• Journal of Microbiology and Biotechnology
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• v.15 no.6
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• pp.1170-1177
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• 2005

Terminal-restriction fragment length polymorphism (T-RFLP) analysis was used to monitor inoculated oil-degrading microorganisms during bioremedial treatability tests. A pair of universal primers, fluorescently labeled 521F and 1392R, was employed to amplify small subunit rDNA in order to simultaneously detect two bacterial strains, Corynebacterium sp. IC10 and Sphingomonas sp. KH3-2, and a yeast strain, Yarrowia lipolytica 180. Digestion of the 5'-end fluorescence/labeled PCR products with HhaI produced specific terminal-restriction fragments (T-RFs) of 185 and 442 bases, corresponding to Corynebacterium sp. IC10 and Y. lipolytica 180, respectively. The enzyme NruI produced a specific T-RF of 338 bases for Sphingomonas sp. KH3-2. The detection limit for oildegrading microorganisms that were inoculated into natural environments was determined to be $0.01\%$ of the total microbial count, regardless of the background environment. When three oil-degrading microorganisms were released into oil-contaminated sand microenvironments, strains IC10 and 180 survived for 35 days after inoculation, whereas strain KH3-2 was detected at 8 days, but not at 35 days. This result implies that T-RFLP could be a useful tool for monitoring the survival and relative abundance of specific microbial strains inoculated into contaminated environments.

• Journal of Environmental Health Sciences
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• v.33 no.5
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• pp.428-433
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• 2007

To clarify the pioneer group in the development of biofilms in high chlorine residual water, a semi-pilot model system was operated and 16S rDNA V3 targeted PCR-DGGE was submitted. Biofilm formation occurred rapidly in the model of a drinking water distribution system. It reached $10^3\;CFU/cm^2$ or more on the surface of stainless steel, PVC, and galvanized iron in chlorinated (1.0 mg/l) water within a week. Within a week, uncultured Proteobacteria- and Bacillales group-like sequences were detected and Sphingomonas-like sequences were identified from all season and all pipe materials tested. Hence Sphingomonas species were regarded as the potential pioneer group in the development of biofilm in drinking water and this results would be useful for the prevention of biofilm formation and safety of drinking tap water.

• KSBB Journal
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• v.21 no.6 s.101
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• pp.428-432
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• 2006

This study investigated the effect of sulfate source on removal efficiency in electrokinetic bioremediation which needs sulfate to degrade contaminants by an applied microorganism. The representative contaminant and the applied microorganism were phenanthrene and Sphingomonas sp. 3Y, respectively. When magnesium sulfate was used, the magnesium ion combined with hydroxyl ion electrically-generated at cathode to cause the decrease of electrolyte pH, and then the microbial activity was inhibited by that. When ammonium sulfate and disodium sulfate were used to solve the pH control problem, the pH values of electrolyte and soil solution were maintained neutrally, and also the high microbial activity was observed. With the former sulfate source, however, ammonium retarded the phenanthrene degradation, and so the removal efficiency decreased to 12.0% rather than 21.8% with magnesium sulfate. On the other hand, the latter improved the removal efficiency to 27.2%. This difference of removal efficiency would be outstanding for an elongated treatment period.

• Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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• 2004.09a
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• pp.181-185
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• 2004

Electrokinetic bioremediation was conducted on phenanthrene-contaminated soil to study the effects of soil temperature and pH on microbial population and removal efficiency at different current densities from 0.63 to 3.13 mA cm$^{-2}$ . Microorganism used in the biodegradation of phenanthrene was Sphingomonas sp. 3Y, which was isolated from a diesel-contaminated site. The microorganism was successfully penetrated into the contaminated soil by electrokinetic phenomena and the highest microbial population was observed in the middle region of soil specimen where soil pH was near neutral. Therefore, phenanthrene removal occurred mainly at anode and middle parts of soil specimen due to a relatively high microbial population. Also, the highest removal efficiency of 68.8% was obtained at 1.88 mA cm$^{-2}$ while low degradation was detected at 3.13 mA cm$^{-2}$ . It was presumably because the soil temperature at 1.88 mAcm$^{-2}$ was close to the appropriate temperature of about 30'c while the temperature increase to above 45$^{\circ}C$ at 3.13 mA cm$^{-2}$ inhibited the microbial activity severely.

• Proceedings of the Zoological Society Korea Conference
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• 1998.10b
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• pp.173.1-173
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• 1998

No Abstract, See Full Text

• Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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• 2004.09a
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• pp.186-190
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• 2004

The electrokinetic bioremediation employing electrolyte circulation method was carried out for the cleanup of phenanthrene-contaminated kaolinite, and microorganism used in the biodegradation of phenanthrene was Sphingomonas sp. 3Y. The electrolyte circulation method supplied ionic nutrientsand the microorganism into soil, and inhibited the significant pH change of soil by increasing the soil buffering capacity by providing phosphate buffer compounds. When the remediation process was conducted without surfactant, the removal efficiency of phenanthrene, at the initial concentration of 200 ppm, was 69% for only 7 days. Higher microbial population and lower phenanthrene concentration were observed in the anode and middle regions of soil specimen than in the cathode region. The higher density of microorganism was because the microbial movement was in the direction of the anode part due to the negative surface charge. When Triton X-100 and APG of 20 g/1 were used to improve the bioavailability of phenanthrene strongly adsorbed onto soil surface, about 90 and 39% of phenanthrene removal were obtained. Consequently, it was confirmed that the microorganism preferred APC to phenanthrene as carbon source and so the removal efficiency with APG decreased less than that without APG.

