Pseudomonas
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ABSTRACT:
PROVIDER: PRJNA414589 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River.
2016-08-02 | GSE85064 | GEO
Project description:<p> Soil contamination with heavy metals, particularly lead (Pb) and cadmium (Cd), has become a growing environmental concern due to rapid industrialization. Salix matsudana, a woody energy plant with notable tolerance to heavy metals, exhibits considerable potential for use in phytoremediation. Although nitrogen (N) fertilization is known to promote the growth of S. matsudana, its dual role in enhancing plant development and improving soil conditions remains insufficiently understood. In this study, we systematically examined the effects of varying nitrogen fertilizer concentrations on the growth of S. matsudana, heavy metal uptake, and rhizosphere soil characteristics through integrated physiological and multi-omics approaches. Our findings revealed that high nitrogen levels significantly increased plant biomass and the accumulation of Pb and Cd compared to control conditions. Detailed physiological analyses demonstrated enhanced heavy metal absorption in roots under nitrogen fertilization. Microbial community analysis further indicated that nitrogen application altered rhizosphere microbial activity, particularly enriching bacterial taxa associated with metal mobilization. Metabolomic profiling corroborated improvements in soil quality, showing significant changes in organic acid metabolites involved in metal chelation. These results provide new insights into the mechanisms by which nitrogen fertilization synergistically enhances both the growth of S. matsudana and the efficiency of soil remediation, offering valuable guidance for optimizing phytoremediation strategies in heavy metal-contaminated environments.</p>
2025-07-19 | MTBLS12749 | MetaboLights
Project description:Anthropogenic pollution has increased the levels of heavy metals in the environment. Bacterial populations continue to thrive in highly polluted environments and bacteria must have mechanisms to counter heavy metal stress. We chose to examine the response of the environmentally-relevant organism Pseudomonas aeruginosa to two different copper treatments. A short, 45 min exposure to copper was done in the Cu shock treatment to examine the immediate transcriptional profile to Cu stress. The Cu adapted treatment was designed to view the transcriptional profile of cells that were actively growing in the presence of Cu. Keywords: stress response
2006-10-04 | GSE4152 | GEO
Project description:Anthropogenic pollution has increased the levels of heavy metals in the environment. Bacterial populations continue to thrive in highly polluted environments and bacteria must have mechanisms to counter heavy metal stress. We chose to examine the response of the environmentally-relevant organism Pseudomonas aeruginosa to two different copper treatments. A short, 45 min exposure to copper was done in the Cu shock treatment to examine the immediate transcriptional profile to Cu stress. The Cu adapted treatment was designed to view the transcriptional profile of cells that were actively growing in the presence of Cu. Experiment Overall Design: We analyzed 2 biological replicates of Pseudomonas aeruginosa exposed to a 45 min Cu shock as compared to a control that was exposed to HCl to bring the pH to similar levels. We analyzed 2 biological replicates of Pseudomonas aeruginosa that were grown in the presence of Cu for approx. 6h (Cu adapted) as compared to an untreated control.
2007-10-24 | E-GEOD-4152 | biostudies-arrayexpress
Project description:Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River. Three groups of samples, A, B and C. Every group has 3 replicates.
