heat stress (38/33 °C, day/night) with or without drought priming. A total of 569 differentially regulated phosphoproteins (DRPs) with 1098 phosphorylation sites were identified in response to drought priming or heat stress individually or sequentially. Most DRPs were nuclear-localized and cytosolic proteins. Motif analysis detected [GS], [DSD], and [S..E] as major phosphorylation sites in casein kinase-II and mitogen-activated protein kinases regulated by drought priming and heat stress. Functional annotation and gene ontology analysis demonstrated that DRPs in response to drought priming and in drought-primed plants subsequently exposed to heat stress were mostly enriched in four major biological processes, including RNA splicing, transcription control, stress protection/defense, and stress perception/signaling. These results suggest the involvement of post-translational regulation of the aforementioned biological processes and signaling pathways in drought priming memory and cross-tolerance with heat stress in a temperate grass species.

The mode of action of plant associated Burkholderia against grey mould disease in grapevine revealed through traits and genomic analyses

Plant-associated Burkholderia spp. have been shown to offer a promising alternative method that may address concerns with ecological issue associated with pesticide overuse in agriculture. However to date, little work has studied the role of Burkholderia species as biocontrol agents for grapevine pathogens. To this end, two Burkholderia strains, BE17 and BE24 isolated from the maize rhizosphere in France, were investigated to determine their biocontrol potential and their ability to induce systemic resistance against grey mould disease in grapevine. Results showed the capacity of both strains to inhibit spore germination and mycelium growth of Botrytis cinerea. Experimental inoculation with BE17 and BE24 showed a significant protection of bacterized-plantlets against grey mould compared to the non-bacterized control. BE17 and BE24-bacterized plants accumulated more reactive oxygen species and an increased callose deposition was observed in leaves of bacterized plantlets compared to the control plantlets. In bacterized plants, gene expression analysis subsequent to B. cinerea challenge showed that strains BE17 and BE24 significantly increased the relative transcript level of pathogenesis-related (PR) proteins PR5 and PR10, two markers involved in the Salicylic acid (SA)-signaling pathway. Furthermore, in silico analysis of strains revealed the presence of genes involved in plant growth promotion and biocontrol highlighting the attractiveness of these strains for sustainable agricultural applications.

Volatile Organic Compounds as Insect Repellents and Plant Elicitors: an Integrated Pest Management (IPM) Strategy for Glasshouse Whitefly (Trialeurodes vaporariorum)

The glasshouse whitefly (Trialeurodes vaporariorum Westwood) is a polyphagous arthropod pest that is of particular detriment to glasshouse grown tomato (Solanum lycopersicum) across temperate regions of the world. Control of whiteflies with synthetic pesticides has resulted in the evolution of resistant genotypes and a reduction in natural enemies, thus highlighting the need for environmentally sound control strategies. Volatile organic compounds (VOCs) offer an environmentally benign alternative to synthetic chemical sprays and this study explored the use of VOCs as insect repellents and plant defence elicitors to control whiteflies on tomato in a commercial glasshouse setting. Limonene in the form of a volatile dispenser system was found to successfully repel whitefly from the target crop and increased fruit yield by 32% during a heavy whitefly infestation. Analysis of tomato herbivore induced plant volatiles (HIPVs) led us to select methyl salicylate (MeSA) as the plant elicitor and application of MeSA to un-infested tomato plants was found to successfully reduce whitefly population development and increase yield by 11%, although this difference was marginally statistically significant. Combination of these two methods was also effective but whitefly abundance in combined plots was similar to the standalone limonene treatment across the course of the experiment. All of the VOC based control methods we used had a negative impact on whitefly performance, with more pronounced effects during the first few weeks of infestation. In subsequent laboratory experiments, we found elevated peroxidase (POD) activity and a significant increase in TPX1 and PR1 transcripts in MeSA treated plants. This led us to deduce that MeSA immediately induced plant defences, rather than priming them. We did however see evidence for residual priming, as plants treated with MeSA and infested with whiteflies produced significantly higher levels of POD activity than whitefly infestation alone. Despite the fact that our treatments failed to synergise, our methods can be optimised further, and the effectiveness of the standalone treatments is promising for future studies. In particular, our repellent limonene dispensers were extremely effective at deterring whiteflies and offer a low economic cost and easy to implement whitefly control option. The methods we have used here could be incorporated into current integrated pest management (IPM) systems, a sustainable approach to pest control which will be central to our efforts to manage whitefly populations under glass in the future.

The Seagrass Methylome Is Associated With Variation in Photosynthetic Performance Among Clonal Shoots

Evolutionary theory predicts that clonal organisms are more susceptible to extinction than sexually reproducing organisms, due to low genetic variation and slow rates of evolution. In agreement, conservation management considers genetic variation as the ultimate measure of a population's ability to survive over time. However, clonal plants are among the oldest living organisms on our planet. Here, we test the hypothesis that clonal seagrass meadows display epigenetic variation that complements genetic variation as a source of phenotypic variation. In a clonal meadow of the seagrass Zostera marina, we characterized DNA methylation among 42 shoots. We also sequenced the whole genome of 10 shoots to correlate methylation patterns with photosynthetic performance under exposure to and recovery from 27°C, while controlling for somatic mutations. Here, we show for the first time that clonal seagrass shoots display DNA methylation variation that is independent from underlying genetic variation, and associated with variation in photosynthetic performance under experimental conditions. It remains unknown to what degree this association could be influenced by epigenetic responses to transplantation-related stress, given that the methylomes showed a strong shift under acclimation to laboratory conditions. The lack of untreated control samples in the heat stress experiment did not allow us to distinguish methylome shifts induced by acclimation from such induced by heat stress. Notwithstanding, the co-variation in DNA methylation and photosynthetic performance may be linked via gene expression because methylation patterns varied in functionally relevant genes involved in photosynthesis, and in the repair and prevention of heat-induced protein damage. While genotypic diversity has been shown to enhance stress resilience in seagrass meadows, we suggest that epigenetic variation plays a similar role in meadows dominated by a single genotype. Consequently, conservation management of clonal plants should consider epigenetic variation as indicator of resilience and stability.

Molecular insights into biochar-mediated plant growth promotion and systemic resistance in tomato against Fusarium crown and root rot disease

Molecular mechanisms associated with biochar-elicited suppression of soilborne plant diseases and improved plant performance are not well understood. A stem base inoculation approach was used to explore the ability of biochar to induce systemic resistance in tomato plants against crown rot caused by a soilborne pathogen, Fusarium oxysporum f. sp. radicis lycopersici. RNA-seq transcriptome profiling of tomato, and experiments with jasmonic and salycilic acid deficient tomato mutants, were performed to elucidate the in planta molecular mechanisms involved in induced resistance. Biochar (produced from greenhouse plant wastes) was found to mediate systemic resistance against Fusarium crown rot and to simultaneously improve tomato plant growth and physiological parameters by up to 63%. Transcriptomic analysis (RNA-seq) of tomato demonstrated that biochar had a priming effect on gene expression and upregulated the pathways and genes associated with plant defense and growth such as jasmonic acid, brassinosteroids, cytokinins, auxin and synthesis of flavonoid, phenylpropanoids and cell wall. In contrast, biosynthesis and signaling of the salicylic acid pathway was downregulated. Upregulation of genes and pathways involved in plant defense and plant growth may partially explain the significant disease suppression and improvement in plant performance observed in the presence of biochar.

