Plant response to biotic stress: Is there a common epigenetic response during plant-pathogenic and symbiotic interactions?

Glutathione-the "master" antioxidant in the regulation of resistant and susceptible host-plant virus-interaction

The interaction between plant hosts and plant viruses is a very unique and complex process, relying on dynamically modulated intercellular redox states and the generation of reactive oxygen species (ROS). Plants strive to precisely control this state during biotic stress, as optimal redox levels enable proper induction of defense mechanisms against plant viruses. One of the crucial elements of ROS regulation and redox state is the production of metabolites, such as glutathione, or the activation of glutathione-associated enzymes. Both of these elements play a role in limiting the degree of potential oxidative damage in plant cells. While the role of glutathione and specific enzymes is well understood in other types of abiotic and biotic stresses, particularly those associated with bacteria or fungi, recent advances in research have highlighted the significance of glutathione modulation and mutations in genes encoding glutathione-associated enzymes in triggering immunity or susceptibility against plant viruses. Apparently, glutathione-associated genes are involved in precisely controlling and protecting host cells from damage caused by ROS during viral infections, playing a crucial role in the host's response. In this review, we aim to outline the significant improvements made in research on plant viruses and glutathione, specifically in the context of their involvement in susceptible and resistant responses, as well as changes in the localization of glutathione. Analyses of essential glutathione-associated enzymes in susceptible and resistant responses have demonstrated that the levels of enzymatic activity or the absence of specific enzymes can impact the spread of the virus and activate host-induced defense mechanisms. This contributes to the complex network of the plant immune system. Although investigations of glutathione during the plant-virus interplay remain a challenge, the use of novel tools and approaches to explore its role will significantly contribute to our knowledge in the field.

Knocking down a DNA demethylase gene affects potato plant defense against a specialist insect herbivore

DNA demethylase (DML) is involved in plant development and responses to biotic and abiotic stresses; however, its role in plant-herbivore interaction remains elusive. Here, we found that herbivory by the potato tuber moth, Phthorimaea operculella, rapidly induced the genome-wide DNA methylation and accumulation of DML gene transcripts in potato plants. Herbivory induction of DML transcripts was suppressed in jasmonate-deficient plants, whereas exogenous application of methyl jasmonate (MeJA) improved DML transcripts, indicating that the induction of DML transcripts by herbivory is associated with jasmonate signaling. Moreover, P. operculella larvae grew heavier on DML gene (StDML2) knockdown plants than on wild-type plants, and the decreased biosynthesis of jasmonates in the former may be responsible for this difference, since the larvae feeding on these two genotypes supplemented with MeJA showed similar growth. In addition, P. operculella adult moths preferred to oviposit on StDML2 knockdown plants than on wild-type plants, which was associated with the reduced emission of β-caryophyllene in the former. In addition, supplementing β-caryophyllene to these two genotypes further disrupted moths' oviposit choice preference for them. Interestingly, in StDML2 knockdown plants, hypermethylation was found at the promoter regions for the key genes StAOS and StAOC in the jasmonate biosynthetic pathway, as well as for the key gene StTPS12 in β-caryophyllene production. Our findings suggest that knocking down StDML2 can affect herbivore defense via jasmonate signaling and defense compound production in potato plants.

Trichoderma as a powerful fungal disease control agent for a more sustainable and healthy agriculture: recent studies and molecular insights

Molecular studies have elucidated Trichoderma's biocontrol mechanisms. Since fungicides have limited use, Trichoderma could control disease by new metabolic routes and epigenetic alterations. Due to environmental and health hazards, agrochemicals have been a concern since they were introduced in agriculture. Trichoderma, a well-known fungal genus with different mechanisms of action, is an alternative to pesticides and a great tool to help minimize disease incidence. Trichoderma-treated plants mainly benefit from disease control and growth promotion through priming, and these fungi can modulate plants' gene expression by boosting their immune system, accelerating their response to threats, and building stress tolerance. The latest studies suggest that epigenetics is required for plant priming and could be essential for growth promotion, expanding the possibilities for producing new resistant plant varieties. Trichoderma's propagules can be mass produced and formulated depending on the delivery method. Microsclerotia-based bioproducts could be a promising way of increasing the reliability and durability of marketed products in the field, as well as help guarantee longer shelf life. Developing novel formulations and selecting efficient Trichoderma strains can be tiresome, but patent search indicates an increase in the industrialization and commercialization of technologies and an expansion of companies' involvement in research and development in this field. Although Trichoderma is considered a well-known fungal genus, it still attracts the attention of large companies, universities, and research institutes around the world.