• Journal of Microbiology and Biotechnology
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• v.22 no.11
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• pp.1532-1539
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• 2012

The ${\alpha}$-galactosidase-coding gene agaAJB13 was cloned from Sphingomonas sp. JB13 showing 16S rDNA (1,343 bp) identities of ${\leq}97.2%$ with other identified Sphingomonas strains. agaAJB13 (2,217 bp; 64.9% GC content) encodes a 738-residue polypeptide (AgaAJB13) with a calculated mass of 82.3 kDa. AgaAJB13 showed the highest identity of 61.4% with the putative glycosyl hydrolase family 36 ${\alpha}$-galactosidase from Granulicella mallensis MP5ACTX8 (EFI56085). AgaAJB13 also showed <37% identities with reported protease-resistant or Sphingomonas ${\alpha}$-galactosidases. A sequence analysis revealed different catalytic motifs between reported Sphingomonas ${\alpha}$-galactosidases (KXD and RXXXD) and AgaAJB13 (KWD and SDXXDXXXR). Recombinant AgaAJB13 (rAgaAJB13) was expressed in Escherichia coli BL21 (DE3). The purified rAgaAJB13 was characterized using p-nitrophenyl-${\alpha}$-D-galactopyranoside as the substrate and showed an apparent optimum at pH 5.0 and $60^{\circ}C$ and strong resistance to trypsin and proteinase K digestion. Compared with reported proteaseresistant ${\alpha}$-galactosidases showing thermolability at $50^{\circ}C$ or $60^{\circ}C$ and specific activities of <71 U/mg with or without protease treatments, rAgaAJB13 exhibited a better thermal stability (half-life of >60 min at $60^{\circ}C$) and higher specific activities (225.0-256.5 U/mg). These sequence and enzymatic properties suggest AgaAJB13 is the first identified and characterized Sphingomonas ${\alpha}$-galactosidase, and shows novel protease resistance with a potential value for basic research and industrial applications.

• Journal of Life Science
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• v.23 no.12
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• pp.1420-1427
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• 2013

A novel acetylalginate esterase (AcAlgE) gene was previously cloned and characterized from Sphingomonas sp. MJ-3. In this study, the synergistic effects of MJ-3 AcAlgE, and KS-408 alginate lyase on the degradation of acetylalginate from Pseudomonas aeruginosa were investigated by using high-field 1H-NMR and an FPLC-equipped peptide column. The alginate lyase coupled assay of AcAlgE showed that degradation of high molecular weight acetylalginate was more difficult than degradation of acid hydrolyzed acetylalginate. The degradation of acetylalginate by alginate lyase was easier after AcAlgE was used to remove the acetyl group from acetylalginate. This result showed that the recombinant AcAlgE enhanced the degradation of acetylalginate by alginate lyase.

• Korean Journal of Microbiology
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• v.34 no.4
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• pp.194-199
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• 1998

Bacterial diversity was determined by amplification and sequencing of 16S rDNA at Tancheon and Jungrang in Han river. Twenty-seven clones constructed were divided 7 groups using RFLP. Fifteen clones were classified 4 groups in Tancheon and the group (HT-1 clone) including many clones was affiliated a high similarity with Aerobacter cryaerophilus (the class Proteobacteria including members of the delta subdivisions). The other two groups (HT-6 and HT-9 clone) including several clones were classified with the class Cytophagales in Tancheon. Twelve clones were classified 3 groups in Jungrang and the group (HJ-1 clone) including many clones was affiliated a high similarity with Sphingomonas sp. (the class Proteobacteria including members of the alpha subdivisions). As a whole results, the class Proteobacteria (alpha, beta and delta subdivision), the order Cytophagales, and the order Actinomycetales were detected.

• BMB Reports
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• v.32 no.4
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• pp.399-404
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• 1999

2,3-Dihydroxybiphenyl 1,2-dioxygenase (2,3-DHBD), which catalyzes the ring meta-cleavage of 2,3-dihydroxybiphenyl, is encoded by the phnQ gene of biphenyl- and phenanthrene-degrading Pseudomonas sp. strain DJ77. We determined the nucleotide sequence of a DNA fragment of 1497 base pairs which included the phnQ gene. The fragment lncluded an open reading frame of 903 base pairs to accommodate the enzyme. The predicted amino acid sequence of the enzyme subunit consisted of 300 residues. In front of the gene, a sequence resembling an E. coli promoter was identified, which led to constitutive expression of the cloned gene in E. coli. The deduced amino acid sequence of the PhnQ enzyme exhibited 85.6% identity with that of the corresponding enzyme in Sphingomonas yanoikuyae Q1 (formerly S. paucimobilis Q1) and 22.1% identity with that of catechol 1,2,3-dioxygenase from the same DJ77 strain. PhnQ showed broader substrate preference than previously-cloned PhnE, catechol 2,3-dioxygenase. Ten amino acid residues, considered to be important for the role of extradiol dioxygenases, were conserved.