Diverse mechanisms of resistance to Pseudomonas syringae in a thousand natural accessions of Arabidopsis thaliana

Roles of microbiota in autoimmunity in Arabidopsis leaves

Over the past three decades, researchers have isolated plant mutants that show constitutively activated defence responses in the absence of pathogen infection. These mutants are called autoimmune mutants and are typically dwarf and/or bearing chlorotic/necrotic lesions. Here, from a genetic screen for Arabidopsis genes involved in maintaining a normal leaf microbiota, we identified TIP GROWTH DEFECTIVE 1 (TIP1), which encodes an S-acyltransferase, as a key player in guarding leaves against abnormal microbiota level and composition under high-humidity conditions. The tip1 mutant has several characteristic phenotypes of classical autoimmune mutants, including a dwarf stature, showing lesions, and having a high basal level of defence gene expression. Gnotobiotic experiments revealed that the autoimmune phenotypes of the tip1 mutant are largely dependent on the presence of microbiota as axenic tip1 plants have markedly reduced autoimmune phenotypes. We found that the microbiota dependency of autoimmune phenotypes is shared by several 'lesion mimic'-type autoimmune mutants in Arabidopsis. It is worth noting that autoimmune phenotypes caused by mutations in two Nucleotide-Binding, Leucine-Rich Repeat (NLR) genes do not require the presence of microbiota and can even be partially alleviated by microbiota. Our results therefore suggest the existence of at least two classes of autoimmunity (microbiota-dependent versus microbiota-independent) in plants. The observed interplay between autoimmunity and microbiota in the lesion mimic class of autoimmunity is reminiscent of the interactions between autoimmunity and dysbiosis in the animal kingdom. These parallels highlight the intricate relationship between host immunity and microbial communities across various biological systems.

Genetic Mapping of Tolerance to Bacterial Stem Blight Caused by Pseudomonas syringae pv. syringae in Alfalfa (Medicago sativa L.)

The bacterial stem blight of alfalfa (Medicago sativa L.), first reported in the United States in 1904, has emerged recently as a serious disease problem in the western states. The causal agent, Pseudomonas syringae pv. syringae, promotes frost damage and disease that can reduce first harvest yields by 50%. Resistant cultivars and an understanding of host-pathogen interactions are lacking in this pathosystem. With the goal of identifying DNA markers associated with disease resistance, we developed biparental F1 mapping populations using plants from the cultivar ZG9830. Leaflets of plants in the mapping populations were inoculated with a bacterial suspension using a needleless syringe and scored for disease symptoms. Bacterial populations were measured by culture plating and using a quantitative PCR assay. Surprisingly, leaflets with few to no symptoms had bacterial loads similar to leaflets with severe disease symptoms, indicating that plants without symptoms were tolerant to the bacterium. Genotyping-by-sequencing identified 11 significant SNP markers associated with the tolerance phenotype. This is the first study to identify DNA markers associated with tolerance to P. syringae. These results provide insight into host responses and provide markers that can be used in alfalfa breeding programs to develop improved cultivars to manage the bacterial stem blight of alfalfa.

Cell specialization and coordination in Arabidopsis leaves upon pathogenic attack revealed by scRNA-seq

Plant defense responses involve several biological processes that allow plants to fight against pathogenic attacks. How these different processes are orchestrated within organs and depend on specific cell types is poorly known. Here, using single-cell RNA sequencing (scRNA-seq) technology on three independent biological replicates, we identified several cell populations representing the core transcriptional responses of wild-type Arabidopsis leaves inoculated with the bacterial pathogen Pseudomonas syringae DC3000. Among these populations, we retrieved major cell types of the leaves (mesophyll, guard, epidermal, companion, and vascular S cells) with which we could associate characteristic transcriptional reprogramming and regulators, thereby specifying different cell-type responses to the pathogen. Further analyses of transcriptional dynamics, on the basis of inference of cell trajectories, indicated that the different cell types, in addition to their characteristic defense responses, can also share similar modules of gene reprogramming, uncovering a ubiquitous antagonism between immune and susceptible processes. Moreover, it appears that the defense responses of vascular S cells, epidermal cells, and mesophyll cells can evolve along two separate paths, one converging toward an identical cell fate, characterized mostly by lignification and detoxification functions. As this divergence does not correspond to the differentiation between immune and susceptible cells, we speculate that this might reflect the discrimination between cell-autonomous and non-cell-autonomous responses. Altogether our data provide an upgraded framework to describe, explore, and explain the specialization and the coordination of plant cell responses upon pathogenic challenge.

Plant and soil-associated microbiome dynamics determine the fate of bacterial wilt pathogen Ralstonia solanacearum

MAIN CONCLUSION

Plant and the soil-associated microbiome is important for imparting bacterial wilt disease tolerance in plants. Plants are versatile organisms that are endowed with the capacity to withstand various biotic and abiotic stresses despite having no locomotory abilities. Being the agent for bacterial wilt (BW) disease, Ralstonia solanacearum (RS) colonizes the xylem vessels and limits the water supply to various plant parts, thereby causing wilting. The havoc caused by RS leads to heavy losses in crop productivity around the world, for which a sustainable mitigation strategy is urgently needed. As several factors can influence plant-microbe interactions, comprehensive understanding of plant and soil-associated microbiome under the influence of RS and various environmental/edaphic conditions is important to control this pathogen. This review mainly focuses on microbiome dynamics associated with BW disease and also provide update on microbial/non-microbial approaches employed to control BW disease in crop plants.

