Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-wide gene expression to dibenzofuran in Sphingomonas wittichii RW1

ABSTRACT: Sphingomonas wittichii RW1 is a bacterium isolated for its ability to degrade the toxic polyaromatic hydrocarbon dibenzofuran (dbf) and its polychlorinated derivatives. Its genome consists of a chromosome and two plasmids, encoding for more than 5300 genes. We studied genome-wide expression of strain RW1 to dbf in three different experimental setups, including both batch cultures and chemostats, comparing in all cases to the transcriptome of cells grown on phenylalanine as carbon source. A short exposure to DBF in chemostat or in batch, provoked the up-regulation of the ECF sigma 24, catalases, peroxiredoxins, chaperones, an aquaporin, several OmpA domain-containing proteins and the down-regulation of genes involved in TCA cycle, oxidative phosphorylation, amino acid metabolism and ribosomal proteins. When growing strain RW1 on DBF, genes known to be involved in DBF degradation were induced 2 to 4 fold. Additionally, two cluster of genes, putatively participating in the gentisate and meta-cleavage branches of the DBF degradation pathway, were induced from 12 to 19 fold. Three experiments are summarized here. 1. Compares the response of exponentially growing S.wittichii RW1 cells on phenylalanine (Phe), washed and resuspended in Phe for 30 min, with that of cells resuspended in DBF medium for 30 min (Phe1_shock, DBF1_schock, etc.). 2. Compares response of RW1 cells grown in batch medium with Phe or DBF as sole carbon and energy source, and harvested in exponential phase (Phe1_long, DBF1_long, etc. triplicates). 3. Comparison of transcriptome of RW1 cells grown continuously in chemostat on phenylalanine as carbon-limited substrate, with cells that have experienced instant exposure to phenylalanine plus DBF. This is done by pulsing DBF to maximum solubility and a simultaneous change in feed medium to Phe+ DBF. Samples before transition (Phe ctrl1-chem, etc. quadruplates), after 30 min (DBF 30m1-chem, etc), 1 h, 2 h and 6 h (DBF6h1-chem, etc.).

ORGANISM(S): Sphingomonas wittichii RW1

SUBMITTER: Edith Coronado

PROVIDER: E-GEOD-37328 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Spingomonas wittichii strain RW1 can completely oxidize dibenzo-p-dioxins and dibenzofurans, which are persistent contaminants of soils and sediments. For successful application in soil bioremediation systems, strain RW1 must cope with fluctuations in water availability, or water potential. The objectives of this study were to characterize how strain RW1 responses to changes in different components of the total water potential (solute and matric potential) and to then connect these responses to more realistic scenarios of soil desiccation. To accomplish this task, transcriptome profiling was used to investigate the effects of decreasing the solute potential with sodium chloride (solute stress), decreasing the matric potential with high-molecular weight polyethylene glycol (matric stress), or inoculating cells directly into unsaturated sand (sand desiccation stress). Transcriptome profiling revealed a general response to solute, matric, and sand desiccation stress that involved synthesizing trehalose and modifying the composition of exopolysaccarides. Transcriptome profiling also revealed responses that were unique to each stress. Only solute and matric stress triggered the down-regulation of flagella genes. Only solute and sand desiccation stress triggered the up-regulation of two RNA polymerase ECF-type sigma factors along with several membrane proteins, mechanosensitive channels, and solute transporters. Finally, only matric stress triggered the up-regulation of the RNA polymerase sigma-32 factor along with several molecular chaperones. Together, this study revealed a general response to solute, matric and sand desiccation stress but also unique responses to only a subset of these stresses, suggesting that each stress affects strain RW1 in a fundamentally different way. Comparative transcriptome profiling was performed to assess the effects of acute (30 min) solute and matric stress (3 samples for acute solute stress, 3 samples for acute matric stress, 3 controls), the effects of chronic (24 hours) solute and matric stress (3 samples for chronic solute stress, 3 samples for chronic matric stress, 3 controls), and the effects of sand desiccation stress (4 samples for sand desiccation treatment, 3 controls).

Project description:The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (i.e., bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of global gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated sand, compared to regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing polycyclic aromatic hydrocarbons such as dioxins, dibenzofurans and other chlorinated congeners. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well during growth and stationary phase in sand. Cells during transition resemble going through stationary phase, showing evidence of stress responses and nutrient scavenging, and even of major adjustments in their primary metabolism if they were not pre-cultured on the same contaminant as found in the soil. Cells growing and surviving in soil show very different signatures as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous soil-specific expressed genes. We conclude that studies focusing on inoculation efficacy should test behavior under conditions as closely as possible mimicking the intended microbiome conditions We were interested to study the global reactions of bacteria with biodegradative properties under near-environmental as compared to laboratory culture conditions. we compared here the genome-wide responses of RW1 between regular laboratory batch growth on the aromatic substrates DBF and salicylate with growth in sandy soil with or without the same aromatic compounds. We analysed the cellular reactions immediately after introduction into the sand, during lag phase, all in carefully controlled and replicated experimental conditions.

Project description:The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (i.e., bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of global gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated sand, compared to regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing polycyclic aromatic hydrocarbons such as dioxins, dibenzofurans and other chlorinated congeners. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well during growth and stationary phase in sand. Cells during transition resemble going through stationary phase, showing evidence of stress responses and nutrient scavenging, and even of major adjustments in their primary metabolism if they were not pre-cultured on the same contaminant as found in the soil. Cells growing and surviving in soil show very different signatures as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous soil-specific expressed genes. We conclude that studies focusing on inoculation efficacy should test behavior under conditions as closely as possible mimicking the intended microbiome conditions. We were interested to study the global reactions of bacteria with biodegradative properties under near-environmental as compared to laboratory culture conditions. We compared here the genome-wide responses of RW1 between regular laboratory batch growth on the aromatic substrates DBF and salicylate with growth in sandy soil with or without the same aromatic compounds. We analysed the cellular reactions immediately after introduction into the sand, during exponential growth and at stationary phase, all in carefully controlled and replicated experimental conditions.

Dataset Information

Genome-wide gene expression to dibenzofuran in Sphingomonas wittichii RW1

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure