Microbiome and plant immunity
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BMC Genomics | Abstract | Dynamics in the resistant and susceptible peanut (Arachis hypogaea L.) root transcriptome on infection with the Ralstonia solanacearum

BMC Genomics | Abstract | Dynamics in the resistant and susceptible peanut (Arachis hypogaea L.) root transcriptome on infection with the Ralstonia solanacearum | Microbiome and plant immunity | Scoop.it
Background

Bacterial wilt caused by Ralstonia solanacearum is a serious soil-borne disease of peanut (Arachis hypogaea L). The molecular basis of peanut response to R. solanacearum remains unknown. To understand the resistance mechanism behind peanut resistance to R. solanacearum, we used RNA-Seq to perform global transcriptome profiling on the roots of peanut resistant (R) and susceptible (S) genotypes under R. solanacearum infection.
Results

A total of 4.95 x 108 raw sequence reads were generated and subsequently assembled into 271, 790 unigenes with an average length of 890 bp and a N50 of 1, 665 bp. 179, 641 unigenes could be annotated by public protein databases. The pairwise transcriptome comparsions of time course (6, 12, 24, 48 and 72 h post inoculation) were conducted 1) between inoculated and control samples of each genotype, 2) between inoculated samples of R and S genotypes. The linear dynamics of transcriptome profile was observed between adjacent samples for each genotype, two genotypes shared similar transcriptome pattern at early time points with most significant up regulation at 12 hour, and samples from R genotype at 24 h and S genotype at 48 h showed similar transcriptome pattern, significant differences of transcriptional profile were observed in pairwise comparisons between R and S genotypes. KEGG analysis showed that the primary metabolisms were inhibited in both genotypes and stronger inhibition in R genotype post inoculation. The defense related genes (R gene, LRR-RLK,cell wall genes, etc.) generally showed a genotype-specific down regulation and different expression between both genotypes.
Conclusion

This transcriptome profiling provided the largest data set that explores the dynamic in crosstalk between peanut and R. solanacearum. The results suggested that the down-regulation of primary metabolism is contributed to the resistance difference between R and S genotypes. The genotype-specific expression pattern of defense related DEGs also contributed to the resistance difference between R and S genotype. This study will strongly contribute to better understand the molecular interaction between plant and R. solanacearum.
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Biosynthesis of redox-active metabolites in response to iron deficiency in plants

Biosynthesis of redox-active metabolites in response to iron deficiency in plants | Microbiome and plant immunity | Scoop.it

Iron is an essential but poorly bioavailable nutrient because of its low solubility, especially in alkaline soils. Here, we describe the discovery of a previously undescribed redox-active catecholic metabolite, termed sideretin, which derives from the coumarin fraxetin and is the primary molecule exuded by Arabidopsis thaliana roots in response to iron deficiency. We identified two enzymes that complete the biosynthetic pathway of fraxetin and sideretin. Chemical characterization of fraxetin and sideretin, and biological assays with pathway mutants, suggest that these coumarins are critical for iron nutrition in A. thaliana. Further, we show that sideretin production also occurs in eudicot species only distantly related to A. thaliana. Untargeted metabolomics of the root exudates of various eudicots revealed production of structurally diverse redox-active molecules in response to iron deficiency. Our results indicate that secretion of small-molecule reductants by roots may be a widespread and previously underappreciated component of reduction-based iron uptake.

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N-hydroxy-pipecolic acid is a mobile signal that induces systemic disease resistance in Arabidopsis

N-hydroxy-pipecolic acid is a mobile signal that induces systemic disease resistance in Arabidopsis | Microbiome and plant immunity | Scoop.it
Systemic acquired resistance (SAR) is a global response in plants induced at the site of infection that leads to long-lasting and broad-spectrum disease resistance at distal, uninfected tissues. Despite the importance of this priming mechanism, the identity of the mobile defense signal that moves systemically throughout plants to initiate SAR has remained elusive. In this paper, we describe a new metabolite, N-hydroxy-pipecolic acid (N-OH-Pip), and provide evidence that this molecule is a mobile signal that plays a central role in initiating SAR signal transduction in Arabidopsis thaliana. We demonstrate that FLAVIN-DEPENDENT MONOOXYGENASE 1 (FMO1), a key regulator of SAR-associated defense priming, can synthesize N-OH-Pip from pipecolic acid in planta, and exogenously applied N-OH-PIP moves systemically in Arabidopsis and can rescue the SAR-deficiency of fmo1 mutants. We also demonstrate that N-OH-Pip treatment causes systemic changes in the expression of pathogenesis-related genes and metabolic pathways throughout the plant, and enhances resistance to a bacterial pathogen. This work provides new insight into the chemical nature of a mobile signal for SAR and also suggests that the N-OH-Pip pathway is a promising target for metabolic engineering to enhance disease resistance.

