• Korean Journal of Environmental Agriculture
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• v.29 no.4
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• pp.388-395
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• 2010

In order to decrease level of an organophosphorus fungicide, tolclofos-methyl, from in situ ginseng cultivating soil, we isolated a tolclofos-methyl degrading bacteria from ginseng cultivating soil samples. The bacterial strain removed tolclofos-methyl around 95% after 3 days incubation with complete liquid media. The strain was identified as Sphingomonas sp. by 16S rDNA sequence comparison, and designated as Sphingomonas sp. 224. Through the GC-MS analysis, Sphingomonas sp. 224 was proposed to have an initiative degradation pathway generating the metabolite such as 2,6-dichloro-4-methyl phenol compound from tolclofos-methyl. In addition, Sphingomonas sp. 224 was confirmed representing the effective degrading capability to tolclofosmethyl in situ soil.

• Korean Journal of Microbiology
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• v.41 no.3
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• pp.201-207
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• 2005

A phenanthrene-degrading bacterium HS362, which is capable of using phenanthrene as a sole carbon and energy source, was isolated from oil contaminated soil. This strain is a gram negative, rod shaped organism that is most closely related to Sphingomonas paucimobilis based on biochemical tests, and belongs to the genus Sphingomonas based on fatty acids analysis. It exhibited more than $99.2{\%}$ nucleotide sequence similarity of 16S rDNA to that of Sphingomonas CF06. Thus, we named this strain as Sphingomonas sp. HS362. It degraded $98{\%}$ of phenanthrene after 10 days of incubation when phenanthrene was added at 500 ppm and $30{\%}$ even when phenanthrene was added at 3000 ppm. Sphingomonas sp. HS362 could also degrade low molecular weight PAHs(Polycyclic aromatic hydrocarbons) such as indole and naphthalene, but was unable to degrade high molecular weight PAHs such as pyrene and fluoranthene. The optimum temperature and pH for phenanthrene degradation were $30^{\circ}C$ and $4{\~}8$, respectively. Sphingomonas sp. HS362 could degrade phenanthrene effectively in the concentration range of NaCl of up to $1{\%}$. Its phenanhrene degrading ability was enhanced by preculture, suggesting the possibility of induction of phenanthrene degrading enzymes. Starch and surfactants such as SDS, Tween 85, and Triton X-100 were also able to enhance phenanthrene degradation by Sphingomonas sp. HS362. It carries five plasmids and one of them, plasmid p4, is considered to be involved in the degradation of phenanthrene according to the plasmid curing experiment by growing at $42^{\circ}C$.

• Journal of Microbiology and Biotechnology
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• v.18 no.1
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• pp.63-66
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• 2008

Anthracene is a PAH that is not readily degraded, plus its degradation mechanism is still not clear. Thus, two strains of anthracene-degrading bacteria were isolated from long-term petroleum-polluted soil and identified as Sphingomonas sp. 12A and Pseudomonas sp. 12B by a 16S rRNA sequence analysis. To further enhance the anthracene-degrading ability of the two strains, the biosurfactants produced by Pseudomonas aeruginosa $W_3$ were used, which were characterized as rhamnolipids. It was found that these rhamnolipids dramatically increased the solubility of anthracene, and a reverse-phase HPLC assay showed that the anthracene degradation percentage after 18 days with Pseudomonas sp. 12B was significantly enhanced from 34% to 52%. Interestingly, their effect on the degradation by Sphingomonas sp. 12A was much less, from 35% to 39%. Further study revealed that Sphingomonas sp. 12A also degraded the rhamnolipids, which may have hampered the effect of the rhamnolipids on the anthracene degradation.

