Plant metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA592876 | ENA |
REPOSITORIES: ENA
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Project description:Plant can perceive and respond natural sound vibration (SV). Artificial SV also served as a novel trigger of induced resistance, although approaches for activating such plant innate immunity intensively studied on the use of biological and chemical agents (BCA). Artificial SV pre-treatment protected Arabidopsis thaliana seedlings against insect pests and fungal pathogens. However, SV-mediated epigenetic modulation remains unexplored while CBA-mediated induced resistance is known as a complicated process involving epigenetic regulation. Here, we performed a ChIP-seq analysis to understand the role of 10 kHz SV-mediated epigenetic modification in induced resistance against a soil-borne pathogenic bacterium Ralstonia solanacearum.
2020-08-03 | GSE133320 | GEO
Project description:A LysM Receptor-like Kinase Mediates Chitin Perception and Fungal Resistance in Arabidopsis; Jinrong Wan,1 Xuecheng Zhang,1 David Neece,2 Katrina M. Ramonell,3 Steve Clough,2,4 Sung-yong Kim,1 Minviluz Stacey,1 and Gary Stacey1*; 1Division of Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO 65211, USA; 2Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; 3Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA; 4US Department of Agriculture, Soybean/Maize Germplasm, Pathology and Genetics Research, Urbana, IL 61801, USA; *To whom correspondence should be addressed. E-mail: staceyg@missouri.edu; Abstract: Chitin, a polymer of N-acetyl-D-glucosamine, is found in fungal cell walls, but not in plants. Plant cells are capable of perceiving chitin fragments (chitooligosaccharides) to trigger various defense responses. We identified a LysM receptor-like protein (AtLysM RLK1) that is required for the perception of chitooligosaccharides in Arabidopsis. Mutation of this gene blocked the induction of almost all chitooligosaccharide-responsive genes (CRGs) and led to more susceptibility to fungal pathogens, but not to a bacterial pathogen. In addition, exogenously applied chitooligosaccharides enhanced resistance against both fungal and bacterial pathogens in the wild-type plants, but not in the mutant. Together, our data strongly suggest AtLysM RLK1 is the chitin receptor or a key part of the receptor complex and chitin is a PAMP (pathogen-associated molecular pattern) in fungi recognized by the receptor leading to the induction of plant innate immunity against fungal pathogens. Since LysM RLKs were also recently shown to be critical for the perception of the rhizobial lipo-chitin Nod signals, our data suggest that LysM RLKs not just recognize friendly symbiotic rhizobia (via their lipo-chitin Nod signals), but also hostile fungal pathogens (via their cell wall chitin). These data suggest a possible evolutionary relationship between the perception mechanisms of Nod signals and chitin by plants. Experiment Overall Design: wild type Col-0 and chitin receptor mutants treated with or without chitooctaose
2008-06-16 | E-GEOD-8319 | biostudies-arrayexpress
Project description:Plant can perceive and respond natural sound vibration (SV). Artificial SV also served as a novel trigger of induced resistance, although approaches for activating such plant innate immunity intensively studied on the use of biological and chemical agents (BCA). Artificial SV pre-treatment protected Arabidopsis thaliana seedlings against insect pests and fungal pathogens. However, SV-mediated epigenetic modulation remains unexplored while CBA-mediated induced resistance is known as a complicated process involving epigenetic regulation. Here, we performed an expression profiling basd on small RNA-seq experiment to understand the role of 10 kHz SV-mediated epigenetic modification in induced resistance against a soil-borne pathogenic bacterium Ralstonia solanacearum.
2020-08-03 | GSE133321 | GEO
Project description:Plant can perceive and respond natural sound vibration (SV). Artificial SV also served as a novel trigger of induced resistance, although approaches for activating such plant innate immunity intensively studied on the use of biological and chemical agents (BCA). Artificial SV pre-treatment protected Arabidopsis thaliana seedlings against insect pests and fungal pathogens. However, SV-mediated epigenetic modulation remains unexplored while CBA-mediated induced resistance is known as a complicated process involving epigenetic regulation. Here, we performed a gene expression profiling basd on RNA-seq experiment to understand the role of 10 kHz SV-mediated epigenetic modification in induced resistance against a soil-borne pathogenic bacterium Ralstonia solanacearum.
