The Pattern Recognition Receptor FLS2 Can Shape the Arabidopsis Rhizosphere Microbiome ß-Diversity but Not EFR1 and CERK1.

Pathogen associated molecular pattern (PAMP) triggered immunity (PTI) is the first line of plant defense. We hypothesized that the absence of pattern recognition receptors (PRRs) in plants could influence the rhizosphere microbiome. Here, we report sequencing of the 16S ribosomal RNA gene and the fungal ribosomal RNA internal transcribed spacer region of rhizosphere DNA from three Arabidopsis PRR mutants involved in plant innate immunity (efr1, fls2, and cerk1). We conducted experiments in a growth chamber using native soil from the Red River Farm (Terral, OK, USA) to detect microbial community shifts in the rhizosphere that may occur in the absence of PRR receptors compared to wild-type (WT; Col-0) plants. No difference in the α-diversity of the rhizosphere microbial population was observed between the PRR mutants tested and the WT. Plant host genotype had a significant impact in bacterial ß-diversity only between the fls2 mutant and the WT. Surprisingly, no significant changes in fungal ß-diversity were observed between the PRR mutants and WT, although we observed an increase in relative abundance for the cup fungi (Pezizaceae) in the cerk1 mutant. This finding suggests that the FLS2 receptor can modulate the rhizosphere-associated microbiome ß-diversity and expands the list of current known genotypes that can modulate the rhizosphere microbiota.

Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture.

Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.

Toward a Resilient, Functional Microbiome: Drought Tolerance-Alleviating Microbes for Sustainable Agriculture.

In recent years, the utilization of novel sequencing techniques opened a new field of research into plant microbiota and was used to explore a wide diversity of microorganisms both inside and outside of plant host tissues, i.e., the endosphere and rhizosphere, respectively. An early realization from such research was that species richness and diversity of the plant microbiome are both greater than believed even a few years ago, and soil is likely home to the most abundant and diverse microbial habitats known. In most ecosystems sampled thus far, overall microbial complexity is determined by the combined influences of plant genotype, soil structure and chemistry, and prevailing environmental conditions, as well as the native "bulk soil" microbial populations from which membership is drawn. Beneficial microorganisms, traditionally referring primarily to nitrogen-fixing bacteria, plant growth-promoting rhizobacteria, and mycorrhizal fungi, play a key role in major functions such as plant nutrition acquisition and plant resistance to biotic and abiotic stresses . Utilization of plant-associated microbes in food production is likely to be critical for twenty-first century agriculture, where arable cropland is limited and food, fiber, and feed productivity must be sustained or even improved with fewer chemical inputs and less irrigation.

Rhizosphere Sampling Protocols for Microbiome (16S/18S/ITS rRNA) Library Preparation and Enrichment for the Isolation of Drought Tolerance-Promoting Microbes.

Natural plant microbiomes are abundant and have a remarkably robust composition, both as epiphytes on the plant surface and as endophytes within plant tissues. Microbes in the former "habitat" face limited nutrients and harsh environmental conditions, while those in the latter likely lead a more sheltered existence. The most populous and diverse of these microbiomes are associated with the zone around the plant roots, commonly referred to as the rhizosphere. A majority of recent studies characterize these plant-associated microbiomes by community profiling of bacteria and fungi, using amplicon-based marker genes and next-generation sequencing (NGS). Here, we collate a group of protocols that incorporate current best practices and optimized methodologies for sampling, handling of samples, and rRNA library preparation for variable regions of V5-V6 and V9 of the bacterial 16S ribosomal RNA (rRNA) gene, and the ITS2 region joining the 5.8S and 28S regions of the fungal rRNA gene. Samples collected for such culture-independent analyses can also be used for the actual isolation of microbes of interest, perhaps even those identified by the libraries described above. One group of microbes that holds promise for mediating plant stress incurred by drought are bacteria that are capable of reducing or eliminating the plant's perception of the stress through degradation of the gaseous plant hormone ethylene, which is abundantly produced in response to drought stimuli. This is accomplished by some types of soil bacteria that can produce the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which is the immediate precursor to ethylene. Here we provide a high-throughput protocol for screening of ACC deaminase-producing bacteria for the applied purpose of mitigating the impact of plant drought stress.