• Journal of Life Science
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• v.19 no.5
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• pp.659-663
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• 2009

Bacterial stain 3Y was isolated from a site that was contaminated with diesel for more than 15 years. The strain could grow on various petroleum using hydrocarbons as the sole carbon source. The strain grew not only on aliphatic hydrocarbons but also on aromatic hydrocarbons. 3Y grew on aliphatic petroleum hydrocarbons hexane or hexadecane, and aromatic petroleum hydrocarbons BTEX, phenol, biphenyl, or phenanthrene. The strain showed aromatic ring dioxygenase and meta-cleavage dioxygenase activities as determined by tests using indole and catechol. Aromatic ring dioxygenase is involved in the initial step of biodegradation of aromatic hydrocarbons while meta-cleavage dioxygenase catalyzes the cleavage of the benzene ring. Based on a nucleotide sequence analysis of its 16S rRNA gene, 3Y belongs to the genus Sphingomonas. A phylogenetic tress was constructed based on the nucleotide sequences of closest relatives of 3Y and petroleum hydrocarbon degrading sphingomonads. 3Y was in a cluster that was different from the cluster that contained well-known sphingomonads. The results of this study suggest that 3Y has the potential to cleanup oil-contaminated sites. Further investigation is warranted to optimize conditions to degrade petroleum hydrocarbons by the strain to develop a better bioremediation strategy.

• Korean Journal of Microbiology
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• v.33 no.2
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• pp.92-96
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• 1997

The 6.8 kb Xhol fragment of chromosomal ONA of Pseudomonas sp. 0177 contains the phnDEFG genes involved in the degradation of polyaromatic hydrocarbons and chlorinated aromatics. Here, we report the nucleotide sequence of the ORF encoding a polypeptide consisted of 143 amino acids with a Mr of 13,859. The nucleotide sequence of the ORF is 99% and 68.6% identical to the downstream region of catE of Sphingomonas sp. strain HV3 and the ORF between xylE and xylG of Sphingomonas yanoikuyae Bl, respectively. The deduced amino acid sequence of the PhnF has 62.3% identity with the amino acid encoded hy orfY region of Citrobacter freundii DSM30040. We now confirm that the ORF is located between the catechol 2,3-dioxygenase (C230), phnE, and 2-hydroxymuconic semialdehyde dehydrogenase (2HMSO), phnG.

• Journal of Microbiology
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• v.37 no.4
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• pp.185-192
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• 1999

A phenanthrene-degrading bacterium was isolated from an oil-spilled intertidal sediment sample and identified as Sphingomonas sp. KH3-2. The strain degraded polycyclic aromatic compounds such naphthalene, fluorene, biphenyl, and dibenzothiophene. When strain KH3-2 was cultured for 28 days at 25C, a total of 500 ppm of phenanthrene was degrated with a concomitant production of biomass and Folin-Ciocalteau reactive aromatic intermediates. Analysis of intermediates during phenanthrene degradation using high-performance liquid chromatography and gas chromatography/mass spectrometry indicated that Sphingomonas sp. KH3-2 primarily degrades phenanthrene to 1-hydroxy-2-naphthoic acid (1H2NA) and further metabolizes 1H2NA through the degradation pathway of naphthalene.

• Journal of Life Science
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• v.25 no.2
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• pp.121-129
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• 2015

Alginates are found in marine brown seaweeds and in extracellular biofilms secreted by some bacteria. Previously, we reported an oligoalginate lyase from Sphingomonas sp. MJ-3 (MJ3-Oal) that had an exolytic activity and protein sequence homology with endolytic polymannuronate (polyM) lyase in the N-terminal region. In this study, the MJ3-Oal was tested for both exolytic and endolytic activity by homology modeling using the crystal structure of Alg17c from Saccharophagus degradans 2-40T. The tyrosine residue at the $426^{th}$ position, which possibly formed a hydrogen bond with the substrate, was mutated to phenylalanine. The FPLC profiles showed that MJ3-Oal degraded alginate quickly to monomers as a final product through the oligmers, whereas the Tyr426Phe mutant showed only exolytic alginate lyase activity. $^1H$-NMR spectra also showed that MJ3-Oal degraded the endoglycosidic bond of polyM and polyMG (polymannuronate-guluronate) blocks. These results indicate that oligoalginate lyase from Sphingomonas sp. MJ-3 probably catalyzes the degradation of both exo- and endo-glycosidic bonds of alginate.