2016-08-02 | E-GEOD-85064 | biostudies-arrayexpress
Project description:Pseudomonas fluorescens strain SS101 (Pf.SS101) promotes growth of Arabidopsis thaliana, enhances greening and lateral root formation, and induces systemic resistance (ISR) against the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). Here, targeted and untargeted approaches were adopted to identify bacterial determinants and underlying mechanisms involved in plant growth promotion and ISR by Pf.SS101. Based on targeted analyses, no evidence was found for volatiles, lipopeptides and siderophores in plant growth promotion by Pf.SS101. Untargeted, genome-wide analyses of 7,488 random transposon mutants of Pf.SS101 led to the identification of 21 mutants defective in both plant growth promotion and ISR. Many of these mutants, however, were auxotrophic and impaired in root colonization. Genetic analysis of three mutants followed by site-directed mutagenesis, genetic complementation and plant bioassays revealed the involvement of the phosphogluconate dehydratase gene edd, the response regulator gene colR and the adenylsulfate reductase gene cysH in both plant growth promotion and ISR. Subsequent comparative plant transcriptomics analyses strongly suggest that modulation of sulfur assimilation, auxin biosynthesis and transport, steroid biosynthesis and carbohydrate metabolism in Arabidopsis are key mechanisms linked to growth promotion and ISR by Pf.SS101. Comparative transcriptome analysis of Arabidopsis treated with Pf. SS101, a growth and ISR promoting rhizobacteria and plants treated with cysH mutant of Pf.SS101 that fails to induce the afformentioned phenotypes
2017-08-26 | GSE103117 | GEO
Project description:Silver nanoparticles (AgNPs) are one of the most promising options for the control of bacterial pathogens. The effectiveness of AgNPs has been proven by several recent research studies in which toxicity against a broad range of human and plant pathogenic bacteria was observed, even when used at low doses compared to other conventional bactericides. Nevertheless, the antibacterial mechanism of AgNPs is yet to be completely understood. This study investiagted the first response of Pseudomonas syringae pv. tomato strain DAPP-PG 215, the causative agent of bacterial speck disease of tomato, to AgNPs. Gene expression of P. syringae pv. tomato in response to AgNPs was observed after 10 and 30 minutes of exposure. A total of 78 and 66 genes were identified as differentially expressed, respectively. Gene ontology and KEGG pathway enrichment analysis revealed a high representation of genes related to stress resistance, energy metabolism, and metal ion binding proteins, with different transporters involved. Validation of four selected genes by quantitative RT-PCR analysis, confirmed these observations. These results not only supported initial findings on the antimicrobial action of AgNPs, but also suggested a significant impact of different heavy metal – toxin transporters in the silver detoxification mechanism of bacteria.
2025-09-23 | GSE308472 | GEO
Project description:This study provides comparative RNA-seq datasets for four freshwater bacterial isolates, Pseudomonas sp. FBCC-B13192, Herbaspirillum sp. FBCC-B12834, Pantoea sp. FBCC-B5559, and Micrococcus sp. FBCC-B5738, cultured under iron-replete (+100 uM FeCl3) and iron-limited (no FeCl3) conditions. Iron availability is a key factor influencing bacterial fitness, and iron limitation is known to activate siderophore biosynthesis, iron transport, and homeostasis pathways. A total of eight libraries generated in 2024 and 2025 were analyzed, comprising 349.9 million processed reads. Reference-guided mapping rates varied among strains, with higher mapping efficiency observed in Pseudomonas, Herbaspirillum, and Pantoea, while Micrococcus showed comparatively lower mapping rates under both conditions. Differential expression analysis revealed strain-specific responses to iron limitation. Genes related to pyoverdine and ferrichrome uptake were enriched in Pseudomonas and Herbaspirillum, enterobactin-associated pathways were prominent in Pantoea, and genes associated with siderophore production, heme utilization, and Fe-S cluster assembly were identified in Micrococcus. Raw sequencing data are available in the NCBI Sequence Read Archive under BioProject PRJNA1456794, and processed data are deposited in a public repository. These datasets provide a valuable resource for understanding bacterial adaptation to iron availability and for comparative transcriptomic analyses.
2026-05-04 | GSE329534 | GEO
Project description:Pseudomonas aeruginosa (P. aeruginosa) lung infection is a significant cause of mortality in patients with cystic fibrosis (CF). Most CF patients acquire unique P. aeruginosa strains from the environment; however clonal strains have been identified in CF communities in several countries. Two clonal strains infect 10% to 40% of patients in three CF clinics in mainland eastern Australia. The expression profiles of four planktonically-grown isolates of one Australian clonal strain (AES-2), and four non–clonal CF P. aeruginosa isolates were compared to each other and to the reference strain PAO1 using the Affymetrix P. aeruginosa PAO1 genome array, to gain insight into properties mediating the enhanced infectivity of AES-1. The isolates were subsequently grown as 3-day old biofilms and similarly extracted for RNA and compared as above. Data analysis was carried out using BIOCONDUCTOR software. Keywords: Comparative strain hybridization
2009-02-05 | GSE10304 | GEO