Roles of microbiota in autoimmunity in Arabidopsis

Over the past three decades, researchers have isolated plant mutants that display constitutively activated defense responses in the absence of pathogen infection. These mutants are called autoimmune mutants and are typically dwarf and/or bearing chlorotic/necrotic lesions. From a genetic screen for Arabidopsis genes involved in maintaining a normal leaf microbiota, we identified TIP GROWTH DEFECTIVE 1 (TIP1), which encodes a S-acyltransferase, as a key player in guarding leaves against abnormal microbiota level and composition under high humidity conditions. The tip1 mutant has several characteristic phenotypes of classical autoimmune mutants, including a dwarf stature, displaying lesions, and having a high basal level of defense gene expression. Gnotobiotic experiments revealed that the autoimmune phenotypes of the tip1 mutant are largely dependent on the presence of microbiota as axenic tip1 plants have markedly reduced autoimmune phenotypes. We found that the microbiota dependency of autoimmune phenotypes is shared by several "lesion mimic"-type autoimmune mutants in Arabidopsis. Interestingly, autoimmune phenotypes caused by mutations in NLR genes do not require the presence of microbiota and can even be partially alleviated by microbiota. Our results therefore suggest the existence of two classes of autoimmunity (microbiota-dependent vs. microbiota-independent) in plants. The observed interplay between autoimmunity and microbiota in the lesion mimic class of autoimmunity is reminiscent of the interactions between autoimmunity and dysbiosis in the animal kingdom.

Laminarin-triggered defence responses are geographically dependent in natural populations of Solanum chilense

Natural plant populations are polymorphic and show intraspecific variation in resistance properties against pathogens. The activation of the underlying defence responses can depend on variation in perception of pathogen-associated molecular patterns or elicitors. To dissect such variation, we evaluated the responses induced by laminarin (a glucan, representing an elicitor from oomycetes) in the wild tomato species Solanum chilense and correlated this to observed infection frequencies of Phytophthora infestans. We measured reactive oxygen species burst and levels of diverse phytohormones upon elicitation in 83 plants originating from nine populations. We found high diversity in basal and elicitor-induced levels of each component. Further we generated linear models to explain the observed infection frequency of P. infestans. The effect of individual components differed dependent on the geographical origin of the plants. We found that the resistance in the southern coastal region, but not in the other regions, was directly correlated to ethylene responses and confirmed this positive correlation using ethylene inhibition assays. Our findings reveal high diversity in the strength of defence responses within a species and the involvement of different components with a quantitatively different contribution of individual components to resistance in geographically separated populations of a wild plant species.

Efficient CRISPR-Cas9 based cytosine base editors for phytopathogenic bacteria

Phytopathogenic bacteria play important roles in plant productivity, and developments in gene editing have potential for enhancing the genetic tools for the identification of critical genes in the pathogenesis process. CRISPR-based genome editing variants have been developed for a wide range of applications in eukaryotes and prokaryotes. However, the unique mechanisms of different hosts restrict the wide adaptation for specific applications. Here, CRISPR-dCas9 (dead Cas9) and nCas9 (Cas9 nickase) deaminase vectors were developed for a broad range of phytopathogenic bacteria. A gene for a dCas9 or nCas9, cytosine deaminase CDA1, and glycosylase inhibitor fusion protein (cytosine base editor, or CBE) was applied to base editing under the control of different promoters. Results showed that the RecA promoter led to nearly 100% modification of the target region. When residing on the broad host range plasmid pHM1, CBE_RecAp is efficient in creating base edits in strains of Xanthomonas, Pseudomonas, Erwinia and Agrobacterium. CBE based on nCas9 extended the editing window and produced a significantly higher editing rate in Pseudomonas. Strains with nonsynonymous mutations in test genes displayed expected phenotypes. By multiplexing guide RNA genes, the vectors can modify up to four genes in a single round of editing. Whole-genome sequencing of base-edited isolates of Xanthomonas oryzae pv. oryzae revealed guide RNA-independent off-target mutations. Further modifications of the CBE, using a CDA1 variant (CBE_RecAp-A) reduced off-target effects, providing an improved editing tool for a broad group of phytopathogenic bacteria.

Characterization of defense responses against bacterial pathogens in duckweeds lacking EDS1

ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) mediates the induction of defense responses against pathogens in most angiosperms. However, it has recently been shown that a few species have lost EDS1. It is unknown how defense against disease unfolds and evolves in the absence of EDS1. We utilize duckweeds; a collection of aquatic species that lack EDS1, to investigate this question. We established duckweed-Pseudomonas pathosystems and used growth curves and microscopy to characterize pathogen-induced responses. Through comparative genomics and transcriptomics, we show that the copy number of infection-associated genes and the infection-induced transcriptional responses of duckweeds differ from other model species. Pathogen defense in duckweeds has evolved along different trajectories than in other plants, including genomic and transcriptional reprogramming. Specifically, the miAMP1 domain-containing proteins, which are absent in Arabidopsis, showed pathogen responsive upregulation in duckweeds. Despite such divergence between Arabidopsis and duckweed species, we found conservation of upregulation of certain genes and the role of hormones in response to disease. Our work highlights the importance of expanding the pool of model species to study defense responses that have evolved in the plant kingdom independent of EDS1.

The Nucleotide Revolution: Immunity at the Intersection of Toll/Interleukin-1 Receptor Domains, Nucleotides, and Ca2

The discovery of the enzymatic activity of the toll/interleukin-1 receptor (TIR) domain protein SARM1 five years ago preceded a flood of discoveries regarding the nucleotide substrates and products of TIR domains in plants, animals, bacteria, and archaea. These discoveries into the activity of TIR domains coincide with major advances in understanding the structure and mechanisms of NOD-like receptors and the mutual dependence of pattern recognition receptor- and effector-triggered immunity (PTI and ETI, respectively) in plants. It is quickly becoming clear that TIR domains and TIR-produced nucleotides are ancestral signaling molecules that modulate immunity and that their activity is closely associated with Ca²⁺ signaling. TIR domain research now bridges the separate disciplines of molecular plant- and animal-microbe interactions, neurology, and prokaryotic immunity. A cohesive framework for understanding the role of enzymatic TIR domains in diverse organisms will help unite the research of these disparate fields. Here, we review known products of TIR domains in plants, animals, bacteria, and archaea and use context gained from animal and prokaryotic TIR domain systems to present a model for TIR domains, nucleotides, and Ca²⁺ at the intersection of PTI and ETI in plant immunity. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Overexpression of NDR1 leads to pathogen resistance at elevated temperatures

Abiotic and biotic environments influence a myriad of plant-related processes, including growth, development, and the establishment and maintenance of interaction(s) with microbes. In the case of the latter, elevated temperature has been shown to be a key factor that underpins host resistance and pathogen virulence. In this study, we elucidate a role for Arabidopsis NON-RACE-SPECIFIC DISEASE RESISTANCE1 (NDR1) by exploiting effector-triggered immunity to define the regulation of plant host immunity in response to both pathogen infection and elevated temperature. We generated time-series RNA sequencing data of WT Col-0, an NDR1 overexpression line, and ndr1 and ics1-2 mutant plants under elevated temperature. Not surprisingly, the NDR1-overexpression line showed genotype-specific gene expression changes related to defense response and immune system function. The results described herein support a role for NDR1 in maintaining cell signaling during simultaneous exposure to elevated temperature and avirulent pathogen stressors.

Metaeffector interactions modulate the type III effector-triggered immunity load of Pseudomonas syringae

The bacterial plant pathogen Pseudomonas syringae requires type III secreted effectors (T3SEs) for pathogenesis. However, a major facet of plant immunity entails the recognition of a subset of P. syringae’s T3SEs by intracellular host receptors in a process called Effector-Triggered Immunity (ETI). Prior work has shown that ETI-eliciting T3SEs are pervasive in the P. syringae species complex raising the question of how P. syringae mitigates its ETI load to become a successful pathogen. While pathogens can evade ETI by T3SE mutation, recombination, or loss, there is increasing evidence that effector-effector (a.k.a., metaeffector) interactions can suppress ETI. To study the ETI-suppression potential of P. syringae T3SE repertoires, we compared the ETI-elicitation profiles of two genetically divergent strains: P. syringae pv. tomato DC3000 (PtoDC3000) and P. syringae pv. maculicola ES4326 (PmaES4326), which are both virulent on Arabidopsis thaliana but harbour largely distinct effector repertoires. Of the 529 T3SE alleles screened on A. thaliana Col-0 from the P. syringae T3SE compendium (PsyTEC), 69 alleles from 21 T3SE families elicited ETI in at least one of the two strain backgrounds, while 50 elicited ETI in both backgrounds, resulting in 19 differential ETI responses including two novel ETI-eliciting families: AvrPto1 and HopT1. Although most of these differences were quantitative, three ETI responses were completely absent in one of the pathogenic backgrounds. We performed ETI suppression screens to test if metaeffector interactions contributed to these ETI differences, and found that HopQ1a suppressed AvrPto1m-mediated ETI, while HopG1c and HopF1g suppressed HopT1b-mediated ETI. Overall, these results show that P. syringae strains leverage metaeffector interactions and ETI suppression to overcome the ETI load associated with their native T3SE repertoires.