Saline and Arid Soils: Impact on Bacteria, Plants, and their Interaction

Salinity and drought are the most important abiotic stresses hampering crop growth and yield. It has been estimated that arid areas cover between 41% and 45% of the total Earth area worldwide. At the same time, the world’s population is going to soon reach 9 billion and the survival of this huge amount of people is dependent on agricultural products. Plants growing in saline/arid soil shows low germination rate, short roots, reduced shoot biomass, and serious impairment of photosynthetic efficiency, thus leading to a substantial loss of crop productivity, resulting in significant economic damage. However, plants should not be considered as single entities, but as a superorganism, or a holobiont, resulting from the intimate interactions occurring between the plant and the associated microbiota. Consequently, it is very complex to define how the plant responds to stress on the basis of the interaction with its associated plant growth-promoting bacteria (PGPB). This review provides an overview of the physiological mechanisms involved in plant survival in arid and saline soils and aims at describing the interactions occurring between plants and its bacteriome in such perturbed environments. The potential of PGPB in supporting plant survival and fitness in these environmental conditions has been discussed.

Primed acclimation: A physiological process offers a strategy for more resilient and irrigation-efficient crop production

Optimizing plant physiological function is essential to maintaining crop yields under water scarcity and in developing more water-efficient production practices. However, the most common strategies in addressing water conservation in agricultural production have focused on water-efficient technologies aimed at managing water application or on improving crop water-use efficiency through breeding. Few management strategies explicitly consider the management or manipulation of plant physiological processes, but one which does is termed primed acclimation (PA). The PA strategy uses the physiological processes involved in priming to pre-acclimate plants to water deficits while reducing irrigation. It has been shown to evoke multi-mechanistic responses across numerous crop species. A combination of existing literature and emerging studies find that mechanisms for pre-acclimating plants to water deficit stress include changes in root:shoot partitioning, root architecture, water use, photosynthetic characteristics, osmotic adjustment and anti-oxidant production. In many cases, PA reduces agricultural water use by improving plant access to existing soil water. Implementing PA in seasonally water-limited environments can mitigate yield losses to drought. Genotypic variation in PA responses offers the potential to screen for crop varieties with the greatest potential for beneficial priming responses and to identify specific priming and acclimation mechanisms. In this review we: 1) summarize the concept of priming within the context of plant stress physiology; 2) review the development of a PA management system that utilizes priming for water conservation in agroecosystems; and 3) address the future of PA, how it should be evaluated across crop species, and its utility in managing crop stress tolerance.

Common Mycorrhizal Network Induced JA/ET Genes Expression in Healthy Potato Plants Connected to Potato Plants Infected by Phytophthora infestans

Most plants are connected belowground via common mycorrhizal networks (CMNs). In their presence, the transmission of warning signals from diseased to uninfected plants has been reported. However, current studies have all been conducted in pots making it difficult to discriminate direct from indirect contribution of hyphae to the transmission of the signals. Here, we conducted an in vitro study with potato plantlets connected by a CMN of the arbuscular mycorrhizal fungus Rhizophagus irregularis. The plantlets were grown in physically separated compartments and their connection ensured only by the CMN. The donor potato plantlets were infected by Phytophthora infestans and defense genes analyzed 24, 48 and 120 h post-infection (hpi) in the uninfected receiver potato plantlets. Twenty-four hpi by the pathogen, PAL, PR-1b, ERF3, and LOX genes were significantly upregulated, whereas no significant transcript variation was noticed 48 and 120 hpi. The exact nature of the warning signals remains unknown but was not associated to microorganisms other than the AMF or to diffusion mechanisms through the growth medium or induced by volatile compounds. The defense response appeared to be transitory and associated with the jasmonic acid or ethylene pathway. These findings demonstrate the direct involvement of hyphae in the transmission of warning signals from diseased to uninfected potato plantlets and their indubitable role in providing a route for activating defense responses in uninfected plants.

Role and mechanisms of callose priming in mycorrhiza-induced resistance

Mycorrhizal plants display enhanced resistance to several pathogens. However, the molecular mechanisms regulating mycorrhiza-induced resistance (MIR) are still elusive. We aim to study the mechanisms underlying MIR against Botrytis cinerea and the role of callose accumulation during this process. Mycorrhizal tomato plants inoculated with Rhizoglomus irregularis displayed callose priming upon B. cinerea infection. The callose inhibitor 2-deoxy-d-glucose abolished MIR, confirming the relevance of callose in the bioprotection phenomena. While studying the mechanisms underlying mycorrhiza-induced callose priming, we found that mycorrhizal plants display an enhanced starch degradation rate that is correlated with increased levels of β-amylase1 transcripts following pathogen infection. Starch mobilization in mycorrhizal plants seems coordinated with the increased transcription of sugar transporter and invertase genes. Moreover, the expression levels of genes encoding the vesicular trafficking proteins ATL31 and SYP121 and callose synthase PMR4 were higher in the mycorrhizal plants and further boosted by subsequent pathogen infection. All these proteins play a key role in the priming of callose accumulation in Arabidopsis, suggesting that callose priming is an induced resistance mechanism conserved in different plant species. This evidence highlights the importance of sugar mobilization and vesicular trafficking in the priming of callose as a defence mechanism in mycorrhiza-induced resistance.

Communication of plants with microbial world: Exploring the regulatory networks for PGPR mediated defense signaling

Agricultural manipulation of potentially beneficial rhizosphere microbes is increasing rapidly due to their multi-functional plant-protective and growth related benefits. Plant growth promoting rhizobacteria (PGPR) are mostly non-pathogenic microbes which exert direct benefits on plants while there are rhizosphere bacteria which indirectly help plant by ameliorating the biotic and/or abiotic stress or induction of defense response in plant. Regulation of these direct or indirect effect takes place via highly specialized communication system induced at multiple levels of interaction i.e., inter-species, intra-species, and inter-kingdom. Studies have provided insights into the functioning of signaling molecules involved in communication and induction of defense responses. Activation of host immune responses upon bacterial infection or rhizobacteria perception requires comprehensive and precise gene expression reprogramming and communication between hosts and microbes. Majority of studies have focused on signaling of host pattern recognition receptors (PRR) and nod-like receptor (NLR) and microbial effector proteins under mining the role of other components such as mitogen activated protein kinase (MAPK), microRNA, histone deacytylases. The later ones are important regulators of gene expression reprogramming in plant immune responses, pathogen virulence and communications in plant-microbe interactions. During the past decade, inoculation of PGPR has emerged as potential strategy to induce biotic and abiotic stress tolerance in plants; hence, it is imperative to expose the basis of these interactions. This review discusses microbes and plants derived signaling molecules for their communication, regulatory and signaling networks of PGPR and their different products that are involved in inducing resistance and tolerance in plants against environmental stresses and the effect of defense signaling on root microbiome. We expect that it will lead to the development and exploitation of beneficial microbes as source of crop biofertilizers in climate changing scenario enabling more sustainable agriculture.