Interplant Aboveground Signaling Prompts Upregulation of Auxin Promoter and Malate Transporter as Part of Defensive Response in the Neighboring Plants.

When disrupted by stimuli such as herbivory, pathogenic infection, or mechanical wounding, plants secrete signals such as root exudates and volatile organic compounds (VOCs). The emission of VOCs induces a response in the neighboring plant communities and can improve plant fitness by alerting nearby plants of an impending threat and prompting them to alter their physiology for defensive purposes. In this study, we investigated the role of plant-derived signals, released as a result of mechanical wounding, that may play a role in intraspecific communication between Arabidopsis thaliana communities. Plant-derived signals released by the wounded plant resulted in more elaborate root development in the neighboring, unwounded plants. Such plant-derived signals also upregulated the Aluminum-activated malate transporter (ALMT1) responsible for the secretion of malic acid (MA) and the DR5 promoter, an auxin responsive promoter concentrated in root apex of the neighboring plants. We speculate that plant-derived signal-induced upregulation of root-specific ALMT1 in the undamaged neighboring plants sharing the environment with stressed plants may associate more with the benign microbes belowground. We also observed increased association of beneficial bacterium Bacillus subtilis UD1022 on roots of the neighboring plants sharing environment with the damaged plants. Wounding-induced plant-derived signals therefore induce defense mechanisms in the undamaged, local plants, eliciting a two-pronged preemptive response of more rapid root growth and up-regulation of ALMT1, resulting in increased association with beneficial microbiome.

Impact of Seed Exudates on Growth and Biofilm Formation of Bacillus amyloliquefaciens ALB629 in Common Bean.

We aimed to unravel the events which favor the seed-rhizobacterium Bacillus amyloliquefaciens strain ALB629 (hereafter ALB629) interaction and which may interfere with the rhizobacterium colonization and growth on the spermosphere of common bean. Seed exudates from common bean were tested in vitro for ALB629 biofilm formation and bacterial growth. Furthermore, the performance of ALB629 on plant-related variables under drought stress was checked. Seed exudates (1 and 5% v/v) increased ALB629 biofilm formation. Additionally, the colony forming units for ALB629 increased both in culture and on the bean seed surface. The bean seed exudates up-regulated biofilm operons in ALB629 TasA and EpsD by ca. two and sixfold, respectively. The high-performance liquid chromatography (HPLC)-coupled with MS showed that malic acid is present as a major organic acid component in the seed exudates. Seeds treated with ALB629 and amended with malic acid resulted in seedlings with a higher bacterial concentration, induced plant drought tolerance, and promoted plant growth. We showed that seed exudates promote growth of ALB629 and malic acid was identified as a major organic acid component in the bean seed exudates. Our results also show that supplementation of ALB629 induced drought tolerance and growth in plants. The research pertaining to the biological significance of seed exudates in plant-microbe interaction is unexplored field and our work shows the importance of seed exudates in priming both growth and tolerance against abiotic stress.

Bacillus subtilis Early Colonization of Arabidopsis thaliana Roots Involves Multiple Chemotaxis Receptors.

