• KSBB Journal
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• v.28 no.5
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• pp.295-302
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• 2013

Indigo is utilized in various industries including textile dyeing, cosmetics, printing and medicinal products and its reduced form, leuco-indigo, is mainly used in these process. Chemical reducing agent (sodium dithionite, sodium sulfide, etc.) is preferred to use for the formation of leucoindigo in industry. In traditional indigo fermentation process, microorganisms can participate in the reduction of indigo and thus it has been known to reduce environmental pollution and noxious byproducts. However, in fermentation method using microorganisms it is difficult to standardize large scale production process due to low yield and reproducibility. In this study, we attempted to develop the indigo reduction process using microbial flora which was isolated from naturally fermented indigo vat or deduced by metagenomic approach. From the results of library analyses of PCR-amplified 16S rRNA genes from the traditional indigo fermentation vat sample (metagenome), it was confirmed that Alkalibacteriums (71%) was distinctly dominant in population. Some strains were identified after confirming that they become pure culture in nutrient media modified slightly. Four strains were separated in this process and each strain showed obvious reducing ability toward indigo in dyeing test. It is expected that the analyzed results will provide important data for standardizing the natural fermentation of indigo and investigating the mechanism of indigo reduction.

• Tuberculosis and Respiratory Diseases
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• v.74 no.4
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• pp.187-190
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• 2013

We report a rare case of lung disease caused by Mycobacterium lentiflavum in a previously healthy woman. A 54-year-old woman was referred to our hospital due to chronic cough and sputum. A computed tomography scan of the chest revealed bilateral bronchiectasis with bronchiolitis in the right middle lobe and the lingular division of the left upper lobe. Nontuberculous mycobacteria were isolated twice from three expectorated sputum specimens. All isolates were identified as M. lentiflavum by multilocus sequence analysis based on rpoB, hsp65, and 16S rRNA fragments. To the best of our knowledge, this is the first documented case of M. lentiflavum lung disease in an immunocompetent adult in Korea.

• ALGAE
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• v.23 no.2
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• pp.119-133
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• 2008

We cultured a tubular marine green alga, originally identified as Capsosiphon groenlandicus (J. Agardh) K.L. Vinogradova, from Amaknak Island, Alaska. The alga had an alternation of heteromorphic generations in which tubular monoecious fronds produced quadriflagellate zoospores and/or biflagellate isogametes. The gametes fused to produce cysts or Codiolum-like zygotes with long, tortuous stalks. Cysts and codiola produced 8-16 aplanospores, which germinated in situ to yield upright fronds. Fronds arising from both aplanospores and zoospores displayed a distinctive development in which non-septate colorless rhizoids from the base of the initially uniseriate, Ulothrix-like filament were transformed into septate uniseriate Ulothrix-like photosynthetic filaments. These transformed filaments then developed new basal non-septate rhizoids. This pattern of rhizoids becoming filaments, which then produced new rhizoids, was repeated to yield a tuft of up to 50 fronds. Periclinal and longitudinal divisions occurred in each filament, starting basally, until the mature tubular thallus was achieved. Pyrenoid ultrastructure revealed several short inward extensions of chloroplast lamellae, each of which was surrounded by pyrenoglobuli. Analysis of ribosomal SSU and ITS sequences placed this alga in the family Ulotrichaceae, order Ulotrichales, together with but as a distinct species from North Atlantic Capsosiphon groenlandicus. Analysis of a partial ITS sequence from authentic Capsosiphon fulvescens, the current name of the type of the genus Capsosiphon, indicated that neither our material nor C. groenlandicus belongs in that genus, and we propose a new genus, Pseudothrix, to accommodate both species. We propose P. borealis for the North Pacific entity formerly called C. groenlandicus and make the new combination P. groenlandica for the Atlantic species.

• The Plant Pathology Journal
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• v.34 no.3
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• pp.208-217
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• 2018