Via Philip Carella, Steve Marek
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Frontiers | Rhizosphere Microbiome Recruited from a Suppressive Compost Improves Plant Fitness and Increases Protection against Vascular Wilt Pathogens of Tomato | Plant Science

Frontiers | Rhizosphere Microbiome Recruited from a Suppressive Compost Improves Plant Fitness and Increases Protection against Vascular Wilt Pathogens of Tomato | Plant Science | Microbiome and plant immunity | Scoop.it
Suppressive composts represent a sustainable approach to combat soil-borne plant pathogens and an alternative to the ineffective chemical fungicides used against those. Nevertheless, suppressiveness to plant pathogens and reliability of composts is often inconsistent with unpredictable effects. While suppressiveness is usually attributed to the compost’s microorganisms, the mechanisms governing microbial recruitment by the roots and the composition of selected microbial communities are not fully elucidated. Herein, the purpose of the study was to evaluate the impact of a compost on tomato plant growth and its suppressiveness against Fusarium oxysporum f. sp. lycopersici (Foxl) and Verticillium dahliae (Vd). First, growth parameters of tomato plants grown in sterile peat-based substrates including 20% and 30% sterile compost (80P/20C-ST and 70P/30C-ST) or non-sterile compost (80P/20C and 70P/30C) were evaluated in a growth room experiment. Plant height, total leaf surface, fresh and dry weight of plants grown in the non-sterile compost mixes were increased compared to the plants grown in the sterile compost substrates, indicating the plant growth promoting activity of the compost’s microorganisms. Subsequently, compost’s suppressiveness against Foxl and Vd was evaluated with pathogenicity experiments on tomato plants grown in 70P/30C-ST and 70P/30C substrates. Disease intensity was significantly less in plants grown in the non-sterile compost than those grown in the sterile compost substrate; AUDPC was 2.3 and 1.4-fold less for Foxl and Vd respectively. Moreover, fungal quantification in planta demonstrated reduced colonization in plants grown in the non-sterile mixture. To further investigate these findings, we characterized the culturable microbiome attracted by the roots compared to the unplanted compost. Bacteria and fungi isolated from unplanted compost and the rhizosphere of plants were sequence-identified. Community-level analysis revealed differential microbial communities between the compost and the rhizosphere, suggesting a clear effect of the plant in the microbiome assembly. Proteobacteria and Actinobacteria were highly enriched in the rhizosphere whereas Firmicutes were strongly represented in both compartments with Bacillus being the most abundant species. Our results shed light on the composition of a microbial consortium that could protect plants against the wilt pathogens of tomato and improve plant overall health.
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Root exudates of stressed plants stimulate and attract Trichoderma soil fungi

Root exudates of stressed plants stimulate and attract Trichoderma soil fungi | Microbiome and plant immunity | Scoop.it
Plant roots release complex mixtures of bioactive molecules including compounds that affect the activity and modify the composition of the rhizosphere microbiome. In this work, we investigated the initial phase of the interaction between tomato and an effective biocontrol strain of Trichoderma harzianum (T22). We found that root exudates (RE), obtained from plants grown in a split root system and exposed to a choice of biotic and abiotic stress factors (wounding, salt, pathogen attack), stimulate the growth and act as chemoattractants of the biocontrol fungus. On the other hand, some of the treatments did not result in an enhanced chemotropism on Fusarium oxysporum f. sp. lycopersici, indicating a mechanism that may be selective for non-pathogenic microbes. The involvement of peroxidases and oxylipins, both known to be released by roots in response to stress, was demonstrated by using RE fractions containing these molecules and their commercial purified analogues, testing the effect of a specific inhibitor, and characterizing the complex pattern of these metabolites released by tomato roots both locally and systemically.
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Transcriptome landscape of a bacterial pathogen under plant immunity

Transcriptome landscape of a bacterial pathogen under plant immunity | Microbiome and plant immunity | Scoop.it
Plants have evolved a powerful innate immune system to defend against microbial pathogens. Despite extensive studies, how plant immunity ultimately inhibits bacterial pathogen growth is largely unknown, due to difficulties in profiling bacterial responses in planta . In this study, we established two methods for in planta bacterial transcriptome analysis using RNA sequencing. By analyzing 27 combinations of plant immunity mutants and Pseudomonas syringae strains, we succeeded in the identification of specific bacterial transcriptomic signatures that are influenced by plant immune activation. In addition, we found that overexpression of an immune-responsive P. syringae sigma factor gene involved in iron regulation could partially counter bacterial growth restriction during plant immunity. This study illuminates the enigmatic mechanisms of bacterial growth inhibition by plant immunity.

Plant pathogens can cause serious diseases that impact global agriculture. The plant innate immunity, when fully activated, can halt pathogen growth in plants. Despite extensive studies into the molecular and genetic bases of plant immunity against pathogens, the influence of plant immunity in global pathogen metabolism to restrict pathogen growth is poorly understood. Here, we developed RNA sequencing pipelines for analyzing bacterial transcriptomes in planta and determined high-resolution transcriptome patterns of the foliar bacterial pathogen Pseudomonas syringae in Arabidopsis thaliana with a total of 27 combinations of plant immunity mutants and bacterial strains. Bacterial transcriptomes were analyzed at 6 h post infection to capture early effects of plant immunity on bacterial processes and to avoid secondary effects caused by different bacterial population densities in planta . We identified specific “immune-responsive” bacterial genes and processes, including those that are activated in susceptible plants and suppressed by plant immune activation. Expression patterns of immune-responsive bacterial genes at the early time point were tightly linked to later bacterial growth levels in different host genotypes. Moreover, we found that a bacterial iron acquisition pathway is commonly suppressed by multiple plant immune-signaling pathways. Overexpression of a P. syringae sigma factor gene involved in iron regulation and other processes partially countered bacterial growth restriction during the plant immune response triggered by AvrRpt2. Collectively, this study defines the effects of plant immunity on the transcriptome of a bacterial pathogen and sheds light on the enigmatic mechanisms of bacterial growth inhibition during the plant immune response.
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Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks

Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks | Microbiome and plant immunity | Scoop.it

Microbial activity in soil is spatially heterogeneous often forming spatial hotspots that contribute disproportionally to biogeochemical processes. Evidence suggests that bacterial spatial organization contributes to the persistence of anoxic hotspots even in unsaturated soils. Such processes are difficult to observe in situ at the microscale, hence mechanisms and time scales relevant for bacterial spatial organization remain largely qualitative. Here we develop an experimental platform based on glass-etched micrometric pore networks that mimics resource gradients postulated in soil aggregates to observe spatial organization of fluorescently tagged aerobic and facultative anaerobic bacteria. Two initially intermixed bacterial species, Pseudomonas putida and Pseudomonas veronii, segregate into preferential regions promoted by opposing gradients of carbon and oxygen (such persistent coexistence is not possible in well-mixed cultures). The study provides quantitative visualization and modeling of bacterial spatial organization within aggregate-like hotspots, a key step towards developing a mechanistic representation of bacterial community organization in soil pores.

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Rescooped by Giannis Stringlis from Host-Microbe Interactions. Plant Biology.
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Pseudomonas syringae: what it takes to be a pathogen

Pseudomonas syringae: what it takes to be a pathogen | Microbiome and plant immunity | Scoop.it

Pseudomonas syringae is one of the best-studied plant pathogens and serves as a model for understanding host–microorganism interactions, bacterial virulence mechanisms and host adaptation of pathogens as well as microbial evolution, ecology and epidemiology. Comparative genomic studies have identified key genomic features that contribute to P. syringae virulence. P. syringae has evolved two main virulence strategies: suppression of host immunity and creation of an aqueous apoplast to form its niche in the phyllosphere. In addition, external environmental conditions such as humidity profoundly influence infection. P. syringae may serve as an excellent model to understand virulence and also of how pathogenic microorganisms integrate environmental conditions and plant microbiota to become ecologically robust and diverse pathogens of the plant kingdom.


Via Tatsuya Nobori
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Chemical priming of immunity without costs to plant growth - Buswell - 2018 - New Phytologist - Wiley Online Library

Chemical priming of immunity without costs to plant growth - Buswell - 2018 - New Phytologist - Wiley Online Library | Microbiome and plant immunity | Scoop.it

β-Aminobutyric acid (BABA) induces broad-spectrum disease resistance, but also represses plant growth, which has limited its exploitation in crop protection. BABA perception relies on binding to the aspartyl-tRNA synthetase (AspRS) IBI1, which primes the enzyme for secondary defense activity. This study aimed to identify structural BABA analogues that induce resistance without stunting plant growth. Using site-directed mutagenesis, we demonstrate that the (l)-aspartic acid-binding domain of IBI1 is critical for BABA perception. Based on interaction models of this domain, we screened a small library of structural BABA analogues for growth repression and induced resistance against biotrophic Hyaloperonospora arabidopsidis (Hpa). A range of resistance-inducing compounds were identified, of which (R)-β-homoserine (RBH) was the most effective. Surprisingly, RBH acted through different pathways than BABA. RBH-induced resistance (RBH-IR) against Hpa functioned independently of salicylic acid, partially relied on camalexin, and was associated with augmented cell wall defense. RBH-IR against necrotrophic Plectosphaerella cucumerina acted via priming of ethylene and jasmonic acid defenses. RBH-IR was also effective in tomato against Botrytis cinerea. Metabolic profiling revealed that RBH, unlike BABA, does not majorly affect plant metabolism. RBH primes distinct defense pathways against biotrophic and necrotrophic pathogens without stunting plant growth, signifying strong potential for exploitation in crop protection.


Via IPM Lab
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Native soils with their microbiotas elicit a state of alert in tomato plants

Native soils with their microbiotas elicit a state of alert in tomato plants | Microbiome and plant immunity | Scoop.it

Several studies have investigated soil microbial biodiversity, but understanding of the mechanisms underlying plant responses to soil microbiota remains in its infancy. Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas. Using transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium). Native soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam-disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil. The ‘state of alert’ detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses.


Via Stéphane Hacquard
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Rhizobia: from saprophytes to endosymbionts

Rhizobia: from saprophytes to endosymbionts | Microbiome and plant immunity | Scoop.it
Rhizobia are some of the best-studied plant microbiota. These oligotrophic Alphaproteobacteria or Betaproteobacteria form symbioses with their legume hosts. Rhizobia must exist in soil and compete with other members of the microbiota before infecting legumes and forming N2-fixing bacteroids. These dramatic lifestyle and developmental changes are underpinned by large genomes and even more complex pan-genomes, which encompass the whole population and are subject to rapid genetic exchange. The ability to respond to plant signals and chemoattractants and to colonize nutrient-rich roots are crucial for the competitive success of these bacteria. The availability of a large body of genomic, physiological, biochemical and ecological studies makes rhizobia unique models for investigating community interactions and plant colonization.


Via Jean-Michel Ané
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Division of tasks - Defense by the spatial separation of antagonistic hormone activities | Plant and Cell Physiology | Oxford Academic

Division of tasks - Defense by the spatial separation of antagonistic hormone activities | Plant and Cell Physiology | Oxford Academic | Microbiome and plant immunity | Scoop.it
Kenichi Tsuda; Division of tasks - Defense by the spatial separation of antagonistic hormone activities, Plant and Cell Physiology, , pcx208, https://doi.org/1

Via Tatsuya Nobori
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Ten simple rules for biologists learning to program

Ten simple rules for biologists learning to program | Microbiome and plant immunity | Scoop.it
As big data and multi-omics analyses are becoming mainstream, computational proficiency and literacy are essential skills in a biologist’s tool kit. All “omics” studies require computational biology: the implementation of analyses requires programming skills, while experimental design and interpretation require a solid understanding of the analytical approach. While academic cores, commercial services, and collaborations can aid in the implementation of analyses, the computational literacy required to design and interpret omics studies cannot be replaced or supplemented. However, many biologists are only trained in experimental techniques. We write these 10 simple rules for traditionally trained biologists, particularly graduate students interested in acquiring a computational skill set.
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Genomic features of bacterial adaptation to plants

Genomic features of bacterial adaptation to plants | Microbiome and plant immunity | Scoop.it
Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3,837 bacterial genomes to identify thousands of plant-associated gene clusters. Genomes of plant-associated bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant-associated genomes do. We experimentally validated candidates from two sets of plant-associated genes: one involved in plant colonization, and the other serving in microbe–microbe competition between plant-associated bacteria. We also identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes. This work expands the genome-based understanding of plant–microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering.