Colonization of plant roots by Bacillus subtilis is mutually beneficial to plants and bacteria. Plants can secrete up to 30% of their fixed carbon via root exudates, thereby feeding the bacteria, and in return the associated B. subtilis bacteria provide the plant with many growth-promoting traits. Formation of a biofilm on the root by matrix-producing B. subtilis is a well-established requirement for long-term colonization. However, we observed that cells start forming a biofilm only several hours after motile cells first settle on the plant. We also found that intact chemotaxis machinery is required for early root colonization by B. subtilis and for plant protection. Arabidopsis thaliana root exudates attract B. subtilis in vitro, an activity mediated by the two characterized chemoreceptors, McpB and McpC, as well as by the orphan receptor TlpC. Nonetheless, bacteria lacking these chemoreceptors are still able to colonize the root, suggesting that other chemoreceptors might also play a role in this process. These observations suggest that A. thaliana actively recruits B. subtilis through root-secreted molecules, and our results stress the important roles of B. subtilis chemoreceptors for efficient colonization of plants in natural environments. These results demonstrate a remarkable strategy adapted by beneficial rhizobacteria to utilize carbon-rich root exudates, which may facilitate rhizobacterial colonization and a mutualistic association with the host. IMPORTANCE: Bacillus subtilis is a plant growth-promoting rhizobacterium that establishes robust interactions with roots. Many studies have now demonstrated that biofilm formation is required for long-term colonization. However, we observed that motile B. subtilis mediates the first contact with the roots. These cells differentiate into biofilm-producing cells only several hours after the bacteria first contact the root. Our study reveals that intact chemotaxis machinery is required for the bacteria to reach the root. Many, if not all, of the B. subtilis 10 chemoreceptors are involved in the interaction with the plant. These observations stress the importance of root-bacterium interactions in the B. subtilis lifestyle.

Killing Two Birds with One Stone: Natural Rice Rhizospheric Microbes Reduce Arsenic Uptake and Blast Infections in Rice.

Our recent work has shown that a rice thizospheric natural isolate, a Pantoea sp (hereafter EA106) attenuates Arsenic (As) uptake in rice. In parallel, yet another natural rice rhizospheric isolate, a Pseudomonas chlororaphis (hereafter EA105), was shown to inhibit rice blast pathogen Magnaporthe oryzae. Considering the above, we envisaged to evaluate the importance of mixed stress regime in rice plants subjected to both As toxicity and blast infections. Plants subjected to As regime showed increased susceptibility to blast infections compared to As-untreated plants. Rice blast pathogen M. oryzae showed significant resistance against As toxicity compared to other non-host fungal pathogens. Interestingly, plants treated with EA106 showed reduced susceptibility against blast infections in plants pre-treated with As. This data also corresponded with lower As uptake in plants primed with EA106. In addition, we also evaluated the expression of defense related genes in host plants subjected to As treatment. The data showed that plants primed with EA106 upregulated defense-related genes with or without As treatment. The data shows the first evidence of how rice plants cope with mixed stress regimes. Our work highlights the importance of natural association of plant microbiome which determines the efficacy of benign microbes to promote the development of beneficial traits in plants.

A perspective on inter-kingdom signaling in plant-beneficial microbe interactions.

Recent work has shown that the rhizospheric and phyllospheric microbiomes of plants are composed of highly diverse microbial species. Though the information pertaining to the diversity of the aboveground and belowground microbes associated with plants is known, an understanding of the mechanisms by which these diverse microbes function is still in its infancy. Plants are sessile organisms, that depend upon chemical signals to interact with the microbiota. Of late, the studies related to the impact of microbes on plants have gained much traction in the research literature, supporting diverse functional roles of microbes on plant health. However, how these microbes interact as a community to confer beneficial traits to plants is still poorly understood. Recent advances in the use of "biologicals" as bio-fertilizers and biocontrol agents for sustainable agricultural practices is promising, and a fundamental understanding of how microbes in community work on plants could help this approach be more successful. This review attempts to highlight the importance of different signaling events that mediate a beneficial plant microbe interaction. Fundamental research is needed to understand how plants react to different benign microbes and how these microbes are interacting with each other. This review highlights the importance of chemical signaling, and biochemical and genetic events which determine the efficacy of benign microbes to promote the development of beneficial traits in plants.

Crucial Roles of Abscisic Acid Biogenesis in Virulence of Rice Blast Fungus Magnaporthe oryzae.