Elicitor hydrophobin Hyd1 interacts with Ubiquilin1-like to induce maize systemic resistance

Trichoderma harzianum is a plant-beneficial fungus that secretes small cysteine-rich proteins that induce plant defense responses; however, the molecular mechanism involved in this induction is largely unknown. Here, we report that the class II hydrophobin ThHyd1 acts as an elicitor of induced systemic resistance (ISR) in plants. Immunogold labeling and immunofluorescence revealed ThHyd1 localized on maize (Zea mays) root cell plasma membranes. To identify host plant protein interactors of Hyd1, we screened a maize B73 root cDNA library. ThHyd1 interacted directly with ubiquilin 1-like (UBL). Furthermore, the N-terminal fragment of UBL was primarily responsible for binding with Hyd1 and the eight-cysteine amino acid of Hyd1 participated in the protein-protein interactions. Hyd1 from T. harzianum (Thhyd1) and ubl from maize were co-expressed in Arabidopsis thaliana, they synergistically promoted plant resistance against Botrytis cinerea. RNA-sequencing analysis of global gene expression in maize leaves 24 h after spraying with Curvularia lunata spore suspension showed that Thhyd1-induced systemic resistance was primarily associated with brassinosteroid signaling, likely mediated through BAK1. Jasmonate/ethylene (JA/ET) signaling was also involved to some extent in this response. Our results suggest that the Hyd1-UBL axis might play a key role in inducing systemic resistance as a result of Trichoderma-plant interactions.

Metabolomics to Exploit the Primed Immune System of Tomato Fruit

Tomato is a major crop suffering substantial yield losses from diseases, as fruit decay at a postharvest level can claim up to 50% of the total production worldwide. Due to the environmental risks of fungicides, there is an increasing interest in exploiting plant immunity through priming, which is an adaptive strategy that improves plant defensive capacity by stimulating induced mechanisms. Broad-spectrum defence priming can be triggered by the compound ß-aminobutyric acid (BABA). In tomato plants, BABA induces resistance against various fungal and bacterial pathogens and different methods of application result in durable protection. Here, we demonstrate that the treatment of tomato plants with BABA resulted in a durable induced resistance in tomato fruit against Botrytis cinerea, Phytophthora infestans and Pseudomonas syringae. Targeted and untargeted metabolomics were used to investigate the metabolic regulations that underpin the priming of tomato fruit against pathogenic microbes that present different infection strategies. Metabolomic analyses revealed major changes after BABA treatment and after inoculation. Remarkably, primed responses seemed specific to the type of infection, rather than showing a common fingerprint of BABA-induced priming. Furthermore, top-down modelling from the detected metabolic markers allowed for the accurate prediction of the measured resistance to fruit pathogens and demonstrated that soluble sugars are essential to predict resistance to fruit pathogens. Altogether, our results demonstrate that metabolomics is particularly insightful for a better understanding of defence priming in fruit. Further experiments are underway in order to identify key metabolites that mediate broad-spectrum BABA-induced priming in tomato fruit.

Priming of inducible defenses protects Norway spruce against tree-killing bark beetles

Plants can form an immunological memory known as defense priming, whereby exposure to a priming stimulus enables quicker or stronger response to subsequent attack by pests and pathogens. Such priming of inducible defenses provides increased protection and reduces allocation costs of defense. Defense priming has been widely studied for short-lived model plants such as Arabidopsis, but little is known about this phenomenon in long-lived plants like spruce. We compared the effects of pretreatment with sublethal fungal inoculations or application of the phytohormone methyl jasmonate (MeJA) on the resistance of 48-year-old Norway spruce (Picea abies) trees to mass attack by a tree-killing bark beetle beginning 35 days later. Bark beetles heavily infested and killed untreated trees but largely avoided fungus-inoculated trees and MeJA-treated trees. Quantification of defensive terpenes at the time of bark beetle attack showed fungal inoculation induced 91-fold higher terpene concentrations compared with untreated trees, whereas application of MeJA did not significantly increase terpenes. These results indicate that resistance in fungus-inoculated trees is a result of direct induction of defenses, whereas resistance in MeJA-treated trees is due to defense priming. This work extends our knowledge of defense priming from model plants to an ecologically important tree species.

Primary Metabolism Is Distinctly Modulated by Plant Resistance Inducers in Coffea arabica Leaves Infected by Hemileia vastatrix

Epidemics of coffee leaf rust (CLR) leads to great yield losses and huge depreciation of coffee marketing values, if no control measures are applied. Societal expectations of a more sustainable coffee production are increasingly imposing the replacement of fungicide treatments by alternative solutions. A protection strategy is to take advantage of the plant immune system by eliciting constitutive defenses. Based on such concept, plant resistance inducers (PRIs) have been developed. The Greenforce CuCa formulation, similarly to acibenzolar-S-methyl (ASM), shows promising results in the control of CLR (Hemileia vastatrix) in Coffea arabica cv. Mundo Novo. The molecular mechanisms of PRIs action are poorly understood. In order to contribute to its elucidation a proteomic, physiological (leaf gas-exchange) and biochemical (enzymatic) analyses were performed. Coffee leaves treated with Greenforce CuCa and ASM and inoculation with H. vastatrix were considered. Proteomics revealed that both PRIs lead to metabolic adjustments but, inducing distinct proteins. These proteins were related with photosynthesis, protein metabolism and stress responses. Greenforce CuCa increased photosynthesis and stomatal conductance, while ASM caused a decrease in these parameters. It was further observed that Greenforce CuCa reinforces the redox homeostasis of the leaf, while ASM seems to affect preferentially the secondary metabolism and the stress-related proteins. So, the PRIs prepare the plant to resist CLR but, inducing different defense mechanisms upon pathogen infection. The existence of a link between the primary metabolism and defense responses was evidenced. The identification of components of the plant primary metabolism, essential for plant growth and development that, simultaneously, participate in the plant defense responses can open new perspectives for plant breeding programs.