• Korean Journal of Microbiology
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• v.43 no.2
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• pp.83-90
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• 2007

Sphingomonas sp. KS 301, which was isolated from oil contaminated soil, was shown to have five different SODs (SODI, II, III, IV, V) which can be separated by DEAE-Sepharose chromatography, and SOD III was finally purified in this study by ammonium sulfate precipitation, DEAE-Sepharose chromatography, Superose 12 gel filtration and Uno-Q1 ion exchange chromatography. The molecular weight of SOD III was 23 kDa as determined by SDS-PAGE and the apparent molecular weight of the native enzyme was estimated to be approximately 71 kDa by Superose-12 gel filtration chromatography. These data suggest that the purified SOD consists of at least two subunits. The specific activity of the SOD III was higher than Mn type or Fe type SOD of Escherichia coli by 5 fold. To determine the type of SOD III, inhibitory effects of $NaN_{3},\;H_{2}O_{2},\;KCN$ were examined. 10 mM $NaN_{3}$ was able to inhibit 56% of the SOD III activity, which indicates that this SOD is Mn type. The optimum pH of the SOD III was 7.0 and the optimum temperature was $20^{\circ}C$. N-terminal amino acid sequence of purified SOD III was most similar to those of Psudomonase ovalis and Vibrio cholerae among bacteria.

• Journal of Microbiology and Biotechnology
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• v.16 no.8
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• pp.1306-1310
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• 2006

Sphingomonas sp. strain SB5 could degrade carbofuran and carbofuran-7-phenol to a hydrolytic product, 2-hydroxy-3-(3-methlypropan-2-o1)phenol, and several red metabolites. However, the chemical structures of the red metabolites have largely remained unidentified. In this study, we identified the structure of one of the red metabolites as 5-(2-hydroxy-2-methyl-propyl)-2,2-dimethyl- 2,3-dihydro-naphtho[2,3-6]furan-4,6,7,9-tetrone by using mass spectrometric and NMR ($^1$H, $^{13}$C) analyses. It is suggested that the red metabolite resulted from condensation of some metabolites in the degradation of 2-hydroxy-3-(3-methlypropan-2-o1)phenol, a hydrolytic product derived from carbofuran. To our knowledge, this is the first paper to report a red metabolite in bacterial degradation of the insecticide carbofuran.

• Korean Journal of Microbiology
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• v.41 no.3
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• pp.195-200
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• 2005

Comamonas sp. strain DJ-12 is a bacterial isolate capable of degrading of 4-chlorobiphenyl (4CB) as a carbon and energy source. The degradation pathway was characterized as being conducted by consecutive reactions of the meta-degradation of 4CB, hydrolytic dechlorination of 4-chlorobenzoate (4CBA), hydroxylation of 4-hydroxybenzoate, and meta-degradation of protocatechuate to product TCA metabolites. The 6.8 kb fragment from the chromosomal DNA of Comamonas sp. strain DJ-12 included the genes encoding for the meta-degradation of PCA; the genes of protocatechuate 4,5-dioxygenase alpha and beta subunits (pmcA and pmcB), 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase (pmcC), 2-pyrone-4,6-dicarboxylate hydrolase (pmcD), 4-oxalomesaconate (OMA) hydratase(pmcE), 4-oxalocitramalate (OCM) aldolase (pmcF), and transporter gene (pmcT). They were organized in the order of pmcT-pmcE-pmcF-pmcD-pmcA-pmcB-pmcC. The amino acid sequences deduced from the nucleotide sequences of pmcABCDEFT genes from Comamonas sp. strain DJ-12 exhibited 94 to $98\%$ homologies with those of Comamonas testosteroni BR6020 and Pseudomonas ochraceae NGJ1, but only 52 to $74\%$ with homologies Sphingomonas paucimobilis SYK-6, Sphingomonas sp. LB126, and Arthrobacter keyseri 12B.