Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns

VAPYRIN attenuates defence by repressing PR gene induction and localized lignin accumulation during arbuscular mycorrhizal symbiosis of Petunia hybrida

The intimate association of host and fungus in arbuscular mycorrhizal (AM) symbiosis can potentially trigger induction of host defence mechanisms against the fungus, implying that successful symbiosis requires suppression of defence. We addressed this phenomenon by using AM-defective vapyrin (vpy) mutants in Petunia hybrida, including a new allele (vpy-3) with a transposon insertion close to the ATG start codon. We explore whether abortion of fungal infection in vpy mutants is associated with the induction of defence markers, such as cell wall alterations, accumulation of reactive oxygen species (ROS), defence hormones and induction of pathogenesis-related (PR) genes. We show that vpy mutants exhibit a strong resistance against intracellular colonization, which is associated with the generation of cell wall appositions (papillae) with lignin impregnation at fungal entry sites, while no accumulation of defence hormones, ROS or callose was observed. Systematic analysis of PR gene expression revealed that several PR genes are induced in mycorrhizal roots of the wild-type, and even more in vpy plants. Some PR genes are induced exclusively in vpy mutants. Our results suggest that VPY is involved in avoiding or suppressing the induction of a cellular defence syndrome that involves localized lignin deposition and PR gene induction.

Uncoupling root hair formation and defence activation from growth inhibition in response to damage-associated Pep peptides in Arabidopsis thaliana

In Arabidopsis thaliana, PROPEPs and their derived elicitor-active Pep epitopes provide damage-associated molecular patterns (DAMPs), which trigger defence responses through cell-surface receptors PEPR1 and PEPR2. In addition, Pep peptides induce root growth inhibition and root hair formation, however their relationships and coordinating mechanisms are poorly understood. Here, we reveal that Pep1-mediated root hair formation requires PEPR-associated kinases BAK1/BKK1 and BIK1/PBL1, ethylene, auxin and root hair differentiation regulators, in addition to PEPR2. Our analysis on 69 accessions unravels intraspecies variations in Pep1-induced root hair formation and growth inhibition. The absence of a positive correlation between the two traits suggests their separate regulation and diversification in natural populations of A. thaliana. Restricted PEPR2 expression to certain root tissues is sufficient to induce root hair formation and growth inhibition in response to Pep1, indicating the capacity of non-cell-autonomous receptor signalling in different root tissues. Of particular note, root hair cell-specific PEPR2 expression uncouples defence activation from root growth inhibition and root hair formation, suggesting a unique property of root hairs in root defence activation following Pep1 recognition.

Dissection of plant microbiota and plant-microbiome interactions

Plants rooted in soil have intimate associations with a diverse array of soil microorganisms. While the microbial diversity of soil is enormous, the predominant bacterial phyla associated with plants include Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. Plants supply nutrient niches for microbes, and microbes support plant functions such as plant growth, development, and stress tolerance. The interdependent interaction between the host plant and its microbes sculpts the plant microbiota. Plant and microbiome interactions are a good model system for understanding the traits in eukaryotic organisms from a holobiont perspective. The holobiont concept of plants, as a consequence of co-evolution of plant host and microbiota, treats plants as a discrete ecological unit assembled with their microbiota. Dissection of plant-microbiome interactions is highly complicated; however, some reductionist approaches are useful, such as the synthetic community method in a gnotobiotic system. Deciphering the interactions between plant and microbiome by this reductionist approach could lead to better elucidation of the functions of microbiota in plants. In addition, analysis of microbial communities' interactions would further enhance our understanding of coordinated plant microbiota functions. Ultimately, better understanding of plantmicrobiome interactions could be translated to improvements in plant productivity.

Pectin lyase enhances cotton resistance to Verticillium wilt by inducing cell apoptosis of Verticillium dahliae

Verticillium wilt caused by Verticillium dahliae Kleb. is a major disease in cotton. We found that pectin lyase can enhance cotton resistance to Verticillium wilt and induce cell apoptosis of V. dahliae strain Vd080. The biocontrol effect of pectin lyase on Vd080 reached 61.9%. Pectin lyase increased ERG4 (Delta (24 (24 (1)))-sterol reductase) expression, the ergosterol content of the cell membrane, the collapse of mitochondrial membrane potential, hydrogen peroxide content, metacaspase activity, and Ca²⁺ content in the cytoplasm in the Vd080 strain and induced endoplasmic reticulum (ER) stress. Pectin lyase also increased the expression levels of the ER molecular chaperone glucose regulating protein Grp78 (BiP), protein disulfide isomerase (PDI) and calnexin (CNX), reduced the expression levels of the protein Hsp40. When the PDI and BiP genes of Vd080 were knocked out, the mutants △BiP and △PDI had reduced sensitivity to pectin lyase. In the absence of external stress, ER stress appeared in mutant △BiP cells. Pectin lyase affects the ergosterol content of the Vd080 cell membrane, which causes ER stress and increases the level of BiP to induce Vd080 cell apoptosis. These results demonstrate that pectin lyase can be used to control Verticillium wilt in cotton.

Systemic propagation of immunity in plants

Systemic immunity triggered by local plant-microbe interactions is studied as systemic acquired resistance (SAR) or induced systemic resistance (ISR) depending on the site of induction and the lifestyle of the inducing microorganism. SAR is induced by pathogens interacting with leaves, whereas ISR is induced by beneficial microbes interacting with roots. Although salicylic acid (SA) is a central component of SAR, additional signals exclusively promote systemic and not local immunity. These signals cooperate in SAR- and possibly also ISR-associated signaling networks that regulate systemic immunity. The non-SA SAR pathway is driven by pipecolic acid or its presumed bioactive derivative N-hydroxy-pipecolic acid. This pathway further regulates inter-plant defense propagation through volatile organic compounds that are emitted by SAR-induced plants and recognized as defense cues by neighboring plants. Both SAR and ISR influence phytohormone crosstalk towards enhanced defense against pathogens, which at the same time affects the composition of the plant microbiome. This potentially leads to further changes in plant defense, plant-microbe, and plant-plant interactions. Therefore, we propose that such inter-organismic interactions could be combined in potentially highly effective plant protection strategies.

Spatially Restricted Immune Responses Are Required for Maintaining Root Meristematic Activity upon Detection of Bacteria

Plants restrict immune responses to vulnerable root parts. Spatially restricted responses are thought to be necessary to avoid constitutive responses to rhizosphere microbiota. To directly demonstrate the importance of spatially restricted responses, we expressed the plant flagellin receptor (FLS2) in different tissues, combined with fluorescent defense markers for immune readouts at cellular resolution. Our analysis distinguishes responses appearing cell autonomous from apparently non-cell-autonomous responses. It reveals lignification as a general immune response, contrasting suberization. Importantly, our analysis divides the root meristem into a central zone refractory to FLS2 expression and a cortex that is sensitized by FLS2 expression, causing meristem collapse upon stimulation. Meristematic epidermal expression generates super-competent lines that detect native bacterial flagellin and bypass the weak or absent response to commensals, providing a powerful tool for studying root immunity. Our manipulations and readouts demonstrate incompatibility of meristematic activity and defense and the importance of cell-resolved studies of plant immune responses.

