Exudate utilization
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB44710 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The secretion of metabolites by plant roots is a key determinant of microbial growth and colonisation. We have used Pisum sativum and its natural symbiont Rhizobium leguminosarum (it can form N2 fixing nodules on pea roots) to study the natural metabolites secreted by roots. To do this root secretion was harvested from pea plants grown under sterile conditions. This root exudate was then concentrated and used as a sole carbon and nitrogen source for growth of the bacteria in the laboratory. These bacteria were harvested in mid-exponential growth and RNA extracted for microarray analysis. As control cultures the bacteria were grown on 30 mM pyruvate as a carbon source and 10 mM ammonium chloride as a nitrogen source and RNA extracted. Two colour microarrays were performed using root exudate cultures versus pyruvate ammonia grown cultures. This was done in biological triplicate.
2016-05-25 | E-MTAB-4790 | biostudies-arrayexpress
Project description:Traumatic strain injury in skeletal muscle is often associated with fluid accumulation on the site of rupture, but the role of this injury exudate in cellular responses and healing is unknown. Exudate fluid from subjects suffering from acute hamstering or calf muscle strain injury was aspirated and the cells isolated. These exudate cells and cells derived from the blood were subjected to RNA sequencing and compared to analyze the nature of the exudate cells.
2019-06-19 | GSE130836 | GEO
Project description:Cercospora armoraciae causes leaf spot disease on Armoracia rusticana. Exudation of droplets, when grown on PDA, distinguishes this fungi from other members of the genus Cercospora. The role this exudate plays in the virulence of this pathogen has not been elucidated. To explore this, we characterized the proteome of exudate associated with this plant pathogen. Nano-HPLC-MS/MS analysis was used to identify proteins in the pathogen exudate. A total of 576 proteins comprising 1,538 peptides, 1,524 unique peptide, were identified from the exudate.
2020-07-16 | PXD019663 | Pride
Project description:The effect of selected adjuvants on the mRNA expression of peritoneal exudate cells.
2009-09-23 | E-MEXP-1814 | biostudies-arrayexpress
Project description:Rice false smut (RFS) is a kind of fungal disease transforming panicles and spikelets into greenish spore balls, caused by Ustilaginoidea virens. During artificial cultivation process, macroscopic exudates could be observed, which is a common feature in many kinds of fungi. We characterized the proteome of exudate associated with this plant pathogen. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis was used to identify proteins in the pathogen exudate. A total of 685 proteins comprising 3,949 peptides were identified from the exudate. This study regarded the biological characteristics of U. virens as an entry point. By studying the protein components of the exudates of U. virens, it is helpful to better understand the occurrence and pathogenic mechanism of pathogen and provide a theoretical basis for the control of RFS.
2021-04-08 | PXD019861 | Pride
Project description:Marine algae convert a substantial fraction of the carbon dioxide they fix into various polysaccharides. Bacteria specialized on the remineralization of these polysaccharides often feature genomic clusters, termed polysaccharide utilization loci (PULs). Such PULs are often prevalent in, but not limited to, marine Flavobacteriia. Since knowledge on extant PUL diversity is sparse, we sequenced the genomes of 53 North Sea Flavobacteriia. We obtained 400 PULs, suggesting usage of a large array of polysaccharides, including laminarin, α- and β-mannans, fucose-, xylose-, galactose-, rhamnose- and arabinose-containing substrates, pectins, and chitins. Many of the PULs were novel, some indicating substrates that have rarely been described in marine environments. PUL repertoires of isolates often differed significantly within genera, corroborating ecological niche-associated glycan partitioning. Polysaccharide uptake in Flavobacteriia is mediated by SusCD. Respective protein trees revealed clustering according to polysaccharide specificities. Analysis of SusCD expression in multiyear phytoplankton bloom-associated metaproteomes indicated changes in microbial utilization of glucan, ß-mannan and sulfated xylan, suggesting that distinct substrates are temporarily abundant.
2018-08-16 | PXD008238 | Pride
Project description:Phytoplankton and bacteria form the base of marine ecosystems and their interactions drive global biogeochemical cycles. The effect of bacteria and bacteria-produced compounds on diatoms range from synergistic to pathogenic and can affect the physiology and transcriptional patterns of the interacting diatom. Here, we investigate physiological and transcriptional changes in the marine diatom Thalassiosira pseudonana induced by extracellular metabolites of a known antagonistic bacterium Croceibacter atlanticus. Mono-cultures of C. atlanticus released compounds that inhibited diatom cell division and elicited a distinctive phenotype of enlarged cells with multiple plastids and nuclei, similar to what was observed when the diatom was co-cultured with the live bacteria. The extracellular C. atlanticus metabolites induced transcriptional changes in diatom pathways that include recognition and signaling pathways, cell cycle regulation, carbohydrate and amino acid production, as well as cell wall stability. Phenotypic analysis showed a disruption in the diatom cell cycle progression and an increase in both intra- and extracellular carbohydrates in diatom cultures after bacterial exudate treatment. The transcriptional changes and corresponding phenotypes suggest that extracellular bacterial metabolites, produced independently of direct bacterial-diatom interaction, may modulate diatom metabolism in ways that support bacterial growth.
2022-06-24 | GSE197934 | GEO
Project description:Polysachharide utilization loci in rumen bacteria
| PRJEB58758 | ENA
Project description:Alkaline hemicellulytic bacteria Bacillus sp. N16-5 has abroad substrate spectrum and exhibits great growth ability on complex carbohydrates. In order to get insight into its carbohydrate utilization mechanism, global transcriptional profiles were separately determined for growth on glucose, fructose, mannose, galactose, arabinose, xylose, galactomannan, xylan, pectin and carboxymethyl cellulose by using one-color microarrays.
2014-06-17 | GSE38276 | GEO
Project description:Transcriptomic, metabolomic, physiological, and computational modeling approaches were integrated to gain insight into the mechanisms of antibiotic tolerance in an in vitro biofilm system. Pseudomonas aeruginosa biofilms were grown in drip-flow reactors on a medium composed to mimic the exudate from a chronic wound (CWE). After 72 hours, the biofilms were treated with CWE (control biofilms) or CWE containing ciprofloxacin (treated biofilms) for an additional 24 hours. Planktonic samples were cultivated to early logarithmic phase in CWE. The biofilm specific growth rate was estimated via elemental balances to be approximately 0.37 h-1, or one-third of the planktonic maximum specific growth rate. Global analysis of gene expression indicated decreased anabolic activity in biofilms compared to planktonic cells. A focused transcriptomic analysis revealed the induction of multiple stress responses in biofilm cells, including those associated with growth arrest, zinc limitation, hypoxia, and acyl-homoserine lactone quorum sensing.
2018-10-03 | GSE120760 | GEO