Shared in planta population and transcriptomic features of nonpathogenic members of endophytic phyllosphere microbiota

Plants evolved in an environment colonized by a vast number of microbes, which collectively constitute the plant microbiota. The majority of microbiota taxa are nonpathogenic and may be beneficial to plants under certain ecological or environmental conditions. We conducted experiments to understand the features of long-term interactions of nonpathogenic microbiota members with plants. We found that a multiplication–death equilibrium explained the shared long-term static populations of nonpathogenic bacteria and that in planta bacterial transcriptomic signatures were characteristic of the stationary phase, a physiological state in which stress protection responses are induced. These results may have significant implications in understanding the bulk of “nonpathogenic” plant–microbiota interactions that occur in agricultural and natural ecosystems.

Plants and animals are in constant association with a variety of microbes. Although much is known about how pathogenic and symbiotic microbes interact with plants, less is known about the population dynamics, adaptive traits, and transcriptional features of the vast number of microbes that make up the bulk of the plant microbiota. The majority of microbiota taxa are either commensal, natural mutants of pathogens, or pathogens that encounter strong immune responses due to plant recognition of pathogen effectors. How these “nonpathogenic” microbes interact with plants is poorly understood, especially during long-term, steady-state interactions, which are more reflective of plant–microbiota interactions in nature. In this study, we embarked upon long-term population and in planta transcriptomic studies of commensal endophytic bacteria and compared them to nonpathogenic or effector-triggered immunity-inducing strains of the bacterial pathogen Pseudomonas syringae. Our results led to the discovery of multiplication–death equilibrium as a common basis for the shared long-term static population densities of these bacteria. A comprehensive in planta transcriptomic analysis using multiple time points after inoculation revealed a striking similarity between the transcriptomic features of nonpathogenic P. syringae to that of bacteria in stationary phase in vitro, a metabolically active physiological state in which the production of adaptive secondary metabolites and stress responses are induced. We propose that the long-term population and transcriptomic features of nonpathogenic bacteria captured in this study likely reflect the physiological steady state encountered by the bulk of endophytic microbiota—excluding virulent pathogens—in their life-long interactions with plants in nature.

Commensal Pseudomonas strains facilitate protective response against pathogens in the host plant

The community structure in the plant-associated microbiome depends collectively on host–microbe, microbe–microbe and host–microbe–microbe interactions. The ensemble of interactions between the host and microbial consortia may lead to outcomes that are not easily predicted from pairwise interactions. Plant–microbe–microbe interactions are important to plant health but could depend on both host and microbe strain variation. Here we study interactions between groups of naturally co-existing commensal and pathogenic Pseudomonas strains in the Arabidopsis thaliana phyllosphere. We find that commensal Pseudomonas prompt a host response that leads to selective inhibition of a specific pathogenic lineage, resulting in plant protection. The extent of protection depends on plant genotype, supporting that these effects are host-mediated. Strain-specific effects are also demonstrated by one individual Pseudomonas isolate eluding the plant protection provided by commensals. Our work highlights how within-species genetic differences in both hosts and microbes can affect host–microbe–microbe dynamics.

The authors conduct competition experiments with multiple strains of Pseudomonas (some pathogenic and some commensal) in the phylosphere microbiome of Arabidopsis plants, showing that both the host and the commensal strains interact to inhibit the pathogenic strains.

A phytobacterial TIR domain effector manipulates NAD+ to promote virulence

The Pseudomonas syringae DC3000 type III effector HopAM1 suppresses plant immunity and contains a Toll/interleukin-1 receptor (TIR) domain homologous to immunity-related TIR domains of plant nucleotide-binding leucine-rich repeat receptors that hydrolyze nicotinamide adenine dinucleotide (NAD⁺ ) and activate immunity. In vitro and in vivo assays were conducted to determine if HopAM1 hydrolyzes NAD⁺ and if the activity is essential for HopAM1's suppression of plant immunity and contribution to virulence. HPLC and LC-MS were utilized to analyze metabolites produced from NAD⁺ by HopAM1 in vitro and in both yeast and plants. Agrobacterium-mediated transient expression and in planta inoculation assays were performed to determine HopAM1's intrinsic enzymatic activity and virulence contribution. HopAM1 is catalytically active and hydrolyzes NAD⁺ to produce nicotinamide and a novel cADPR variant (v2-cADPR). Expression of HopAM1 triggers cell death in yeast and plants dependent on the putative catalytic residue glutamic acid 191 (E191) within the TIR domain. Furthermore, HopAM1's E191 residue is required to suppress both pattern-triggered immunity and effector-triggered immunity and promote P. syringae virulence. HopAM1 manipulates endogenous NAD⁺ to produce v2-cADPR and promote pathogenesis. This work suggests that HopAM1's TIR domain possesses different catalytic specificity than other TIR domain-containing NAD⁺ hydrolases and that pathogens exploit this activity to sabotage NAD⁺ metabolism for immune suppression and virulence.