Via Matt Agler, Stéphane Hacquard
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Steve Marek's curator insight, December 19, 2017 10:30 AM
"identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes"
WillistonPlantPath's curator insight, December 20, 2017 2:43 PM
484 bacterial genomes. wow.
Rescooped by Giannis Stringlis from The Plant Microbiome
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Microbial interactions within the plant holobiont | Microbiome |

Microbial interactions within the plant holobiont | Microbiome | | Microbiome and plant immunity | Scoop.it
Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a “holobiont.” Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.

Via Stéphane Hacquard
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Fungal Phytotoxin Lasiojasmonate A Activates the Plant Jasmonic Acid Pathway | Journal of Experimental Botany | Oxford Academic

Fungal Phytotoxin Lasiojasmonate A Activates the Plant Jasmonic Acid Pathway | Journal of Experimental Botany | Oxford Academic | Microbiome and plant immunity | Scoop.it
Jasmonates are signaling compounds that regulate plant responses to stress. Jasmonic acid (JA) is the direct precursor of the bioactive plant hormone JA-Ile, the ligand of the COI1-JAZ co-receptor complex. JA, its methyl ester and three furanonyl esters were recently isolated from the grapevine pathogen Lasiodiplodia mediterannea sp. The JA ester lasiojasmonate A (LasA) is the first reported naturally occurring JA-furanone, whose mode of action is currently unexplored. Here we show that LasA activates many JA-regulated responses in planta, including protein degradation, gene expression, and physiological processes. These in vivo effects required LasA conversion into JA, formation of JA-Ile and its recognition by the plant JA-Ile perception complex. These data suggest a mode of action of the natural fungal LasA as an inactive JA pool that can be transformed into the bioactive JA-Ile form. We propose that fungal production of JA derivates such as LasA occur at late infection stages to induce plant JA responses such as cell death, and facilitate fungal infection.

Via Philip Carella, Francis Martin, Steve Marek
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Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly

Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly | Microbiome and plant immunity | Scoop.it

Like all higher organisms, plants have evolved in the context of a microbial world, shaping both their evolution and their contemporary ecology. Interactions between plant roots and soil microorganisms are critical for plant fitness in natural environments. Given this co-evolution and the pivotal importance of plant–microbial interactions, it has been hypothesized, and a growing body of literature suggests, that plants may regulate the composition of their rhizosphere to promote the growth of microorganisms that improve plant fitness in a given ecosystem. Here, using a combination of comparative genomics and exometabolomics, we show that pre-programmed developmental processes in plants (Avena barbata) result in consistent patterns in the chemical composition of root exudates. This chemical succession in the rhizosphere interacts with microbial metabolite substrate preferences that are predictable from genome sequences. Specifically, we observed a preference by rhizosphere bacteria for consumption of aromatic organic acids exuded by plants (nicotinic, shikimic, salicylic, cinnamic and indole-3-acetic). The combination of these plant exudation traits and microbial substrate uptake traits interact to yield the patterns of microbial community assembly observed in the rhizosphere of an annual grass. This discovery provides a mechanistic underpinning for the process of rhizosphere microbial community assembly and provides an attractive direction for the manipulation of the rhizosphere microbiome for beneficial outcomes.

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Convergent and Divergent Signaling in PAMP-Triggered Immunity and Effector-Triggered Immunity | Molecular Plant-Microbe Interactions

Convergent and Divergent Signaling in PAMP-Triggered Immunity and Effector-Triggered Immunity | Molecular Plant-Microbe Interactions | Microbiome and plant immunity | Scoop.it
Plants use diverse immune receptors to sense pathogen attacks. Recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors localized on the plasma membrane leads to PAMP-triggered immunity (PTI). Detection of pathogen effectors by intracellular or plasma membrane–localized immune receptors results in effector-triggered immunity (ETI). Despite the large variations in the magnitude and duration of immune responses triggered by different PAMPs or pathogen effectors during PTI and ETI, plasma membrane–localized immune receptors activate similar downstream molecular events such as mitogen-activated protein kinase activation, oxidative burst, ion influx, and increased biosynthesis of plant defense hormones, indicating that defense signals initiated at the plasma membrane converge at later points. On the other hand, activation of ETI by immune receptors localized to the nucleus appears to be more directly associated with transcriptional regulation of defense gene expression. Here, we review recent progress in signal transductions downstream of different groups of plant immune receptors, highlighting the converging and diverging molecular events.
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Disease-induced assemblage of a plant-beneficial bacterial consortium - ISME Journal

