Pseudomonas
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA642738 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome sequences of four Pseudomonads from Oak Ridge Field Research Center
| PRJEB15108 | ENA
Project description:Groundwater from Oak Ridge Integrated Field Research Center, Tennessee - FW301 metagenome
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Project description:Draft genome sequences of Pseudomonas isolates collected at Oak Ridge Field Research Center
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Project description:Oak Ridge Integrated Field Research Challenge (OR-IFRC) Metagenomes
| PRJNA258175 | ENA
Project description:Bacteria are known to adhere to surfaces via self-produced extracellular polymeric substances organized as biofilms. In subsurface areas with low oxygen, limited nutrients, and toxic contaminants, biofilms are crucial for microbial survival and persistence. However, the relationship between biofilm formation and survival in such environments is not well-documented. At the Oak Ridge Reservation Field Research Center (ORRFRC), we observed a high abundance of Rhodanobacter species in conditions with elevated nitrate, metals, organics, and nitric acid. This study investigated the role of biofilm formation in their survival and the underlying molecular mechanisms in diverse geochemical niches. We examined sixteen phylogenetically diverse Rhodanobacter strains for biofilm formation under varying nutrient, pH, and nitrate conditions. Our findings indicate that biofilm formation is a strain-specific phenotype, correlating with environmental stresses, especially in low pH and nitrate conditions. Comparative genomic analysis revealed unique traits in the high biofilm-forming FW021-MT20 strain, such as the absence of flagella and chemotaxis genes and the presence of unique secretion system VI genes, as supported by pangenomic results. Additional tests on biofilm formation in response to field-relevant metals highlighted increased biofilm formation under aluminum stress in strains typically exhibiting weaker biofilm capabilities. Further investigation using RB-Tnseq, proteomics, and TEM indicated flagellar loss under aluminum stress, linked to increased cyclic AMP and di-GMP levels. Our results shed light on the adaptive strategies of Rhodanobacter strains in subsurface environments, suggesting genetic factors linked to biofilm formation and metal stress tolerance, thereby enhancing our understanding of microbial survival under environmental stress.
2025-03-08 | PXD049428 | Pride
Project description:Parental and BXD mouse lines were received from Jackson Laboratory and The Oak Ridge National Laboratory. Splenocytes were isolated and stained with anti-CD4 and anti-CD25 antibodies. CD4+ T cells were separated into CD4+CD25+ Treg and CD4+CD25- Th cells. Tregs and Th cell were collected from spleens of 31 BXD recombinant inbred strains and of the parental mouse strains DBA/2J and C57BL/6J. Gene expression was measured by microarrays. The comparative analysis of the transcriptomes from the two cell populations allowed us to identify many novel differentially expressed genes. Furthermore, the analysis of cis- and trans-expression Quantitative Trail Loci (eQTLs) showed that both common and unique regulatory mechanisms are active in the two cell types.
2011-12-15 | E-MTAB-836 | biostudies-arrayexpress
Project description:The purpose of this study was to make a single comparison between Cqf genes expressed during the vegetative stages of infection on the telial host (oak leaf) versus the aecial host (pine stem). A large proportion of genes were expressed in both hosts and significantly differentially expressed genes were enriched for candidate fungal effectors (small secreted proteins). These results suggest that the Cqf rust fungus uses a largely common set of genes to create two very different infection phenotypes. This study was based on hybridizations to custom microarrays containing features representing 8692 gene models from a Cqf genome sequencing project midpoint assembly. Two Agilent 4 X 44K microarray slides were populated with 60-mer probes (1 to 5 per transcript), designed using AgilentM-bM-^@M-^Ys web-based eArray software. Labeled target cRNA (complementary RNA) was generated using AgilentM-bM-^@M-^Ys Low Input Quick Amp Labeling Kit, such that oak and pine samples were labeled with either cy3 or cy5 an equal number of times across the experiment. Each microarray was hybridized with labeled cRNA target derived from a single oak sample and labeled cRNA target derived from a single pine sample. There were a total of eight oak sample replications and eight pine sample replications. Target hybridization and scanning were performed by the University of FloridaM-bM-^@M-^Ys Interdisciplinary Center for Biotechnology Research using standard procedures and an Agilent G250B Scanner.
2013-10-25 | E-GEOD-51655 | biostudies-arrayexpress
Project description:Three different strains of PGPR pseudomonads and their respective Tn5 mutants. Metabolomic extraction in dichloromethane.
2022-07-06 | MSV000089821 | MassIVE