• 한국미생물·생명공학회지
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• 제37권3호
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• pp.189-196
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• 2009

Bacteria were isolated from roots of plants belonging to family Solanaceae and Gramineae, inhabited in Dokdo island. Fifty six endospore-forming bacteria grown on tryptic soy broth (TSB) agar medium and 23 nitrogen-fixing bacteria (NFB) grown on nitrogen free agar medium were isolated, respectively. The isolates were partially identified by analyzing the 16S rDNA and categorized into phylogenetic groups. The 16S rDNA sequences of each identified isolates were compared with sequences of each type strains to analyze phylogenetic relationship by phylogenetic tree. As a result, endospore-forming bacteria and nitrogen-fixing bacteria were classified into 4 and 6 lineage groups, respectively. Among these isolated, 18 were presumed to be novel species candidates based on the similarity (lower than 98%) analysis of the l6S rDNA sequences.

• Journal of Microbiology and Biotechnology
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• 제16권1호
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• pp.92-101
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• 2006

The bacterial diversity of the bovine rumen was examined using a PCR-based approach. 16S rDNA sequences were amplified and cloned from three fractions of rumen (solid, fluid, and epithelium) that are likely to represent different bacterial niches. A total of 113 clones were sequenced, and similarities to known l6S rDNA sequences were examined. About $47.8\%$ of the sequences had $90-97\%$ similarity to 16S rDNA database sequences. Furthermore, about $62.2\%$ of the sequences were $98-100\%$ similar to 16S rDNA database sequences. For the remaining $6.1\%$, the similarity was less than $90\%$. Phylogenetic analysis was also used to infer the makeup of the bacterial communities in the different rumen fractions. The Cytophaga-Flexibacter-Bacteroides group (CFB, $67.5\%$), low G+C Gram-positive bacteria (LGCGPB, $30\%$), and Proteobacteria $(2.5\%)$ were represented in the rumen fluid clone set; LGCGPB $(75.7\%)$, CFB$(10.8\%)$, Proteobacteria $(5.4\%)$, high G+C Gram-positive bacteria (HGCGPB, $5.4\%$), and Spirochaetes $(2.7\%)$ were represented in the rumen solid clone set; and the CFB group $(94.4\%)$ and LGCGPB $(5.6\%)$ were represented in the rumen epithelium clone set. These findings suggest that the rumen fluid, solid, and epithelium support different microbial populations that may play specific roles in rumen function.

• Animal Systematics, Evolution and Diversity
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• 제37권4호
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• pp.349-353
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• 2021

Scolelepis (Parascolelepis) papillosa (Okuda, 1937), originally described from a single incomplete individual from Jeju Island in Korea, was collected from the intertidal sandflats of Soan Island (Jeollanam-do province) in Korea. The examined specimens of S. (P.) papillosa agree well with the original description in having the papillae on the basal sheath of the palps, presence of occipital antenna, absence of notochaetae in chaetiger 1, branchiae completely fused with notopodial postchaetal lamellae at the anterior chaetigers, and neuropodial hooded hooks appearing from chaetiger 16. In this study, the sequences of partial mitochondrial cytochrome c oxidase subunit I (COI), 16S ribosomal DNA (16S rDNA), and the nuclear 18S ribosomal DNA (18S rDNA) of the species were determined. We also provide the detailed description and illustrations on this species based on the complete specimens newly collected in this study.

• The Plant Pathology Journal
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• 제21권4호
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• pp.383-386
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• 2005

In 2003 typical phytoplasma symptoms of witches' broom and flower malformation were observed on statice (Limonium sinuatum) plants grown at commercial greenhouses in Busan, South Korea. The DNA extracted from the infected leaves was amplified using universal primer pair of Pl/P6 derived from conserved 16S rRNA gene of Mollicutes giving the expected Polymerase chain reaction (PCR) product of 1.5 kb. In the nested PCR assays, the expected DNA fragment of 1.1 kb was amplified with the specific primer pair 16Fl/Rl that was designed on the basis of aster yellows (AY) phytoplasma 16S rDNA sequences. The 1.1 kb PCR products were cloned and nucleotide sequences were determined. The sequences were identical to that of Onion yellows OY phytoplasma (GenBank accession no. D12569) isolated from Onion in Japan. Electron microscopy of thin sections of leaf veins showed phytoplasma bodies in the phloem. Statice witches' broom symptom occurred on statice in commercial greenhouses in Korea was confirmed as infection of AY phytoplasma by transmission electron microscopy observation, and by determination of 16S rRNA gene sequences of phytoplasma.

• Journal of Microbiology
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• 제42권1호
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• pp.9-13
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• 2004

Culture-independent approaches, based on 16S rDNA sequences, are extensively used in modern microbial ecology. Sequencing of the clone library generated from environmental DNA has advantages over fingerprint-based methods, such as denaturing gradient gel electrophoresis, as it provides precise identification and quantification of the phylotypes present in samples. However, to date, no method exists for comparing multiple bacterial community structures using clone library sequences. In this study, an automated method to achieve this has been developed, by applying pair wise alignment, hierarchical clustering and principle component analysis. The method has been demonstrated to be successful in comparing samples from various environments. The program, named CommCluster, was written in JAVA, and is now freely available, at http://chunlab.snu.ac.kr/commcluster/.