Disease-induced assemblage of a plant-beneficial bacterial consortium - ISME Journal | Microbiome and plant immunity | Scoop.it

Disease suppressive soils typically develop after a disease outbreak due to the subsequent assembly of protective microbiota in the rhizosphere. The role of the plant immune system in the assemblage of a protective rhizosphere microbiome is largely unknown. In this study, we demonstrate that Arabidopsis thaliana specifically promotes three bacterial species in the rhizosphere upon foliar defense activation by the downy mildew pathogen Hyaloperonospora arabidopsidis. The promoted bacteria were isolated and found to interact synergistically in biofilm formation in vitro. Although separately these bacteria did not affect the plant significantly, together they induced systemic resistance against downy mildew and promoted growth of the plant. Moreover, we show that the soil-mediated legacy of a primary population of downy mildew infected plants confers enhanced protection against this pathogen in a second population of plants growing in the same soil. Together our results indicate that plants can adjust their root microbiome upon pathogen infection and specifically recruit a group of disease resistance-inducing and growth-promoting beneficial microbes, therewith potentially maximizing the chance of survival of their offspring that will grow in the same soil.


Via Max-Bernhard Ballhausen
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International Society of Root Research Conference – ISRR 2018

International Society of Root Research Conference – ISRR 2018 | Microbiome and plant immunity | Scoop.it

The Symposium will promote fundamental understanding of the diverse aspects of root biology. The symposium, titled: “Exposing the Hidden Half - Root Research at the Forefront of Science”, will assemble multiple disciplines in order to facilitate exploration of novel approaches and investigation of complex processes and mechanisms. The intersections of root physiology, root development, root architecture and root interactions with the environment will be tackled by researchers from around the globe through talks, poster sessions and discussions. Basic research at multiple scales (proteins, cells, tissues and the root system as a whole) and cutting-edge methodologies will be highlighted as important means to advance agriculture. Graduate students, young researchers and senior scientists will find the conference setting in the scenic Jerusalem hills conducive for both formal and informal interactions promoting a rich exchange of ideas and knowledge and opportunity for fostering collaborations.

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Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice

Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice | Microbiome and plant immunity | Scoop.it

Plant roots are colonized by complex communities of bacterial and archaeal microbiota from the soil, with the potential to affect plant nutrition and fitness. Although root-associated microbes are known to have the potential to be utilized to promote crop productivity, their exploitation has been hindered by a lack of understanding of the compositional dynamics of these communities. Here we investigate temporal changes in the root-associated bacterial and archaeal communities throughout the plant life cycle in field-grown rice over multiple seasons and locations. Our results indicate that root microbiota composition varies with both chronological age and the developmental stage of the plants. We find that a major compositional shift correlates with the transition to reproductive growth, suggestive of distinct root microbiota associations for the juvenile and adult plant phases. The results from this study highlight dynamic relationships between plant growth and associated microbiota that should be considered in strategies for the successful manipulation of microbial communities to enhance crop performance.


Via Stéphane Hacquard
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The soil microbiome — from metagenomics to metaphenomics

The soil microbiome — from metagenomics to metaphenomics | Microbiome and plant immunity | Scoop.it
Soil microorganisms carry out important processes, including support of plant growth and cycling of carbon and other nutrients. However, the majority of soil microbes have not yet been isolated and their functions are largely unknown. Although metagenomic sequencing reveals microbial identities and functional gene information, it includes DNA from microbes with vastly varying physiological states. Therefore, metagenomics is only predictive of community functional potential. We posit that the next frontier lies in understanding the metaphenome, the product of the combined genetic potential of the microbiome and available resources. Here we describe examples of opportunities towards gaining understanding of the soil metaphenome.

