• Journal of Microbiology and Biotechnology
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• 제11권3호
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• pp.428-434
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• 2001

A viscous substance producer strain BS62, which was isolated from conventional Chungkookjang, was examined for its productivity of levansucrase and levan during soybean fermentation at $37{\circ}C$. After one day of cultivation, the enzyme activity reached the highest level, 8 units $ml^{-1}$. Extracts of fermented soybeans were precipitated by ethanol and hydrolyzed by either 0.1 N HCl or invertase, and the hydrolyzates were analyzed using thin layer and ion chromatographies. Fructose was the only sugar detected. This suggest that fructose was derived from the levan produced by the strain BS62 during soybean fermentation. The aerobic, endospore-forming bacterium BS62 was identified as a Bacillus subtilis sp., based on the composition of its cellular fatty acids and phylogeny, which was determined by its 16S rDNA sequence.

• Animal Systematics, Evolution and Diversity
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• 제16권2호
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• pp.203-211
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• 2000

한국에서 양식되어지고 있는 한국산 굴류 4종, 굴(Crassostrea gigas Thunberg), 바위굴(C. nippona Seki), 강굴(C. ariakensis Fujita et Wakiya), 토굴(Ostrea denselamellosa Lischke)의 유전적 근연관계를 조사하고자 미토콘드리아 DNA의 16S rDNA와 cytochrome c oxidase I (COI) 유전자 일부분의 염기서열을 분석하였다. 16S rDNA의 319 bp와 COI유전자의 710 bp를 PCR 증폭하여 염기서열을 결정하였으며, 염기서열과 아미노산서열을 자료로 하여 UPGMA와 neighbor-joining 방법으로 계통수를 작성하고, 종간 유연관계를 확인하였다. Crassostrea 속과 Ostrea 속간 비교에서는 뚜렷한 유전적 분화를 나타내었으며 계통분석 결과, neighbor-joining 방법에 의한 COI의 아미노산 서열분석에서는 굴과 강굴이 자매군을 형성하는 양상을 보였으나 두 유전자의 염기서열과 A+T 비율 비교에서는 굴과 바위굴이 자매군을 형성하는 것으로 나타났다.

• Journal of Microbiology and Biotechnology
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• 제17권6호
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• pp.985-992
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• 2007

The diversity of archaeal strains from six hypersaline environments in Turkey was analyzed by comparing their phenotypic characteristics and 16S rDNA sequences. Thirty-three isolates were characterized in terms of their phenotypic properties including morphological and biochemical characteristics, susceptibility to different antibiotics, and total lipid and plasmid contents, and finally compared by 16S rDNA gene sequences. The results showed that all isolates belong to the family Halobacteriaceae. Phylogenetic analyses using approximately 1,388 bp comparisions of 16S rDNA sequences demonstrated that all isolates clustered closely to species belonging to 9 genera, namely Halorubrum (8 isolates), Natrinema (5 isolates), Haloarcula (4 isolates), Natronococcus (4 isolates), Natrialba (4 isolates), Haloferax (3 isolates), Haloterrigena (3 isolates), Halalkalicoccus (1 isolate), and Halomicrobium (1 isolate). The results revealed a high diversity among the isolated halophilic strains and indicated that some of these strains constitute new taxa of extremely halophilic archaea.

• Animal cells and systems
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• 제6권2호
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• pp.145-151
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• 2002

Phylogenetic signal present in the mitochondrial 16S ribosomal RNA gene (16S rDNA) and the nuclear large subunit ribosomal RNA gene (28S rDNA) was explored to assess their utility in resolving family level relationships of the superfamily Tephritoidea. These two genes were chosen because they appear to evolve at different rates, and might contribute to resolve both shallow and deeper phylogenetic branches within a highly diversified group. For the 16S rDNA data set, the number of aligned sites was 1,258 bp, but 1,204 bp were used for analysis after excluding sites of ambiguous alignment. Among these 1,204 sites, 662 sites were variable and 450 sites were informative for parsimony analysis. For the 28S rDNA data set, the number of aligned sites was 1,102 bp, but 1,000 bp were used for analysis after excluding sites of ambiguous alignment. Among these 1000 sites, 235 sites were variable and 95 sites were informative for parsimony analysis. Our analyses suggest that: (1) while 16S rDNA is useful for resolving more recent phylogenetic divergences, 28S rDNA can be used to define much deeper phylogenetic branches; (2) the combined analysis of the 16S and 28S rDNAs enhances the overall resolution without losing phylogenetic signal from either single gene analysis; and (3) additional genes that evolve at intermediate rates between the 16S and 28S rDNAs are needed to further resolve relationships among the tephritoid families.

• 미생물학회지
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• 제46권3호
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• pp.296-302
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• 2010

남조세균 Microcystis (Cyanobacteria, Chroococcales)는 담수 녹조원인 생물의 하나로써 일부 종은 microcystin이라는 간 독소를 분비한다. 따라서 담수 수질관리 및 보건위생 측면에서 이들에 대한 관리가 필요하다. 본 연구는 Microcystis 분자 검출을 위한 신규 마커로 RNA polymerase beta subunit (rpoB) 유전자 염기서열을 분석하여 이들의 분자적 특성을 규명하였다. Microcystis rpoB 유전자는 16S rRNA보다 염기 유사도와 유전거리에서 큰 변이가 있는 것으로 조사되었으며, 통계적으로 유의한 차이를 보였다(Student t-test, p<0.05). Parsimony 분석을 통해 rpoB 유전자가 16S rRNA 유전자보다 2배 이상 빠르게 진화하는 것으로 파악되었다. 또한 rpoB 유전자 phylogeny 분석에서 16S rRNA tree 보다 M. aeruginosa 균주를 명확하게 구분해 주었다. Microcystis가 속하는 Chroococcales 목은 염색체 안에 2개 정도의 rRNA 오페론이 있고 rpoB 유전자는 1개 있는 것으로 조사되었다. 본 연구결과는 rpoB 유전자가 Microcystis의 분자계통분류 및 분자검출 마커로 유용하다는 것을 제시해 준다.