2020-08-03 | GSE133324 | GEO
Project description:Plants establish mutualistic association with beneficial microbes while deploy the immune system to defend against pathogens. Little is known about the interplay between mutualism and immunity and about the mediator molecules. Here we show that plants respond differently to a bacterial volatile compound through integral modulation of the immune system and the phosphate starvation response (PSR) system, resulting in either mutualism or immunity. We found that the same exposure of a recognized plant growth-promoting rhizobacterium unexpectedly causes either beneficial or deleterious effects to plants. The beneficial-to-deleterious transition is dependent on plant nutrition of phosphorus (P) and is mediated by diacetyl (DA), a bacterial volatile compound. In P-sufficient plants, DA partially suppresses plant production of reactive oxygen species (ROS) and enhances symbiont colonization without compromising disease resistance. In P-deficient plants, DA elevates phytohormone-mediated immunity and consequently causes plant hypersensitivity to P deficiency. Therefore, DA affects the types of relation between plants and certain rhizobacteria in a way that depends on plant PSR system and phytohormone-mediated immunity.
2019-12-03 | GSE138478 | GEO
Project description:Bacterial diversity analysis of banana plant samples
| PRJNA494050 | ENA
Project description:Development of cereal crops with high nitrogen-use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improve crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse sorghum lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry (GC-MS) were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxa, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low-N stress. This indicates that the shift in the sorghum microbiome due to low-N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low-N stress.
2023-08-29 | MSV000092783 | MassIVE
Project description:Arabidopsis DEK2, a nuclear protein involved in multiple chromatin-related processes, was found to be phosphorylated in response to flg22 treatment suggesting a role in plant immunity to bacterial pathogens. dek2 loss of function mutants were susceptible to bacterial as well as fungal pathogens. Transcriptome data of the dek2-1 mutant shows that AtDEK2 is a transcriptional repressor of defense related genes, hormone synthesis & signaling genes. ChIP-Seq analysis indicates that DEK2 binds to motifs of several families of transcription factors (TFs) and to class I TCP binding motif regions with the highest affinity. We determined that DEK2 is recruited to specific regions on the chromatin by transcription factors. Our data suggests that DEK2 is a reader of the dual histone mark, H3K4me3K27me3. Finally, based on our data we postulate a hypothetical working model for the function of DEK2 as a transcriptional repressor and targets regions with H3K4me3K27me3 marks.
2026-03-13 | GSE244560 | GEO
Project description:Arabidopsis DEK2, a nuclear protein involved in multiple chromatin-related processes, was found to be phosphorylated in response to flg22 treatment suggesting a role in plant immunity to bacterial pathogens. dek2 loss of function mutants were susceptible to bacterial as well as fungal pathogens. Transcriptome data of the dek2-1 mutant shows that AtDEK2 is a transcriptional repressor of defense related genes, hormone synthesis & signaling genes. ChIP-Seq analysis indicates that DEK2 binds to motifs of several families of transcription factors (TFs) and to class I TCP binding motif regions with the highest affinity. We determined that DEK2 is recruited to specific regions on the chromatin by transcription factors. Our data suggests that DEK2 is a reader of the dual histone mark, H3K4me3K27me3. Finally, based on our data we postulate a hypothetical working model for the function of DEK2 as a transcriptional repressor and targets regions with H3K4me3K27me3 marks.
2026-02-23 | GSE244561 | GEO
Project description:Quorum sensing (QS) enhances bacterial pathogenesis. How plants perceive QS signals remains elusive. Here, we report that Arabidopsis thaliana perceives 2'-aminoacetophenone (2’-AA), a QS-regulated volatile compound emitted from Pseudomonas aeruginosa, through cell-surface pattern recognition receptor (PRR) complexes that require BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE (BAK1). 2’-AA activates PRR-mediated immunity and enhances plant resistance to Pseudomonas pathogens. The 2’-AA-activated immunity displayed structural specificity of the elicitor and genetic specificity of the PRR complexes. 2’-AA induces in vivo protein interactions between BAK1 and its co-functioning PPRs, meanwhile the plant transcriptome responded to 2’-AA similarly as to flg22, a bacterial immunogenic elicitor that activates BAK1-dependent immunity. Hence bacterial QS signals can be sensed by plant cell-surface immune receptors.
2025-07-15 | GSE208376 | GEO