• Korean Journal of Microbiology
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• v.26 no.4
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• pp.312-317
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• 1988

The genes for ribosomal RNA in Rhizobium meliloti and Bradyrhizobium japonicum were analyzed by southern hybridization of BamHI, EcoRI, HindIII digested chromosomal DNA with purified 5' $^{32}P$-labeled 16S and 23S rRNA. The big differences in the hybridization pattern of both rhizobia were found. The comparative results were discussed in relation to the copy number and conservativity of restriction sites in the rRNA genes of both rhizobia.

• Ocean Science Journal
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• v.41 no.4
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• pp.315-318
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• 2006

Three Synechococcus strains were isolated from seawater near the Ieodo Ocean Research Station (IORS), and their 16S rDNA genes and the internal transcribed spacer (ITS) between the 16S and 23S rRNA genes were sequenced to investigate their phylogenetic relationships. Phylogenetic trees based on the 16S rDNA and ITS sequences showed that they clustered in the main MC-A Synechococcus group (subcluster 5.1), but formed branches differentiating them from the described clades. As the IORS is located in an area affected by diverse water masses, high Synechococcus diversity is expected in the area. Therefore, the IORS might be a good site to study the diversity, physiology, and distribution of the Synechococcus group.

• ALGAE
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• v.39 no.2
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• pp.59-74
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• 2024

Terrestrial cyanobacteria are extremely diverse. In urban areas, they can be found as black stains on the surface of building walls, stone monuments, or man-made structures. Many of the terrestrial cyanobacteria are still understudied. To expand knowledge of terrestrial cyanobacterial diversity, a polyphasic characterization was performed to identify 12 strains isolated from campus of University of the Ryukyus, Okinawa, Japan. Multigene phylogenetic analyses based on 16S rRNA gene and 16S-23S rRNA internal transcribed spacer (ITS) region showed that the isolated strains formed two independent subclades within Nodosilinea, and were distantly related to all described Nodosilinea species. The 16S-23S rRNA ITS secondary structures showed variations for D1-D1' and Box B domain, while V3 domain was almost identical among entire species of Nodosilinea, including the studied strains. In addition, a unique morphological character, i.e. forming nodule or spiral shape, was also observed in certain studied strains. According to polyphasic characterization, Nodosilinea coculeatus sp. nov. and Nodosilinea terrestrialis sp. nov., were proposed as two new species of terrestrial cyanobacteria from Okinawa.

• Proceedings of the Korean Aquaculture Society Conference
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• 2002.08a
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• pp.234-235
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• 2002

• Journal of fish pathology
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• v.17 no.3
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• pp.159-169
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• 2004

Bacterial wihte enteritis ocurred by infection of V. ichthyoenteri is a devastating disease in olive flounder (Paralichthys olivaceus) hatcheries in Korea. Since white enteritis has been a problem in aquqtic industries, necessity of a rapid detection method is increased. In an attempt to develop rapid PCR method the detection of V. ichthyoenteri, we examined the 16S-23S rRNA intergenic spacer region(ISR) of V. ichthyoenteri and developed species-specific primer for V. ichthyoenteri. The intergenic spacers were amplified by primers complementary to conserved region of 16S and 23S rRNA genes. The intergenic spacer region between the 16S and 23S rRNA genes of V. ichthoenteri were investigated by PCR fragment length typing and DNA sequencing. Analysis of the ISR sequences showed that V. ichthyoenteri contains one types of polymorphic ISRs. The size of ISRs ranged 348bp length and not contains tRNA genes. Mutiple alignment of representative sequences from different Vibrio species revealed several domains of high sequence variability, and allowed to design species-specific primer for detection of Vibrio ichthyoenteri. PCR. The specific of the primer was examined using genomic DNA prepared from 19 different Vibrio species, isolated 18group Vibrio species. The results showed that the PCR reaction using species-specific primer designed in this study can be used to detect V. ichthyoenteri.