Rice suffers dramatic yield losses due to blast pathogen Magnaporthe oryzae. Pseudomonas chlororaphis EA105, a bacterium that was isolated from the rice rhizosphere, inhibits M. oryzae. It was shown previously that pre-treatment of rice with EA105 reduced the size of blast lesions through jasmonic acid (JA)- and ethylene (ETH)-mediated ISR. Abscisic acid (ABA) acts antagonistically toward salicylic acid (SA), JA, and ETH signaling, to impede plant defense responses. EA105 may be reducing the virulence of M. oryzae by preventing the pathogen from up-regulating the key ABA biosynthetic gene NCED3 in rice roots, as well as a ß-glucosidase likely involved in activating conjugated inactive forms of ABA. However, changes in total ABA concentrations were not apparent, provoking the question of whether ABA concentration is an indicator of ABA signaling and response. In the rice-M. oryzae interaction, ABA plays a dual role in disease severity by increasing plant susceptibility and accelerating pathogenesis in the fungus itself. ABA is biosynthesized by M. oryzae. Further, exogenous ABA increased spore germination and appressoria formation, distinct from other plant growth regulators. EA105, which inhibits appressoria formation, counteracted the virulence-promoting effects of ABA on M. oryzae. The role of endogenous fungal ABA in blast disease was confirmed through the inability of a knockout mutant impaired in ABA biosynthesis to form lesions on rice. Therefore, it appears that EA105 is invoking multiple strategies in its protection of rice from blast including direct mechanisms as well as those mediated through plant signaling. ABA is a molecule that is likely implicated in both tactics.

A natural rice rhizospheric bacterium abates arsenic accumulation in rice (Oryza sativa L.).

MAIN CONCLUSION: A natural rice rhizospheric isolate abates arsenic uptake in rice by increasing Fe plaque formation on rice roots. Rice (Oryza sativa L.) is the staple food for over half of the world's population, but its quality and yield are impacted by arsenic (As) in some regions of the world. Bacterial inoculants may be able to mitigate the negative impacts of arsenic assimilation in rice, and we identified a nonpathogenic, naturally occurring rice rhizospheric bacterium that decreases As accumulation in rice shoots in laboratory experiments. We isolated several proteobacterial strains from a rice rhizosphere that promote rice growth and enhance the oxidizing environment surrounding rice root. One Pantoea sp. strain (EA106) also demonstrated increased iron (Fe)-siderophore in culture. We evaluated EA106's ability to impact rice growth in the presence of arsenic, by inoculation of plants with EA106 (or control), subsequently grew the plants in As-supplemented medium, and quantified the resulting plant biomass, Fe and As concentrations, localization of Fe and As, and Fe plaque formation in EA106-treated and control plants. These results show that both arsenic and iron concentrations in rice can be altered by inoculation with the soil microbe EA106. The enhanced accumulation of Fe in the roots and in root plaques suggests that EA106 inoculation improves Fe uptake by the root and promotes the formation of a more oxidative environment in the rhizosphere, thereby allowing more expansive plaque formation. Therefore, this microbe may have the potential to increase food quality through a reduction in accumulation of toxic As species within the aerial portions of the plant.

Functional soil microbiome: belowground solutions to an aboveground problem.

There is considerable evidence in the literature that beneficial rhizospheric microbes can alter plant morphology, enhance plant growth, and increase mineral content. Of late, there is a surge to understand the impact of the microbiome on plant health. Recent research shows the utilization of novel sequencing techniques to identify the microbiome in model systems such as Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). However, it is not known how the community of microbes identified may play a role to improve plant health and fitness. There are very few detailed studies with isolated beneficial microbes showing the importance of the functional microbiome in plant fitness and disease protection. Some recent work on the cultivated microbiome in rice (Oryza sativa) shows that a wide diversity of bacterial species is associated with the roots of field-grown rice plants. However, the biological significance and potential effects of the microbiome on the host plants are completely unknown. Work performed with isolated strains showed various genetic pathways that are involved in the recognition of host-specific factors that play roles in beneficial host-microbe interactions. The composition of the microbiome in plants is dynamic and controlled by multiple factors. In the case of the rhizosphere, temperature, pH, and the presence of chemical signals from bacteria, plants, and nematodes all shape the environment and influence which organisms will flourish. This provides a basis for plants and their microbiomes to selectively associate with one another. This Update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.

Factors other than root secreted malic acid that contributes toward Bacillus subtilis FB17 colonization on Arabidopsis roots.

