• Title/Summary/Keyword: ARDRA

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Bacterial diversity of the Marine Sponge, Halichondria panicea by ARDRA and DGGE (ARDRA와 DGGE를 이용한 Halichondria panicea 해면의 공생세균 다양성)

  • Park, Jin-Sook
    • Korean Journal of Microbiology
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    • v.51 no.4
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    • pp.398-406
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    • 2015
  • Culture-dependent ARDRA and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Halichondria panicea collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and Marine agar media. PCR amplicons of the 16S rRNA gene from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rRNA gene sequences derived from ARDRA patterns showed more than 96% similarities compared with known bacterial species, and the isolates belonged to four classes, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Firmicutes, of which Alphaproteobacteria was dominant. DGGE fingerprinting of 16S rRNA genes amplified from the sponge-derived total gDNA showed 14 DGGE bands, and their sequences showed 100% similarities compared with the sequences available in GenBank. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven classes, including Alphaproteobacteria, Gammaproteobacteria, Acidobacteria, Actinobacteira, Bacteroidetes, Cyanobacteria, and Chloroflexi. According to both the ARDRA and DGGE methods, three classes, Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, were commonly found in H. panicea. However, overall bacterial community in the sponge differed depending on the analysis methods. Sponge showed more various bacterial community structures in culture independent method than in culture-dependent method.

The Genetic Diversity of Bacterial Communities in the Groundwater (지하수 세균 군집의 유전적 다양성)

  • 김여원;민병례;최영길
    • Korean Journal of Environmental Biology
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    • v.18 no.1
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    • pp.53-61
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    • 2000
  • In order to characterize the genetic diversity of bacterial community in groundwater, samples were collected from used for drinking water and polluted with heavy metal wastewater in Seoul city and natural cave of Kangwondo. The DNA was amplified with 165 rDNA-based primers by use of the PCR, and then analysed ARDRA (amplified ribosomal DNA restriction analysis). Restriction endonuclease analysis patterns of amplified 165 rDNA in drinking water and wastewater relatively showed high genetic diversity in situ and drinking groundwater. The number of DNA fragments varied with in situ and drinking water. This method of ARDRA of bacterial communities in groundwater could be used for a quick assessment of genotypic changes between different locations reflecting different environmental conditions and the diversity reflected pollution of groundwater (natural cave water>drinking water>waste water, as in order of grade). [Genetic diversity, Groundwater, 165 rDNA, PCR, ARDRA].

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Genomic Species Identification of Acinetobacter calcoaceticus - Acinetobacter baumannii Complex Strains by Amplified Ribosomal DNA Restriction Analysis (ARDRA) (Amplified Ribosomal DNA Restriction Analysis (ARDRA) 방법을 이용한 국내 분리 Acinetobacter calcoaceticus - Acinetobacter baumannii Complex 균주의 유전자종 동정)

  • Oh, Jae-Young;Cho, Jae-We;Park, Jong-Chun;Lee, Je-Chul
    • The Journal of the Korean Society for Microbiology
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    • v.35 no.1
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    • pp.69-76
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    • 2000
  • Members of the genus Acinetobacter are recognized as newer pathogens of the nosocomial infection with an increasing frequency in recent years. Strains that belonged to A. calcoaceticus A. baumannii complex (genomic species 1, 2, 3, and 13TU) were major groups associated with nosocomial infection. Phenotypic identification was unreliable and laborious method to classify Acinetobacter strains into 19 genomic species. Rapid and reliable identification of clinical isolates is essential to diagnosis and epidemiology of Acinetobacter. We investigated the suitability of amplified ribosomal DNA restriction analysis (ARDRA) to identify genomic species of 131 Acinetobacter isolates. The 16S rRNA genes (ribosomal DNA) were enzymatically amplified and the amplified PCR products were restricted independently with the enzymes, AluI, CfoI, and MboI. Genomic species of Acinetobacter was classified by the combinations of restriction patterns. The analysis was showed that restriction profiles were characteristic for each genomic species. One hundred fourteen isolates were identified as A. baumannii, twelve were identified as genomic species 13TU, and one was identified as genomic species 3. Four isolates were found to be unknown organisms. All of the isolates which were identified to A. baumannii by phenotypic tests were completely discriminated into A. baumannii and genomic species 13TU by ARDRA. This study demonstrates that ARDRA is a rapid and simple techniques for the identification of Acinetobacter species according to the genomic species.