The root endophytic bacterial community of Ricinus communis L. resembles the seeds community more than the rhizosphere bacteria independent of soil water content

Rhizosphere and root endophytic bacteria are crucial for plant development, but the question remains if their composition is similar and how environmental conditions, such as water content, affect their resemblance. Ricinus communis L., a highly drought resistant plant, was used to study how varying soil water content affected the bacterial community in uncultivated, non-rhizosphere and rhizosphere soil, and in its roots. Additionally, the bacterial community structure was determined in the seeds of R. communis at the onset of the experiment. Plants were cultivated in soil at three different watering regimes, i.e. 50% water holding capacity (WHC) or adjusted to 50% WHC every two weeks or every month. Reducing the soil water content strongly reduced plant and root dry biomass and plant development, but had little effect on the bacterial community structure. The bacterial community structure was affected significantly by cultivation of R. communis and showed large variations over time. After 6 months, the root endophytic bacterial community resembled that in the seeds more than in the rhizosphere. It was found that water content had only a limited effect on the bacterial community structure and the different bacterial groups, but R. communis affected the bacterial community profoundly.

Pinpointing secondary metabolites that shape the composition and function of the plant microbiome

One of the major questions in contemporary plant science involves determining the functional mechanisms that plants use to shape their microbiome. Plants produce a plethora of chemically diverse secondary metabolites, many of which exert bioactive effects on microorganisms. Several recent publications have unequivocally shown that plant secondary metabolites affect microbiome composition and function. These studies have pinpointed that the microbiome can be influenced by a diverse set of molecules, including: coumarins, glucosinolates, benzoxazinoids, camalexin, and triterpenes. In this review, we summarize the role of secondary metabolites in shaping the plant microbiome, highlighting recent literature. A body of knowledge is now emerging that links specific plant metabolites with distinct microbial responses, mediated via defined biochemical mechanisms. There is significant potential to boost agricultural sustainability via the targeted enhancement of beneficial microbial traits, and here we argue that the newly discovered links between root chemistry and microbiome composition could provide a new set of tools for rationally manipulating the plant microbiome.

CGTase, a novel antimicrobial protein from Bacillus cereus YUPP-10, suppresses Verticillium dahliae and mediates plant defence responses

Verticillium wilt is a plant vascular disease caused by the soilborne fungus Verticillium dahliae that severely limits cotton production. In a previous study, we screened Bacillus cereus YUPP-10, an efficient antagonistic bacterium, to uncover mechanisms for controlling verticillium wilt. Here, we report a novel antimicrobial cyclodextrin glycosyltransferase (CGTase) from YUPP-10. Compared to other CGTases, six different conserved domains were identified, and six mutants were constructed by gene splicing with overlap extension PCR. Functional analysis showed that domain D was important for hydrolysis activity and domains A1 and C were important for inducing disease resistance. Direct effects of recombinant CGTase on V. dahliae included reduced mycelial growth, spore germination, spore production, and microsclerotia germination. In addition, CGTase also elicited cotton's innate defence reactions. Transgenic Arabidopsis thaliana lines that overexpress CGTase showed higher resistance to verticillium wilt. Transgenic CGTase A. thaliana plants grew faster and resisted disease better. CGTase overexpression enabled a burst of reactive oxygen species production and activated pathogenesis-related gene expression, indicating that the transgenic cotton was better prepared to protect itself from infection. Our work revealed that CGTase could inhibit the growth of V. dahliae, activate innate immunity, and play a major role in the biocontrol of fungal pathogens.

Bulked Segregant RNA-Seq Provides Distinctive Expression Profile Against Powdery Mildew in the Wheat Genotype YD588

Wheat powdery mildew, caused by the fungal pathogen Blumeria graminis f. sp. tritici (Bgt), is a destructive disease leading to huge yield losses in production. Host resistance can greatly contribute to the control of the disease. To explore potential genes related to the powdery mildew (Pm) resistance, in this study, we used a resistant genotype YD588 to investigate the potential resistance components and profiled its expression in response to powdery mildew infection. Genetic analysis showed that a single dominant gene, tentatively designated PmYD588, conferred resistance to powdery mildew in YD588. Using bulked segregant RNA-Seq (BSR-Seq) and single nucleotide polymorphism (SNP) association analysis, two high-confidence candidate regions were detected in the chromosome arm 2B, spanning 453,752,054-506,356,791 and 584,117,809-664,221,850 bp, respectively. To confirm the candidate region, molecular markers were developed using the BSR-Seq data and mapped PmYD588 to an interval of 4.2 cM by using the markers YTU588-004 and YTU588-008. The physical position was subsequently locked into the interval of 647.1-656.0 Mb, which was different from those of Pm6, Pm33, Pm51, Pm52, Pm63, Pm64, PmQ, PmKN0816, MlZec1, and MlAB10 on the same chromosome arm in its position, suggesting that it is most likely a new Pm gene. To explore the potential regulatory genes of the R gene, 2,973 differentially expressed genes (DEGs) between the parents and bulks were analyzed using gene ontology (GO), clusters of orthologous group (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Based on the data, we selected 23 potential regulated genes in the enriched pathway of plant-pathogen interaction and detected their temporal expression patterns using an additional set of wheat samples and time-course analysis postinoculation with Bgt. As a result, six disease-related genes showed distinctive expression profiles after Bgt invasion and can serve as key candidates for the dissection of resistance mechanisms and improvement of durable resistance to wheat powdery mildew.

Plant roots employ cell-layer-specific programs to respond to pathogenic and beneficial microbes

Plant roots are built of concentric cell layers that are thought to respond to microbial infections by employing specific, genetically defined programs. Yet, the functional impact of this radial organization remains elusive, particularly due to the lack of genome-wide techniques for monitoring expression at a cell-layer resolution. Here, cell-type-specific expression of tagged ribosomes enabled the isolation of ribosome-bound mRNA to obtain cell-layer translatomes (TRAP-seq, translating ribosome affinity purification and RNA sequencing). After inoculation with the vascular pathogen Verticillium longisporum, pathogenic oomycete Phytophthora parasitica, or mutualistic endophyte Serendipita indica, root cell-layer responses reflected the fundamentally different colonization strategies of these microbes. Notably, V. longisporum specifically suppressed the endodermal barrier, which restricts fungal progression, allowing microbial access to the root central cylinder. Moreover, localized biosynthesis of antimicrobial compounds and ethylene differed in response to pathogens and mutualists. These examples highlight the power of this resource to gain insights into root-microbe interactions and to develop strategies in crop improvement.