The plant growth promoting rhizobacterium (PGPR) Bacillus subtilis FB17 (hereafter FB17) induces resistance against broad pathogen including Pseudomonas syringae pv tomato (PstDC3000). The extent of plant protection by FB17 depends on establishment of root colonization followed by biofilm formation. The general convention dictates that beneficial rhizobacterium may suppress the root innate immune system to establish a robust colonization. However, it is still not well understood which genetic targets FB17 affects in plants to facilitate a symbiotic association. Our recent study, involving whole transcriptome analysis of Arabdiopsis thaliana roots treated with FB17 post 24 h of treatment showed totally 279 genes that were significantly up- or/ downregulated. Further, we found that the mutants for upregulated and downregulated genes post-FB17 colonization showed a differential phenotype for FB17 root colonization. Interestingly, plants mutated in the FB17-responsive genes showed increased Aluminum activated malate transporter (ALMT1) expression under foliar pathogen PstDC3000, infections, indicating the independent functionality of ALMT1 for bacterial recruitment. Taken together this, present study suggests that the establishment of interaction between the plant host and PGPR is a complex phenomenon which is regulated by multiple genetic components.

Overexpression of AtALMT1 in the Arabidopsis thaliana ecotype Columbia results in enhanced Al-activated malate excretion and beneficial bacterium recruitment.

AtALMT1 (Arabidopsis thaliana ALuminum activated Malate Transporter 1) encodes an Arabidopsis thaliana malate transporter that has a pleiotropic role in Arabidopsis stress tolerance. Malate released through AtALMT1 protects the root tip from Al rhizotoxicity, and recruits beneficial rhizobacteria that induce plant immunity. To examine whether the overexpression of AtALMT1 can improve these traits, the gene, driven by the cauliflower mosaic virus 35S promoter, was introduced into the Arabidopsis ecotype Columbia. Overexpression of the gene enhanced both Al-activated malate excretion and the recruitment of beneficial bacteria Bacillus subtilis strain FB17. These findings suggest that overexpression of AtALMT1 can be used as an approach to enhance a plant's ability to release malate into the rhizosphere, which can enhance plant tolerance to some environmental stress factors.

Root transcriptome analysis of Arabidopsis thaliana exposed to beneficial Bacillus subtilis FB17 rhizobacteria revealed genes for bacterial recruitment and plant defense independent of malate efflux.

Our previous work has demonstrated that Arabidopsis thaliana can actively recruit beneficial rhizobacteria Bacillus subtilis strain FB17 (hereafter FB17) through an unknown shoot-to-root long-distance signaling pathway post a foliar bacterial pathogen attack. However, it is still not well understood which genetic targets FB17 affects in plants. Microarray analysis of A. thaliana roots treated with FB17 post 24 h of treatment showed 168 and 129 genes that were up- and down-regulated, respectively, compared with the untreated control roots. Those up-regulated include auxin-regulated genes as well as genes involved in metabolism, stress response, and plant defense. In addition, other defense-related genes, as well as cell-wall modification genes were also down-regulated with FB17 colonization. Expression patterns of 20 selected genes were analyzed by semi-quantitative RT-PCR, validating the microarray results. A. thaliana insertion mutants were used against FB17 to further study the functional response of the differentially expressed genes. Five mutants for the up-regulated genes were tested for FB17 colonization, three (at3g28360, at3g20190 and at1g21240) mutants showed decreased FB17 colonization on the roots while increased FB17 titers was seen with three mutants of the down-regulated genes (at3g27980, at4g19690 and at5g56320). Further, these mutants for up-regulated genes and down-regulated genes were foliar infected with Pseudomonas syringae pv. tomato (hereafter PstDC3000) and analyzed for Aluminum activated malate transporter (ALMT1) expression which showed that ALMT1 may be the key regulator for root FB17 colonization. Our microarray showed that under natural condition, FB17 triggers plant responses in a manner similar to known plant growth-promoting rhizobacteria and to some extent also suppresses defense-related genes expression in roots, enabling stable colonization. The possible implication of this study opens up a new dialogin terms of how beneficial microbes regulate plant genetic response for mutualistic associations.