Proteomic Changes in the Sound Vibration-Treated Arabidopsis thaliana Facilitates Defense Response during Botrytis cinerea Infection

Sound vibration (SV) treatment can trigger various molecular and physiological changes in plants. Previously, we showed that pre-exposure of Arabidopsis plants to SV boosts its defense response against Botrytis cinerea fungus. The present study was aimed to investigate the changes in the proteome states in the SV-treated Arabidopsis during disease progression. Proteomics analysis identified several upregulated proteins in the SV-infected plants (i.e., SV-treated plants carrying Botrytis infection). These upregulated proteins are involved in a plethora of biological functions, e.g., primary metabolism (i.e., glycolysis, tricarboxylic acid cycle, ATP synthesis, cysteine metabolism, and photosynthesis), redox homeostasis, and defense response. Additionally, our enzyme assays confirmed the enhanced activity of antioxidant enzymes in the SV-infected plants compared to control plants. Broadly, our results suggest that SV pre-treatment evokes a more efficient defense response in the SV-infected plants by modulating the primary metabolism and reactive oxygen species scavenging activity.

Target of rapamycin signaling is tightly and differently regulated in the plant response under distinct abiotic stresses

TOR signaling is finely regulated under diverse abiotic stresses and may be required for the plant response with a different time-course depending on the duration and nature of the stress. Target of rapamycin (TOR) signaling is a central regulator of growth and development in eukaryotic organisms. However, its regulation under stress conditions has not yet been elucidated. In Arabidopsis, we show that TOR transcripts and activity in planta are finely regulated within hours after the onset of salt, osmotic, cold and oxidative stress. The expression of genes encoding the partner proteins of the TOR complex, RAPTOR3G and LST8-1, is also regulated. Besides, the data indicate that TOR activity increases at some time during the adverse condition. Interestingly, in oxidative stress, the major TOR activity increment occurred transiently at the early phase of treatment, while in salt, osmotic and cold stress, it was around 1 day after the unfavorable condition was applied. Those results suggest that the TOR signaling has an important role in the plant response to an exposure to stress. Moreover, basal ROS (H₂O₂) levels and their modification under abiotic stresses were altered in TOR complex mutants. On the other hand, the root phenotypic analysis of the effects caused by the diverse abiotic stresses on TOR complex mutants revealed that they were differently affected, being in some cases less sensitive, than wild-type plants to long-term unfavorable conditions. Therefore, in this work, we demonstrated that TOR signaling is tightly regulated under abiotic stresses, at transcript and activity level, with different and specific time-course patterns according to the type of abiotic stress in Arabidopsis. Taking our results together, we propose that TOR signaling should be necessary during the plant stress response.

A Microbial Fermentation Mixture Primes for Resistance Against Powdery Mildew in Wheat

Since many fungal pathogens develop resistance to fungicides, novel and low-cost alternative methods to improve plant health and fitness need to be developed. An approach to improve productivity in crops is to stimulate the plant's own defence mechanisms via priming. Therefore, we investigated if a fermentation-based elicitor could prime plant defences against powdery mildew in wheat by inducing the expression of endogenous defence-related genes. Wheat seedlings were spray-treated with a fermentation-based elicitor 8 days prior to inoculation with powdery mildew. Disease assays showed a significantly reduced number of powdery mildew pustules were formed on wheat treated with the mixed elicitor. In vitro sensitivity assays tested the ability of powdery mildew conidia to germinate on agar amended with the fermentation-based product and concluded that fungal germination and differentiation were also inhibited. Tissue samples were taken at time points pertaining to different developmental stages of powdery mildew infection. Significantly higher expression of PR genes (PR1, PR4, PR5, and PR9) was observed in the microbial fermentation mixture-treated plants compared with untreated plants. These genes are often associated with the elicitation of plant defence responses to specific biotrophic pathogens, such as powdery mildew, suggesting an elicitor-mediated response in the wheat plants tested. The product components were assessed, and the components were found to act synergistically in the microbial fermentation mixture. Therefore, this fermentation-based elicitor provides an effective method for powdery mildew control.

Roles of plant volatiles in defence against microbial pathogens and microbial exploitation of volatiles

Plants emit a large variety of volatile organic compounds during infection by pathogenic microbes, including terpenes, aromatics, nitrogen-containing compounds, and fatty acid derivatives, as well as the volatile plant hormones, methyl jasmonate, and methyl salicylate. Given the general antimicrobial activity of plant volatiles and the timing of emission following infection, these compounds have often been assumed to function in defence against pathogens without much solid evidence. In this review, we critically evaluate current knowledge on the toxicity of volatiles to fungi, bacteria, and viruses and their role in plant resistance as well as how they act to induce systemic resistance in uninfected parts of the plant and in neighbouring plants. We also discuss how microbes can detoxify plant volatiles and exploit them as nutrients, attractants for insect vectors, and inducers of volatile emissions, which stimulate immune responses that make plants more susceptible to infection. Although much more is known about plant volatile-herbivore interactions, knowledge of volatile-microbe interactions is growing and it may eventually be possible to harness plant volatiles to reduce disease in agriculture and forestry. Future research in this field can be facilitated by making use of the analytical and molecular tools generated by the prolific research on plant-herbivore interactions.

Leaf metabolic signatures induced by real and simulated herbivory in black mustard (Brassica nigra)

INTRODUCTION

The oxylipin methyl jasmonate (MeJA) is a plant hormone active in response signalling and defence against herbivores. Although MeJA is applied experimentally to mimic herbivory and induce plant defences, its downstream effects on the plant metabolome are largely uncharacterized, especially in the context of primary growth and tissue-specificity of the response.

OBJECTIVES

We investigated the effects of MeJA-simulated and real caterpillar herbivory on the foliar metabolome of the wild plant Brassica nigra and monitored the herbivore-induced responses in relation to leaf ontogeny.

METHODS

As single or multiple herbivory treatments, MeJA- and mock-sprayed plants were consecutively exposed to caterpillars or left untreated. Gas chromatography (GC) and liquid chromatography (LC) time-of-flight mass-spectrometry (TOF-MS) were combined to analyse foliar compounds, including central primary and specialized defensive plant metabolites.

RESULTS

Plant responses were stronger in young leaves, which simultaneously induced higher chlorophyll levels. Both MeJA and caterpillar herbivory induced similar, but not identical, accumulation of tricarboxylic acids (TCAs), glucosinolates (GSLs) and phenylpropanoids (PPs), but only caterpillar feeding led to depletion of amino acids. MeJA followed by caterpillars caused higher induction of defence compounds, including a three-fold increase in the major defence compound allyl-GSL (sinigrin). When feeding on MeJA-treated plants, caterpillars gained less weight indicative of the reduced host-plant quality and enhanced resistance.

CONCLUSIONS

The metabolomics approach showed that plant responses induced by herbivory extend beyond the regulation of defence metabolism and are tightly modulated throughout leaf development. This leads to a new understanding of the plant metabolic potential that can be exploited for future plant protection strategies.

