Ontology highlight
ABSTRACT:
PROVIDER: PRJNA497930 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8088581_1.fastq.gz | Fastqsanger.gz | |||
| SRR8088581_2.fastq.gz | Fastqsanger.gz |
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Project description:The survival, pollutant degradation activity and transcriptome response was monitored in Sphingomonas sp. LH128 inoculated into soil. Cultivable cell numbers were determined by plating, while phenanthrene degradation was monitored by HPLC. The genetic base for the adaptive strategy of LH128 in soil was investigated by using microarray consisting 7,200 gene-coding ORFs. During 4 hours of incubation, 510 genes were differentially expressed (317 increased and 193 reduced expression) while 610 genes were differentially expressed (318 increased and 292 reduced) after 10 days of incubation. Genes with increased expression comprised of gene encoding PAH catabolic enzymes, stress resistance, oxidative stress tolerance, outer membrane proteins/porins and efflux pump proteins while the downregulated genes comprised of genes encoding flagellar biosynthesis, ribosomal proteins and ATPase. Transcriptomic response of phenanthrene degrading Sphingomonas sp. LH128 inoculated into phenanthrene contaminated soil after 4h and after 10 days of incubation was studied using genome-wide gene expression analysis. For this purpose, the strain was pregrown in minimal medium and inoculated at appropriated celld densitites. RNA was extracted both from soil and and from initial inoculum and cDNA was synthesized and labeled with Cy3. Transcriptomic response in soil of three replicates per conditions after both incubation duration were analyzed and compared with the initial inoculum
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Project description:Polycyclic aromatic hydrocarbons (PAHs) are widely distributed pollutants. As in saturated PAH-contaminated sites oxygen is rapidly depleted, microorganisms able to use these compounds as a carbon source in the absence of molecular oxygen are crucial for their consumption. Here, we described the metabolic pathway for anaerobic degradation of phenanthrene by a sulfate-reducing enrichment culture (TRIP) obtained from a natural asphalt lake. The dominant organism of this culture belongs to the Desulfobacteraceae family of deltaproteobacteria. Proteogenome analysis revealed that the metabolic capacity of this bacterium includes the key enzymes for dissimilatory sulfate reduction, the Embden-Meyerhof-Parnas pathway, a complete tricarboxylic acid cycle as well as the key elements of the Wood-Ljungdahl pathway. Genes encoding enzymes potentially involved in the degradation of phenanthrene were identified in the genome of this bacterium. Two gene clusters were identified encoding a carboxylase enzyme involved in the activation of phenanthrene, as well as genes encoding reductases potentially involved in subsequent ring dearomatization and reduction steps. The predicted metabolic pathways were corroborated by transcriptome and proteome analyses and provide the first metabolic pathway for anaerobic degradation of three-rings PAHs.
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Project description:au10-04_phytoremediation; impact of sucrose on the tolerance of phenanthrene Effect of phenanthrene and sucrose - We test 3 conditions plants non-treated (C or t0), plants treated with phenanthrene (P) and plants tread with phenanthrene and sucrose (S). The plants were grown on MS/2 media for 17 days and then transferred on the corresponding condition. We took a sample of 30 plants at different times (0, 30 min, 2h, 4h, 8h and 24h).
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Project description:This study examines genome-wide expression of the phenanthrene-degrading Sphingomonas sp. LH128 as a response to long-term starvation stress. For this purpose, the strain was subjected to complete nutrient starvation for 6 months after growth on a rich medium. Survival was monitored by plating, physiological response was examined by flow cytometry and FAME analysis, and this response was related to transcriptomic response as determined by whole-genome microarray analysis. The data showed that decreased gene functions involved in ribosomal proteins biosynthesis, decreased chromosomal replication, increased gene functions involved in stringent regulation of gene expression, increased gene functions involved in genetic exchange and recombination, increased efflux systems, increased degradation of rRNA, and increased M-NM-2-oxidation of fatty acids to access stored nutrients. Genes involved in PAH degradations appears to be with decreased expression. Transcriptomic response of phenanthrene degrading Sphingomonas sp. LH128 starved for 6 month in isotonic solution of 0.01 mM MgS04 was studied using genome-wide gene expression analysis. For this purpose, the strain was pregrown in minimal medium to an OD600 of 0.5, washed twice with 0.01 mM MgS04 and resuspended in the same solution to an OD of 0.5. RNA was extracted both from starved cells and from the initial culture (non-starved cells) and cDNA was synthesized and labeled with Cy3. Transcriptomic response of three replicates were analyzed and compared with the initial inoculum
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