Identification of two compounds able to improve flax resistance towards Fusarium oxysporum infection

Plants are surrounded by a diverse range of microorganisms that causes serious crop losses and requires the use of pesticides. Flax is a major crop in Normandy used for its fibres and is regularly challenged by the pathogenic fungus Fusarium oxysporum (Fo) f. sp. lini. To protect themselves, plants use "innate immunity" as a first line of defense level against pathogens. Activation of plant defense with elicitors could be an alternative for crop plant protection. A previous work was conducted by screening a chemical library and led to the identification of compounds able to activate defense responses in Arabidopsis thaliana. Four compounds were tested for their abilities to improve resistance of two flax varieties against Fo. Two of them, one natural (holaphyllamine or HPA) and one synthetic (M4), neither affected flax nor Fo growth. HPA and M4 induced oxidative burst and callose deposition. Furthermore, HPA and M4 caused changes in the expression patterns of defense-related genes coding a glucanase and a chitinase-like. Finally, plants pre-treated with HPA or M4 exhibited a significant decrease in the disease symptoms. Together, these findings demonstrate that HPA and M4 are able to activate defense responses in flax and improve its resistance against Fo infection.

Simultaneous visualization of callose deposition and plasma membrane for live-cell imaging in plants

The appropriate combination of fluorescent probes enabled the simultaneous visualization of callose deposition and plasma membrane in living Arabidopsis and can be useful for the cell biological study of papilla formation in plants. Localized callose deposition at the site of fungal infection is a central part of papilla formation, which creates a barrier between the host plasma membrane and the cell wall and plays an important role in preventing the penetration of fungal hyphae into the host cells. Using chitin-induced callose deposition as a model system, we examined suitable conditions for the simultaneous visualization of callose deposition and plasma membrane dynamics in living Arabidopsis cotyledons. We found that aniline blue fluorochrome (ABF) for callose staining selectively interferes with FM dyes for membrane visualization depending on the structure of the latter compounds and the proper combination of these fluorescent dyes and staining conditions is a key for successful live-cell imaging. The established conditions enabled the live-cell imaging of chitin-induced callose deposition and host membrane systems. The established system/conditions would also be useful for the cell biological studies on the localized callose deposition in other stress/development-associated processes. The finding that the slight difference in the structure of FM dyes affects the interaction with another fluorescent dye, ABF, would also give useful suggestions for the studies where multiple fluorescent dyes are utilized for live-cell imaging.

Structural specificity in plant-filamentous pathogen interactions

Plant diseases bear names such as leaf blights, root rots, sheath blights, tuber scabs, and stem cankers, indicating that symptoms occur preferentially on specific parts of host plants. Accordingly, many plant pathogens are specialized to infect and cause disease in specific tissues and organs. Conversely, others are able to infect a range of tissues, albeit often disease symptoms fluctuate in different organs infected by the same pathogen. The structural specificity of a pathogen defines the degree to which it is reliant on a given tissue, organ, or host developmental stage. It is influenced by both the microbe and the host but the processes shaping it are not well established. Here we review the current status on structural specificity of plant-filamentous pathogen interactions and highlight important research questions. Notably, this review addresses how constitutive defence and induced immunity as well as virulence processes vary across plant organs, tissues, and even cells. A better understanding of the mechanisms underlying structural specificity will aid targeted approaches for plant health, for instance by considering the variation in the nature and the amplitude of defence responses across distinct plant organs and tissues when performing selective breeding.

Danger-Associated Peptide Regulates Root Growth by Promoting Protons Extrusion in an AHA2-Dependent Manner in Arabidopsis

Plant elicitor peptides (Peps) are damage/danger-associated molecular patterns (DAMPs) that are derived from precursor proteins PROPEPs and perceived by a pair of leucine-rich repeat receptor-like kinases (LRR-RLKs), PEPR1 and PEPR2, to enhance innate immunity and to inhibit root growth in Arabidopsis thaliana. In this study, we show that Arabidopsis Pep1 inhibits the root growth by interfering with pH signaling, as acidic condition increased, but neutral and alkaline conditions decreased the Pep1 effect on inhibiting the root growth. The perception of Pep1 to PEPRs activated the plasma membrane-localized H+-ATPases (PM H+-ATPases) -the pump proton in plant cell-to extrude the protons into apoplast, and induced an overly acidic environment in apoplastic space, which further promoted the cell swelling in root apex and inhibited root growth. Furthermore, we revealed that pump proton AUTOINHIBITED H⁺-ATPase 2 (AHA2) physically interacted with PEPR2 and served downstream of the Pep1-PEPRs signaling pathway to regulate Pep1-induced protons extrusion and root growth inhibition. In conclusion, this study demonstrates a previously unrecognized signaling crosstalk between Pep1 and pH signaling to regulate root growth.

Plant Immune Mechanisms: From Reductionistic to Holistic Points of View

After three decades of the amazing progress made on molecular studies of plant-microbe interactions (MPMI), we have begun to ask ourselves "what are the major questions still remaining?" as if the puzzle has only a few pieces missing. Such an exercise has ultimately led to the realization that we still have many more questions than answers. Therefore, it would be an impossible task for us to project a coherent "big picture" of the MPMI field in a single review. Instead, we provide our opinions on where we would like to go in our research as an invitation to the community to join us in this exploration of new MPMI frontiers.

The Soil-Borne Identity and Microbiome-Assisted Agriculture: Looking Back to the Future

Looking forward includes looking back every now and then. In 2007, David Weller looked back at 30 years of biocontrol of soil-borne pathogens by Pseudomonas and signified that the progress made over decades of research has provided a firm foundation to formulate current and future research questions. It has been recognized for more than a century that soil-borne microbes play a significant role in plant growth and health. The recent application of high-throughput omics technologies has enabled detailed dissection of the microbial players and molecular mechanisms involved in the complex interactions in plant-associated microbiomes. Here, we highlight old and emerging plant microbiome concepts related to plant disease control, and address perspectives that modern and emerging microbiomics technologies can bring to functionally characterize and exploit plant-associated microbiomes for the benefit of plant health in future microbiome-assisted agriculture.

eIF2α Phosphorylation by GCN2 Is Induced in the Presence of Chitin and Plays an Important Role in Plant Defense against B. cinerea Infection

Translation plays an important role in plant adaptation to different abiotic and biotic stresses; however, the mechanisms involved in translational regulation during each specific response and their effect in translation are poorly understood in plants. In this work, we show that GCN2 promotes eIF2α phosphorylation upon contact with Botrytis cinerea spores, and that this phosphorylation is required for the proper establishment of plant defense against the fungus. In fact, independent gcn2 mutants display an enhanced susceptibility to B. cinerea infection, which is highlighted by an increased cell death and reduced expression of ethylene- and jasmonic-related genes in the gcn2 mutants. eIF2α phosphorylation is not only triggered in the presence of the fungus, but interestingly, is also achieved in the sole presence of the microbe-associated molecular pattern (MAMP) chitin. Moreover, analysis of de novo protein synthesis by ^35SMet-^35SCys incorporation indicates that chitin treatment promotes a global inhibition of translation. Taken together, these results suggest that eIF2α phosphorylation by GCN2 is promoted in the presence of chitin and plays an important role in plant defense against B. cinerea infection.

