Characterization and genomic analysis of a nitrate reducing bacterium from shale oil in the Ordos Basin and the associated biosurfactant production

Xu, Yuanyuan; Wei, Fengdan; Xu, Rui; Cheng, Tao; Ma, Yi

doi:10.1016/j.jece.2022.108776

Cited by 4 publications

(4 citation statements)

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“…and compared to other sequences in GenBank through the Basic Local Alignment Search Tool (BLAST) to construct a phylogenetic tree using the neighbor-joining method in MEGA 7 software (Yoo et al, 2021;Uyar and Avcı, 2023). The NS-6 strain was stored at −80°C in 30% glycerol (Xu et al, 2022).…”

Section: Isolation and Identification Of Urease Producing Bacterial S...mentioning

confidence: 99%

Characterization and genome analysis of Neobacillus mesonae NS-6, a ureolysis-driven strain inducing calcium carbonate precipitation

Xu,

Zhang,

et al. 2023

Front. Microbiol.

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In this study, a highly promising bacterium was isolated from sandstone oil in the Ordos Basin, named strain NS-6 which exhibited exceptional urease production ability and demonstrated superior efficiency in inducing the deposition of calcium carbonate (CaCO3). Through morphological and physiochemical characteristics analysis, as well as 16S rRNA sequencing, strain NS-6 was identified as Neobacillus mesonae. The activity of urease and the formation of CaCO3 increased over time, reaching a maximum of 7.9 mmol/L/min and 184 mg (4.60 mg/mL) respectively at 32 h of incubation. Scanning Electron Microscopy (SEM) revealed CaCO3 crystals ranging in size from 5 to 6 μm, and Energy Dispersive X-ray (EDX) analysis verified the presence of calcium, carbon, and oxygen within the crystals. X-ray Diffraction (XRD) analysis further confirmed the composition of these CaCO3 crystals as calcite and vaterite. Furthermore, the maximum deposition of CaCO3 by strain NS-6 was achieved using response surface methodology (RSM), amounting to 193.8 mg (4.845 mg/mL) when the concentration of calcium ions was 0.5 mmol/L supplemented with 0.9 mmol/L of urea at pH 8.0. Genome-wide analysis revealed that strain NS-6 possesses a chromosome of 5,736,360 base pairs, containing 5,442 predicted genes, including 3,966 predicted functional genes and 1,476 functionally unknown genes. Genes like ureA, ureB, and ureC related to urea catabolism were identified by gene annotation, indicating that strain NS-6 is a typical urease-producing bacterium and possesses a serial of genes involved in metabolic pathways that mediated the deposition of CaCO3 at genetic level.

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Section: Isolation and Identification Of Urease Producing Bacterial S...mentioning

confidence: 99%

Characterization and genome analysis of Neobacillus mesonae NS-6, a ureolysis-driven strain inducing calcium carbonate precipitation

Xu,

Zhang,

et al. 2023

Front. Microbiol.

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“…Chemical reagent DBT (analytical purity and chromatographic grade) was purchased from Comio (Tianjin, China) and dissolved in acetone that was placed in a test tube, followed by complete evaporation of acetone under nitrogen (N 2 ) gas. The sandstone oil used in this study was obtained from the Ordos Basin located at latitudes 37°35′24 to 40°51′40 N and longitudes 106°42′40 to 111°27′20 E in Changqing Oil elds (China), and transported back to the laboratory at 4 •C (Xu et al 2022). Luria-Bertani (LB) broth was used as bacterial enrichment, including tryptone 10.0 g/L, yeast extract 5.0 g/L, and NaCl 5.0 g/L per liter.…”

Section: Chemicals and Culture Mediamentioning

confidence: 99%

“…Diverse strains of the Gordonia genus have been extensively studied and applied in industrial desulfurization processes. Some strains of Gordonia have the ability to utilize sul des as electron donors for energy metabolism, even under acidic or neutral conditions (Alves et al 2007a;Xu et al 2022). .…”

Section: Isolation and Identi Cation Of Strain Swx-4mentioning

confidence: 99%

“…In our previous research on petroleum-contaminated bioremediation, a sulfur-utilizing strain named SWX-4 was screened, which demonstrated the capability of degrading oil and utilizing dibenzothiophene (DBT) as a sulfur source (Xu et al 2022). After 2 d of cultivation at 37°C on LB agar plates, colonies of the SWX-4 strain exhibited a pink color with a smooth surface, regular edges, a convex center, opaque appearance, and an approximate colony diameter of 0.8 µm (Fig.…”

Section: Isolation and Identi Cation Of Strain Swx-4mentioning

confidence: 99%

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Genetic and comparative genome analysis of the dibenzothiophene-desulfurizing Gordonia SWX-4

Xu,

Cheng,

et al. 2023

Preprint

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Biodesulfurization of crude oil is a highly promising technology for achieving thorough desulfurization. In this study, a bacterial strain, designated as SWX-4, was isolated from sandstone oil in the Ordos Basin that had the ability to utilize dibenzothiophene (DBT) as a carbon source. Through physiological and biochemical characterization as well as 16S rRNA sequencing, the isolate was identified as Gordonia sp. The genome of strain SWX-4 was found to be 5,303,410 bp in size, with a GC content of 67.44%. It comprised 12 rRNA genes, 51 tRNA genes, and two plasmids. Genome analysis revealed the presence of 4,683 functional genes potentially involved in DBT desulfurization, as well as the oxidation of alkanes and aromatic compounds. Notably, the genome of strain SWX-4 also contained genes encoding sfnG, sfnB, and terD, which are known to be responsible for the desulfurization activity of DBT. These genes exhibited functional similarity to the well-conserved dszABC operons. Furthermore, a comparative genomic analysis of 43 Gordonia strains isolated from various habitats was conducted to explore their genetic diversity. The results revealed that Gordonia sp. possesses an open pan-genome with a total of 774 core genes present across all strains. On average, these core genes accounted for 18% of each individual genome. Additionally, phylogenetic tree analysis and the distribution of accessory genes showed that each strain harbored a distinct set of unique genes. Interestingly, genes associated with biodesulfurization were found to be distributed among different branches of the phylogenetic tree. This suggests that these strains have the capacity to acquire new genes through horizontal gene transfer from their environments, thereby increasing the diversity of their bacterial genomes. However, we did not observe a direct evolutionary correlation between the bacterial genome and desulfurization metabolism. Overall, our findings provide valuable insights into the biodegradation of DBT by the SWX-4 strain and offer an efficient bacterial resource for biodesulfurization.

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Enhanced organic matter degradation in shale gas wastewater treatment using Biofilm-Membrane bioreactors with varied filler Types, Pre-ozonation, and filler ratios

Zhang,

Tang,

Chen

et al. 2024

Separation and Purification Technology

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Characterization and genomic analysis of a nitrate reducing bacterium from shale oil in the Ordos Basin and the associated biosurfactant production

Cited by 4 publications

References 55 publications

Characterization and genome analysis of Neobacillus mesonae NS-6, a ureolysis-driven strain inducing calcium carbonate precipitation

Characterization and genome analysis of Neobacillus mesonae NS-6, a ureolysis-driven strain inducing calcium carbonate precipitation

Genetic and comparative genome analysis of the dibenzothiophene-desulfurizing Gordonia SWX-4

Enhanced organic matter degradation in shale gas wastewater treatment using Biofilm-Membrane bioreactors with varied filler Types, Pre-ozonation, and filler ratios

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