Unravelling the Metabolic Reconfiguration of the Post-Challenge Primed State in Sorghum bicolor Responding to Colletotrichum sublineolum Infection

Priming is a natural phenomenon that pre-conditions plants for enhanced defence against a wide range of pathogens. It represents a complementary strategy, or sustainable alternative that can provide protection against disease. However, a comprehensive functional and mechanistic understanding of the various layers of priming events is still limited. A non-targeted metabolomics approach was used to investigate metabolic changes in plant growth-promoting rhizobacteria (PGPR)-primed Sorghum bicolor seedlings infected with the anthracnose-causing fungal pathogen, Colletotrichum sublineolum, with a focus on the post-challenge primed state phase. At the 4-leaf growth stage, the plants were treated with a strain of Paenibacillus alvei at 10⁸ cfu mL⁻¹. Following a 24 h PGPR application, the plants were inoculated with a C. sublineolum spore suspension (10⁶ spores mL⁻¹), and the infection monitored over time: 1, 3, 5, 7 and 9 days post-inoculation. Non-infected plants served as negative controls. Intracellular metabolites from both inoculated and non-inoculated plants were extracted with 80% methanol-water. The extracts were chromatographically and spectrometrically analysed on an ultra-high performance liquid chromatography (UHPLC) system coupled to high-definition mass spectrometry. The acquired multidimensional data were processed to create data matrices for chemometric modelling. The computed models indicated time-related metabolic perturbations that reflect primed responses to the fungal infection. Evaluation of orthogonal projection to latent structure-discriminant analysis (OPLS-DA) loading shared and unique structures (SUS)-plots uncovered the differential stronger defence responses against the fungal infection observed in primed plants. These involved enhanced levels of amino acids (tyrosine, tryptophan), phytohormones (jasmonic acid and salicylic acid conjugates, and zeatin), and defence-related components of the lipidome. Furthermore, other defence responses in both naïve and primed plants were characterised by a complex mobilisation of phenolic compounds and de novo biosynthesis of the flavones, apigenin and luteolin and the 3-deoxyanthocyanidin phytoalexins, apigeninidin and luteolinidin, as well as some related conjugates.

β-Aminobutyric Acid Priming Acquisition and Defense Response of Mango Fruit to Colletotrichum gloeosporioides Infection Based on Quantitative Proteomics

β-aminobutyric acid (BABA) is a new environmentally friendly agent to induce disease resistance by priming of defense in plants. However, molecular mechanisms underlying BABA-induced priming defense are not fully understood. Here, comprehensive analysis of priming mechanism of BABA-induced resistance was investigated based on mango-Colletotrichum gloeosporioides interaction system using iTRAQ-based proteome approach. Results showed that BABA treatments effectively inhibited the expansion of anthracnose caused by C. gleosporioides in mango fruit. Proteomic results revealed that stronger response to pathogen in BABA-primed mango fruit after C. gleosporioides inoculation might be attributed to differentially accumulated proteins involved in secondary metabolism, defense signaling and response, transcriptional regulation, protein post-translational modification, etc. Additionally, we testified the involvement of non-specific lipid-transfer protein (nsLTP) in the priming acquisition at early priming stage and memory in BABA-primed mango fruit. Meanwhile, spring effect was found in the primed mango fruit, indicated by inhibition of defense-related proteins at priming phase but stronger activation of defense response when exposure to pathogen compared with non-primed fruit. As an energy-saving strategy, BABA-induced priming might also alter sugar metabolism to provide more backbone for secondary metabolites biosynthesis. In sum, this study provided new clues to elucidate the mechanism of BABA-induced priming defense in harvested fruit.

Gene networks underlying the early regulation of Paraburkholderia phytofirmans PsJN induced systemic resistance in Arabidopsis

Plant defense responses to biotic stresses are complex biological processes, all governed by sophisticated molecular regulations. Induced systemic resistance (ISR) is one of these defense mechanisms where beneficial bacteria or fungi prime plants to resist pathogens or pest attacks. In ISR, the defense arsenal in plants remains dormant and it is only triggered by an infection, allowing a better allocation of plant resources. Our group recently described that the well-known beneficial bacterium Paraburkholderia phytofirmans PsJN is able to induce Arabidopsis thaliana resistance to Pseudomonas syringae pv. tomato (Pst) DC3000 through ISR, and that ethylene, jasmonate and salicylic acid are involved in this protection. Nevertheless, the molecular networks governing this beneficial interaction remain unknown. To tackle this issue, we analyzed the temporal changes in the transcriptome of PsJN-inoculated plants before and after being infected with Pst DC3000. These data were used to perform a gene network analysis to identify highly connected transcription factors. Before the pathogen challenge, the strain PsJN regulated 405 genes (corresponding to 1.8% of the analyzed genome). PsJN-inoculated plants presented a faster and stronger transcriptional response at 1-hour post infection (hpi) compared with the non-inoculated plants, which presented the highest transcriptional changes at 24 hpi. A principal component analysis showed that PsJN-induced plant responses to the pathogen could be differentiated from those induced by the pathogen itself. Forty-eight transcription factors were regulated by PsJN at 1 hpi, and a system biology analysis revealed a network with four clusters. Within these clusters LHY, WRKY28, MYB31 and RRTF1 are highly connected transcription factors, which could act as hub regulators in this interaction. Concordantly with our previous results, these clusters are related to jasmonate, ethylene, salicylic, acid and ROS pathways. These results indicate that a rapid and specific response of PsJN-inoculated plants to the virulent DC3000 strain could be the pivotal element in the protection mechanism.

Discussion paper: Sustainable increase of crop production through improved technical strategies, breeding and adapted management - A European perspective

During the next decade it will be necessary to develop novel combinations of management strategies to sustainably increase crop production and soil resilience. Improving agricultural productivity, while conserving and enhancing biotic and abiotic resources, is an essential requirement to increase global food production on a sustainable basis. The role of farmers in increasing agricultural productivity growth sustainably will be crucial. Farmers are at the center of any process of change involving natural resources and for this reason they need to be encouraged and guided, through appropriate incentives and governance practices, to conserve natural ecosystems and their biodiversity, and minimize the negative impact agriculture can have on the environment. Farmers and stakeholders need to revise traditional approaches not as productive as the modern approaches but more friendly with natural and environmental ecosystems values as well as emerging novel tools and approaches addressing precise farming, organic amendments, lowered water consumption, integrated pest control and beneficial plant-microbe interactions. While practical solutions are developing, science based recommendations for crop rotations, breeding and harvest/postharvest strategies leading to environmentally sound and pollinator friendly production and better life in rural areas have to be provided.

