Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: PGPR and Biocontrol Bacillus strains

PROVIDER: PRJNA1095867 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR28539087_1.fastq.gz	Fastqsanger.gz
	SRR28539087_2.fastq.gz	Fastqsanger.gz
	SRR28539088_1.fastq.gz	Fastqsanger.gz
	SRR28539088_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 11

Similar Datasets

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 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

Transcriptome profiling of Bacillus subtilis OKB105 in response to rice seedlings

2014-10-17 | GSE62421 | GEO

The flavonoid-sensing regulator AefR is involved in modulating quorum sensing through repressing the MexEF-OprN efflux pump in Pseudomonas fluorescens

Project description:Pseudomonas fluorescens is an important plant growth-promoting rhizobacteria (PGPR) for its biocontrol properties, which are mostly influenced by the quorum sensing (QS) system. Plants produce multiple metabolites like flavonoids to regulate physiology of PGPR. However, it remains under-explored how flavonoids produced by plant roots influence the QS system of PGPR. In this study, we found the TetR-family regulator AefR was capable of binding to flavonoids and could inhibit production of AHLs by suppressing the expression of mexEF-oprN in P. fluorescens 2P24. We further showed that the efflux pump MexEF-OprN could attenuate the quorum sensing system PcoR/PcoI by extruding homoserine lactone (AHLs) molecules, leading to reduced biosynthesis of secondary metabolite mupirocin. Taken together, this study identified a TetR-like regulator responding to plant flavonoids and regulating the quorum sensing, providing insights into the interaction between PGPR and plant roots.

2025-02-15 | PXD052702 | Pride

The flavonoid-sensing regulator AefR is involved in modulating quorum sensing through repressing the MexEF-OprN efflux pump in Pseudomonas fluorescens

2025-02-15 | PXD052703 | Pride

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

Soil Pseudomonas - GAC signal identification

Project description:Three different strains of PGPR pseudomonads and their respective Tn5 mutants. Metabolomic extraction in dichloromethane.

2022-07-06 | MSV000089821 | MassIVE

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

2013-05-31 | GSE47092 | GEO

Transcriptional reprogramming underpins enhanced plant growth promotion by the biocontrol fungus Trichoderma hamatum GD12 during antagonistic interactions with Sclerotinia sclerotiorum in soil

Project description:The free-living soil fungus Trichoderma hamatum GD12 is notable amongst other Trichoderma strains in exhibiting both biocontrol and plant growth promotion (PGP) activities, which are coincident with a markedly expanded genome when compared to other characterised biocontrol and PGP isolates. Here, we make direct comparisons of T. hamatum GD12 transcription during PGP, and during antagonism of the root-infecting pathogen Sclerotinia sclerotiorum, in peat-based microcosms. An extensive mRNA-seq analysis sampling six time-points, 1, 2, 4, 7, 10 and 15 days after microcosm establishment revealed dynamic and biphasic signatures in the transcriptional responses of T. hamatum GD12 during Sclerotinia biocontrol and lettuce growth promotion. Functional analysis of differentially expressed genes demonstrated up-regulation of transportation and oxidation-reduction genes during both processes. Sclerotinia biocontrol is most likely mediated by the synthesis and secretion of antifungal compounds. Notably, the biphasic response during biocontrol was further characterised by the expression of a number of uncharacterised GD12 genes, small-secreted cysteine rich proteins and secondary metabolite producing gene clusters. This work demonstrates that T. hamatum GD12 harnesses a reservoir of uncharacterised genes that are actively engaged during effective biological control of a plurivorous plant pathogen.

2016-05-16 | GSE67909 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data