Fungi-Bacteria Associations in Wilt Diseased Rhizosphere and Endosphere by Interdomain Ecological Network Analysis

In the plant rhizosphere and endosphere, some fungal and bacterial species regularly co-exist, however, our knowledge about their co-existence patterns is quite limited, especially during invasion by bacterial wilt pathogens. In this study, the fungal communities from soil to endophytic compartments were surveyed during an outbreak of tobacco wilt disease caused by Ralstonia solanacearum. It was found that the stem endophytic fungal community was significantly altered by pathogen invasion in terms of community diversity, structure, and composition. The associations among fungal species in the rhizosphere and endosphere infected by R. solanacearum showed more complex network structures than those of healthy plants. By integrating the bacterial dataset, associations between fungi and bacteria were inferred by Inter-Domain Ecological Network (IDEN) approach. It also revealed that infected samples, including both the rhizosphere and endosphere, had more complex interdomain networks than the corresponding healthy samples. Additionally, the bacterial wilt pathogenic Ralstonia members were identified as the keystone genus within the IDENs of both root and stem endophytic compartments. Ralstonia members was negatively correlated with the fungal genera Phoma, Gibberella, and Alternaria in infected roots, as well as Phoma, Gibberella, and Diaporthe in infected stems. This suggested that those endophytic fungi may play an important role in resisting the invasion of R. solanacearum.

Polymorphisms in plants to restrict losses to pathogens: From gene family expansions to complex network evolution

Genetic polymorphisms are the basis of the natural diversity seen in all life on earth, also in plant-pathogen interactions. Initially, studies on plant-pathogen interaction focused on reporting phenotypic variation in resistance properties and on the identification of underlying major genes. Nowadays, the field of plant-pathogen interactions is moving from focusing on families of single dominant genes involved in gene-for-gene interactions to an understanding of the plant immune system in the context of a much more complex signaling network and quantitative resistance. Simultaneously, studies on pathosystems from the wild and genome analyses advanced, revealing tremendous variation in natural plant populations. It is now imperative to place studies on genetic diversity and evolution of plant-pathogen interactions in the appropriate molecular biological, as well as evolutionary, context.

Effects of Root-Colonizing Fluorescent Pseudomonas Strains on Arabidopsis Resistance to a Pathogen and an Herbivore

Rhizobacteria in the genus Pseudomonas can enhance plant resistance to a range of pathogens and herbivores. However, resistance to these different classes of plant antagonists is mediated by different molecular mechanisms, and the extent to which induced systemic resistance by Pseudomonas can simultaneously protect plants against both pathogens and herbivores remains unclear. We screened 12 root-colonizing Pseudomonas strains to assess their ability to induce resistance in Arabidopsis thaliana against a foliar pathogen (Pseudomonas syringae DC3000) and a chewing herbivore (Spodoptera littoralis). None of our 12 strains increased plant resistance against herbivory; however, four strains enhanced pathogen resistance, and one of these (Pseudomonas strain P97-38) also made plants more susceptible to herbivory. Phytohormone analyses revealed stronger salicylic acid induction in plants colonized by P97-38 (versus controls) following subsequent pathogen infection but weaker induction of jasmonic acid (JA)-mediated defenses following herbivory. We found no effects of P97-38 inoculation on herbivore-relevant nutrients such as sugars and protein, suggesting that the observed enhancement of susceptibility to S. littoralis is due to effects on plant defense chemistry rather than nutrition. These findings suggest that Pseudomonas strains that enhance plant resistance to pathogens may have neutral or negative effects on resistance to herbivores and provide insight into potential mechanisms associated with effects on different classes of plant antagonists. Improved understanding of these effects has potentially important implications for the use of rhizobacteria inoculation in agriculture. IMPORTANCE Plant-associated microbes have significant potential to enhance agricultural production, for example, by enhancing plant resistance to pathogens and pests. Efforts to identify beneficial microbial strains typically focus on a narrow range of desirable plant traits; however, microbial symbionts can have complex effects on plant phenotypes, including susceptibility and resistance to different classes of plant antagonists. We examined the effects of 12 strains of Pseudomonas rhizobacteria on plant (Arabidopsis) resistance to a lepidopteran herbivore and a foliar pathogen. None of our strains increased plant resistance against herbivory; however, four strains enhanced pathogen resistance, and one of these made plants more susceptible to herbivory (likely via effects on plant defense chemistry). These findings indicate that microbial strains that enhance plant resistance to pathogens can have neutral or negative effects on resistance to herbivores, highlighting potential pitfalls in the application of beneficial rhizobacteria as biocontrol agents.

Quantitative resistance differences between and within natural populations of Solanum chilense against the oomycete pathogen Phytophthora infestans

The wild tomato species Solanum chilense is divided into geographically and genetically distinct populations that show signs of defense gene selection and differential phenotypes when challenged with several phytopathogens, including the oomycete causal agent of late blight Phytophthora infestans. To better understand the phenotypic diversity of this disease resistance in S. chilense and to assess the effect of plant genotype versus pathogen isolate, respectively, we evaluated infection frequency in a systematic approach and with large sample sizes. We studied 85 genetically distinct individuals representing nine geographically separated populations of S. chilense. This showed that differences in quantitative resistance can be observed between but also within populations at the level of individual plants. Our data also did not reveal complete immunity in any of the genotypes. We further evaluated the resistance of a subset of the plants against P. infestans isolates with diverse virulence properties. This confirmed that the relative differences in resistance phenotypes between individuals were mainly determined by the plant genotype under consideration with modest effects of pathogen isolate used in the study. Thus, our report suggests that the observed quantitative resistance against P. infestans in natural populations of a wild tomato species S. chilense is the result of basal defense responses that depend on the host genotype and are pathogen isolate-unspecific.