In this study, samples were collected from the leaves and stems of healthy wild Pistachio trees (Pistacia atlantica L.) from various locations of Baneh and Marivan regions, Iran. In total, 61 endophytic bacteria were isolated and grouped according to phenotypic properties. Ten selected isolates from each group were further identified by partial sequencing of the 16S rRNA gene. Based on the results, isolates were identified as bacteria belonging to Pseudomonas, Stenotrophomonas, Bacillus, Pantoea and Serratia genus. The ability of these isolates was evaluated to phytohormone production such as auxin and gibberellin, siderophore production, phosphate solubilization, atmospheric nitrogen fixation, protease and hydrogen cyanide production. All strains were able to produce the plant growth hormone auxin and gibberellin in different amounts. The majority of strains were able to solubilize phosphate. The results of atmospheric nitrogen fixation ability, protease and siderophore production were varied among strains. Only Ba66 could produce a low amount of hydrogen cyanide. The results of biocontrol assay showed that Pb78 and Sp15 strains had the highest and lowest inhibition effects on bacterial plant pathogens, Pseudomonas syringae pv. syringae Pss20 and Pseudomonas tolaasii Pt18 under in vitro condition. Pb3, Pb24 and Pb71 strains significantly promote root formation on carrot slices. To our knowledge this is the first report of the isolation of endophytic bacterial strains belonging to Pantoea, Bacillus, Pseudomonas, Serratia and Stenotrophomonas genus from wild pistachio trees with plant growth promoting potential and biocontrol activity.

• Journal of Life Science
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• v.14 no.5
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• pp.815-820
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• 2004

A bacterum containing antitumor activity was isolated from traditional korean food, Jeotgal. Through the 16s rRNA sequence analysis, the bacterium was identitied as a strain of Bacillus subtilis SW-l. The best culture condition for antitumor activity of the bacterium is 3% of soluble starch and 1 % of yeast extract as corbon and nitrogen sources, respectively. Cytotoxicitic concentrations of the culture supernatant of B. subtilis SW-1 against cancer cell lines, A549 and SK-OV3 were 30 ul/ml and 40 ul/ml, respectively, as $IC_{50}$/ values. In DNA fragmentation assay, the culture supernatant showed the programmed cell death (apoptosis) to cause degrading the chromosomal DNA like ladder. Taken together, the culture supernatant of the B. subtilis SW-1 has some possibility to be used as an antitumor agent.

• Journal of Ginseng Research
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• v.36 no.3
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• pp.291-297
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• 2012

Ginsenoside (ginseng saponin), the principal component of ginseng, is responsible for the pharmacological and biological activities of ginseng. We isolated lactic acid bacteria from Kimchi using esculin agar, to produce ${\beta}$-glucosidase. We focused on the bio-transformation of ginsenoside. Phylogenetic analysis was performed by comparing the 16S rRNA sequences. We identified the strain as Lactobacillus (strain 6105). In order to determine the optimal conditions for enzyme activity, the crude enzyme was incubated with 1 mM ginsenoside Rb1 to catalyse the reaction. A carbon substrate, such as cellobiose, lactose, and sucrose, resulted in the highest yields of ${\beta}$-glucosidase activity. Biotransformations of ginsenoside Rb1 were analyzed using TLC and HPLC. Our results confirmed that the microbial enzyme of strain 6105 significantly transformed ginsenoside as follows: Rb1${\rightarrow}$gypenoside XVII, Rd${\rightarrow}$F2 into compound K. Our results indicate that this is the best possible way to obtain specific ginsenosides using microbial enzymes from 6105 culture.

• The Plant Pathology Journal
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• v.28 no.1
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• pp.68-74
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• 2012

Biocontrol microbes have mainly been screened among large collections of microorganisms $via.$ nutrient-rich $in$ $vitro$ assays to identify novel and effective isolates. However, thus far, isolates from only a few genera, mainly spore-forming bacilli, have been commercially developed. In order to isolate field-effective biocontrol microbes, we screened for more than 200 oligotrophic bacterial strains, isolated from rhizospheres of various soil samples in Korea, which induced systemic resistance against the soft-rot disease caused by $Pectobacterium$ $carotovorum$ SCC1; we subsequently conducted in $planta$ bioassay screening. Two oligotrophic bacterial strains were selected for induced systemic disease resistance against the $Tobacco$ $Mosaic$ $Virus$ and the gray mold disease caused by $Botrytis$ $cinerea$. The oligotrophic bacterial strains were identified as $Pseudomonas$ $manteilii$ B001 and $Bacillus$ $cereus$ C003 by biochemical analysis and the phylogenetic analysis of the 16S rRNA sequence. These bacterial strains did not exhibit any antifungal activities against plant pathogenic fungi but evidenced several other beneficial biocontrol traits, including phosphate solubilization and gelatin utilization. Collectively, our results indicate that the isolated oligotrophic bacterial strains possessing induced systemic disease resistance could provide useful tools as effective biopesticides and might be successfully used as cost-effective and preventive biocontrol agents in the field.

