• Journal of Microbiology and Biotechnology
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• v.11 no.6
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• pp.1046-1054
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• 2001

Bioleaching is the process in which insoluble metal sulfide is oxidized by specialized iron- and/or sulfur-oxidizing lithotrophic bacteria in acidic, metal-rich environments. Most of these processes are carried out by the genus Thiobacillus. Three novel Thiobacillus strains (Thiobacillus thiooxidans AZ11, Thiobacillus thiooxidans MET, and thiobacillus thiooxidans TAS) associated with bioleaching have been isolated from soil and sludge (Korean patent No. 1999-0073060 for T. thiooxidans AZ11, Korean patent No. 1999-0005798 for T. thiooxidans MET, and Korean patent No. 1999-0073059 for T. thiooxidans TAS). A partial sequence of 16S ribosomal RNA gene (16S rDNA) and the entire sequence of 16S/23S intergenic spacer region (ISR) were determined in the three above novel strains and in Thiobacillus ferrooxidans ATCC19859 as a reference strain. When phylogenetic analysis was performed based on G+C contents and sequence alignments, T. ferroxidans ATCC19859 was found to be closely related to previously registered T. ferrooxidans strains in a monophyletic manner, while the three novel T. thiooxidans strains were classified in a paraphyletic manner. Close examination on the base composition of 16S/23S ISR revealed that the 5\` part (nucleotide residues 21-200) was specific for the genus Thiobacillus. On the other end, the 3\` part (nucleotide residues 201-520) showed specificity in T. ferrooxidans strains, but not in T. thiooxidans strains. These results suggest that the proximal and distal halves of 16S/23S could be used as a genetic marker for the identification of the genus Thiobacillus and the species T. ferrooxidans, respectively.

• Microbiology and Biotechnology Letters
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• v.44 no.1
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• pp.98-105
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• 2016

The presence of bacterial strains showing antagonistic activity to common pathogens found in a variety of fermented foods in Korea was explored. A bacterium inhibiting the growth of pathogens such as Aspergillus terreus (KCTC6178), A. flavus (KCTC6984), Staphylococcus aureus (KCCM12214), Escherichia coli O157:H7 (KCCM40406), Bacillus cereus (KCTC1012), Cryptococcus neoformans (ATCC208821), Salmonella typhimurium (ATCC19430), and Listeria monocytogenes (KCTC3569) was isolated from Makgeolli, a Korean traditional rice wine. The strain showing high antipathogenic activity was identified as B. amyloliquefaciens based on the nucleotide sequence of the 16S ribosomal RNA gene. Compared with B. amyloliquefaciens KCTC1660, whose genome has been sequenced, the isolate exhibited significantly low activities of starch-degrading enzymes and high resistance to high temperature and low pH.

• 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.

• Animal cells and systems
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• v.6 no.1
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• pp.13-18
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• 2002

Phylogenetic relationships of Korean Acidiella species were tested using mitochondrial 16S ribosomal RNA gene sequences. We used 16 published sequences as outgroup, and 10 new sequences for nine Korean Acidiella species as ingroup. The number of aligned sites was 1,281 bp, but 1,135 bp were used for the analysis after excluding sites with missing data or gaps. Among these 1,135 sites, 464 sites were variable and 340 were informative for parsimony analysis. Phylogenetic information was extracted from this data set using neighbor-joining, maximum likelihood and maximum parsimony methods and compared to a morphology-based phylogenetic hypothesis. Our molecular data suggest that: (1) the tribe Trypetini appears to be monophyletic even when the nine additional Acidiella species are added to our previous phylogenetic analysis; (2) all the Korean Acidiella species belong to the Trypeta group, but the genus Acidiella is not supported as monophyletic; (3) the close relationship of A. circumvaga, A. issikii, and A. sapporensis is supported; (4) the close relationship of A. pachypogon and two additional new Acidiella species is strongly supported; and (5) the possible presence of two or more cryptic species among the specimens previously identified as A. obscuripennis is suggested. Sequence data from the mitochondrial 16S rDNA allowed us to better understand the systematic status of Korean Acidiella species. They indicated that the current concept about the genus Acidiella is insufficient and needs to be refined further. This study also showed a few interesting relationships, that had not been recognized by morphological study alone. Based on this study, we were able to plan further experiments to analyze relationships within the Trypeta Group.