Comprehensive Survey of ChIP-Seq Datasets to Identify Candidate Iron Homeostasis Genes Regulated by Chromatin Modifications

Vital biochemical reactions including photosynthesis to respiration require iron, which should be tightly regulated. Although increasing evidence reveals the importance of epigenetic regulation in gene expression and signaling, the role of histone modifications and chromatin remodeling in plant iron homeostasis is not well understood. In this study, we surveyed publicly available ChIP-seq datasets of Arabidopsis wild-type and mutants defective in key enzymes of histone modification and chromatin remodeling and compared the deposition of epigenetic marks on loci of genes involved in iron regulation. Based on the analysis, we compiled a comprehensive list of iron homeostasis genes with differential enrichment of various histone modifications. This report will provide a resource for future studies to investigate epigenetic regulatory mechanisms of iron homeostasis in plants.

Leaf rust responsive miRNA and their target genes in wheat

Small RNA sequencing (sRNA-seq) and degradome analysis were used for the identification of miRNAs and their target host genes in a pair of near-isogenic lines (NILs), which differed for the presence of leaf rust resistance gene Lr28. The study led to identification of (i) 506 known and 346 novel miRNAs; and (ii) 5054 target genes including 4557 in silico predicted and 497 degradome-based genes using 105 differentially expressed (DE) miRNAs. A subset of 128 targets (67 in silico + 61 degradome-based) was differentially expressed in RNA-seq data that was generated by us earlier using the same pair of NILs; among these 128 targets, 58 target genes exhibited an inverse relationship with the DE miRNAs (expression of miRNAs and activation/suppression of target genes). Eight miRNAs which belonged to the conserved miRNA families and were known to be induced in response to fungal diseases in plants included the following: miR156, miR158, miR159, miR168, miR169, miR172, miR319, miR396. The target genes belonged to the following classes of genes known to be involved in downstream disease resistance pathways; peroxidases, sugar transporters, auxin response signaling, oxidation-reduction, etc. It was also noticed that although a majority of miRNAs and target genes followed the above classical inverse relationship, there were also examples, where no such relationship was observed. Among the target genes, there were also 51 genes that were not only regulated by miRNAs, but were also differentially methylated at sequences including the following segments: promotors, introns, TSS, exons. The results of the present study suggest a complex interplay among miRNA genes, target genes, and various epigenetic controls, which regulate the expression of genes involved in downstream pathways for disease resistance.

A pH- and redox-stimulated responsive hollow mesoporous silica for triggered delivery of fungicides to control downy mildew of Luffa cylindrica

BACKGROUND

Downy mildew, a devastating disease of cucurbitaceous crops caused by Pseudoperonospora cubensis. Although a variety of fungicides are used to control downy mildew, choosing an effective product can be challenging. Environmental stimulus-responsive pesticide delivery systems have great potential to improve the effectiveness of disease and pest control and reduce the impact on environmentally beneficial organisms.

RESULTS

In this work, a disulfide bond (SS)-modified and chitosan oligosaccharide (COS)-capped hollow mesoporous silica (HMS) pesticide delivery system was synthesized using a hard template method for the control of downy mildew in cucurbit crops. The synthesized nanoparticles were loaded with dimethomorph (DMM), denoted as DMM@HMS-SS-COS, and the developmental toxicity of these nanoparticles to zebrafish embryos were evaluated. The results showed that the prepared DMM@HMS-SS-COS exhibited excellent dual response properties to pH and glutathione (GSH), with an encapsulation rate of up to 24.36%. DMM@HMS-SS-COS has good ultraviolet (UV) radiation stability and adhesion properties. Compared with dimethomorph suspension concentrate (SC), DMM@HMS-SS-COS was more effective against downy mildew for up to 21 days. Toxicity tests showed that DMM@HMS-SS-COS significantly reduced the effect of DMM on the hatching rate and survival rate of zebrafish embryos.

CONCLUSIONS

This work not only demonstrates that DMM@HMS-SS-COS could be used as a nanodelivery system for intelligent control of downy mildew but also emphasizes the necessity of increasing the acute toxicity of nanoformulations to non-target organisms in environmental risk assessment. © 2022 Society of Chemical Industry.

