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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE36730 | GEO | 2012/06/01

SECONDARY ACCESSION(S): PRJNA167819

REPOSITORIES: GEO

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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. 6 dye-swap - dose response,organ comparison,treated vs untreated comparison

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

Transcriptome profiling of Bacillus subtilis OKB105 in response to rice seedlings

2014-10-17 | GSE62421 | GEO

Effects of bacterium Burkholderia phytofirmans PsJN in Arabidopsis

2013-05-31 | GSE47092 | GEO

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

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

Nitrogen nutrition of E. coli in the mammalian intestine

Project description:Our focus of this study is to determine the differential expression of genes related to uptake and degradation of nitrogenous compounds in E. coli colonizing the mouse intestine as compared to E. coli grown in minimal medium in vitro. We colonized CD-1 male mice with E. coli MG1655 StrR wild type and extracted the total RNA from mouse cecal mucus (GSE217743). We also colonized CD-1 male mice with E. coli MG1655 ∆glnG StrR CamR and extracted the total RNA from mouse cecal mucus. We grew E. coli MG1655 StrR wild type in MOPS minimal medium containing high nitrogen (10 mM NH4Cl) and low nitrogen (3 mM NH4Cl) and extracted the total RNA from exponential phase and stationary phase culture. We also grew E. coli MG1655 ∆glnG StrR CamR in MOPS minimal medium containing low nitrogen (3 mM NH4Cl) and extracted the total RNA from exponential phase culture. The extracted RNA samples were sequenced, and differential expression analysis was done to determine the genes related to uptake and degradation of nitrogenous compounds that are important for E. coli colonization. Our results indication nitrogen is not limiting for E. coli in the intestine and genes related to uptake and degradation of several aminoacids, di- and tripeptides, aminosugars, ethanolamine, urea among others are upregualated in the mouse intestine as compared to invitro culture grown in high nitrogen conditions.

2024-01-29 | GSE241658 | GEO

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

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

profiling of the pgpr induced systemic resistance (isr)-Arabidopsis thaliana transcriptome analysis in respons...

Project description:ra04-07_pgpr - profiling of the pgpr induced systemic resistance (isr) - Experiment 1 : Which genes are up- or down-regulated in Arabidopsis thaliana cultivated in vitro with increased lateral root development in response to Phyllobacterium STM196 inoculation. Experiment 2 : Which genes are up- or down-regulated during the ISR triggered by a rhizobacteria, in comparison with those affected by a pathogenic interaction. Experiment 3 : which genes are specifically induced or repressed in Arabidopsis thaliana by inoculation of the soil with a PGPR vs a bacteria that has the ability to trigger nodule formation in a Legume. - Seeds were sawn on 0.8% (W/V) agar mineral medium (see below). 4 days after storage in the dark at 4degreeC, seedling were cultivated 6 days in a growth chamber (16 h daily, 20-22degreeC) and then transferred on soil inoculated or not with 107 cfu.g-1 of Bradyrhizobium strain ORS278. Three weeks later, 3 leaves per plant were infiltrated with a suspension of Pseudomonas syringae pv. tomato (2.105 cfu.ml-1) or with MgSO4 10 mM alone for control plants. Infiltrated leaves were collected 24h later. Keywords: normal vs rnai mutant comparaison,treated vs untreated comparison

2007-06-20 | GSE7990 | GEO

barley responses to nitrate limitation-BarIEy Stress Tolerance

Project description:ngs2020_19_arimnet-barley responses to nitrate limitation-What are the molecular mechanisms taking place in barley under nitrate limitation?-Barley were grown on sand under 0.5 mM nitrate (Low nitrate= LN) or 5 mM nitrate (high nitrate = HN)

2022-01-24 | GSE188216 | GEO

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