Ammonium mediated changes in carbon and nitrogen metabolisms induce resistance against Pseudomonas syringae in tomato plants

Predominant NH₄⁺ nutrition causes an "ammonium syndrome" that induces metabolic changes and thereby provides resistance against Pseudomonas syringae infection through the activation of systemic acquired acclimation (SAA). Hence, to elucidate the mechanisms underlying NH₄⁺-mediated SAA, the changes in nutrient balance and C and N skeletons were studied in NH₄⁺-treated plants upon infection by P. syringae. A general decrease in cation and an increase in anion levels was observed in roots and leaves of NH₄⁺-treated plants. Upon NH₄⁺-based nutrition and infection, tomato leaves showed an accumulation of S, P, Zn, and of Mn. Mn accumulation might be required for ROS detoxification since it acts as a cofactor of superoxide dismutase (SOD). Primary metabolism was modified in both tissues of NH₄⁺-fed plants to counteract NH₄⁺ toxicity by decreasing TCA intermediates. A significant increase in Arg, Gln, Asn, Lys, Tyr, His and Leu was observed in leaves of NH₄⁺-treated plants. The high level of the putrescine precursor Arg hints towards the importance of the Glu pathway as a key metabolic check-point in NH₄⁺-treated and infected plants. Taken together, NH₄⁺-fed plants displayed a high level of basal responses allowing them to activate SAA and to trigger defense responses against P. syringae through nutrient imbalances and changes in primary metabolism.

Transcriptome and Metabolome Reprogramming in Tomato Plants by Trichoderma harzianum strain T22 Primes and Enhances Defense Responses Against Aphids

Beneficial fungi in the genus Trichoderma are among the most widespread biocontrol agents of plant pathogens. Their role in triggering plant defenses against pathogens has been intensely investigated, while, in contrast, very limited information is available on induced barriers active against insects. The growing experimental evidence on this latter topic looks promising, and paves the way toward the development of Trichoderma strains and/or consortia active against multiple targets. However, the predictability and reproducibility of the effects that these beneficial fungi is still somewhat limited by the lack of an in-depth understanding of the molecular mechanisms underlying the specificity of their interaction with different crop varieties, and on how the environmental factors modulate this interaction. To fill this research gap, here we studied the transcriptome changes in tomato plants (cultivar "Dwarf San Marzano") induced by Trichoderma harzianum (strain T22) colonization and subsequent infestation by the aphid Macrosiphum euphorbiae. A wide transcriptome reprogramming, related to metabolic processes, regulation of gene expression and defense responses, was induced both by separate experimental treatments, which showed a synergistic interaction when concurrently applied. The most evident expression changes of defense genes were associated with the multitrophic interaction Trichoderma-tomato-aphid. Early and late genes involved in direct defense against insects were induced (i.e., peroxidase, GST, kinases and polyphenol oxidase, miraculin, chitinase), along with indirect defense genes, such as sesquiterpene synthase and geranylgeranyl phosphate synthase. Targeted and untargeted semi-polar metabolome analysis revealed a wide metabolome alteration showing an increased accumulation of isoprenoids in Trichoderma treated plants. The wide array of transcriptomic and metabolomics changes nicely fit with the higher mortality of aphids when feeding on Trichoderma treated plants, herein reported, and with the previously observed attractiveness of these latter toward the aphid parasitoid Aphidius ervi. Moreover, Trichoderma treated plants showed the over-expression of transcripts coding for several families of defense-related transcription factors (bZIP, MYB, NAC, AP2-ERF, WRKY), suggesting that the fungus contributes to the priming of plant responses against pest insects. Collectively, our data indicate that Trichoderma treatment of tomato plants induces transcriptomic and metabolomic changes, which underpin both direct and indirect defense responses.

Transcriptome analysis of the model grass Lolium temulentum exposed to green leaf volatiles

BACKGROUND

Forage and turf grasses are routinely cut and grazed upon throughout their lifecycle. When grasses are cut or damaged, they rapidly release a volatile chemical cocktail called green leaf volatiles (GLV). Previously we have shown that mechanical wounding or exposure to GLV released from cut grass, activated a Lt 46 kDa mitogen-activated protein kinase (MAPK) within 3 min and a 44 kDa MAPK within 15-20 min in the model grass species Lolium temulentum (Lt). Currently very little is known concerning the perception, signaling or molecular responses associated with wound stress in grasses. Since GLV are released during wounding, we wanted to investigate what genes and signaling pathways would be induced in undamaged plants exposed to GLV.

RESULTS

RNA-Seq generated transcriptome of Lolium plants exposed to GLV identified 4308 up- and 2794 down-regulated distinct differentially-expressed sequences (DES). Gene Ontology analysis revealed a strong emphasis on signaling, response to stimulus and stress related categories. Transcription factors and kinases comprise over 13% of the total DES found in the up-regulated dataset. The analysis showed a strong initial burst within the first hour of GLV exposure with over 60% of the up-regulated DES being induced. Specifically sequences annotated for enzymes involved in the biosynthesis of jasmonic acid and other plant hormones, mitogen-activated protein kinases and WRKY transcription factors were identified. Interestingly, eleven DES for ferric reductase oxidase, an enzyme involved in iron uptake and transport, were exclusively found in the down-regulated dataset. Twelve DES of interest were selected for qRT-PCR analysis; all displayed a rapid induction one hour after GLV exposure and were also strongly induced by mechanical wounding.

CONCLUSION

The information gained from the analysis of this transcriptome and previous studies suggests that GLV released from cut grasses transiently primes an undamaged plant's wound stress pathways for potential oncoming damage, and may have a dual role for inter- as well as intra-plant signaling.

Role of Multiple Infections on Immunological Variation in Wild Populations

A central challenge in the fields of evolutionary immunology and disease ecology is to understand the causes and consequences of natural variation in host susceptibility to infectious diseases. As hosts progress from birth to death in the wild, they are exposed to a wide variety of microorganisms that influence their physical condition, immune system maturation, and susceptibility to concurrent and future infection.

A central challenge in the fields of evolutionary immunology and disease ecology is to understand the causes and consequences of natural variation in host susceptibility to infectious diseases. As hosts progress from birth to death in the wild, they are exposed to a wide variety of microorganisms that influence their physical condition, immune system maturation, and susceptibility to concurrent and future infection. Thus, multiple exposures to the same or different microbes can be important environmental drivers of host immunological variation and immune priming. In this perspective, I discuss parasite infracommunity interactions and their imprint on host immunity in space and time. I further consider feedbacks from parasite community dynamics within individual hosts on the transmission of disease at higher levels of biological organization and highlight the promise of systems biology approaches, using flour beetles as an example, for studying the role of multiple infections on immunological variation in wild populations.

