Petroleum-contaminated soil
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1091787 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28682752.fastq.gz | Fastqsanger.gz | |||
| SRR28682753.fastq.gz | Fastqsanger.gz | |||
| SRR28682754.fastq.gz | Fastqsanger.gz | |||
| SRR28682754_1.fastq.gz | Fastqsanger.gz | |||
| SRR28682754_2.fastq.gz | Fastqsanger.gz |
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Project description:A novel Gram-stain positive, aerobic, non-motile bacterial strain, designated Z1T, was isolated from a sample of petroleum-contaminated soil collected in Daqing, Heilongjiang province, China and characterised with a series of taxonomic approaches. The morphological and chemotaxonomic properties of the isolate were typical of those of members of the genus Rhodococcus. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Z1T belongs to the genus Rhodococcus and clustered with Rhodococcus maanshanensis DSM 44675T (99.2%, sequence similarity) and Rhodococcus tukisamuensis JCM 11308T (97.9%), respectively. However, the DNA-DNA hybridizations between strain Z1T and R. maanshanensis DSM 44675T and R. tukisamuensis JCM 11308T were both less than 70%. The optimal growth temperature and pH for strain Z1T were found to be at 28 °C and at pH 7.0. The peptidoglycan was found to contain meso-diaminopimelic acid; arabinose, galactose and glucose were detected as diagnostic sugars. The main polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified lipid; MK-8(H2) was found as the major menaquinone. The major fatty acids were identified as C16:0, 10-methyl C18:0 and C18:1ω9c. Mycolic acids were found to be present. The G + C content of the genomic DNA was determined to be 66.7 mol%. Based on a comparative analysis of phenotypic and genotypic characteristics, in combination with DNA-DNA hybridization results, strain Z1T can be distinguished from the type strains of its two close neighbours as a novel species of the genus Rhodococcus, for which the name Rhodococcus daqingensis sp. nov. is proposed. The type strain is Z1T (= CGMCC 1.13630T = DSM 107227T).
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Project description:Microbial community analysis with DNA oligonucleotide microarrays targeting ribosomal RNA (rRNA) provides a highly parallel interrogation of nucleic acids isolated from environmental samples. High fidelity readout is essential for accurate interpretation of hybridisations. We describe the hybridisation of in vitro transcribed 16S rRNA from an uncontaminated and 2,4,6-trinitrotoluene contaminated soil to an oligonucleotide microarray containing group- and species-specific perfect match (PM) probes and their 2 corresponding mismatch (MM) probes. Thermal dissociation analysis was used to determine the specificity of each PM-MM probe set. Functional ANOVA often discriminated PM-MM probe sets when Td values (temperature at 50% probe-target dissociation) could not. Maximum discrimination for many PM and MM probes often occurred at temperatures greater than the Td. Comparison of signal intensities measured prior to dissociation analysis from hybridisations of the two soil samples revealed significant differences in domain-, group- and species-specific probes. Functional ANOVA showed significantly different dissociation curves for 11 PM probes when hybridisations from the two soil samples were compared, even though initial signal intensities for 3 of the 11 did not vary. This approach provides a highly parallel, multi-level analysis that incorporates MM probes and dissociation curves into high fidelity microarray analysis of complex environmental nucleic acid profiles. Keywords: Microbial diversity, thermal dissociation analysis
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Project description:Soil health deteriorates through the contamination and remediation processes, resulting in the limitation of the reuse and recycling of the remediated soils. Therefore, soil health should be recovered for the intended purposes of reuse and recycling. This study aimed to evaluate the applicability and effectiveness of several amendments to revitalize total petroleum hydrocarbon contaminated soils remediated by the landfarming process. Ten inorganic, organic, and biological amendments were investigated for their dosage and duration, and nine physicochemical, four fertility, and seven microbial (soil enzyme activity) factors were compared before and after the treatment of amendments. Finally, the extent of recovery was quantitatively estimated, and the significance of results was confirmed with statistical methods, such as simple regression and correlation analyses assisted by principal component analysis. The landfarming process is considered a somewhat environmentally friendly remediation technology to minimize the adverse effect on soil quality, but four soil properties-such as water holding capacity (WHC), exchangeable potassium (Ex. K), nitrate-nitrogen (NO3-N), available phosphorus (Av. P), and urease-were confirmed to deteriorate through the landfarming process. The WHC was better improved by organic agents, such as peat moss, biochar, and compost. Zeolite was evaluated as the most effective material for improving Ex. K content. The vermicompost showed the highest efficacy in recovering the NO3-N content of the remediated soil. Chlorella, vermicompost, and compost were investigated for their ability to enhance urease activity effectively. Although each additive showed different effectiveness according to different soil properties, their effect on overall soil properties should be considered for cost-effectiveness and practical implementation. Their overall effect was evaluated using statistical methods, and the results showed that compost, chlorella, and vermicompost were the most relevant amendments for rehabilitating the overall health of the remediated soil for the reuse and/or recycling of agricultural purposes. This study highlighted how to practically improve the health of remediated soils for the reuse and recycling of agricultural purposes.
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Project description:Pollution after oil spill represents extreme habitat for survival and is a major concern for loss of species diversity in the affected area. In this study, we investigated soil samples collected from a petrochemical industry, Ulsan, South Korea. The soil was in the phase of recovery from the contamination of crude oil spill. Detailed investigation, based on morphology, ontogenesis, and molecular phylogenetic methods, resulted in discovery of a novel hypotrich ciliate, i.e., Metasterkiella koreana n. gen., n. sp., which is morphologically characterized by a semirigid body, undulating membranes in Oxytricha pattern, 18 frontal-ventral-transverse cirri with cirrus V/3 placed posteriorly, one right and one left row of marginal cirri, four dorsal kineties, two dorsomarginal rows, and caudal cirri at the end of dorsal kineties 1, 2, and 4. Interestingly, during ontogenesis, formation of three common anlagen for the proter and the opisthe and involvement of cirrus V/3 in anlagen formation was observed. The dorsal ontogenesis was typical of oxytrichids, i.e., simple fragmentation of dorsal kinety 3 and formation of dorsomarginal rows close to the right marginal row. The new species was found to be similar with Sterkiella subtropica, except for some minor differences in morphometry, and at gene level with only one base pair difference. In phylogenetic analyses, based on SSU rRNA gene sequence, M. koreana cluster in a clade away from Sterkiella species, which could be explained by the differences in the morphogenetic pattern between these two genera. It is proposed that S. subtropica probably belongs to Metasterkiella; however, we do not perform changes and wait for the reinvestigation of its morphogenetic pattern.
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Project description:Genes that encode for enzymes that can degrade petroleum hydrocarbons (PHs) are critical for the ability of microorganisms to bioremediate soils contaminated with PHs. Distributions of two petroleum-degrading genes AlkB and Nah in soils collected from three zones of the Dagang Oilfield, Tianjin, China were investigated. Numbers of copies of AlkB ranged between 9.1 × 10(5) and 1.9 × 10(7) copies/g dry mass (dm) soil, and were positively correlated with total concentrations of PHs (TPH) (R(2) = 0.573, p = 0.032) and alkanes (C33 ~ C40) (R(2)?= 0.914, p < 0.01). The Nah gene was distributed relatively evenly among sampling zones, ranging between 1.9 × 10(7) and 1.1 × 10(8) copies/g dm soil, and was negatively correlated with concentrations of total aromatic hydrocarbons (TAH) (R(2) = -0.567, p = 0.035) and ?16 PAHs (R(2) = -0.599, p = 0.023). Results of a factor analysis showed that individual samples of soils were not ordinated as a function of the zones.
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