• Research in Plant Disease
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• v.16 no.1
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• pp.94-96
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• 2010

In May of 2004 through 2007, Leptosphaerulina leaf blight caused by Leptosphaerulina trifolii occurred on Kentucky bluegrass (Poa pratensis) at golf courses in Gangwon Province, Korea. Symptoms on the turfgrass caused by L. trifolii were leaf blights, dying from the leaf tip downwards to the crown, which appeared patches in the field because of local pockets of severely infected (blighted) grass. Perithecia were produced on old or weak leaves, including club-shaped asci, each of which contained 8 pale brown muriform ascospores with cross and longitudinal septa. Ascospores of the fungus isolated from the diseased leaf tissue and cultured on potato-dextrose agar (PDA) were muriform multicellular (composed of 3-6 cells) and $23.4-40.5{\times}7.8-15.6{\mu}m$ in size with 3-4 transverse and 0-3 longitudinal septa, which were morphologically identical to L. trifolii reported previously. DNA sequences of ribosomal RNA gene (internal transcribed spacer) of the fungus were homologous with similarity of 99% to those of L. trifolii isolates in GenBank database, confirming the identity of the causal agent of the disease. Pathogenicity of the fungus was also confirmed on the creeping bentgrass by Koch's postulates. This is first report of Leptosphaerulina leaf blight on turfgrass caused by L. trifolii in Korea.

• Korean Journal of Microbiology
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• v.45 no.2
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• pp.170-176
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• 2009

Culture-independent 16S rDNA-DGGE profiling and phylogenetic analysis were used to examine the predominant bacterial communities associated with the two sponges, Dictyonella sp. and Spirastrella abata from Jeju island. The culture-independent approach involved extraction of total bacterial DNA, PCR amplification of the 16S ribosomal DNA using primer pair 341f-GC and 518r, and separation of the amplicons on a denaturing gradient gel. Denaturing gradient gel electrophoresis banding patterns indicated 8 and 7 bands from the two sponge species, Dictyonella sp. and Spirastrella abata, respectively. There were not common major bands in two different sponges. Comparative sequence analysis of variable DGGE bands revealed from 93% to 98% similarity to the known published sequences. The dominant bacterial group of Dictyonella sp. belonged to uncultured Gammaproteobacteria, while, that of Spirastrella abata belonged to uncultured Alphaproeobacteria and Firmicutes. DGGE analysis indicated predominant communities of the sponge-associated bacteria differ in the two sponges from the same geographical location. This result revealed that bacterial community profiles of the sponges were host species-specific.

• Journal of Microbiology and Biotechnology
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• v.16 no.2
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• pp.193-199
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• 2006

Halotolerant spore-forming Gram-positive bacteria were isolated from the root, rhizosphere, and non-rhizosphere soil of Blutaparon portulacoides. The different isolates were characterized genetically using an amplified ribosomal DNA restriction analysis (ARDRA), and phenotypically based on their colonial morphology, physiology, and nutritional requirements. Three different 16S rRNA gene-based genotypes were observed at a 100% similarity using the enzymes HinfI, MspI, and RsaI, and the phenotypic results also followed the ARDRA groupings. Selected strains, representing the different ARDRA groups, were analyzed by 16S rDNA sequencing, and members of the genera Halobaeillus, Virgibacillus, and Oceanobacillus were found. Two isolates showed low 16S rDNA sequence similarities with the closest related species of Halobacillus, indicating the presence of new species among the isolates. The majority of the strains isolated in this study seemed to belong to the species O. iheyensis and were compared using an AP-PCR to determine whether they had a clonal origin or not. Different patterns allowed the grouping of the strains according to Pearson's coefficient, and the resulting dendrogram revealed the formation of two main clusters, denoted as A and B. All the strains isolated from the soil were grouped into cluster A, whereas cluster B was exclusively composed of the strains associated with the B. portulacoides roots. This is the first report on the isolation and characterization of halotolerant spore-forming Gram-positive bacteria that coexist with B. portulacoides. As such, these new strains may be a potential source for the discovery of bioactive compounds with industrial value.

