Paraburkholderia caffeinilytica strain:CF1
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ABSTRACT:
PROVIDER: PRJNA564949 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Paraburkholderia caffeinilytica CF1 Genome sequencing
| PRJNA479521 | ENA
Project description:Escherichia coli strain:CF1-2 Genome sequencing and assembly
| PRJNA362211 | ENA
Project description:Starmerella floricola CF1 Transcriptome - CF13.3c
| PRJNA697085 | ENA
Project description:Characterization of the transcriptomic responses of grafted tomato seedlings leaves after the root inoculations with the two beneficial microorganisms Paraburkholderia graminis and Azospirillum brasiliensis. Paraburkholderia graminis treatment led to a higher number of differentially expressed genes than Azospirillum brasiliensis, with a higher amount of up-regulated than down-regulated genes for both treatments. These DEGs were manly involved in response to oxidative stress, response to biotic and abiotic stress, water transport, regulation of transcription and hormones. Only few DEGs were shared among the two treatments, including genes involved in flowering time and in tolerance against abiotic stresses.
2022-10-16 | E-MTAB-11398 | biostudies-arrayexpress
Project description:Volatilization of lower-chlorinated polychlorinated biphenyls (LC-PCBs) from sediment poses health threats to nearby communities and ecosystems. Biodegradation combined with black carbon (BC) materials is an emerging approach to remove PCBs from sediment, but development of aerobic biofilms on BC for long-term, sustained LC-PCBs remediation is poorly understood. This work aimed to characterize cell enrichment and activity of biphenyl- and benzoate-grown Paraburkholderia xenovorans strain LB400 on various BCs. Biphenyl dioxygenase gene (bphA) abundance on four BC types demonstrated corn kernel biochar hosted at least four orders of magnitude more attached cells per gram than other feedstocks, and microscopic imaging revealed the attached live cell fraction was >1.5X more on corn kernel biochar than GAC. BC characteristics (i.e., sorption potential, surface area, pH) drove cell attachment differences. Reverse transcription qPCR indicated BC feedstocks significantly influenced bphA expression in attached cells. The bphA transcript-per-gene ratio of attached cells was >10-fold more than suspended cells, confirmed by transcriptomics. RNA-seq also demonstrated significant upregulation of biphenyl and benzoate degradation pathways on attached cells, revealing biofilm formation potential and cell-cell communication pathway connections. These novel findings demonstrate aerobic PCB-degrading cell abundance and activity could be tuned by adjusting BC feedstocks/ attributes to improve LC-PCBs biodegradation.
2023-11-03 | GSE246487 | GEO
Project description:Bacterial aromatic degradation may cause oxidative stress. The long-chain flavodoxin FldX1 of Paraburkholderia xenovorans LB400 counteracts reactive oxygen species (ROS). The aim of this study was to evaluate the protective role of FldX1 in P. xenovorans LB400 during the degradation of 4-hydroxyphenylacetate (4-HPA) and 3-hydroxyphenylacetate (3-HPA). Functionality of FldX1 was assessed by P. xenovorans p2-fldX1 that overexpresses FldX1. The effects of FldX1 on P. xenovorans were studied measuring growth on hydroxyphenylacetates, degradation of 4-HPA and 3-HPA, and ROS formation. The effects of hydroxyphenylacetates on the proteome (LC–MS/MS) and gene expression (qRT-PCR) were quantified. Bioaugmentation with strain p2-fldX1 of 4-HPA-polluted soil was assessed, measuring aromatic degradation (HPLC), 4-HPA-degrading bacteria, and plasmid stability.
2024-03-27 | PXD047097 | Pride
Project description:Paraburkholderia phymatum is a beta-proteobacterium, which lives in the soil and is able to enter nitrogen-fixing symbiosis with different legumes. The biological nitrogen fixation (BNF) process is of great ecological and agronomic importance. We previously showed that the expression of the key P. phymatum BNF enzyme – the nitrogenase –is regulated by the sigma factor σ54 (or RpoN) inside root nodules. This study focused on identifying the σ54 regulon of P. phymatum grown in nitrogen limited conditions using RNA-Sequencing. Among the genes significantly down-regulated in absence of σ54 we found those coding for a C4-dicarboxylate transport system (Bphy_0225-27), a flagellar biosynthesis cluster (Bphy_2926-64) and one of the two type 6 secretion system (T6SS-b) present in P. phymatum genome (Bphy_5978-97). Indeed, the σ54 mutant was unable to grow on C4 dicarboxylates (fumarate, malate and succinate) as the sole carbon source and was less motile compared to the wild-type strain. Both defects were complemented by adding rpoN in trans. Additionally, using reporter fusions we confirmed that T6SS-b expression is regulated by σ54. Finally, a σ54 mutant was less competitive than its parental strain against P. diazotrophica, suggesting a role of σ54 in controlling interbacterial competition.