Molecular Dissection of Early Defense Signaling Underlying Volatile-Mediated Defense Regulation and Herbivore Resistance in Rice

Herbivore-induced plant volatiles prime plant defenses and resistance, but how they are integrated into early defense signaling and whether a causal relationship exists between volatile defense priming and herbivore resistance is unclear. Here, we investigated the impact of indole, a common herbivore-induced plant volatile and modulator of many physiological processes in plants, bacteria, and animals, on early defense signaling and herbivore resistance in rice (Oryza sativa). Rice plants infested by fall armyworm (Spodoptera frugiperda) caterpillars release indole at a rate of up to 25 ng*h^-1 Exposure to equal doses of exogenous indole enhances rice resistance to S. frugiperda Screening of early signaling components revealed that indole pre-exposure directly enhances the expression of the leucine-rich repeat-receptor-like kinase OsLRR-RLK1 Pre-exposure to indole followed by simulated herbivory increases (i.e. primes) the transcription, accumulation, and activation of the mitogen-activated protein kinase OsMPK3 and the expression of the downstream WRKY transcription factor gene OsWRKY70 as well as several jasmonate biosynthesis genes, resulting in higher jasmonic acid (JA) accumulation. Analysis of transgenic plants defective in early signaling showed that OsMPK3 is required and that OsMPK6 and OsWRKY70 contribute to indole-mediated defense priming of JA-dependent herbivore resistance. Therefore, herbivore-induced plant volatiles increase plant resistance to herbivores by positively regulating early defense signaling components.

Accumulation patterns of endogenous β-aminobutyric acid during plant development and defence in Arabidopsis thaliana

We recently discovered that β-aminobutyric acid (BABA), a molecule known for its ability to prime defences in plants, is a natural plant metabolite. However, the role played by endogenous BABA in plants is currently unknown. In this study we investigated the systemic accumulation of BABA during pathogen infection, levels of BABA during plant growth and development and analysed mutants possibly involved in BABA transport or regulation. BABA was quantified by LC-MS using an improved method adapted from a previously published protocol. Systemic accumulation of BABA was determined by analysing non-infected leaves and roots after localised infections with Plectosphaerella cucumerina or Pseudomonas syringae pv. tomato (Pst) DC3000 avrRpt2. The levels of BABA were also quantified in different plant tissues and organs during normal plant growth, and in leaves during senescence. Mutants affecting amino acid transport (aap6, aap3, prot1 and gat1), γ-aminobutyric acid levels (pop2) and senescence/defence (cpr5-2) were analysed. BABA was found to accumulate only locally after bacterial or fungal infection, with no detectable increase in non-infected systemic plant parts. In leaves, BABA content increased during natural and induced senescence. Reproductive organs had the highest levels of BABA, and the mutant cpr5-2 produced constitutively high levels of BABA. Synthetic BABA is highly mobile in the receiving plant, whereas endogenous BABA appears to be produced and accumulated locally in a tissue-specific way. We discuss a possible role for BABA in age-related resistance and propose a comprehensive model for endogenous and synthetic BABA.

Induced, Imprinted, and Primed Responses to Changing Environments: Does Metabolism Store and Process Information?

Metabolism is the system layer that determines growth by the rate of matter uptake and conversion into biomass. The scaffold of enzymatic reaction rates drives the metabolic network in a given physico-chemical environment. In response to the diverse environmental stresses, plants have evolved the capability of integrating macro- and micro-environmental events to be prepared, i.e., to be primed for upcoming environmental challenges. The hierarchical view on stress signaling, where metabolites are seen as final downstream products, has recently been complemented by findings that metabolites themselves function as stress signals. We present a systematic concept of metabolic responses that are induced by environmental stresses and persist in the plant system. Such metabolic imprints may prime metabolic responses of plants for subsequent environmental stresses. We describe response types with examples of biotic and abiotic environmental stresses and suggest that plants use metabolic imprints, the metabolic changes that last beyond recovery from stress events, and priming, the imprints that function to prepare for upcoming stresses, to integrate diverse environmental stress histories. As a consequence, even genetically identical plants should be studied and understood as phenotypically plastic organisms that continuously adjust their metabolic state in response to their individually experienced local environment. To explore the occurrence and to unravel functions of metabolic imprints, we encourage researchers to extend stress studies by including detailed metabolic and stress response monitoring into extended recovery phases.

Root colonization by Pseudomonas chlororaphis primes tomato (Lycopersicum esculentum) plants for enhanced tolerance to water stress

Previous research demonstrated that Pseudomonas chlororaphis subsp. aureofaciens strain M71, a plant growth promoting bacterium (PGPB), exerts beneficial effects on plant metabolism and primes tolerance mechanisms against biotic stresses in tomatoes. We designed an experiment to assess whether root colonization with P. chlororaphis is also able to improve tolerance to water stress in tomatoes. Our results show that inoculation with P. chlororaphis stimulates the antioxidant activity of well-watered tomatoes while maintaining a steady-state level of reactive oxygen species (ROS), increases the expression of genes encoding for the biosynthesis of leaf terpenes, stimulates the production of both the phytohormones ABA and IAA, in turn affecting plant shape (number of leaves) and height (length of internodes), without altering photosynthesis. Upon exposure to mild water stress conditions, an improved antioxidant activity in tomatoes 'primed' by P. chlororaphis inoculation limited the accumulation of reactive oxygen species (ROS) in leaves and thus enhanced tolerance, also through increase of the (osmolyte) proline content. Moreover, P. chlororaphis inoculation further enhanced the ABA level in leaves of water-stressed tomatoes allowing a more efficient modulation of stomatal closure that resulted in an improved water use efficiency (WUE) and biomass accumulation.

Trichoderma Species: Versatile Plant Symbionts

Because of the need to provide food for the growing population, agricultural activity is faced with the huge challenge of counteracting the negative effects generated by adverse environmental factors and diseases caused by pathogens on crops, while avoiding environmental pollution due to the excessive use of agrochemicals. The exploitation of biological systems that naturally increase plant vigor, preparing them against biotic and abiotic stressors that also promote their growth and productivity represents a useful and viable strategy to help face these challenges. Fungi from the genus Trichoderma have been widely used in agriculture as biocontrol agents because of their mycoparasitic capacity and ability to improve plant health and protection against phytopathogens, which makes it an excellent plant symbiont. The mechanisms employed by Trichoderma include secretion of effector molecules and secondary metabolites that mediate the beneficial interaction of Trichoderma with plants, providing tolerance to biotic and abiotic stresses. Here we discuss the most recent advances in understanding the mechanisms employed by this opportunistic plant symbiont as biocontrol agent and plant growth promoter. In addition, through genome mining we approached a less explored factor that Trichoderma could be using to become successful plant symbionts, the production of phytohormones-auxins, cytokinins, abscisic acid, gibberellins, among others. This approach allowed us to detect sets of genes encoding proteins potentially involved in phytohormone biosynthesis and signaling. We discuss the implications of these findings in the physiology of the fungus and in the establishment of its interaction with plants.