• Journal of Microbiology
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• 제44권5호
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• pp.566-571
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• 2006

An archaeal 16S rRNA gene library was constructed from mangrove soil. Phylogenetic analysis revealed archaea in mangrove soil including the Crenarchaeota (80.4%) and Euryarchaeota (19.6%) phyla. The archaeal community in mangrove soil appears to be a mixture of organisms found in a variety of environments with the majority being of marine origin.

• Journal of Microbiology and Biotechnology
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• 제14권1호
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• pp.205-211
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• 2004

A 16S rDNA clone library was generated to investigate the bacterial diversity in tidal flat sediment in Ganghwa Island, Republic of Korea. A total of 103 clones were sequenced and analyzed by comprehensive phylogenetic analyses. No clones were identical to any of known 16S rRNA sequences in public databases. Sequenced clones fell into thirteen lineages of the domain Bacteria: the alpha, beta, gamma, delta, and epsilon Proteobacteria, Actinobacteria, CFB group, Chloroflexi, Acidobacteria, Planctomycetes, Verrucomicrobia, and known uncultured candidate divisions (OP11, BRC1, KSB1, and WS1). Two clones were not associated with any known bacterial divisions. The majority of clones belonged to the gamma and delta Proteobacteria (46.7%). Clones of Actinobacteria were distantly related to known taxa. It is evident from 16S rDNA-based community analysis that the bacterial community in tidal flat sediment is remarkably diverse and unique among other marine environments examined so far.

• The Plant Pathology Journal
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• 제18권3호
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• pp.109-114
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• 2002

To evaluate the phylogenetic and taxonomic status of the phytoplasmas associated with water dropwort (Oenanthe javanica DC) disease in Korea and Japan, their 16S rDNA was analyzed. DNAs extracted from water dropworts collected in Korea (Kyongnam province) and Japan (Chiba prefecture) affected by witches' broom and yellows were subjected to PCR using phytoplasma-specific primers, which amplified a 1.4-kbp fragment that included the 16S rDNA. Phytoplasmas were characterized by RFLP analysis using AluI, HaeIII, HhaI, KpnI, MseI, and RsaI restriction enzymes and by sequence analysis of the PCR products. The mater dropwort witches'broom (WDWB) and water dropwort yellows (WDY) 16S rDNA sequences were identical and closely related to onion yellows (OY, 99.9% identity), which belong to the aster yellows (AY) 16S-subgroup. However, the KpnI RFLP analyses clearly distinguished the WDY and WDWB phytoplasmas from the OY phytoplasma. The phylogenetic analysis based on 16S rDNA showed that WDWE and WDY phytoplasmas are members of a relatively homogeneous group that evolved from a common ancestor.

• 미생물학회지
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• 제47권3호
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• pp.268-274
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• 2011

남조세균 Anabaena (Cyanobacteria, Nostocales)는 담수 생태계에서 녹조 현상을 유발하거나 일부 종은 간독소(hepatotoxin)를 갖고 있어 수질관리 차원에서 주목 받아 왔다. 본 연구는 Anabaena RNA polymerase beta subunit (rpoB) 유전자 염기서열을 규명하였으며, 분류학적 분자 마커로 사용하기 위하여 이들 염기서열의 특성을 평가하였다. Anabaena rpoB 유전자는 16S rRNA 유전자와 비교하여 염기 유사도가 낮으며 유전자 변이가 큰 것으로 분석되었으며, 통계적으로 유의한 차이를 보였다(Student t-test, p<0.01). Parsimony 분석을 통해 rpoB 유전자가 4.8배의 속도로 빠르게 진화하는 것으로 파악되었다. 또한 rpoB 유전자 phylogeny 분석에서 16S rRNA tree보다 높은 해상도로 Anabaena 균주를 명확하게 구분해 주었다. 본 연구 결과는 Anabaena의 종 식별, 분자계통 분류, 분자적 검출을 위해 rpoB 유전자가 매우 효과적이라는 것을 제시해 준다.

• Molecules and Cells
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• 제22권1호
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• pp.78-88
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• 2006

The phylogeny of the subfamily Tephritinae (Diptera: Tephritidae) was reconstructed from mitochondrial 16S ribosomal RNA gene sequences using 53 species representing 11 currently recognized tribes of the Tephritinae and 10 outgroup species. The minimum evolution and Bayesian trees suggested the following phylogenetic relationships: (1) monophyly of the Tephritinae was strongly supported; (2) a sister group relationship between the Tephritinae and Plioreocepta was supported by the Bayesian tree; (3) the tribes Tephrellini, Myopitini, and Terelliini (excluding Neaspilota) were supported as monophyletic groups; (4) the non-monophyletic nature of the tribes Dithrycini, Eutretini, Noeetini, Tephritini, Cecidocharini, and Xyphosiini; and (5) recognition of 10 putative tribal groups, most of which were supported strongly by the statistical tests of the interior branches. Our results, therefore, convincingly suggest that an extensive rearrangement of the tribal classification of the Tephritinae is necessary. Since our sampling of taxa heavily relied on the current accepted classification, some lineages identified by the present study were severely under-sampled and other possible major lineages of the Tephritinae were probably not even represented in our dataset. We believe that our results provide baseline information for a more rigorous sampling of additional taxa representing all possible major lineages of the subfamily, which is essential for a comprehensive revision of the tephritine tribal classification.