Moving Beyond DNA Sequence to Improve Plant Stress Responses

Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.

Recent Advances in Minimizing Cadmium Accumulation in Wheat

Cadmium (Cd), a toxic heavy metal, affects the yield and quality of crops. Wheat (Triticum aestivum L.) can accumulate high Cd content in the grain, which poses a major worldwide hazard to human health. Advances in our understanding of Cd toxicity for plants and humans, different parameters influencing Cd uptake and accumulation, as well as phytoremediation technologies to relieve Cd pollution in wheat have been made very recently. In particular, the molecular mechanisms of wheat under Cd stress have been increasingly recognized. In this review, we focus on the recently described omics and functional genes uncovering Cd stress, as well as different mitigation strategies to reduce Cd toxicity in wheat.

Bacillus subtilis Impact on Plant Growth, Soil Health and Environment: Dr. Jekyll and Mr. Hyde

The increased dependence of farmers on chemical fertilizers poses a risk to soil fertility and ecosystem stability. Plant growth-promoting rhizobacteria (PGPR) are at the forefront of sustainable agriculture, providing multiple benefits for the enhancement of crop production and soil health. Bacillus subtilis is a common PGPR in soil that plays a key role in conferring biotic and abiotic stress tolerance to plants by induced systemic resistance (ISR), biofilm formation, and lipopeptide production. As a part of bioremediating technologies, Bacillus spp. can purify metal contaminated soil. It acts as a potent denitrifying agent in agroecosystems while improving the carbon sequestration process when applied in a regulated concentration. Although it harbors several antibiotic resistance genes (ARGs), it can reduce the horizontal transfer of ARGs during manure composting by modifying the genetic makeup of existing microbiota. In some instances, it affects the beneficial microbes of the rhizosphere. External inoculation of B. subtilis has both positive and negative impacts on the endophytic and semi-synthetic microbial community. Soil texture, type, pH, and bacterial concentration play a crucial role in the regulation of all these processes. Soil amendments and microbial consortia of Bacillus produced by microbial engineering could be used to lessen the negative effect on soil microbial diversity. The complex plant-microbe interactions could be decoded using transcriptomics, proteomics, metabolomics, and epigenomics strategies which would be beneficial for both crop productivity and the well-being of soil microbiota. Bacillus subtilis has more positive attributes similar to the character of Dr. Jekyll and some negative attributes on plant growth, soil health, and the environment akin to the character of Mr. Hyde.

Inheritance of DNA methylation differences in the mangrove Rhizophora mangle

The capacity to respond to environmental challenges ultimately relies on phenotypic variation which manifests from complex interactions of genetic and nongenetic mechanisms through development. While we know something about genetic variation and structure of many species of conservation importance, we know very little about the nongenetic contributions to variation. Rhizophora mangle is a foundation species that occurs in coastal estuarine habitats throughout the neotropics where it provides critical ecosystem functions and is potentially threatened by anthropogenic environmental changes. Several studies have documented landscape-level patterns of genetic variation in this species, but we know virtually nothing about the inheritance of nongenetic variation. To assess one type of nongenetic variation, we examined the patterns of DNA sequence and DNA methylation in maternal plants and offspring from natural populations of R. mangle from the Gulf Coast of Florida. We used a reduced representation bisulfite sequencing approach (epi-genotyping by sequencing; epiGBS) to address the following questions: (a) What are the levels of genetic and epigenetic diversity in natural populations of R. mangle? (b) How are genetic and epigenetic variation structured within and among populations? (c) How faithfully is epigenetic variation inherited? We found low genetic diversity but high epigenetic diversity from natural populations of maternal plants in the field. In addition, a large portion (up to ~25%) of epigenetic differences among offspring grown in common garden was explained by maternal family. Therefore, epigenetic variation could be an important source of response to challenging environments in the genetically depauperate populations of this foundation species.