• 식물병연구
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• 제9권4호
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• pp.189-195
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• 2003

참외의 발효과를 유발하는 세균은 16S rDNA 염기분석에 의해 3 group으로 분류되었다. CM2105균주의 16S rDNA 염기서열은 Microbacterium phyllosphaerae의 염기서열과 99.6%의 높은 상동성을 나타냈고, M. holiorum과도 99.5%의 높은 상동성을 나타냈다. CM2101과 CM2121균주의 16S rDNA 염기서열은 "P. pavonaceae"와 각각 98.9%, 98.8, CM2126균주는 P. costantinii와 99.5%, P. grimontii와 99.0%의 높은 상동성을 나타냈다. CM21131균주의 16S rDNA 염기서열은 Enterobacter cloacae와 99.7%의 높은 상동성 나타냈다. 검정균주의 생리적, 생화학적 특성과 16S rDNA의 염기분석에 따라 CM2105 균주는 M. phyllosphaerae, CM2101, CM2121, CM2126 균주는 Pseudomonas spp., 그리고 CM2113 균주는 E. cloacae로 동정하였다.

• 미생물학회지
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• 제48권4호
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• pp.275-283
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• 2012

해양 해면 Asteropus simplex를 제주도에서 채집하여 배양에 의한 RFLP와 비배양에 의한 DGGE 분석 방법에 의해 세균군집 구조를 조사하였다. 16S rDNA-RFLP 분석을 위해 변형된 Zobell 배지와 MA를 이용하여 120균주를 선별하고 제한효소, HaeIII와 MspI을 사용하여 각각의 다른 RFLP 패턴으로 구분하였다. RFLP 패턴으로부터 유래한 16S rDNA 염기서열 분석결과, 알려진 세균 종과 94% 이상의 유사도를 나타내었으며 Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, 5개의 문이 관찰되었다. 그 중 Gammaproteobacteria가 우점하였다. 같은 해면, A. simplex의 DGGE 분석을 위해 total genomic DNA로부터 16S rDNA를 증폭하여 DGGE fingerprinting을 수행한 결과 12개의 서로 다른 밴드가 관찰되었다. 각 밴드의 16S rDNA 염기서열은 알려진 세균의 염기서열과 90% 이상의 유사성을 나타내었으며 대부분의 염기서열은 uncultured bacteria에 속하였다. DGGE 분석으로부터 미생물의 군집은 Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteria, Chloroflexi, Nitrospira, 7개의 문으로 나타났다. RFLP와 DGGE 방법에 의해 Alphaproteobacteria, Gammaproteobacteria, Actinobacteria가 공통적으로 발견되었으나 전체적인 공생세균의 군집구조는 분석방법에 따른 차이를 나타내었다. 배양에 의한 방법보다 비배양 방법에서 더 다양한 세균군집구조를 나타내었다.

• Animal Systematics, Evolution and Diversity
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• 제38권3호
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• pp.144-147
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• 2022

The polychaete Scolelepis (Scolelepis) sagittaria was originally described from Japanese waters and subsequently reported from Korean waters. In this study, we determined for the first time the mitochondrial cytochrome c oxidase subunit I (COI), 16S ribosomal DNA (16S rDNA), and nuclear 18S ribosomal DNA (18S rDNA) sequences of Korean specimens of S. (S.) sagittaria. We also assessed intraspecific variation in the shape of the prostomium of this species based on an examination of 247 individuals. All materials were collected from intertidal sandy beaches of the Korea Strait. The molecular data and morphological observations reported herein will contribute to gaining a better understanding of the taxonomic relationships among members of the genus Scolelepis.

• Animal Systematics, Evolution and Diversity
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• 제36권4호
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• pp.382-386
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• 2020

In this study, Prionospio depauperata Imajima, 1990 is newly reported in Korean fauna. Prionospio depauperata can be distinguished from other relatives by the four pairs of branchiae which are pinnate on chaetigers 2 and 5, and apinnate on chaetigers 3 and 4; caruncle extending to the end of chaetiger 2; and moderate dorsal crest present on chaetigers 7-13. The morphological diagnosis of P. depauperata are provided with the photographs of four Prionospio species. The mitochondrial cytochrome c oxidase subunit 1 (CO1), 16S ribosomal DNA (16S rDNA), and the nuclear 18S ribosomal DNA (18S rDNA) sequences of four Prionospio species from Korean waters, P. depauperata Imajima, 1990, P. japonica Okuda, 1935, P. krusadensis Fauvel, 1929, and P. membranacea Imajima, 1990, were determined for the first time. The inter-specific genetic distances among the congeners of four Prionospio species were 22.3-29.6% in CO1, 10.5-25.0% in 16S rDNA, and 0.3-3.6% in 18S rDNA.

• 미생물학회지
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• 제50권2호
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• pp.152-157
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• 2014

이 논문은 Callyspongia elegans에서 서식하는 세균군집에 관한 내용이다. 해양세균은 marine agar를 사용하여 해면동물 C. elelgans에서 분리하였다. 그 결과 112균주를 분리하였으며, 본 연구에 사용하였다. 현미경 및 그람 염색을 통해 형태학적 표현형질을 측정하였다. 분리균주의 집락 색소는 노란색, 갈색, 아이보리색, 흰색으로 나타났다. 그람염색 결과 37균주는 그람양성균이였으며, 75균주는 그람 음성균이었다. 균주의 형태는 분리균주 중 79균주는 구균형태로 관찰되었고, 16균주는 간균이었다. 16S rDNA 유전자 염기서열 분석을 통해 분리균주들의 계통학적 특성을 파악하였다. 그 결과, 분리된 112균주는 5개의 주요 계통군이 확인되었으며, Alphaproteobacteria는 39%, Gammaproteobacteria는 22%, Acinobacteria는 14%, Firmicutes는 9%, Bacteroidetes는 6%에 속하는 것으로 나타났다. 그리고 16S rDNA 유전자 염기서열을 통해 계통분석 결과 15균주가 새로운 속 또는 종으로 분류될 가능성을 나타났으며, 앞으로 추가적인 실험이 필요한 실정이다.