• The Plant Pathology Journal
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• v.28 no.1
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• pp.20-31
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• 2012

Endophytic bacterial communities of tidal flat plants antagonistic to oomycete plant pathogens were studied by the isolation of 256 root colonizing endophytic bacteria from surface-disinfected root tissues of six plants ($Rosa$ $rugosa$, $Suaeda$ $maritima$, $Vitex$ $rotundifolia$, $Carex$ $scabrifolia$, $Glehnia$ $littoralis$ and $Elymus$ $mollis$) growing in a tidal flat area of Namhae Island, Korea. To understand the antagonistic potential, an $in$ $vitro$ antagonistic assay was performed to characterize and identify strains that were antagonistic to the oomycete plant pathogens $Phytophthora$ $capsici$ and $Pythium$ $ultimum$ from the total population. Nine percent of the total number of isolated bacteria exhibited in vitro inhibitory activity against target plant pathogenic oomycetes. Taxonomic and phylogenetic placement of the antagonistic bacteria was investigated by analysis of the 16S rRNA gene sequences. The sequence analysis classified the antagonistic strains into four major classes of the domain bacteria ($Firmicutes$, ${\alpha}-Proteobacteria$, ${\gamma}-Proteobacteria$ and $Actinomycetes$) and 10 different genera. Further production of secondary metabolites, hydrolytic enzymes and plant growth promoting traits were determined for the putative new species of antagonistic endophytic bacteria. These new strains could not be identified as known species of ${\alpha}-Proteobacteria$, and so may represent novel bacterial taxa. The unexpected high antagonistic bacterial diversity associated with the tidal flat plants may be indicative of their importance in tidal flat plants as a promising source of novel antimicrobial compounds and biocontrol agents.

• Journal of Soil and Groundwater Environment
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• v.17 no.3
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• pp.49-58
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• 2012

Batch experiments using indigenous and commercialized adventive microorganisms were performed to investigate the feasibility of the biodegradation process for the diesel contaminated soil, which was taken in US Military Camp 'Hialeah', Korea. TPH concentration of the soil was determined as 3,819 mg/kg. Four indigenous microorganisms having high TPH degradation activity were isolated from the soil and by 16S rRNA gene sequence analysis, they were identified as Arthrobacter sp., Burkholderia sp., Cupriavidus sp. and Bacillus sp.. Two kinds of commercialized solutions cultured with adventive microorganisms were also used for the experiments. Various biodegradation conditions such as the amount of microorganism, water content and the temperature were applied to decide the optimal bioavailability condition in the experiments. In the case of soils without additional microorganisms (on the natural attenuation condition), 35% of initial TPH was removed from the soil by inhabitant microorganisms in soil for 30 days. When the commercialized microorganism cultured solutions were added into the soil, their average TPH removal efficiencies were 64%, and 54%, respectively, which were higher than that without additional microorganisms. When indigenous microorganisms isolated from the contaminated soil were added into the soil, TPH removal efficiency increased up to 95% (for Bacillus sp.). According to the calculation of the average biodegradation rates for Bacillus sp., the remediation goal (87% of the removal efficiency: 500 mg/kg) for the soil would reach within 24 days. Results suggested that TPH removal efficiency of biodegradation by injecting indigenous microorganisms is better than those by injecting commercialized adventive microorganisms and only by using the natural attenuation.

• Journal of Soil and Groundwater Environment
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• v.22 no.2
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• pp.41-51
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• 2017

Microbial processes that bind heavy metals and form minerals are widespread, and they represent a basic aspect of biogeochemistry. Some microorganisms can crystallize minerals by secreting a specific enzyme. In particular, calcite ($CaCO_3$) precipitation is an important part of biomineralization, and has been studied extensively because of its wide application in civil engineering technology. This process provides an effective way to stabilize heavy metals within a relatively stable crystal phase. In this study, biomineralization of calcite by three urea-hydrolyzing indigenous bacterial strains was investigated by microbiological analyses. Three bacterial strains were isolated from the sludge of B mine in Mexico and each bacterial strain was identified by the cellular fatty acid composition and 16S rRNA partial sequencing analysis. The results of the identification analysis showed that these strains were closest to Sporosarcina pasteurii, Kurthia gibsonii, and Paenibacillus polymyxa. We found that the optimum conditions for growth of these indigenous bacteria were $30-40^{\circ}C$ and pH range of 7-8. Microbiological analyses showed the possibility that the bioaccumulated heavy metals ions were deposited around the cell as crystalline carbonate minerals under the optimum conditions. The findings of our study suggest that the indigenous bacterial strains play an important role in heavy metal immobilization.