• Weed & Turfgrass Science
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• v.2 no.3
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• pp.306-311
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• 2013

Pythium blight occurred by Pythium aphanidermatum on chewing fescue cv. "Jamestowm II" from early June, 2010 and 2011 at the test field in Daegu University in Gyeongbuk Province, Korea. Disease symptoms on the turfgrass were leaf blights dying from the leaf tip and root rot, which appeared patches of brown to dark brown color or gray brown color in the field. The pathogens (40-1 isolate) of Pythium blight was isolated from the diseased leaf and crown tissue and cultured on potato-dextrose agar (PDA) for identification. Lobulate sporangia were inflated, complex structures, and filamentous sporangia were usually indistinguishable from vegetative hyphae. Sequences of ribosomal RNA gene of the fungus were homologous with similarity of 100% to those of P. aphanidermatum isolates in GenBank database. Pathogenicity was also confirmed on the chewing fescue, creeping betgrass and Kentucky bluegrass by Koch's postulates. This is the first report of Pythium blight on chewing fescue caused by P. aphanidermatum in Korea.

• Korean journal of food and cookery science
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• v.31 no.1
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• pp.9-17
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• 2015

Shindari is a traditional fermented drink of Jeju in Korea, which is made with boiled barley and nuruk for short fermentation periods. This study determined chemical, microbiological, and sensory characteristics of the modified Shindari with 15% carrots as an additive (carrot Shindari), and this study compared it with a traditional Shindari as a control. After fermentation at $30^{\circ}C$ for a day, the pHs of the carrot Shindari and traditional Shindari largely decreased, and the total acidities increased in both of the Shindari. The significantly higher scores of Hunter's color values were observed more in carrot Shindari than in traditional Shindari. Also, carrot Shindari (0.4954 g/100 g) had a significantly higher content of vitamin C than traditional Shindari (0.0030 g/100 g). The most abundant free sugar and organic acid were glucose and lactic acid, respectively, in both of the Shindari. The total numbers of bacteria, fungi and lactic-acid bacteria in both samples increased by log 3 CFU/mL after fermentation. Based on 16S ribosomal RNA gene analysis, the dominant lactic-acid bacteria was Pediococcus acidilactici in both samples. The DPPH (1.1-diphenyl-2-picrylhydrazyl) radical scavenging activity of carrot Shindari (60.13%) was higher than that of traditional Shindari (23.70%). In sensory evaluations (taste, flavor, color, and overall acceptance), the carrot Shindari had higher scores in all these values. In this study, the modified Shindari with carrot presenting high sensory characteristic as well as chemical and microbiologic characteristics provide an opportunity to improve the application of a traditional fermented drink of Jeju, Shindari.

• Archives of Plastic Surgery
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• v.39 no.1
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• pp.18-24
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• 2012

Background : Infection caused by rapidly growing mycobacteria (RGM) is not uncommon, and the prevalence of RGM infection has been increasing. Clinical diagnosis is difficult because there are no characteristic clinical features. There is also no standard antibiotic regimen for treating RGM infection. A small series of patients with RGM infections was studied to examine their treatments and outcomes. Methods : A total of 5 patients who had developed postoperative infections from January 2009 to December 2010 were retrospectively reviewed. Patients were initially screened using a mycobacteria rapid screening test (polymerase chain reaction [PCR]-reverse blot hybridization assay). To confirm mycobacterial infection, specimens were cultured for nontuberculous mycobacteria and analyzed by 16 S ribosomal RNA and rpoB gene PCR. Results : The patients were treated with intravenous antibiotics during hospitalization, and oral antibiotics were administered after discharge. The mean duration of follow-up was 9 months, and all patients were completely cured of infection with a regimen of a combination of antibiotics plus surgical treatment. Although none of the patients developed recurrence, there were complications at the site of infection, including hypertrophic scarring, pigmentation, and disfigurement. Conclusions : Combination antibiotic therapy plus drainage of surgical abscesses appeared to be effective for the RGM infections seen in our patients. Although neither the exact dosage nor a standardized regimen has been firmly established, we propose that our treatment can provide an option for the management of rapidly growing mycobacterial infection.