Ectomycorrhizal fungi induce systemic resistance against insects on a nonmycorrhizal plant in a CERK1-dependent manner

Below-ground microbes can induce systemic resistance against foliar pests and pathogens on diverse plant hosts. The prevalence of induced systemic resistance (ISR) among plant-microbe-pest systems raises the question of host specificity in microbial induction of ISR. To test whether ISR is limited by plant host range_, we tested the ISR-inducing ectomycorrhizal fungus Laccaria bicolor on the nonmycorrhizal plant Arabidopsis thaliana. We used the cabbage looper Trichoplusia ni and bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pto) as readouts for ISR on Arabidopsis. We found that root inoculation with L. bicolor triggered ISR against T. ni and induced systemic susceptibility (ISS) against the bacterial pathogen Pto. We found that L. bicolor-triggered ISR against T. ni was dependent on jasmonic acid signaling and salicylic acid biosynthesis and signaling. Heat-killed L. bicolor and chitin were sufficient to trigger ISR against T. ni and ISS against Pto. The chitin receptor CERK1 was necessary for L. bicolor-mediated effects on systemic immunity. Collectively our findings suggest that some ISR responses might not require intimate symbiotic association, but rather might be the result of root perception of conserved microbial signals.

Regulation of Cell Type-Specific Immunity Networks in Arabidopsis Roots

While root diseases are among the most devastating stresses in global crop production, our understanding of root immunity is still limited relative to our knowledge of immune responses in leaves. Considering that root performance is based on the concerted functions of its different cell types, we undertook a cell type-specific transcriptome analysis to identify gene networks activated in epidermis, cortex, and pericycle cells of Arabidopsis (Arabidopsis thaliana) roots challenged with two immunity elicitors, the bacterial flagellin-derived flg22 and the endogenous Pep1 peptide. Our analyses revealed distinct immunity gene networks in each cell type. To further substantiate our understanding of regulatory patterns underlying these cell type-specific immunity networks, we developed a tool to analyze paired transcription factor binding motifs in the promoters of cell type-specific genes. Our study points toward a connection between cell identity and cell type-specific immunity networks that might guide cell types in launching immune response according to the functional capabilities of each cell type.

Co-incidence of Damage and Microbial Patterns Controls Localized Immune Responses in Roots

Recognition of microbe-associated molecular patterns (MAMPs) is crucial for the plant's immune response. How this sophisticated perception system can be usefully deployed in roots, continuously exposed to microbes, remains a mystery. By analyzing MAMP receptor expression and response at cellular resolution in Arabidopsis, we observed that differentiated outer cell layers show low expression of pattern-recognition receptors (PRRs) and lack MAMP responsiveness. Yet, these cells can be gated to become responsive by neighbor cell damage. Laser ablation of small cell clusters strongly upregulates PRR expression in their vicinity, and elevated receptor expression is sufficient to induce responsiveness in non-responsive cells. Finally, localized damage also leads to immune responses to otherwise non-immunogenic, beneficial bacteria. Damage-gating is overridden by receptor overexpression, which antagonizes colonization. Our findings that cellular damage can "switch on" local immune responses helps to conceptualize how MAMP perception can be used despite the presence of microbial patterns in the soil.

Plant resistance and leaf chemical characteristic jointly shape phyllosphere bacterial community

Phyllosphere bacteria have an important role in plant growth and resistance to pathogen infection and are partially influenced by plant genotype and leaf environment. How plant resistance to pathogens and leaf chemical characteristics shape the phyllosphere bacterial communities is unclear. In this study, the phyllosphere bacterial communities of maize hybrids with various resistance to Setosphaeria turcica were compared using the high-throughput sequencing and large-scale culturing methods. The results showed that Shannon and Simpson indices of phyllosphere bacterial communities were markedly higher in the highly resistant hybrid (HR) compared with the susceptible one. Hierarchical clustering analysis, unweighted UniFrac principal component analysis (PCoA) and the analysis of similarities (ANOSIM) demonstrated that the phyllosphere bacterial communities were significantly distinct between resistant and susceptible hybrids. The redundancy analysis (RDA) demonstrated that leaf chemical characteristics, including nitrogen and phosphorus concentration, and disease resistance play an important role in shaping the phyllosphere bacterial community. Linear discriminant effect size (LEfSe) analysis indicated that Bacillus, Pseudomonas and Tumebacillus were the biomarker species in the phyllosphere of HR. Biocontrol bacteria against S. turcica (such as Pseudomonas and Bacillus) were isolated from the phyllosphere of HR by large-scale culturing. The work contributes to understanding of the phyllosphere bacterial community assembly and provides a new clue to screening for strong biocontrol bacteria from HR and to facilitating future breeding efforts for enhancing disease resistance.

Single-stranded oligodeoxynucleotides induce plant defence in Arabidopsis thaliana

BACKGROUND AND AIMS

Single-stranded DNA oligodeoxynucleotides (ssODNs) have been shown to elicit immune responses in mammals. In plants, RNA and genomic DNA can activate immunity, although the exact mechanism through which they are sensed is not clear. The aim of this work was to study the possible effect of ssODNs on plant immunity.

KEY RESULTS

The ssODNs IMT504 and 2006 increased protection against the pathogens Pseudomonas syringae pv. tomato DC3000 and Botrytis cinerea but not against tobacco mosaic virus-Cg when infiltrated in Arabidopsis thaliana. In addition, ssODNs inhibited root growth and promoted stomatal closure in a concentration-dependent manner, with half-maximal effective concentrations between 0.79 and 2.06 µm. Promotion of stomatal closure by ssODNs was reduced by DNase I treatment. It was also diminished by the NADPH oxidase inhibitor diphenyleneiodonium and by coronatine, a bacterial toxin that inhibits NADPH oxidase-dependent reactive oxygen species (ROS) synthesis in guard cells. In addition it was found that ssODN-mediated stomatal closure was impaired in bak1-5, bak1-5/bkk1, mpk3 and npr1-3 mutants. ssODNs also induced early expression of MPK3, WRKY33, PROPEP1 and FRK1 genes involved in plant defence, an effect that was reduced in bak1-5 and bak1-5/bkk1 mutants.

CONCLUSIONS

ssODNs are capable of inducing protection against pathogens through the activation of defence genes and promotion of stomatal closure through a mechanism similar to that of other elicitors of plant immunity, which involves the BAK1 co-receptor, and ROS synthesis.

Modulation of Plant Defense System in Response to Microbial Interactions

At different stages throughout their life cycle, plants often encounter several pathogenic microbes that challenge plant growth and development. The sophisticated innate plant immune system prevents the growth of harmful microbes via two interconnected defense strategies based on pathogen perception. These strategies involve microbe-associated molecular pattern-triggered immunity and microbial effector-triggered immunity. Both these immune responses induce several defense mechanisms for restricting pathogen attack to protect against pathogens and terminate their growth. Plants often develop immune memory after an exposure to pathogens, leading to systemic acquired resistance. Unlike that with harmful microbes, plants make friendly interactions with beneficial microbes for boosting their plant immune system. A spike in recent publications has further improved our understanding of the immune responses in plants as triggered by interactions with microbes. The present study reviews our current understanding of how plant–microbe interactions can activate the sophisticated plant immune system at the molecular level. We further discuss how plant-microbe interaction boost the immune system of plants by demonstrating the examples of Mycorrhizal and Rhizobial association and how these plant-microbe interactions can be exploited to engineer disease resistance and crop improvement.

Dual Activities of Receptor-Like Kinase OsWAKL21.2 Induce Immune Responses

Plant pathogens secrete cell wall-degrading enzymes that degrade various components of the plant cell wall. Plants sense this cell wall damage as a mark of infection and induce immune responses. However, the plant functions that are involved in the elaboration of cell wall damage-induced immune responses remain poorly understood. Transcriptome analysis revealed that a rice (Oryza sativa) receptor-like kinase, WALL-ASSOCIATED KINASE-LIKE21 (OsWAKL21.2), is up-regulated following treatment with either Xanthomonas oryzae pv oryzae (a bacterial pathogen) or lipaseA/esterase (LipA; a cell wall-degrading enzyme of X. oryzae pv oryzae). Overexpression of OsWAKL21.2 in rice induces immune responses similar to those activated by LipA treatment. Down-regulation of OsWAKL21.2 attenuates LipA-mediated immune responses. Heterologous expression of OsWAKL21.2 in Arabidopsis (Arabidopsis thaliana) also activates plant immune responses. OsWAKL21.2 is a dual-activity kinase that has in vitro kinase and guanylate cyclase activities. Interestingly, kinase activity of OsWAKL21.2 is necessary to activate rice immune responses, whereas in Arabidopsis, OsWAKL21.2 guanylate cyclase activity activates these responses. Our study reveals a rice receptor kinase that activates immune responses in two different species via two different mechanisms.

Danger-Associated Peptide Regulates Root Immune Responses and Root Growth by Affecting ROS Formation in Arabidopsis

Plant elicitor peptides (Peps) are damage/danger-associated molecular patterns (DAMPs) that are perceived by a pair of receptor-like kinases, PEPR1 and PEPR2, to enhance innate immunity and induce the growth inhibition of root in Arabidopsis thaliana. In this study, we show that PEPR1 and PEPR2 function vitally in roots to regulate the root immune responses when treating the roots with bacterial pathogen Pst DC3000. PEPR2, rather than PEPR1, played a predominant role in the perception of Pep1 in the roots and further triggered a strong ROS accumulation—the substance acts as an antimicrobial agent or as a secondary messenger in plant cells. Consistently, seedlings mutating two major ROS-generating enzyme genes, respiratory burst oxidase homologs D and F (RBOHD and RBOHF), abolished the root ROS accumulation and impaired the growth inhibition of the roots induced by Pep1. Furthermore, we revealed that botrytis-induced kinase 1 (BIK1) physically interacted with PEPRs and RBOHD/F, respectively, and served downstream of the Pep1-PEPRs signaling pathway to regulate Pep1-induced ROS production and root growth inhibition. In conclusion, this study demonstrates a previously unrecognized signaling crosstalk between Pep1 and ROS signaling to regulate root immune response and root growth.

Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application

Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.

Calcium channel CNGC19 mediates basal defense signaling to regulate colonization by Piriformospora indica in Arabidopsis roots

The activation of calcium signaling is a crucial event for perceiving environmental stress. Colonization by Piriformospora indica, a growth-promoting root endosymbiont, activates cytosolic Ca2+ in Arabidopsis roots. In this study, we examined the role and functional relevance of calcium channels responsible for Ca2+ fluxes. Expression profiling revealed that CYCLIC NUCLEOTIDE GATED CHANNEL 19 (CNGC19) is an early-activated gene, induced by unidentified components in P. indica cell-wall extract. Functional analysis showed that loss-of-function of CNGC19 resulted in growth inhibition by P.indica, due to increased colonization and loss of controlled fungal growth. The cngc19 mutant showed reduced elevation of cytosolic Ca2+ in response to P. indica cell-wall extract in comparison to the wild-type. Microbe-associated molecular pattern-triggered immunity was compromised in the cngc19 lines, as evidenced by unaltered callose deposition, reduced cis-(+)-12-oxo-phytodienoic acid, jasmonate, and jasmonoyl isoleucine levels, and down-regulation of jasmonate and other defense-related genes, which contributed to a shift towards a pathogenic response. Loss-of-function of CNGC19 resulted in an inability to modulate indole glucosinolate content during P. indica colonization. CNGC19-mediated basal immunity was dependent on the AtPep receptor, PEPR. CNGC19 was also crucial for P. indica-mediated suppression of AtPep-induced immunity. Our results thus demonstrate that Arabidopsis CNGC19 is an important Ca2+ channel that maintains a robust innate immunity and is crucial for growth-promotion signaling upon colonization by P. indica.

Extensin arabinosylation is involved in root response to elicitors and limits oomycete colonization

BACKGROUND AND AIMS

Extensins are hydroxyproline-rich glycoproteins thought to strengthen the plant cell wall, one of the first barriers against pathogens, through intra- and intermolecular cross-links. The glycan moiety of extensins is believed to confer the correct structural conformation to the glycoprotein, leading to self-assembly within the cell wall that helps limit microbial adherence and invasion. However, this role is not clearly established.

METHODS

We used Arabidopsis thaliana mutants impaired in extensin arabinosylation to investigate the role of extensin arabinosylation in root-microbe interactions. Mutant and wild-type roots were stimulated to elicit an immune response with flagellin 22 and immunolabelled with a set of anti-extensin antibodies. Roots were also inoculated with a soilborne oomycete, Phytophthora parasitica, to assess the effect of extensin arabinosylation on root colonization.

KEY RESULTS

A differential distribution of extensin epitopes was observed in wild-type plants in response to elicitation. Elicitation also triggers altered epitope expression in mutant roots compared with wild-type and non-elicited roots. Inoculation with the pathogen P. parasitica resulted in enhanced root colonization for two mutants, specifically xeg113 and rra2.

CONCLUSIONS

We provide evidence for a link between extensin arabinosylation and root defence, and propose a model to explain the importance of glycosylation in limiting invasion of root cells by pathogenic oomycetes.

Ectopic Expression of a Cell-Wall-Degrading Enzyme-Induced OsAP2/ERF152 Leads to Resistance against Bacterial and Fungal Infection in Arabidopsis

Pathogen secreted cell-wall-degrading enzymes (CWDEs) induce plant innate immune responses. The expression of rice transcription factor APETALA2/ethylene response factor-152 (OsAP2/ERF152) is enhanced in leaves upon treatment with different CWDEs and upon wounding. Ectopic expression of OsAP2/ERF152 in Arabidopsis leads to induction of immune responses such as callose deposition and upregulation of both salicylic acid- and jasmonic acid/ethylene-responsive defense genes. Arabidopsis transgenics expressing OsAP2/ERF152 exhibited resistance to infections caused by both bacterial and fungal pathogens (Pseudomonas syringae pv. tomato DC3000 and Rhizoctonia solani AG1-IA, respectively). Ectopic expression of OsAP2/ERF152 results in transient activation of mitogen-activated protein kinases 3/6 (MPK3/6), which could be leading to the induction of a broad range immunity in Arabidopsis.

Damage Control: Cellular Logic in the Root Immune Response

The organizational principles of the root immune system are largely uncharacterized. In the February 6, 2020 issue of Cell, Zhou et al. showed roots are built entirely by immunocompetent cells that require distinct instructions to unlock cell-autonomous immune programs. A root cell's developmental identity combined with its spatial distribution fine-tunes immune signal sensitivity, enabling sector-specific immune responses.

Vascular bundle sheath and mesophyll cells modulate leaf water balance in response to chitin

Plants can detect pathogen invasion by sensing microbe-associated molecular patterns (MAMPs). This sensing process leads to the induction of defense responses. Numerous MAMP mechanisms of action have been described in and outside the guard cells. Here, we describe the effects of chitin, a MAMP found in fungal cell walls and insects, on the cellular osmotic water permeability (P_f ) of the leaf vascular bundle-sheath (BS) and mesophyll cells (MCs), and its subsequent effect on leaf hydraulic conductance (K_leaf ). BS is a parenchymatic tissue that tightly encases the vascular system. BS cells (BSCs) have been shown to influence K_leaf through changes in their P_f , for example, after sensing the abiotic stress response-regulating hormone abscisic acid. It was recently reported that, in Arabidopsis, the chitin receptors-like kinases, chitin elicitor receptor kinase 1 (CERK1) and LYSINE MOTIF RECEPTOR KINASE 5 (LYK5) are highly expressed in the BS as well as the neighboring mesophyll. Therefore, we studied the possible impact of chitin on these cells. Our results revealed that BSCs and MCs exhibit a sharp decrease in P_f in response to chitin treatment. In addition, xylem-fed chitin decreased K_leaf and led to stomatal closure. However, Atlyk5 mutant showed none of these responses. Complementing AtLYK5 in the BSCs (using the SCARECROW promoter) resulted in the response to chitin that was similar to that observed in the wild-type. These results suggest that BS play a role in the perception of apoplastic chitin and in initiating chitin-triggered immunity.

Microbes Attaching to Endoparasitic Phytonematodes in Soil Trigger Plant Defense Upon Root Penetration by the Nematode

Root-knot nematodes (Meloidogyne spp.) are among the most aggressive phytonematodes. While moving through soil to reach the roots of their host, specific microbes attach to the cuticle of the infective second-stage juveniles (J2). Reportedly, the attached microorganisms affect nematodes and reduce their performance on the host plants. We have previously shown that some non-parasitic bacterial strains isolated from the cuticle of Meloidogyne hapla in different soils affected J2 mortality, motility, hatching, and root invasion. Here we tested whether cuticle-attached microbes trigger plant defenses upon penetration of J2. In in vitro assays, M. hapla J2-attached microbes from a suppressive soil induced pathogen-associated molecular pattern-triggered immunity (PTI) in tomato roots. All tested PTI-responsive defense genes were upregulated after root invasion of J2 with attached microbes, compared to surface-sterilized J2, particularly the jasmonic acid-mediated PTI marker genes TFT1 and GRAS4.1. The strain Microbacterium sp. K6, that was isolated from the cuticle, significantly reduced root invasion when attached to the J2. Attached K6 cells supported plant defense and counteracted suppression of plant basal defense in roots by invaded J2. The plant response to the J2-attached K6 cells was stronger in leaves than in roots, and it increased from 1 to 3 days post inoculation (dpi). At 1 dpi, the plant responded to J2-attached K6 cells by ameliorating the J2-triggered down-regulation of defense genes mostly in roots, while at 3 dpi this response was systemic and more pronounced in leaves. In a reactive oxygen species (ROS) assay, the compounds released from J2 with attached K6 cells triggered a stronger ROS burst in tomato roots than the compounds from nematodes without K6, or the metabolites released from strain K6 alone. Leaves showed a 100 times more sensitive response than roots, and the metabolites of K6 with or without J2 induced strong ROS bursts. In conclusion, our results suggest the importance of microorganisms that attach to M. hapla in suppressive soil, inducing early basal defenses in plants and suppressing nematode performance in roots.

Biocontrol by Fusarium oxysporum Using Endophyte-Mediated Resistance

Interactions between plants and the root-colonizing fungus Fusarium oxysporum (Fo) can be neutral, beneficial, or detrimental for the host. Fo is infamous for its ability to cause wilt, root-, and foot-rot in many plant species, including many agronomically important crops. However, Fo also has another face; as a root endophyte, it can reduce disease caused by vascular pathogens such as Verticillium dahliae and pathogenic Fo strains. Fo also confers protection to root pathogens like Pythium ultimum, but typically not to pathogens attacking above-ground tissues such as Botrytis cinerea or Phytophthora capsici. Endophytes confer biocontrol either directly by interacting with pathogens via mycoparasitism, antibiosis, or by competition for nutrients or root niches, or indirectly by inducing resistance mechanisms in the host. Fo endophytes such as Fo47 and CS-20 differ from Fo pathogens in their effector gene content, host colonization mechanism, location in the plant, and induced host-responses. Whereas endophytic strains trigger localized cell death in the root cortex, and transiently induce immune signaling and papilla formation, these responses are largely suppressed by pathogenic Fo strains. The ability of pathogenic strains to compromise immune signaling and cell death is likely attributable to their host-specific effector repertoire. The lower number of effector genes in endophytes as compared to pathogens provides a means to distinguish them from each other. Co-inoculation of a biocontrol-conferring Fo and a pathogenic Fo strain on tomato reduces disease, and although the pathogen still colonizes the xylem vessels this has surprisingly little effect on the xylem sap proteome composition. In this tripartite interaction the accumulation of just two PR proteins, NP24 (a PR-5) and a β-glucanase, was affected. The Fo-induced resistance response in tomato appears to be distinct from induced systemic resistance (ISR) or systemic acquired resistance (SAR), as the phytohormones jasmonate, ethylene, and salicylic acid are not required. In this review, we summarize our molecular understanding of Fo-induced resistance in a model and identify caveats in our knowledge.

Elicitor and Receptor Molecules: Orchestrators of Plant Defense and Immunity

Pathogen-associated molecular patterns (PAMPs), microbe-associated molecular patterns (MAMPs), herbivore-associated molecular patterns (HAMPs), and damage-associated molecular patterns (DAMPs) are molecules produced by microorganisms and insects in the event of infection, microbial priming, and insect predation. These molecules are then recognized by receptor molecules on or within the plant, which activates the defense signaling pathways, resulting in plant’s ability to overcome pathogenic invasion, induce systemic resistance, and protect against insect predation and damage. These small molecular motifs are conserved in all organisms. Fungi, bacteria, and insects have their own specific molecular patterns that induce defenses in plants. Most of the molecular patterns are either present as part of the pathogen’s structure or exudates (in bacteria and fungi), or insect saliva and honeydew. Since biotic stresses such as pathogens and insects can impair crop yield and production, understanding the interaction between these organisms and the host via the elicitor–receptor interaction is essential to equip us with the knowledge necessary to design durable resistance in plants. In addition, it is also important to look into the role played by beneficial microbes and synthetic elicitors in activating plants’ defense and protection against disease and predation. This review addresses receptors, elicitors, and the receptor–elicitor interactions where these components in fungi, bacteria, and insects will be elaborated, giving special emphasis to the molecules, responses, and mechanisms at play, variations between organisms where applicable, and applications and prospects.