Via Stéphane Hacquard
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Rescooped by Giannis Stringlis from MycorWeb Plant-Microbe Interactions
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Trends in Genetics: Transposable Elements Direct The Coevolution between Plants and Microbes (2016)

Trends in Genetics: Transposable Elements Direct The Coevolution between Plants and Microbes (2016) | Microbiome and plant immunity | Scoop.it

Transposable elements are powerful drivers of genome evolution in many eukaryotes. Although they are mostly considered as ‘selfish’ genetic elements, increasing evidence suggests that they contribute to genetic variability; particularly under stress conditions. Over the past few years, the role of transposable elements during host–microbe interactions has been recognised. It has been proposed that many pathogenic microbes have evolved a ‘two-speed’ genome with regions that show increased variability and that are enriched in transposable elements and pathogenicity-related genes. Plants similarly display structured genomes with transposable-element-rich regions that mediate accelerated evolution. Immune receptor genes typically reside in such regions. Various mechanisms have recently been identified through which transposable elements contribute to the coevolution between plants and their associated microbes.


Via Kamoun Lab @ TSL, Francis Martin
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intimate talk between plants and microorganisms at the leaf surface | Journal of Experimental Botany | Oxford Academic

intimate talk between plants and microorganisms at the leaf surface | Journal of Experimental Botany | Oxford Academic | Microbiome and plant immunity | Scoop.it

The plant epidermis or cuticle is constantly exposed to external and internal environmental factors, including an enriched and diverse community of bacteria, yeast, fungi, viruses, and mites. It is not only where the plant has its first physical barrier, but also where organisms can be recognized and potentially where the plant defense responses can be triggered. The plant cuticle is a polymeric composite formed by an array of structurally and chemically heterogeneous compounds, including cutin and wax. A few studies have shown that cuticular components are essential and important drivers of the structure and size of the bacterial community. On the other hand, cuticular components are also important for both pathogens and plants, to initiate the pre-invasion and infection process and to activate the innate immune response, respectively. In this review, we explore current knowledge on the role of the cuticle during the intimate interactions between plants and microorganisms, in particular pathogenic and non-pathogenic bacteria and fungi. Finally, we propose new perspectives on the potential use of this information for agriculture.


Via Steve Marek
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QHG's curator insight, January 14, 7:46 PM
Please sharing your work with us
Rescooped by Giannis Stringlis from The Plant Microbiome
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Frontiers | A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome | Plant Science

Frontiers | A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome | Plant Science | Microbiome and plant immunity | Scoop.it
The soil-plant ecosystem harbors an immense microbial diversity that challenges investigative approaches to study traits underlying plant-microbe association. Studies solely based on culture-dependent techniques have overlooked most microbial diversity. Here we describe the concomitant use of culture-dependent and -independent techniques to target plant-beneficial microbial groups from the sugarcane microbiome. The community-based culture collection (CBC) approach was used to access microbes from roots and stalks. The CBC recovered 399 unique bacteria representing 15.9% of the rhizosphere core microbiome and 61.6–65.3% of the endophytic core microbiomes of stalks. By cross-referencing the CBC (culture-dependent) with the sugarcane microbiome profile (culture-independent), we designed a synthetic community comprised of naturally occurring highly abundant bacterial groups from roots and stalks, most of which has been poorly explored so far. We then used maize as a model to probe the abundance-based synthetic inoculant. We show that when inoculated in maize plants, members of the synthetic community efficiently colonize plant organs, displace the natural microbiota and dominate at 53.9% of the rhizosphere microbial abundance. As a result, inoculated plants increased biomass by 3.4-fold as compared to uninoculated plants. The results demonstrate that abundance-based synthetic inoculants can be successfully applied to recover beneficial plant microbes from plant microbiota.

Via Stéphane Hacquard
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Rescooped by Giannis Stringlis from Host-Microbe Interactions. Plant Biology.
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Know your Enemy, Embrace your Friend: Using omics to understand how plants respond differently to pathogenic and mutualistic microorganisms

Know your Enemy, Embrace your Friend: Using omics to understand how plants respond differently to pathogenic and mutualistic microorganisms | Microbiome and plant immunity | Scoop.it
Micro‐organisms, or ‘microbes’, have formed intimate associations with plants throughout the length of their evolutionary history. In extant plant systems microbes still remain an integral part o

Via Tatsuya Nobori
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