Characterization of the complex regulation of AtALMT1 expression in response to phytohormones and other inducers.

In Arabidopsis (Arabidopsis thaliana), malate released into the rhizosphere has various roles, such as detoxifying rhizotoxic aluminum (Al) and recruiting beneficial rhizobacteria that induce plant immunity. ALUMINUM-ACTIVATED MALATE TRANSPORTER1 (AtALMT1) is a critical gene in these responses, but its regulatory mechanisms remain unclear. To explore the mechanism of the multiple responses of AtALMT1, we profiled its expression patterns in wild-type plants, in transgenic plants harboring various deleted promoter constructs, and in mutant plants with defects in signal transduction in response to various inducers. AtALMT1 transcription was clearly induced by indole-3-acetic acid (IAA), abscisic acid (ABA), low pH, and hydrogen peroxide, indicating that it was able to respond to multiple signals, while it was not induced by methyl jasmonate and salicylic acid. The IAA-signaling double mutant nonphototropic hypocotyls4-1; auxin-responsive factor19-1 and the ABA-signaling mutant aba insensitive1-1 did not respond to auxin and ABA, respectively, but both showed an Al response comparable to that of the wild type. A synthetic microbe-associated molecular pattern peptide, flagellin22 (flg22), induced AtALMT1 transcription but did not induce the transcription of IAA- and ABA-responsive biomarker genes, indicating that both Al and flg22 responses of AtALMT1 were independent of IAA and ABA signaling. An in planta ß-glucuronidase reporter assay identified that the ABA response was regulated by a region upstream (-317 bp) from the first ATG codon, but other stress responses may share critical regulatory element(s) located between -292 and -317 bp. These results illustrate the complex regulation of AtALMT1 expression during the adaptation to abiotic and biotic stresses.

Microbe-associated molecular patterns-triggered root responses mediate beneficial rhizobacterial recruitment in Arabidopsis.

This study demonstrated that foliar infection by Pseudomonas syringae pv tomato DC3000 induced malic acid (MA) transporter (ALUMINUM-ACTIVATED MALATE TRANSPORTER1 [ALMT1]) expression leading to increased MA titers in the rhizosphere of Arabidopsis (Arabidopsis thaliana). MA secretion in the rhizosphere increased beneficial rhizobacteria Bacillus subtilis FB17 (hereafter FB17) titers causing an induced systemic resistance response in plants against P. syringae pv tomato DC3000. Having shown that a live pathogen could induce an intraplant signal from shoot-to-root to recruit FB17 belowground, we hypothesized that pathogen-derived microbe-associated molecular patterns (MAMPs) may relay a similar response specific to FB17 recruitment. The involvement of MAMPs in triggering plant innate immune response is well studied in the plant's response against foliar pathogens. In contrast, MAMPs-elicited plant responses on the roots and the belowground microbial community are not well understood. It is known that pathogen-derived MAMPs suppress the root immune responses, which may facilitate pathogenicity. Plants subjected to known MAMPs such as a flagellar peptide, flagellin22 (flg22), and a pathogen-derived phytotoxin, coronatine (COR), induced a shoot-to-root signal regulating ALMT1 for recruitment of FB17. Micrografts using either a COR-insensitive mutant (coi1) or a flagellin-insensitive mutant (fls2) as the scion and ALMT1(pro):ß-glucuronidase as the rootstock revealed that both COR and flg22 are required for a graft transmissible signal to recruit FB17 belowground. The data suggest that MAMPs-induced signaling to regulate ALMT1 is salicylic acid and JASMONIC ACID RESISTANT1 (JAR1)/JASMONATE INSENSITIVE1 (JIN1)/MYC2 independent. Interestingly, a cell culture filtrate of FB17 suppressed flg22-induced MAMPs-activated root defense responses, which are similar to suppression of COR-mediated MAMPs-activated root defense, revealing a diffusible bacterial component that may regulate plant immune responses. Further analysis showed that the biofilm formation in B. subtilis negates suppression of MAMPs-activated defense responses in roots. Moreover, B. subtilis suppression of MAMPs-activated root defense does require JAR1/JIN1/MYC2. The ability of FB17 to block the MAMPs-elicited signaling pathways related to antibiosis reflects a strategy adapted by FB17 for efficient root colonization. These experiments demonstrate a remarkable strategy adapted by beneficial rhizobacteria to suppress a host defense response, which may facilitate rhizobacterial colonization and host-mutualistic association.

