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Effects of bacterium Burkholderia phytofirmans PsJN in Arabidopsis

ABSTRACT: Plant growth promoting rhizobacteria (PGPR) induce positive effects in plants, such as increased growth or reduced stress susceptibility. The mechanisms behind PGPR/plant interaction are poorly understood, as most studies have described short- term responses on plants and only a few studies have analyzed plant molecular responses under PGPR colonization. Transcriptional profiles were determined by microarray analysis (Affymetrix ATH1 Genome Array) in Arabidopsis thaliana plants inoculated with the PGPR bacterial model Burkholderia phytofirmans PsJN

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE47092 | GEO | 2013/05/31

SECONDARY ACCESSION(S): PRJNA203542

REPOSITORIES: GEO

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Effects of bacterium Burkholderia phytofirmans PsJN in Arabidopsis

Project description:Plant growth promoting rhizobacteria (PGPR) induce positive effects in plants, such as increased growth or reduced stress susceptibility. The mechanisms behind PGPR/plant interaction are poorly understood, as most studies have described short- term responses on plants and only a few studies have analyzed plant molecular responses under PGPR colonization. Transcriptional profiles were determined by microarray analysis (Affymetrix ATH1 Genome Array) in Arabidopsis thaliana plants inoculated with the PGPR bacterial model Burkholderia phytofirmans PsJN Arabidopsis seeds were sown on square Petri dishes with half strength Murashige and Skoog medium (MS) 0.8% agar, and inoculated or not (control) with strain PsJN. To assess the effect of inactivated bacteria, an inoculum was heated at 95M-BM-0C for 20 min and then was used at the same dilution.Three biological replicates, consisting of ten plantlets of 13 days after sowing (DAS) each, for control and strain PsJN treatments, were used for global gene expression.

2013-05-31 | E-GEOD-47092 | biostudies-arrayexpress

Improving coriander yield and quality with a beneficial bacterium

Project description:Plant growth-promoting rhizobacteria (PGPR) are soil microbes that can promote plant growth and/or increase plant resistance to one or multiple stress conditions. These natural resources are environmentally friendly tools for reducing the use of chemical fertilizers and pesticides and for improving the nutritional quality of plants, including pharmacological metabolites. Coriander (Coriandrum sativumL.), commonly known as cilantro or Chinese parsley, is a worldwide culinary and medicinal plant with both nutritional and medicinal properties. Little is known about how PGPR may promote plant growth or affect metabolite profiles in coriander. Here, by usingAeromonassp. H1 that is a PGPR strain, we investigate how coriander yield and quality could be affected by PGPR with transcriptome insights.

2024-03-11 | GSE247080 | GEO

Transcriptome profiling of Bacillus subtilis OKB105 in response to rice seedlings

2014-10-17 | GSE62421 | GEO

arcole / pgpr-Nitrogenous nutrition efficiency of canola in spring : identification of targets for plant breeding

Project description:pc_arcole - arcole / pgpr - What are the genes implicated in the efficiency of nitrogenous nutrition when A.thaliana is inoculated with a PGPR (Plant Growth Promoting Rhizobacteria)? - A.thaliana seeds germinated and grew during ten days until they were transfered in 6 different media: 0,5 mM nitrate with PGPR (Plant Growth Promoting Rhizobacteria), 0,5mM nitrate without PGPR, 2mM nitrate with PGPR, 2mM nitrate without PGPR, 20 mM nitrate with PGPR, 20 mM nitrate without PGPR. Young plantlets grew 7 days in these new mediums. Shoots are collected in eppendorf.

2012-06-01 | GSE36730 | GEO

arcole / pgpr-Nitrogenous nutrition efficiency of canola in spring : identification of targets for plant breeding

2012-05-31 | E-GEOD-36730 | biostudies-arrayexpress

Transcriptome profiling of Bacillus subtilis OKB105 in response to rice seedlings

Project description:Plant growth-promoting rhizobacteria (PGPR) are soil beneficial microorganisms that colonize plant roots for nutritional purposes and accordingly benefit plants by increasing plant growth or reducing disease. But it still remains unclear which mechanisms or pathways are involved in the interactions between PGPR and plants. To understand the complex plant-PGPR interactions, the changes in the transcriptome of typical PGPR standard Bacillus subtilis in responding to rice seedlings were analyzed. We compared and anylyzed the transcriptome changes of the bacteria Bacillus subtilis OKB105 in response to rice seedings for 2 h. Total RNA was extracted and Random priming cDNA synthesis, cDNA fragmentation and terminal labeling with biotinylated GeneChip DNA labeling reagent, and hybridization to the Affymetrix GeneChip Bacillus subtilis Genome Array.