2020-08-12 | GSE156048 | GEO
Project description:Starmerella floricola CF1 Standard Draft genome sequencing
| PRJNA697083 | ENA
Project description:<p>We used time-resolved metabolic footprinting, an important technical approach used to monitor changes in extracellular compound concentrations during microbial growth, to study the order of substrate utilization (i.e., substrate preferences) and kinetics of a fast-growing soil isolate, <em>Paraburkholderia</em> sp. strain 1N. The growth of <em>Paraburkholderia</em> sp. 1N was monitored under aerobic conditions in a soil-extracted solubilized organic matter medium, representing a realistic diversity of available substrates and gradient of initial concentrations. We combined multiple analytical approaches to track over 150 compounds in the medium and complemented this with bulk carbon and nitrogen measurements, allowing estimates of carbon use efficiency throughout the growth curve. Targeted methods allowed the quantification of common low-molecular-weight substrates: glucose, 20 amino acids, and 9 organic acids. All targeted compounds were depleted from the medium, and depletion followed a sigmoidal curve where sufficient data were available. Substrates were utilized in at least three distinct temporal clusters as <em>Paraburkholderia</em> sp. 1N produced biomass at a cumulative carbon use efficiency of 0.43. The two substrates with highest initial concentrations, glucose and valine, exhibited longer usage windows, at higher biomass-normalized rates, and later in the growth curve. Contrary to hypotheses based on previous studies, we found no clear relationship between substrate nominal oxidation state of carbon (NOSC) or maximal growth rate and the order of substrate depletion. Under soil solution conditions, the growth of <em>Paraburkholderia</em> sp. 1N induced multiauxic substrate depletion patterns that could not be explained by the traditional paradigm of catabolite repression.</p><p><strong>IMPORTANCE:</strong> Exometabolomic footprinting methods have the capability to provide time-resolved observations of the uptake and release of hundreds of compounds during microbial growth. Of particular interest is microbial phenotyping under environmentally relevant soil conditions, consisting of relatively low concentrations and modeling pulse input events. Here, we show that growth of a bacterial soil isolate, <em>Paraburkholderia</em> sp. 1N, on a dilute soil extract resulted in a multiauxic metabolic response, characterized by discrete temporal clusters of substrate depletion and metabolite production. Our data did not support the hypothesis that compounds with lower energy content are used preferentially, as each cluster contained compounds with a range of nominal oxidation states of carbon. These new findings with <em>Paraburkholderia</em> sp. 1N, which belongs to a metabolically diverse genus, provide insights on ecological strategies employed by aerobic heterotrophs competing for low-molecular-weight substrates in soil solution.</p>
2020-09-28 | MTBLS1692 | MetaboLights
Project description:RpoN (σ54) is the key sigma factor for the regulation of transcription of nitrogen fixation genes in diazotrophic bacteria, which include alpha- and beta-rhizobia. Our previous studies showed that a rpoN mutant of the beta-rhizobial strain Paraburkholderia phymatum formed root nodules on Phaseolus vulgaris that were unable to reduce atmospheric nitrogen into ammonia. In an effort to further characterize the RpoN regulon of P. phymatum, transcriptomics was combined with a powerful metabolomics approach. The metabolome of P. vulgaris root nodules infected by the P. phymatum rpoN Fix- mutant revealed statistically significant metabolic changes compared to wild-type Fix+ nodules, including reduced amounts of chorismate and elevated levels of flavonoids. A transcriptome analysis on Fix+ and Fix- nodules – combined with a search for RpoN binding sequences in promoter regions of regulated genes – confirmed the expected control of σ54 on nitrogen fixation genes in nodules. The transcriptomic data also identified additional target genes, whose differential expression was able to explain the observed metabolite changes in a numerous cases. Moreover, the genes encoding the two-component regulatory system NtrBC were downregulated in root nodules induced by the rpoN mutant and contained a putative RpoN binding motif in their promoter region, suggesting direct regulation. The construction and characterization of an ntrB mutant strain revealed impaired nitrogen assimilation in free-living conditions, as well as a noticeable symbiotic phenotype by forming less but heavier nodules on P. vulgaris roots.
2018-06-06 | GSE111993 | GEO