• Journal of fish pathology
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• v.19 no.2
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• pp.127-139
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• 2006

From 2002 to 2004, various vibrios were isolated from the olive flounder, Paralichthys olivaceus of culturing size with disease signs. During this survey, it was known that the high proportion of Vibrio ichthyoenteri was occupied among the isolated vibrios. Generally, V. ichthyoenteri is well known as the pathogen of bacterial enteritis of olive flounder larvae. The aim of the present study was the compare the characteristics of two groups of V. ichthyoenteri, culturing sized olive flounder, and larvae of olive flounder showing the intestinal necrosis. The research was focused on the physiology, biochemistry, genetics in the two bacterial groups. The physiological and biochemical characteristics of the tested strains were very similar. The intergenic spacer (IGS) region between the 16S and 23S rRNA genes of 21 isolated strains and 3 reference strains, V. ichthyoenteri, were investigated by PCR fragment length typing and DNA sequencing. After the isolated strains were identified as V. ichthyoenteri, not only phenotypic characteristics of the isolated and reference strains but also homology of 16S-23S IGS of all isolated strains and reference strains as 99.1~100%. The V. ichthyoenteri showed 4 specific 16S-23S patterns and contained no-tRNA, tRNAGlu(TTC) , tRNAIle(GAT) tRNAAla(TGC) type .

• The Plant Pathology Journal
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• v.23 no.3
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• pp.151-154
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• 2007

Phytoplasma was identified from leaf lettuce (Lactuca sativa) cultivated in commercial green-house in Korea. Diseased leaf lettuce revealed proliferation of shoots, and yellowing and shrinking of leaves (lettuce proliferation-K). Polymerase chain reaction (PCR) with universal primer pair P1/P6, and aster yellows (AY) specific primer pair R16F1/R1 amplified 1.5kb and 1.1kb length of DNA fragments, respectively. Nucleotide sequences of 16S rRNA gene were determined (Gen Bank accession no EF489024). Phylogenetic analysis of 16S rDNA showed the closest relationship with AY phytoplasma (GenBank accession no. AY389822 and AY389826), indicating that lettuce proliferation-K is a member of AY. Phytoplasma bodies were detected in phloem sieve tubes of diseased lettuce by transmission electron microscopy. The structures had round or pleomorphic shapes with a diameter of 130-300nm. Phylogenetic analysis of 16S rRNA gene, microscopic observation of phytoplasma bodies and symptomatology indicated that lettuce proliferation-K is caused by phytoplasma in the AY group. This is the first report of phytoplasma disease in lettuce in Korea.

• Journal of Microbiology and Biotechnology
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• v.17 no.3
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• pp.490-495
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• 2007

Lactic acid bacteria (LAB) are beneficial for the gastrointestinal tract and reinforce immunity in human health. Recently, many functional products using the lactic acid bacteria have been developed. Among these LAB, Lactobacillus acidophilus, Lactobacillus rhamnosus, Bifidobacterium longum, and Bifidobacterium bifidum are frequently used for probiotic products. In order to monitor these LAB in commercial probiotic products, a multiplex PCR method was developed. We designed four species-specific primer pairs for multiplex PCR from the 16S rRNA, 16S-23S rRNA intergenic spacer region, and 23S rRNA genes in Lactobacillus acidophilus, Lactobacillus rhamnosus, Bifidobacterium longum, and Bifidobacterium bifidum. Using these primer pairs, 4 different LAB were detected with high specificity in functional foods. We suggest that the multiplex PCR method developed in this study would be an efficient tool for simple, rapid, and reliable identification of LAB used as probiotic strains.

• Proceedings of the Korean Aquaculture Society Conference
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• 2004.05a
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• pp.240-241
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• 2004

• Microbiology and Biotechnology Letters
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• v.23 no.4
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• pp.384-389
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• 1995

Streptoalloteichus hindustanus ATCC 31219, a nebramycin complex producer, is similar to Streptomyeces tenebrarius in a viewpoint of resistance to a wide range of aminoglycoside antibiotics. S. tenebrarius has resistance mechanisms of 16s rRNA methylation and aminogycoside modification. However, it is not known whether resistance mechanisms of Stall. hindustanus are the same as in S. tenebrarius. Therefore, we have tried to isolate resistance determinants from Stall. hindustanus. Two different types of aminoglycoside resistance determinants were isolated from Stall. hindustanus and expressed in Streptomyces lividans TK24. The apramycin resistance gene (amr) and the tobramycin resistance gene (tmr) isolated from Stall. hindustanus showed broad resistance spectrum against a dozen of aminoglycoside antibiotics. The complete nucleotide sequences of apramycin resistance gene (amr) were determined. The deduced amino acid sequence of the amr gene of Stall hindustanus ATCC 31219 showed extensive sequence homology to the 16s rRNA methylase gene (kamB) of S. tenebrarius.