2014-10-17 | E-GEOD-62421 | biostudies-arrayexpress

RNA-Seq gene expression profiling in the plant growth promoting Bacillus atrophaeus UCMB-5137 revealed an alternative strategy of plant colonization compared to Bacillus amyloliquefaciens endophytes

Project description:Plant growth promoting rhizobacteria (PGPR) of the genus Bacillus are successfully used as biofertilizers and biopesticides. They potentially can reduce the use of chemicals in agriculture as an ecologically safe alternative, but to optimize the application of PGPR, more profound knowledge on specific gene regulation and molecular mechanisms of interaction with plants is needed. Advance in sequencing technologies made it affordable to compare transcriptom profiles of relative organisms to check to which extend PGPR strains or closely related species differ in their strategies of plant colonization. This work aimed at analysis of gene regulation in a biotechnological strain Bacillus atrophaeus UCMB-5137 to compare it with the gene expression profile of a generally recognized PGPR strain B. amyloliquefaciens FZB42. It was found out that despite the close taxonomic relatedness, these two organisms developed ability to colonize plants independently and use different strategies of plant colonization. Root exudate has triggered in UCMB-5137 alteration in expression in many genes controlled by stress response transcription factors (TF) SigB and SigD, while SigF, SigH, SigW, CcpA and several other TFs regulated genes associated with quorum sensing and biofilm formation, and adjusted the carbohydrate metabolism. Counting to peculiarities of gene regulation in different PGPR strains will allow optimization of their practical application.

2015-05-06 | GSE68543 | GEO

Transcriptome analysis of rice roots in response to plant growth promoting bacterium Bacillus subtilis RR4

Project description:The aim of our study is to elucidate the gene expression changes in rice in response to colonization by a plant growth promoting rhizobacteria such as the Bacillus subtilis through microarray high throughput technology. In particular, the effect of B.subtilis on root exudation (secretion of phytochemicals through roots) will be analysed. For this rice plantlets were grown in hydroponics and treated with B.subtilis RR4 for 48 hrs. The root samples of the control and treated plants were then used for the microarray experiment. The data obtained through microarray revealed genes related to cell wall modification, phytohormone synthesis, defense response, root exudation, etc. to be differentially regulated in response to B.subtilis RR4. Real time PCR analysis of few chosen genes (OsMS, OsALMT, OsABC, OsSDH, etc) also confirmed the validity of the microarray data. The initial responses of a plant in response to colonization by the microbe will be changes in cell wall of the plant tissues and the secretion of phytochemicals to attract/repel the colonizing beneficial/pathogenic organism. From analysis of microarray data we found the cell wall related genes which aid in root colonization and the root exudate related genes (biosynthesis and transport) which play a role in providing nutrition for the bacterial growth to be differentially regulated significantly. Analysis of specific genes and their biosynthesis pathways indicated that rice plants responded positively to root colonization by B.subtilis RR4. Notable among the exudation related genes such as Malate synthase and ALMT were found to be upregulated which indicates the significant role played by organic acids particularly malate in recruiting the PGPR towards the plant roots. This recruitment will thereby facilitate plant growth. Subsequently, these genes can be engineered in crop plants to recruit beneficial bacteria which might further open new avenues for improved crop production.

2017-01-05 | GSE80800 | GEO

Volatiles of two growth-inhibiting rhizobacteria commonly enroll AtWRKY18 function

Project description:Volatiles of certain rhizobacteria can cause growth inhibitory effects on plants/ Arabidopsis thaliana. How these effects are initiated and which mechanisms are enrolled is not yet understood. Obviously the plant can survive/live with the bacteria in the soil, which suggest the existance of a regulatory mechanism/network that provide the possibility for coexistance with the bacteria. To shed light on this regulatory mechanism/network we performed a microarray anlaysis of Arabidopsis thaliana co-cultivated with two different rhizobacteria strains. In this study we used the ATH1 GeneChip microarray to investigate the transcriptional response of 4 to 5 days old Arabidopsis thaliana seedlings at 6 h, 12 h and 24 h exposure to volatiles of the rhizobacteria Serratia plymuthica HRO-C48 or Stenotrophomonas maltophilia R3089.

2012-01-25 | GSE35325 | GEO

PGPR isolated from the rhizosphere of a wheat ancestor and active in an elite cultivar: metabolomics and proteomics of bacterial exudates affecting root development

Project description:Two diazotrophic bacteria, BPMP-PU-28 and BPMP-EL-40, isolated from the rhizosphere of a wild wheat ancestor (T. t. dicoccoides) grown in soil from its refuge area in the Fertile Crescent or from south of France, respectively, were shown to behave as efficient Plant Growth Promoting Rhizobacteria (PGPR) upon interaction with an elite wheat cultivar (Anvergur), providing about 50% of the seed nitrogen content in plants grown under low assimilable nitrogen availability. A bacterial growth medium was developed to investigate the effects of bacterial exudates on root development in the elite cultivar and to analyze the exo-metabolomes and exo-proteomes of the two strains. Altered root development was observed, with distinctive responses according to the strain, BPMP-PU-28 also inducing a strong increase in root hair length and density. Exo-metabolome analysis revealed a complex set of secondary metabolites including fatty acids potentially involved in volatile organic compounds (VOCs) metabolism, cyclopeptides that could act as phytohomone mimetics, quorum sensing molecules having inter-kingdom signaling properties and nutrient ion chelators. The exo-proteome comprised a set of strain specific enzymatic activities (e.g., proteases) and structural proteins belonging to outer-membrane vesicles likely to sequester metabolites, peptides and enzymes in their lumen. Thus, the wheat ability to establish efficient beneficial interactions with PGPR has not been profoundly reprogrammed during domestication and breeding, and PGPR constitutively exude rich and complex metabolomes and proteomes, in absence of partner roots, which could allow numerous mechanisms to simultaneously contribute to plant growth promotion and thereby broaden the range of responsive plant species.

2023-03-08 | PXD034914 | Pride

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