Underground Azelaic Acid-Conferred Resistance to Pseudomonas syringae in Arabidopsis

Local interactions between individual plant organs and diverse microorganisms can lead to whole plant immunity via the mobilization of defense signals. One such signal is the plastid lipid-derived oxylipin azelaic acid (AZA). Arabidopsis lacking AZI1 or EARLI1, related lipid transfer family proteins, exhibit reduced AZA transport among leaves and cannot mount systemic immunity. AZA has been detected in roots as well as leaves. Therefore, the present study addresses the effects on plants of AZA application to roots. AZA but not the structurally related suberic acid inhibits root growth when directly in contact with roots. Treatment of roots with AZA also induces resistance to Pseudomonas syringae in aerial tissues. These effects of AZA on root growth and disease resistance depend, at least partially, on AZI1 and EARLI1. AZI1 in roots localizes to plastids, similar to its known location in leaves. Interestingly, kinases previously shown to modify AZI1 in vitro, MPK3 and MPK6, are also needed for AZA-induced root-growth inhibition and aboveground immunity. Finally, deuterium-labeled AZA applied to the roots does not move to aerial tissues. Thus, AZA application to roots triggers systemic immunity through an AZI1/EARLI1/MPK3/MPK6-dependent pathway and AZA effects may involve one or more additional mobile signals.

BABA-Induced DNA Methylome Adjustment to Intergenerational Defense Priming in Potato to Phytophthora infestans

We provide evidence that alterations in DNA methylation patterns contribute to the regulation of stress-responsive gene expression for an intergenerational resistance of β-aminobutyric acid (BABA)-primed potato to Phytophthora infestans. Plants exposed to BABA rapidly modified their methylation capacity toward genome-wide DNA hypermethylation. De novo induced DNA methylation (5-mC) correlated with the up-regulation of Chromomethylase 3 (CMT3), Domains rearranged methyltransferase 2 (DRM2), and Repressor of silencing 1 (ROS1) genes in potato. BABA transiently activated DNA hypermethylation in the promoter region of the R3a resistance gene triggering its downregulation in the absence of the oomycete pathogen. However, in the successive stages of priming, an excessive DNA methylation state changed into demethylation with the active involvement of potato DNA glycosylases. Interestingly, the 5-mC-mediated changes were transmitted into the next generation in the form of intergenerational stress memory. Descendants of the primed potato, which derived from tubers or seeds carrying the less methylated R3a promoter, showed a higher transcription of R3a that associated with an augmented intergenerational resistance to virulent P. infestans when compared to the inoculated progeny of unprimed plants. Furthermore, our study revealed that enhanced transcription of some SA-dependent genes (NPR1, StWRKY1, and PR1) was not directly linked with DNA methylation changes in the promoter region of these genes, but was a consequence of methylation-dependent alterations in the transcriptional network.

Activation of the phenylpropanoid biosynthesis pathway reveals a novel action mechanism of the elicitor effect of chitosan on avocado fruit epicarp

Secondary metabolites play an important role in the avocado fruit defense system. Phenolic compounds are the main biosynthesized metabolites of this system response. Our objective in this investigation was to evaluate the induction of specific metabolic pathways using chitosan as an elicitor. Extracts obtained from avocado in intermediate and consumption maturity stages treated with chitosan exhibited an increase in antifungal activity, which caused inhibition of mycelial growth and a decrease in sporulation as well as spore germination of Colletotrichum gloeosporioides. Additionally, RNA from epicarp of the fruits treated and untreated with chitosan was obtained in order to evaluate the expression of genes related to phenylpropanoids and the antifungal compound 1-acetoxy-2-hydroxy-4-oxo-heneicosa-12,15-diene biosynthesis. An increased in gene expression of genes that participates in the phenylpropanoids route was observed during the stage of physiological fruit maturity, others genes such as Flavonol synthase (Fls), increased only in samples obtained from fruit treated with chitosan at consumption maturity. Our results reveal a new molecular mechanism where chitosan induces a specific accumulation of phenylpropanoids and antifungal diene; this partially explains avocado's resistance against fungal pathogens. Finally, we discuss the molecular connections between chitosan induction and gene expression to explain the biological events that orchestrate the resistance pathways in fruits.

Induced Systemic Resistance Against Citrus Canker Disease by Rhizobacteria

Citrus canker, caused by Xanthomonas citri subsp. citri, is an important citrus disease that causes significant economic losses worldwide. All commercial citrus varieties are susceptible to citrus canker. Currently, chemical control with copper based products is the main approach to control X. citri subsp. citri dispersal and plant colonization. However, extensive use of copper compounds can result in copper-resistant strains and cause adverse effects on the environment. Alternatives to chemical control involve the activation of citrus immunity to control the disease. Here, we investigated the ability of multiple rhizobacteria to induce a systemic defense response in cultivar Duncan grapefruit. Burkholderia territorii strain A63, Burkholderia metallica strain A53, and Pseudomonas geniculata strain 95 were found to effectively activate plant defense and significantly reduce symptom development in leaves challenged with X. citri subsp. citri. In the priming phase, root application of P. geniculata induced the expression of salicylic acid (SA)-signaling pathway marker genes (PR1, PR2, PR5, and salicylic acid carboxyl methyltransferase [SAM-SACM]). Gene expression analyses after X. citri subsp. citri challenge showed that root inoculation with P. geniculata strain 95 increased the relative levels of phenylalanine ammonia lyase 1 and SAM-SACM, two genes involved in the phenylpropanoid pathway as well as the biosynthesis of SA and methyl salicylate (MeSA), respectively. However, hormone analyses by UPLC-MS/MS showed no significant difference between SA in P. geniculata-treated plants and control plants at 8 days post-beneficial bacteria root inoculation. Moreover, P. geniculata root-treated plants contained higher reactive oxygen species levels in aerial tissues than control plants 8 days post-treatment application. This study demonstrates that rhizobacteria can modulate citrus immunity resulting in a systemic defense response against X. citri subsp. citri under greenhouse conditions.

Tricarboxylates Induce Defense Priming Against Bacteria in Arabidopsis thaliana

Exposure of plants to biotic stress results in an effective induction of numerous defense mechanisms that involve a vast redistribution within both primary and secondary metabolisms. For instance, an alteration of tricarboxylic acid (TCA) levels can accompany the increase of plant resistance stimulated by various synthetic and natural inducers. Moreover, components of the TCA flux may play a role during the set-up of plant defenses. In this study, we show that citrate and fumarate, two major components of the TCA cycle, are able to induce priming in Arabidopsis against the bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Both citrate and fumarate show no direct antimicrobial effect and therefore enhanced bacterial resistance found in planta is solely based on the induction of the plant defense system. During the priming phase, both TCA intermediates did not induce any changes in transcript abundances of a set of defense genes, and in phytohormones and camalexin levels. However, at early time points of bacterial challenge, citrate induced a stronger salicylic acid and camalexin accumulation followed later by a boost of the jasmonic acid pathway. On the other hand, adaptations of hormonal pathways in fumarate-treated plants were more complex. While jasmonic acid was not induced, mutants impaired in jasmonic acid perception failed to mount a proper priming response induced by fumarate. Our results suggest that changes in carboxylic acid abundances can enhance Arabidopsis defense through complex signaling pathways. This highlights a promising feature of TCAs as novel defense priming agents and calls for further exploration in other pathosystems and stress situations.