Ontology highlight
ABSTRACT:
PROVIDER: PRJNA523725 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8607580_1.fastq.gz | Fastqsanger.gz | |||
| SRR8607580_2.fastq.gz | Fastqsanger.gz | |||
| SRR8607590_1.fastq.gz | Fastqsanger.gz | |||
| SRR8607590_2.fastq.gz | Fastqsanger.gz | |||
| SRR8607600_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 62 |
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Project description:Petroleum hydrocarbons are recalcitrant contaminants, which has caused most serious environmental problems. Acinetobacter calcoaceticus Aca13 was isolated from petroleum polluted soil for petroleum biodegradation. Hexadecane and naphthalene were used to incubate with Acinetobacter calcoaceticus Aca13. After incubation, the whole transcriptome was obtained from treated groups and control groups, and then used for RNA sequence and analysis. Obtained data in this project will help us understand the biodegradation mechanism of hexadecane and naphthalene, and will be helpful for the bioremediation of petroleum hydrocarbons.
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Project description:A significant part of the heavier petroleum fraction resulting from offshore oil-spills sinks to the deep-sea. Its fate and biodegradation by microbial communities is unclear. In particular, the physiological and metabolic features of hydrostatic pressure (HP) adapted oil-degraders have been neglected. In this study, hydrocarbon-free sediment from 1km below surface water (bsl) was incubated at 0.1, 10 and 20MPa (equivalent to surface waters, 1 and 2km bsl) using triacontane (C30) as sole carbon source for a 3-month enrichment period. HP strongly impacted biodegration, as it selected for microbial communities with small cells, high O2 respiration and nutrients requirements, but low biomass and C30-degradation yields. The alkane-degrading metaproteome linked to β-oxidation was detected but its expression was reduced under HP contrary to several housekeeping genes. This was reflected in the enriched communities, as atmospheric pressure was dominated by hydrocarbonoclastic bacteria while non-specialized or previously unrecognized oil-degrading genera were enriched under HP.
2018-12-19 | PXD004328 | Pride
Project description:Enhancing the anaerobic biodegradation of petroleum hydrocarbons in soils with electrically conductive materials
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Project description:We have developed a 60-mer oligonucleotide multibacterial microarray for detection and expression profiling of biodegradative genes and bacterial diversity (16S rRNA gene) in different habitats contaminated with varieties of hazardous chemicals. The genes selected were involved in biodegradation and biotransformation of various groups of compounds viz. nitroaromatic compounds (148 genes), chloroaromatic compounds (75 genes), monoaromatic compounds (373 genes), polyaromatic hydrocarbons (174 genes), pesticides/ herbicides (34 genes), alkanes/aliphatics (185 genes) and heavy metals (68 genes), which covered a total number of 133 chemicals. The efficiency (specificity, detection sensitivity) of the developed array was evaluated using the labeled genomic DNA of pure bacterial strains, Escherichia coli DH5α and Sphingomonas sp. strain NM-05 (involved in the biodegradation of γ-hexachlorohexane isolated from IPL, Lucknow) at different concentrations of 300ng, 500ng, 800ng, 1000ng and 1250ng. The specificity of the developed array was further validated using mixed cultures containing three strains (Sphingomonas sp. strain NM-05, Rhodococcus sp. strain RHA1 and Bordetella sp. strain IITR-02) involved in biodegradation of γ-hexachlorohexane, biphenyl and chlorobenzenes respectively. The mixed culture also contained non-target/non-degrader strains (E. coli DHα, E.coli BL21 and E.coli K12 NCTC50192). The developed array was applied for profiling using the total soil DNA in five contaminated habitats of north India, viz. chloroaromatic chemicals contaminated site (India Pesticide Limited, Chinhat, Lucknow), a river sediments (Gomti river sediment, Lucknow), heavy metal industry dump site (Jajmau industrial area Kanpur), a effluent treatment plant (CETP along Ganges river near Kanpur), and an oil refinery (Mathura oil refinery). Hybridization of 16S rRNA probes revealed the presence of bacteria similar to well characterized genera involved in biodegradation of pollutants. Genes involved in complete degradation pathways for hexachlorocyclohexane (lin), 1,2,4-trichlorobenzene (tcb), naphthalene (nah), phenol (mph), biphenyl (bph), benzene (ben), toluene (tbm), xylene (xyl), phthalate (pht), Salicylate (sal) and resistance to mercury (mer) were detected with highest intensity. The most abundant genes belonged to hydroxylases, monooxygenases and dehydrogenases which were present in all the five samples. Many compound specific genes which initiate the degradation pathway were also detected. Thus, the array developed and validated here may be useful in assessing the biodegradative potential and composition of environmentally useful bacteria in hazardous ecosystems.