Rhizobacteria Bacillus subtilis restricts foliar pathogen entry through stomata.

Plants exist in a complex multitrophic environment, where they interact with and compete for resources with other plants, microbes and animals. Plants have a complex array of defense mechanisms, such as the cell wall being covered with a waxy cuticle serving as a potent physical barrier. Although some pathogenic fungi infect plants by penetrating through the cell wall, many bacterial pathogens invade plants primarily through stomata on the leaf surface. Entry of the foliar pathogen, Pseudomonas syringae pathovar tomato DC3000 (hereafter PstDC3000), into the plant corpus occurs through stomatal openings, and consequently a key plant innate immune response is the transient closure of stomata, which delays disease progression. Here, we present evidence that the root colonization of the rhizobacteria Bacillus subtilis FB17 (hereafter FB17) restricts the stomata-mediated pathogen entry of PstDC3000 in Arabidopsis thaliana. Root binding of FB17 invokes abscisic acid (ABA) and salicylic acid (SA) signaling pathways to close light-adapted stomata. These results emphasize the importance of rhizospheric processes and environmental conditions as an integral part of the plant innate immune system against foliar bacterial infections.

Natural variation among Arabidopsis accessions reveals malic acid as a key mediator of Nickel (Ni) tolerance.

Plants have evolved various mechanisms for detoxification that are specific to the plant species as well as the metal ion chemical properties. Malic acid, which is commonly found in plants, participates in a number of physiological processes including metal chelation. Using natural variation among Arabidopsis accessions, we investigated the function of malic acid in Nickel (Ni) tolerance and detoxification. The Ni-induced production of reactive oxygen species was found to be modulated by intracellular malic acid, indicating its crucial role in Ni detoxification. Ni tolerance in Arabidopsis may actively involve malic acid and/or complexes of Ni and malic acid. Investigation of malic acid content in roots among tolerant ecotypes suggested that a complex of Ni and malic acid may be involved in translocation of Ni from roots to leaves. The exudation of malic acid from roots in response to Ni treatment in either susceptible or tolerant plant species was found to be partially dependent on AtALMT1 expression. A lower concentration of Ni (10 µM) treatment induced AtALMT1 expression in the Ni-tolerant Arabidopsis ecotypes. We found that the ecotype Santa Clara (S.C.) not only tolerated Ni but also accumulated more Ni in leaves compared to other ecotypes. Thus, the ecotype S.C. can be used as a model system to delineate the biochemical and genetic basis of Ni tolerance, accumulation, and detoxification in plants. The evolution of Ni hyperaccumulators, which are found in serpentine soils, is an interesting corollary to the fact that S.C. is also native to serpentine soils.

A plasmodesmata-localized protein mediates crosstalk between cell-to-cell communication and innate immunity in Arabidopsis.

Plasmodesmata (PD) are thought to play a fundamental role in almost every aspect of plant life, including normal growth, physiology, and developmental responses. However, how specific signaling pathways integrate PD-mediated cell-to-cell communication is not well understood. Here, we present experimental evidence showing that the Arabidopsis thaliana plasmodesmata-located protein 5 (PDLP5; also known as HOPW1-1-INDUCED GENE1) mediates crosstalk between PD regulation and salicylic acid-dependent defense responses. PDLP5 was found to localize at the central region of PD channels and associate with PD pit fields, acting as an inhibitor to PD trafficking, potentially through its capacity to modulate PD callose deposition. As a regulator of PD, PDLP5 was also essential for conferring enhanced innate immunity against bacterial pathogens in a salicylic acid-dependent manner. Based on these findings, a model is proposed illustrating that the regulation of PD closure mediated by PDLP5 constitutes a crucial part of coordinated control of cell-to-cell communication and defense signaling.