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Pseudomonas fluorescens transcriptome in flowback water

ABSTRACT: The goal of the study was to examine the influence of flowback water exposure on bacterial survival and biocide tolerance. The transcriptome of P. fluorescens was analyzed using RNA-seq to determine the gene rxpression profile changes occuring upon flowback water exposure. The results indicate that that P. fluorescens induces a well-coordinated genetic response that aids in its survival in flowback water as well as imparts enhanced tolerance against typically used slow acting biocides such as gluteraldehyde but increased susceptibity towards sodium hypochlorite. RNA-seq data demonstrated significant induction of genes involved in osmotic stress, energy production and conversion, membrane integrity, protein transport among others.

ORGANISM(S): Pseudomonas fluorescens

PROVIDER: GSE55388 | GEO | 2014/12/23

SECONDARY ACCESSION(S): PRJNA239456

REPOSITORIES: GEO

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Pseudomonas fluorescens transcriptome in flowback water

Project description:The goal of the study was to examine the influence of flowback water exposure on bacterial survival and biocide tolerance. The transcriptome of P. fluorescens was analyzed using RNA-seq to determine the gene rxpression profile changes occuring upon flowback water exposure. The results indicate that that P. fluorescens induces a well-coordinated genetic response that aids in its survival in flowback water as well as imparts enhanced tolerance against typically used slow acting biocides such as gluteraldehyde but increased susceptibity towards sodium hypochlorite. RNA-seq data demonstrated significant induction of genes involved in osmotic stress, energy production and conversion, membrane integrity, protein transport among others. Examination of P. fluorescens transcriptome exposed to flowback water for one hour and compare with PBS exposed cells.

2014-12-23 | E-GEOD-55388 | biostudies-arrayexpress

Glutaraldehyde resistance mechanisms in Pseudomonas fluorescens and Pseudomonas aeruginosa biofilms

Project description:The objective of the current study was to understand the glutaraldehyde resistance mechanisms in P. fluorescens and P. aeruginosa biofilms. Glutaraldehyde is a common biocide used in various industries to control the microbial growth. Recent reports of emergence of glutaraldehyde resistance in several bacterial species motivated this study to understand the genetic factors responsible got glutaraldehyde resistance. Using a combination of phenotypic assays, chemical genetic assays and RNA-seq, we demonstrate that novel efflux pump, polyamine biosynthesis, lipid biosynthesis and phosphonate degradation play significant role in glutaraldehyde resistance and post-glutaraldehyde recovery of Psudomonad biofilms. Examination of P. fluorescens 72 h biofilm transcriptome was elucidated upon exposure to glutaraldehyde. The results were confirmed using qRT--PCR and chemical genetic appraoches in P. fluorescens and P. aeruginosa.

2015-04-06 | E-GEOD-64448 | biostudies-arrayexpress

Glutaraldehyde resistance mechanisms in Pseudomonas fluorescens and Pseudomonas aeruginosa biofilms

2015-04-06 | GSE64448 | GEO

Pseudomonas fluorescens

Project description:Pseudomonas fluorescens transcriptome in flowback water

| PRJNA239456 | ENA

RNA-Seq of Pseudomonas fluorescens SBW25 isolated from axenic rhizospheres of the barley varieties Chevallier and Tipple one and five days post-inoculation.

Project description:Pseudomonas fluorescens SBW25 cultures were inoculated into the rhizospheres of barley seedlings of the Chevallier and Tipple varieties growing in axenic cultures. Bacterial cells were collected from the rhizosphere one and five days after inculation and RNA extracted from them. Culture used for inoculation (but not exposed to the rhizospheres) were used as control. The aim of the experiment was to determine the changes in gene expression of P. fluorescens SBW25 upon exposure to barley rhizosphere and also to determine if the rhizospehres of the two varieties of Barley had different effects on gene expression of P. fluorescens SBW25.

2023-05-15 | E-MTAB-12918 | biostudies-arrayexpress

Early gene expression in Pseudomonas fluorescens exposed to a polymetallic solution

Project description:Our main objective was to study the changes in cDNA microarray gene expression profiles of P. fluorescens cells exposed to different doses of a polymetallic solution containing Ag (I), Pb (II), Cd (II), Cu (II), Ni (II) and Zn (II)) over two exposure times (5 and 15 minutes). Control cells grown in the absence of metals were also included in the experiment.

2014-11-26 | E-MTAB-3094 | biostudies-arrayexpress

Iron deficiency response of interactions between Brachypodium and Pseudomonas fluorescens SBW25 under controlled growth conditions.

Project description:The goal of this study was to evaluate the molecular mechanisms by which Brachypodium distachyon grown with and without Pseudomonas fluorescens (P. fluorescens) strain SBW25 respond to Fe deprivation. Fe deprivation induced Brachypodium secretion of phytosiderophores and reduced biomass production while inoculation with P. fluorescens resulted in alterations of extracellular metabolite abundances. Results provide insight into the role of iron in interactions between a host plant and root associated bacteria.

2020-09-22 | GSE158273 | GEO

Iron-starvation effect on transcriptome of Pseudomonas fluorescens Pf-5

Project description:This SuperSeries is composed of the following subset Series: GSE29319: Iron-starvation effect on transcriptome of Pseudomonas fluorescens Pf-5: iron(II) chloride GSE29320: Iron-starvation effect on transcriptome of Pseudomonas fluorescens Pf-5: iron(III) chloride Refer to individual Series

2011-05-16 | E-GEOD-29322 | biostudies-arrayexpress

Tannic acid treatment effect on transcriptome of Pseudomonas fluorescens Pf-5

Project description:This SuperSeries is composed of the following subset Series: GSE33907: Tannic acid (20 µg/ mL) treatment effect on transcriptome of Pseudomonas fluorescens Pf-5 GSE33908: Tannic acid (160 µg/ mL) treatment effect on transcriptome of Pseudomonas fluorescens Pf-5 Refer to individual Series

2011-11-24 | E-GEOD-33909 | biostudies-arrayexpress

Combining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescens

Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.

2019-11-12 | PXD010845 | Pride

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