Plant Responses to Abiotic Stresses and Rhizobacterial Biostimulants: Metabolomics and Epigenetics Perspectives

In response to abiotic stresses, plants mount comprehensive stress-specific responses which mediate signal transduction cascades, transcription of relevant responsive genes and the accumulation of numerous different stress-specific transcripts and metabolites, as well as coordinated stress-specific biochemical and physiological readjustments. These natural mechanisms employed by plants are however not always sufficient to ensure plant survival under abiotic stress conditions. Biostimulants such as plant growth-promoting rhizobacteria (PGPR) formulation are emerging as novel strategies for improving crop quality, yield and resilience against adverse environmental conditions. However, to successfully formulate these microbial-based biostimulants and design efficient application programs, the understanding of molecular and physiological mechanisms that govern biostimulant-plant interactions is imperatively required. Systems biology approaches, such as metabolomics, can unravel insights on the complex network of plant-PGPR interactions allowing for the identification of molecular targets responsible for improved growth and crop quality. Thus, this review highlights the current models on plant defence responses to abiotic stresses, from perception to the activation of cellular and molecular events. It further highlights the current knowledge on the application of microbial biostimulants and the use of epigenetics and metabolomics approaches to elucidate mechanisms of action of microbial biostimulants.

Epigenetics in plant organismic interactions

Plants are hubs of organismic interactions. They constantly engage in beneficial or competitive interactions with fungi, oomycetes, bacteria, insects, nematodes, and other plants. To adjust the molecular processes necessary for the establishment and maintenance of beneficial interactions and for the defense against pathogens and herbivores, plants have evolved intricate regulatory mechanisms. Besides the canonical plant immune system that acts as the primary defense, epigenetic mechanisms have started to emerge as another regulatory entity and as a target of pathogens trying to overcome the plant's defenses. In this review, we highlight recent advances in understanding the contribution of various epigenetic components and of epigenetic diversity to plant-organismic interactions.

Subcellular Roles of Glutathione in Mediating Plant Defense during Biotic Stress

Glutathione and reactive oxygen species (ROS) play important roles, within different cell compartments, in activating plant defense and the development of resistance. In mitochondria, the accumulation of ROS and the change of glutathione towards its oxidized state leads to mitochondrial dysfunction, activates cell death, and triggers resistance. The accumulation of glutathione in chloroplasts and peroxisomes at the early stages of plant pathogen interactions is related to increased tolerance and resistance. The collapse of the antioxidative system in these two cell compartments at the later stages leads to cell death through retrograde signaling. The cytosol can be considered to be the switchboard during biotic stress where glutathione is synthesized, equally distributed to, and collected from different cell compartments. Changes in the redox state of glutathione and the accumulation of ROS in the cytosol during biotic stress can initiate the activation of defense genes in nuclei through pathways that involve salicylic acid, jasmonic acid, auxins, and abscisic acid. This review dissects the roles of glutathione in individual organelles during compatible and incompatible bacterial, fungal, and viral diseases in plants and explores the subcelluar roles of ROS, glutathione, ascorbate, and related enzymes in the development of resistance.

Biological Control of Plant-Parasitic Nematodes by Filamentous Fungi Inducers of Resistance: Trichoderma, Mycorrhizal and Endophytic Fungi

Plant-parasitic-nematodes represent a major threat to the agricultural production of different crops worldwide. Due to the high toxicity of chemical nematicides, it is necessary to develop new control strategies against nematodes. In this respect, filamentous fungi can be an interesting biocontrol alternative. The genus Trichoderma, mycorrhizal and endophytic fungi are the main groups of filamentous fungi studied and used as biological control agents (BCAs) against nematodes as resistance inducers. They are able to reduce the damage caused by plant-parasitic nematodes directly by parasitism, antibiosis, paralysis and by the production of lytic enzymes. But they also minimize harm by space and resource-competition, by providing higher nutrient and water uptake to the plant, or by modifying the root morphology, and/or rhizosphere interactions, that constitutes an advantage for the plant-growth. Besides, filamentous fungi are able to induce resistance against nematodes by activating hormone-mediated (salicylic and jasmonic acid, strigolactones among others) plant-defense mechanisms. Additionally, the alteration of the transport of chemical defense components through the plant or the synthesis of plant secondary metabolites and different enzymes can also contribute to enhancing plant defenses. Therefore, the use of filamentous fungi of the mentioned groups as BCAs is a promising durable biocontrol strategy in agriculture against plant-parasitic nematodes.