Natural variation in temperature-modulated immunity uncovers transcription factor bHLH059 as a thermoresponsive regulator in Arabidopsis thaliana

Temperature impacts plant immunity and growth but how temperature intersects with endogenous pathways to shape natural variation remains unclear. Here we uncover variation between Arabidopsis thaliana natural accessions in response to two non-stress temperatures (22°C and 16°C) affecting accumulation of the thermoresponsive stress hormone salicylic acid (SA) and plant growth. Analysis of differentially responding A. thaliana accessions shows that pre-existing SA provides a benefit in limiting infection by Pseudomonas syringae pathovar tomato DC3000 bacteria at both temperatures. Several A. thaliana genotypes display a capacity to mitigate negative effects of high SA on growth, indicating within-species plasticity in SA—growth tradeoffs. An association study of temperature x SA variation, followed by physiological and immunity phenotyping of mutant and over-expression lines, identifies the transcription factor bHLH059 as a temperature-responsive SA immunity regulator. Here we reveal previously untapped diversity in plant responses to temperature and a way forward in understanding the genetic architecture of plant adaptation to changing environments.

Temperature has a profound effect on plant innate immune responses but little is known about the mechanisms underlying natural variation in transmission of temperature signals to defence pathways. Much of our understanding of temperature effects on plant immunity and tradeoffs between activated defences and growth has come from analysis of the common Arabidopsis thaliana genetic accession, Col-0. Here we examine A. thaliana genetic variation in response to temperature (within the non-stress range—22 ^oC and 16 ^oC) at the level of accumulation of the thermoresponsive biotic stress hormone salicylic acid (SA), bacterial pathogen resistance, and plant biomass. From analysis of 105 genetically diverse A. thaliana accessions we uncover plasticity in temperature-modulated SA homeostasis and in the relationship between SA levels and plant growth. We find that high SA amounts prior to infection provide a robust benefit of enhancing bacterial resistance. In some accessions this benefit comes without compromised plant growth, suggestive of altered defence–growth tradeoffs. Based on a temperature x SA association study we identify the transcription factor gene, bHLH059, and show that it has features of a temperature-sensitive immunity regulator that are unrelated to PIF4, a known thermosensitive coordinator of immunity and growth.

Oligogalacturonides induce resistance in Arabidopsis thaliana by triggering salicylic acid and jasmonic acid pathways against Pst DC3000

Oligogalacturonides (OGAs) are a biologically active carbohydrate derived from homogalacturonan, a major element of cell wall pectin. OGAs induced resistance and mechanism were assessed in Arabidopsis thaliana-Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) interaction. The effective resistance was mainly observed at 25 mg/L OGAs with reduced disease index, bacterial multiplication, higher transcript level of salicylic acid (SA) pathway related genes (PR1, PR2, PR5) and jasmonic acid (JA) pathway related genes (PDF1.2, VSP2) as well as SA, JA content and production of reactive oxygen species (ROS), nitric oxide (NO). In SA (NahG, sid2) and JA (jar1) deficient mutants, disease severity indicated that both SA and JA pathways are necessary for Arabidopsis response to Pst DC3000. OGAs triggered less resistance to Pst DC3000 in JA-deficient mutant, and SA-deficient mutants signifying that SA and JA play redundant roles in OGAs induced resistance. Therefore, these evidences further reveal the signaling pathways of OGAs resistance, which is conducive to its application in agriculture to protect plants from diseases.

The Arabidopsis exocyst subunits EXO70B1 and EXO70B2 regulate FLS2 homeostasis at the plasma membrane

The plasma membrane (PM)-localized receptor kinase FLAGELLIN SENSING 2 (FLS2) recognizes bacterial flagellin or its immunogenic epitope flg22, and initiates microbe-associated molecular pattern-triggered immunity, which inhibits infection by bacterial pathogens. The localization, abundance and activity of FLS2 are under dynamic control. Here, we demonstrate that Arabidopsis thaliana EXO70B1, a subunit of the exocyst complex, plays a critical role in FLS2 signaling that is independent of the truncated Toll/interleukin-1 receptor-nucleotide binding sequence protein TIR-NBS2 (TN2). In the exo70B1-3 mutant, the abundance of FLS2 protein at the PM is diminished, consistent with the impaired flg22 response of this mutant. EXO70B1-GFP plants showed increased FLS2 accumulation at the PM and therefore enhanced FLS2 signaling. The EXO70B1-mediated trafficking of FLS2 to the PM is partially independent of the PENETRATION 1 (PEN1)-containing secretory pathway. In addition, EXO70B1 interacts with EXO70B2, a close homolog of EXO70B1, and both proteins associate with FLS2 and contribute to the accumulation of FLS2 at the PM. Taken together, our data suggest that the exocyst complex subunits EXO70B1 and EXO70B2 regulate the trafficking of FLS2 to the PM, which represents a new layer of regulation of FLS2 function in plant immunity.

Network analysis infers the wilt pathogen invasion associated with non-detrimental bacteria

The microbiota colonizing the root endophytic compartment and surrounding rhizosphere soils contribute to plant growth and health. However, the key members of plant soil and endophytic microbial communities involved in inhibiting or assisting pathogen invasion remain elusive. By utilizing 16S high-throughput sequencing and a molecular ecological network (MEN) approach, we systematically studied the interactions within bacterial communities in plant endophytic compartments (stem and root) and the surrounding soil (bulk and rhizosphere) during bacterial wilt invasion. The endophytic communities were found to be strongly influenced by pathogen invasion according to analysis of microbial diversity and community structure and composition. Endophytic communities of the infected plants were primarily derived from soil communities, as assessed by the SourceTracker program, but with rare migration from soil communities to endophytic communities observed in healthy plants. Soil and endophytic microbiomes from infected plants showed modular topology and greater complexity in network analysis, and a higher number of interactions than those in healthy plants. Furthermore, interactions among microbial members revealed that pathogenic Ralstonia members were positively correlated with several bacterial genera, including Delftia, Stenotrophomonas, Bacillus, Clostridium XlVa, Fontibacillus, Acidovorax, Herminiimonas, and three unclassified bacterial genera, in infected plant roots. Our findings indicated that the pathogen invasion in the rhizosphere and endophytic compartments may be highly associated with bacteria that are normally not detrimental, and sometimes even beneficial, to plants.

Plant-Pathogen Warfare under Changing Climate Conditions

Global environmental changes caused by natural and human activities have accelerated in the past 200 years. The increase in greenhouse gases is predicted to continue to raise global temperature and change water availability in the 21^st century. In this Review, we explore the profound effect the environment has on plant diseases - a susceptible host will not be infected by a virulent pathogen if the environmental conditions are not conducive for disease. The change in CO₂ concentrations, temperature, and water availability can have positive, neutral, or negative effects on disease development, as each disease may respond differently to these variations. However, the concept of disease optima could potentially apply to all pathosystems. Plant resistance pathways, including pattern-triggered immunity to effector-triggered immunity, RNA interference, and defense hormone networks, are all affected by environmental factors. On the pathogen side, virulence mechanisms, such as the production of toxins and virulence proteins, as well as pathogen reproduction and survival are influenced by temperature and humidity. For practical reasons, most laboratory investigations into plant-pathogen interactions at the molecular level focus on well-established pathosystems and use a few static environmental conditions that capture only a fraction of the dynamic plant-pathogen-environment interactions that occur in nature. There is great need for future research to increasingly use dynamic environmental conditions in order to fully understand the multidimensional nature of plant-pathogen interactions and produce disease-resistant crop plants that are resilient to climate change.

Natural variation for unusual host responses and flagellin-mediated immunity against Pseudomonas syringae in genetically diverse tomato accessions

The interaction between tomato and Pseudomonas syringae pv tomato (Pst) is a well-developed model for investigating the molecular basis of the plant immune system. There is extensive natural variation in Solanum lycopersicum (tomato) but it has not been fully leveraged to enhance our understanding of the tomato-Pst pathosystem. We screened 216 genetically diverse accessions of cultivated tomato and a wild tomato species for natural variation in their response to three strains of Pst. The host response to Pst was investigated using multiple Pst strains, tomato accessions with available genome sequences, reactive oxygen species (ROS) assays, reporter genes and bacterial population measurements. The screen uncovered a broad range of previously unseen host symptoms in response to Pst, and one of these, stem galls, was found to be simply inherited. The screen also identified tomato accessions that showed enhanced responses to flagellin in bacterial population assays and in ROS assays upon exposure to flagellin-derived peptides, flg22 and flgII-28. Reporter genes confirmed that the host responses were due primarily to pattern recognition receptor-triggered immunity. This study revealed extensive natural variation in tomato for susceptibility and resistance to Pst and will enable elucidation of the molecular mechanisms underlying these host responses.

The Pseudomonas Syringae Effector AvrPtoB Associates With and Ubiquitinates Arabidopsis Exocyst Subunit EXO70B1

Many bacterial pathogens secret effectors into host cells to disable host defenses and thus promote infection. The exocyst complex functions in the transport and secretion of defense molecules, and loss of function of the EXO70B1 subunit leads to autoimmunity by activation of a truncated Toll/interleukin-1 receptor-nucleotide-binding sequence protein (TIR-NBS2; herein referred to as TN2). Here, we show that EXO70B1 is required for pathogen-associated molecular pattern-triggered immune responses in Arabidopsis thaliana. The effector AvrPtoB, an E3 ligase from Pseudomonas syringae pv. tomato (Pto) strain DC3000, associates with EXO70B1. AvrPtoB ubiquitinates EXO70B1 and mediates EXO70B1 degradation via the host's 26S proteasome in a manner requiring E3 ligase activity. AvrPtoB enhances Pto DC3000 virulence by overcoming EXO70B1-mediated resistance. Moreover, overexpression of AvrPtoB in Arabidopsis leads to autoimmunity, which is partially dependent on TN2. Expression of TN2 in tobacco (Nicotiana tabacum and Nicotiana benthamiana) triggers strong and rapid cell death, which is suppressed by co-expression with EXO70B1 but reoccurs when co-expressed with AvrPtoB. Taken together, our data highlight that AvrPtoB targets the Arabidopsis thaliana EXO70 protein family member EXO70B1 to manipulate the defense molecule secretion machinery or immunity.