2011-04-15 | GSE24353 | GEO
Project description:Petroleum hydrocarbons contaminated soil metagenome (VLK)
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Project description:Petroleum hydrocarbons contaminated soil metagenome (VLN)
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Project description:Petroleum hydrocarbons contaminated soil metagenome (VDK)
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Project description:We have developed a 60-mer oligonucleotide multibacterial microarray for detection and expression profiling of biodegradative genes and bacterial diversity (16S rRNA gene) in different habitats contaminated with varieties of hazardous chemicals. The genes selected were involved in biodegradation and biotransformation of various groups of compounds viz. nitroaromatic compounds (148 genes), chloroaromatic compounds (75 genes), monoaromatic compounds (373 genes), polyaromatic hydrocarbons (174 genes), pesticides/ herbicides (34 genes), alkanes/aliphatics (185 genes) and heavy metals (68 genes), which covered a total number of 133 chemicals. The efficiency (specificity, detection sensitivity) of the developed array was evaluated using the labeled genomic DNA of pure bacterial strains, Escherichia coli DH5M-NM-1 and Sphingomonas sp. strain NM-05 (involved in the biodegradation of M-NM-3-hexachlorohexane isolated from IPL, Lucknow) at different concentrations of 300ng, 500ng, 800ng, 1000ng and 1250ng. The specificity of the developed array was further validated using mixed cultures containing three strains (Sphingomonas sp. strain NM-05, Rhodococcus sp. strain RHA1 and Bordetella sp. strain IITR-02) involved in biodegradation of M-NM-3-hexachlorohexane, biphenyl and chlorobenzenes respectively. The mixed culture also contained non-target/non-degrader strains (E. coli DHM-NM-1, E.coli BL21 and E.coli K12 NCTC50192). The developed array was applied for profiling using the total soil DNA in five contaminated habitats of north India, viz. chloroaromatic chemicals contaminated site (India Pesticide Limited, Chinhat, Lucknow), a river sediments (Gomti river sediment, Lucknow), heavy metal industry dump site (Jajmau industrial area Kanpur), a effluent treatment plant (CETP along Ganges river near Kanpur), and an oil refinery (Mathura oil refinery). Hybridization of 16S rRNA probes revealed the presence of bacteria similar to well characterized genera involved in biodegradation of pollutants. Genes involved in complete degradation pathways for hexachlorocyclohexane (lin), 1,2,4-trichlorobenzene (tcb), naphthalene (nah), phenol (mph), biphenyl (bph), benzene (ben), toluene (tbm), xylene (xyl), phthalate (pht), Salicylate (sal) and resistance to mercury (mer) were detected with highest intensity. The most abundant genes belonged to hydroxylases, monooxygenases and dehydrogenases which were present in all the five samples. Many compound specific genes which initiate the degradation pathway were also detected. Thus, the array developed and validated here may be useful in assessing the biodegradative potential and composition of environmentally useful bacteria in hazardous ecosystems. Agilent one-color CGH experiment,Organism: Genotypic designed Agilent-17159 Genotypic designed Agilent Multibacterial 8x15k Array , Labeling kit: Agilent Genomic DNA labeling Kit (Part Number: 5190-0453)
2011-04-15 | E-GEOD-24353 | biostudies-arrayexpress