The role of CYP71A12 monooxygenase in pathogen-triggered tryptophan metabolism and Arabidopsis immunity

Effective defense of Arabidopsis against filamentous pathogens requires two mechanisms, both of which involve biosynthesis of tryptophan (Trp)-derived metabolites. Extracellular resistance involves products of PEN2-dependent metabolism of indole glucosinolates (IGs). Restriction of further fungal growth requires PAD3-dependent camalexin and other, as yet uncharacterized, indolics. This study focuses on the function of CYP71A12 monooxygenase in pathogen-triggered Trp metabolism, including the biosynthesis of indole-3-carboxylic acid (ICA). Moreover, to investigate the contribution of CYP71A12 and its products to Arabidopsis immunity, we analyzed infection phenotypes of multiple mutant lines combining pen2 with pad3, cyp71A12, cyp71A13 or cyp82C2. Metabolite profiling of cyp71A12 lines revealed a reduction in ICA accumulation. Additionally, analysis of mutant plants showed that low amounts of ICA can form during an immune response by CYP71B6/AAO1-dependent metabolism of indole acetonitrile, but not via IG hydrolysis. Infection assays with Plectosphaerella cucumerina and Colletotrichum tropicale, two pathogens with different lifestyles, revealed cyp71A12-, cyp71A13- and cyp82C2-associated defects associated with Arabidopsis immunity. Our results indicate that CYP71A12, but not CYP71A13, is the major enzyme responsible for the accumulation of ICA in Arabidopsis in response to pathogen ingression. We also show that both enzymes are key players in the resistance of Arabidopsis against selected filamentous pathogens after they invade.

Alteration of Bacterial Wilt Resistance in Tomato Plant by Microbiota Transplant

Plant-associated microbiota plays an important role in plant disease resistance. Bacterial wilt resistance of tomato is a function of the quantitative trait of tomato plants; however, the mechanism underlying quantitative resistance is unexplored. In this study, we hypothesized that rhizosphere microbiota affects the resistance of tomato plants against soil-borne bacterial wilt caused by Ralstonia solanacearum. This hypothesis was tested using a tomato cultivar grown in a defined soil with various microbiota transplants. The bacterial wilt-resistant Hawaii 7996 tomato cultivar exhibited marked suppression and induction of disease severity after treatment with upland soil-derived and forest soil-derived microbiotas, respectively, whereas the transplants did not affect the disease severity in the susceptible tomato cultivar Moneymaker. The differential resistance of Hawaii 7996 to bacterial wilt was abolished by diluted or heat-killed microbiota transplantation. Microbial community analysis revealed the transplant-specific distinct community structure in the tomato rhizosphere and the significant enrichment of specific microbial operational taxonomic units (OTUs) in the rhizosphere of the upland soil microbiota-treated Hawaii 7996. These results suggest that the specific transplanted microbiota alters the bacterial wilt resistance in the resistant cultivar potentially through a priority effect.

Dynamic infection of Verticillium dahliae in upland cotton

Verticillium wilt, an infection caused by the soilborne fungus Verticillium dahliae, is one of the most serious diseases in cotton. No effective control method against V. dahliae has been established, and the infection mechanism of V. dahliae in upland cotton remains unknown. GFP-tagged V. dahliae isolates with different pathogenic abilities were used to analyse the colonisation and infection of V. dahliae in the roots and leaves of different upland cotton cultivars, the relationships among infection processes, the immune responses and the resistance ability of different cultivars against V. dahliae. Here, we report a new infection model for V. dahliae in upland cotton plants. V. dahliae can colonise and infect any organ of upland cotton plants and then spread to the entire plant from the infected organ through the surface and interior of the organ. Vascular tissue was found to not be the sole transmission route of V. dahliae in cotton plants. In addition, the rate of infection of a V. dahliae isolate with strong pathogenicity was notably faster than that of an isolate with weak pathogenicity. The resistance of upland cotton to Verticillium wilt was related to the degree of the immune response induced in plants infected with V. dahliae. These results provide a theoretical basis for studying the mechanism underlying the interaction between V. dahliae and upland cotton. These results provide a theoretical basis for studying the mechanism underlying the interaction between V. dahliae and upland cotton.

Biocontrol of Root Diseases and Growth Promotion of the Tuberous Plant Aconitum carmichaelii Induced by Actinomycetes Are Related to Shifts in the Rhizosphere Microbiota

Soil Actinomycetes have been used as biocontrol agents against soil-borne plant diseases, yet little is known about their effects on the structure of the rhizosphere microbiota and the long-term effects on crop yield and disease intensity after the application of Actinomycetes is stopped. Here, we conducted 3-year plot experiments to investigate the roles of two Actinomycetes strains (Streptomyces pactum Act12 and Streptomyces rochei D74) in the biocontrol of soil-borne root diseases and growth promotion of monkhood (Aconitum carmichaelii). We also examined their long-term effects after soil application of a mixed Actinomycetes preparation (spore powder) was completed. High-throughput sequencing was used to analyze shifts in the rhizosphere microbiota. The antifungal activity and root colonization ability of the two Actinomycetes were also tested. Disease severity of southern blight and root rot decreased following application of the Actinomycetes preparation, whereas biomass yield of tubers increased compared with the control group. Significant effects of disease control and plant growth promotion were also observed after application was stopped. The Actinomycetes preparation induced marked increases in the abundance of beneficial microbes and decreases in the abundance of harmful microbes in rhizosphere soil. Adding cell-free culture filtrates of both strains Act12 and D74 inhibited the growth of fungal pathogens capable of causing southern blight (Sclerotium rolfsii) and root rot (Fusarium oxysporum) in A. carmichaelii. A GFP-labeled strain was used to show that D74 can colonize roots of A. carmichaelii. In conclusion, a preparation of two Actinomycetes plays a role in the biocontrol of root diseases and growth promotion of A. carmichaelii by inhibiting pathogen growth and shaping the rhizosphere microbiota.

Crying out for help with root exudates: adaptive mechanisms by which stressed plants assemble health-promoting soil microbiomes

Plants employ immunological and ecological strategies to resist biotic stress. Recent evidence suggests that plants adapt to biotic stress by changing their root exudation chemistry to assemble health-promoting microbiomes. This so-called 'cry-for-help' hypothesis provides a mechanistic explanation for previously characterized soil feedback responses to plant disease, such as the development of disease-suppressing soils upon successive cultivations of take all-infected wheat. Here, we divide the hypothesis into individual stages and evaluate the evidence for each component. We review how plant immune responses modify root exudation chemistry, as well as what impact this has on microbial activities, and the subsequent plant responses to these activities. Finally, we review the ecological relevance of the interaction, along with its translational potential for future crop protection strategies.

Root Transcriptomic Analysis Reveals Global Changes Induced by Systemic Infection of Solanum lycopersicum with Mild and Severe Variants of Potato Spindle Tuber Viroid

Potato spindle tuber viroid (PSTVd) causes systemic infection in plant hosts. There are many studies on viroid-host plant interactions, but they have predominantly focused on the aboveground part of the plant. Here, we investigated transcriptomic profile changes in tomato roots systemically infected with mild or severe PSTVd variants using a combined microarray/RNA-seq approach. Analysis indicated differential expression of genes related to various Gene Ontology categories depending on the stage of infection and PSTVd variant. A majority of cell-wall-related genes were down-regulated at early infection stages, but at the late stage, the number of up-regulated genes increased significantly. Along with observed alterations of many lignin-related genes, performed lignin quantification indicated their disrupted level in PSTVd-infected roots. Altered expression of genes related to biosynthesis and signaling of auxin and cytokinin, which are crucial for lateral root development, was also identified. Comparison of both PSTVd infections showed that transcriptional changes induced by the severe variant were stronger than those caused by the mild variant, especially at the late infection stage. Taken together, we showed that similarly to aboveground plant parts, PSTVd infection in the underground tissues activates the plant immune response.