Transcriptome reprogramming, epigenetic modifications and alternative splicing orchestrate the tomato root response to the beneficial fungus Trichoderma harzianum

Beneficial interactions of rhizosphere microorganisms are widely exploited for plant biofertilization and mitigation of biotic and abiotic constraints. To provide new insights into the onset of the roots-beneficial microorganisms interplay, we characterised the transcriptomes expressed in tomato roots at 24, 48 and 72 h post inoculation with the beneficial fungus Trichoderma harzianum T22 and analysed the epigenetic and post-trascriptional regulation mechanisms. We detected 1243 tomato transcripts that were differentially expressed between Trichoderma-interacting and control roots and 83 T. harzianum transcripts that were differentially expressed between the three experimental time points. Interaction with Trichoderma triggered a transcriptional response mainly ascribable to signal recognition and transduction, stress response, transcriptional regulation and transport. In tomato roots, salicylic acid, and not jasmonate, appears to have a prominent role in orchestrating the interplay with this beneficial strain. Differential regulation of many nutrient transporter genes indicated a strong effect on plant nutrition processes, which, together with the possible modifications in root architecture triggered by ethylene/indole-3-acetic acid signalling at 72 h post inoculation may concur to the well-described growth-promotion ability of this strain. Alongside, T. harzianum-induced defence priming and stress tolerance may be mediated by the induction of reactive oxygen species, detoxification and defence genes. A deeper insight into gene expression and regulation control provided first evidences for the involvement of cytosine methylation and alternative splicing mechanisms in the plant-Trichoderma interaction. A model is proposed that integrates the plant transcriptomic responses in the roots, where interaction between the plant and beneficial rhizosphere microorganisms occurs.

The role of plant epigenetics in biotic interactions

Contents Summary 731 I. Biotic interactions in the context of genetic, epigenetic and environmental diversity 731 II. Biotic interactions affect epigenetic configuration 732 III. Plant epigenetic configuration influences biotic interactions 733 IV. Epigenetic memory in the context of biotic interactions 734 V. Conclusions and future research 735 Acknowledgements 735 Author contributions 735 References 735 SUMMARY: Plants are hubs of a wide range of biotic interactions with mutualist and antagonist animals, microbes and neighboring plants. Because the quality and intensity of those relationships can change over time, a fast and reversible response to stress is required. Here, we review recent studies on the role of epigenetic factors such as DNA methylation and histone modifications in modulating plant biotic interactions, and discuss the state of knowledge regarding their potential role in memory and priming. Moreover, we provide an overview of strategies to investigate the contribution of epigenetics to environmentally induced phenotypic changes in an ecological context, highlighting possible transitions from whole-genome high-resolution analyses in plant model organisms to informative reduced representation analyses in genomically less accessible species.

Survival Mechanisms to Selective Pressures and Implications

Organisms have evolved a spectrum of strategies that facilitate survival in the face of adverse environmental conditions. In order to make full use of the unfavorable resources of nature, human beings usually impose selective pressures to breed phenotypic traits that can survive in adverse environments. Animals are frequently under attack by biotic stress, such as bacterial and viral infections, while plants are more often subjected to abiotic stress, including high salinity, drought, and cold. In response to these diverse stresses, animals and plants initiate wide-ranging changes in gene expression by altering regulation of transcriptional and post-transcriptional activities. Recent studies have identified a number of key responsive components that promote survival of animals and plants in response to biotic and abiotic stresses. Importantly, with recent developments in genome-editing technology based on the CRISPR/Cas9 system, manipulation of genetic elements to generate stress-resistant animals and plants has become both feasible and cost-effective. Herein, we review important mechanisms that govern the response of organisms to biotic and abiotic stresses with the aim of applying our understanding to the agriculture and animal husbandry industries.

Roles of Non-Coding RNA in Sugarcane-Microbe Interaction

Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae. Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae, while the siRNAs were repressed in the presence of A. avenae. Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408-a copper-microRNA-was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5'RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly.

Gene Silencing of Argonaute5 Negatively Affects the Establishment of the Legume-Rhizobia Symbiosis

The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, can bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance, AGO5 regulates the systemic resistance of Arabidopsis against Potato Virus X as well as the pigmentation of soybean (Glycine max) seeds. Here, we show that AGO5 is also playing a central role in legume nodulation based on its preferential expression in common bean (Phaseolus vulgaris) and soybean roots and nodules. We also report that the expression of AGO5 is induced after 1 h of inoculation with rhizobia. Down-regulation of AGO5 gene in P. vulgaris and G. max causes diminished root hair curling, reduces nodule formation and interferes with the induction of three critical symbiotic genes: Nuclear Factor Y-B (NF-YB), Nodule Inception (NIN) and Flotillin2 (FLOT2). Our findings provide evidence that the common bean and soybean AGO5 genes play an essential role in the establishment of the symbiosis with rhizobia.