Chitosan Oligosaccharide Induces Resistance to Pseudomonas syringae pv. tomato DC3000 in Arabidopsis thaliana by Activating Both Salicylic Acid- and Jasmonic Acid-Mediated Pathways

Chitosan oligosaccharide (COS) is an effective plant immunity elicitor; however, its induction mechanism in plants is complex and needs further investigation. In this study, the Arabidopsis-Pseudomonas syringae pv. tomato DC3000 (hereafter called DC3000) interaction was used to investigate the induction effect and the underlying mechanisms of COS. COS is effective in inducing resistance to DC3000 in Arabidopsis, and our results demonstrate that treatment with COS 3 days before DC3000 inoculation provided the most effective resistance. Disease severity in jar1 (jasmonic acid [JA]-deficient mutant), NahG, and sid2 (salicylic acid [SA]-deficient mutants) suggest both the SA and JA pathways are required for the Arabidopsis response to DC3000. COS pretreatment induced resistance in wild type (WT), jar1, and also, although to a lesser degree, in NahG and sid2 plants, implying that the SA and JA pathways play redundant roles in COS-induced resistance to DC3000. In COS-pretreated plants, expression of genes related to the SA pathway (PR1, PR2, and PR5) and SA content increased in both WT and jar1. Moreover, expression of genes related to the JA pathway (PDF1.2 and VSP2) and JA content both increased in WT and NahG. In conclusion, COS induces resistance to DC3000 in Arabidopsis by activating both SA- and JA-mediated pathways, although SA and JA pathways play redundant roles in this COS-induced resistance.

Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales

Crop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild pathosystems, we carried out a multi-year, multi-site survey of Pseudomonas in its natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a ubiquitous pathogenic clade. Sequencing of 1,524 genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically identifiable pathogenic sublineages. There is differentiation at the level of both gene content and disease phenotype, although the differentiation may not provide fitness advantages to specific sublineages. The coexistence of sublineages indicates that in contrast to crop systems, no single strain has been able to overtake the studied A. thaliana populations in the recent past. Our results suggest that selective pressures acting on a plant pathogen in wild hosts are likely to be much more complex than those in agricultural systems.

Defining essential processes in plant pathogenesis with Pseudomonas syringae pv. tomato DC3000 disarmed polymutants and a subset of key type III effectors

Pseudomonas syringae pv. tomato DC3000 and its derivatives cause disease in tomato, Arabidopsis and Nicotiana benthamiana. The primary virulence factors include a repertoire of 29 effector proteins injected into plant cells by the type III secretion system and the phytotoxin coronatine. The complete repertoire of effector genes and key coronatine biosynthesis genes have been progressively deleted and minimally reassembled to reconstitute basic pathogenic ability in N. benthamiana, and in Arabidopsis plants that have mutations in target genes that mimic effector actions. This approach and molecular studies of effector activities and plant immune system targets have highlighted a small subset of effectors that contribute to essential processes in pathogenesis. Most notably, HopM1 and AvrE1 redundantly promote an aqueous apoplastic environment, and AvrPtoB and AvrPto redundantly block early immune responses, two conditions that are sufficient for substantial bacterial growth in planta. In addition, disarmed DC3000 polymutants have been used to identify the individual effectors responsible for specific activities of the complete repertoire and to more effectively study effector domains, effector interplay and effector actions on host targets. Such work has revealed that AvrPtoB suppresses cell death elicitation in N. benthamiana that is triggered by another effector in the DC3000 repertoire, highlighting an important aspect of effector interplay in native repertoires. Disarmed DC3000 polymutants support the natural delivery of test effectors and infection readouts that more accurately reveal effector functions in key pathogenesis processes, and enable the identification of effectors with similar activities from a broad range of other pathogens that also defeat plants with cytoplasmic effectors.

Constant vigilance: plant functions guarded by resistance proteins

Unlike animals, plants do not have an adaptive immune system and have instead evolved sophisticated and multi-layered innate immune mechanisms. To overcome plant immunity, pathogens secrete a diverse array of effectors into the apoplast and virtually all cellular compartments to dampen immune signaling and interfere with plant functions. Here we describe the scope of the arms race throughout the cell and summarize various strategies used by both plants and pathogens. Through studying the ongoing evolutionary battle between plants and key pathogens, we may yet uncover potential ways to achieve the ultimate goal of engineering broad-spectrum resistant crops without affecting food quality or productivity.