A Comparative Transcriptomic and Proteomic Analysis of Hexaploid Wheat's Responses to Colonization by Bacillus velezensis and Gaeumannomyces graminis, Both Separately and Combined

Tritrophic interactions involving a biocontrol agent, a pathogen, and a plant have been analyzed predominantly from the perspective of the biocontrol agent. To explore the adaptive strategies of wheat in response to beneficial, pathogenic, and combined microorganisms, we performed the first comprehensive transcriptomic, proteomic, and biochemical analysis in wheat roots after exposure to Bacillus velezensis CC09, Gaeumannomyces graminis var. tritici, and their combined colonization, respectively. The transcriptional or translational programming of wheat roots inoculated with beneficial B. velezensis showed mild alterations compared with that of pathogenic G. graminis var. tritici. However, the combination of B. velezensis and G. graminis var. tritici activated a larger transcriptional or translational program than for each single microorganism, although the gene expression pattern was similar to that of individual infection by G. graminis var. tritici, suggesting a prioritization of defense against G. graminis var. tritici infection. Surprisingly, pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity made wheat pretreated with B. velezensis more sensitive to subsequent G. graminis var. tritici infection. Additionally, B. velezensis triggered a salicylic acid (SA)-dependent mode of induced systemic resistance that resembles pathogen-induced systemic acquired resistance. Wheat plants mainly depend on SA-mediated resistance, and not that mediated by jasmonic acid (JA), against the necrotrophic pathogen G. graminis var. tritici. Moreover, SA-JA interactions resulted in antagonistic effects regardless of the type of microorganisms in wheat. Further enhancement of SA-dependent defense responses such as lignification to the combined infection was shown to reduce the level of induced JA-dependent defense against subsequent infection with G. graminis var. tritici. Altogether, our results demonstrate how the hexaploid monocot wheat responds to beneficial or pathogenic microorganisms and prolongs the onset of take-all disease through modulation of cell reprogramming and signaling events.

Beneficial microbes going underground of root immunity

Plant roots interact with an enormous diversity of commensal, mutualistic, and pathogenic microbes, which poses a big challenge to roots to distinguish beneficial microbes from harmful ones. Plants can effectively ward off pathogens following immune recognition of conserved microbe-associated molecular patterns (MAMPs). However, such immune elicitors are essentially not different from those of neutral and beneficial microbes that are abundantly present in the root microbiome. Recent studies indicate that the plant immune system plays an active role in influencing rhizosphere microbiome composition. Moreover, it has become increasingly clear that root-invading beneficial microbes, including rhizobia and arbuscular mycorrhiza, evade or suppress host immunity to establish a mutualistic relationship with their host. Evidence is accumulating that many free-living rhizosphere microbiota members can suppress root immune responses, highlighting root immune suppression as an important function of the root microbiome. Thus, the gate keeping functions of the plant immune system are not restricted to warding off root-invading pathogens but also extend to rhizosphere microbiota, likely to promote colonization by beneficial microbes and prevent growth-defense tradeoffs triggered by the MAMP-rich rhizosphere environment.

Beyond pathogens: microbiota interactions with the plant immune system

Plant immune receptors perceive microbial molecules and initiate an array of biochemical responses that are effective against most invaders. The role of the plant immune system in detecting and controlling pathogenic microorganism has been well described. In contrast, much less is known about plant immunity in the context of the wealth of commensals that inhabit plants. Recent research indicates that, just like pathogens, commensals in the plant microbiome can suppress or evade host immune responses. Moreover, the plant immune system has an active role in microbiome assembly and controls microbial homeostasis in response to environmental variation. We propose that the plant immune system shapes the microbiome, and that the microbiome expands plant immunity and acts as an additional layer of defense against pathogenic organisms.

Monitoring of Rice Transcriptional Responses to Contrasted Colonizing Patterns of Phytobeneficial Burkholderia s.l. Reveals a Temporal Shift in JA Systemic Response

In the context of plant-pathogen and plant-mutualist interactions, the underlying molecular bases associated with host colonization have been extensively studied. However, it is not the case for non-mutualistic beneficial interactions or associative symbiosis with plants. Particularly, little is known about the transcriptional regulations associated with the immune tolerance of plants towards beneficial microbes. In this context, the study of the Burkholderia rice model is very promising to describe the molecular mechanisms involved in associative symbiosis. Indeed, several species of the Burkholderia sensu lato (s.l.) genus can colonize rice tissues and have beneficial effects; particularly, two species have been thoroughly studied: Burkholderia vietnamiensis and Paraburkholderia kururiensis. This study aims to compare the interaction of these species with rice and especially to identify common or specific plant responses. Therefore, we analyzed root colonization of the rice cultivar Nipponbare using DsRed-tagged bacterial strains and produced the transcriptomes of both roots and leaves 7 days after root inoculation. This led us to the identification of a co-expression jasmonic acid (JA)-related network exhibiting opposite regulation in response to the two strains in the leaves of inoculated plants. We then monitored by quantitative polymerase chain reaction (qPCR) the expression of JA-related genes during time course colonization by each strain. Our results reveal a temporal shift in this JA systemic response, which can be related to different colonization strategies of both strains.

Danger-Associated Peptides Interact with PIN-Dependent Local Auxin Distribution to Inhibit Root Growth in Arabidopsis

Plant elicitor peptides (Peps) are damage/danger-associated molecular patterns that are perceived by the receptor-like kinases, PEPR1 and PEPR2, to enhance innate immunity and to inhibit root growth in Arabidopsis (Arabidopsis thaliana). Here, we show that Arabidopsis Pep1 inhibits root growth in a PEPR2-dependent manner, which is accompanied by swelling epidermal and cortex cells and root hair formation in the transition zone (TZ). These Pep1-induced changes were mimicked by exogenous auxin application and were suppressed in the auxin perception mutants transport inhibitor response1 (tir1) and tir1 afb1 afb2 Pep1-induced auxin accumulation in the TZ region preceded cell expansion in roots. Because local auxin distribution depends on PIN-type auxin transporters, we examined Pep1-PEPR-induced root growth inhibition in several pin mutants and found that pin2 was highly sensitive but pin3 was less sensitive to Pep1. The pin2 pin3 double mutant was as sensitive to Pep1 treatment as wild-type plants. Pep1 reduced the abundance of PIN2 in the plasma membrane through activating endocytosis while increasing PIN3 expression in the TZ, leading to changes in local auxin distribution and inhibiting root growth. These results suggest that Pep-PEPR signaling undergoes crosstalk with auxin accumulation to control cell expansion and differentiation in roots during immune responses.