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Comparison of the Phylogenetic Diversity of Humus Forest Soil Bacterial Populations via Different Direct DNA Extyaction Methods (DNA 직접추출법에 따른 산림토양 부식층 내 세균군집의 계통학적 다양성 비교)

  • Son, Hee-Seong;Han, Song-Ih;Whang, Kyung-Sook
    • Korean Journal of Microbiology
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    • v.43 no.3
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    • pp.210-216
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    • 2007
  • The principal objective of this study was to analyze 16S rDNA-ARDRA of the humus forest soil via an improved manual method and an ISOIL kit on the basis of the UPGMA clustering of the 16S rDNA combined profile, 44 ARDRA clusters of 76 clones via the ISOIL kit method and 45 ARDRA clusters of 136 clones via the improved manual method. On the basis of the 16S rDNA sequences, 44 clones from the ARDRA clusters by the ISOIL kit were classified into 3 phyla : ${\alpha}-,\;{\beta}-,\;{\gamma}-,\;{\delta}-Proteobacteria$, Acidobacteria and Actinobacteria. Using the improved manual method, the specimens were classified into 6 phyla : the ${\alpha}-,\;{\beta}-,\;{\gamma}-,\;{\delta}-Proteobacteria$, Acidobacteria, Bacteroides, Verrucomicrobia, Planctomycetes and Gemmatomonadetes. As a result, the modified manual method indicated greater phylogenetic diversity than was detected by the ISOIL kit. Approximately 40 percent of the total clones were identified as ${\alpha}-Proteobacteria$ and 30 percent of the total clones were ${\gamma}-Proteobacteria$ and assigned to dominant phylogenetic groups using the ISOIL kit. Using the modified manual method, 41 percent of the total clones were identified as Acidobacteria and 28 percent of total clones were identified as ${\alpha}-proteobacteria$ and assigned to dominant phylogenetic groups.

Seasonal Differences of Cultivable Bacterial Communities Associated with the Marine Sponge, Petrosia corticata, Collected from Jeju Island (제주도에 서식하는 Petrosia corticata 해면의 배양가능한 공생세균 군집구조의 계절적 차이)

  • Jeong, Jong-Bin;Park, Jin-Sook
    • Journal of Marine Bioscience and Biotechnology
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    • v.7 no.2
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    • pp.42-51
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    • 2015
  • The community structure of cultivable bacteria associated with the marine sponge, Petrosia corticata, collected from Jeju Island in summer (September) of 2012 and winter (January) of 2013, were compared by the PCR-ARDRA method. Bacterial strains were cultured for 4 days at $26^{\circ}C$ on Zobell medium and marine agar medium. After PCR amplification of 16S rRNA gene of individual strains, the restriction enzymes MspI and HaeIII were used to make restriction patterns. As a result, 24 ARDRA patterns from the summer sponge and 20 ARDRA patterns from the winter sponge were obtained. The sequencing result of 1-3 selected strains from each pattern showed over 98% similarities with the known sequences from the public database. At the phylum level, the bacterial community structures of both sponges (summer and winter) were identical qualitatively and composed of 4 phyla : Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Alphaproteobacteria accounted for 42.5% of total in summer sponge and 25.2% in winter, decreasing in the winter sample. Gammaproteobacteria accounted for 27.5% of total in summer sponge and 35.2% in winter, increasing in the winter sample. At the genus and species level, summer sponge had more diverse bacterial communities than winter sponge. Actinobacteria, Bacteroidetes, and Firmicutes increased in the winter sample.

Comparison of Phylogenetic Characteristics of Viable but Non-Culturable (VBNC) Bacterial Populations in the Pine and Quercus Forest Soil by 16S rDNA-ARDRA (16S rDNA-ARDRA법을 이용한 소나무림과 상수리나무림 토양 내 VBNC 세균군집의 계통학적 특성 비교)

  • Han Song-Ih;Kim Youn-Ji;Whang Kyung-Sook
    • Korean Journal of Microbiology
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    • v.42 no.2
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    • pp.116-124
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    • 2006
  • In this study was performed to analyze quantitatively the number of viable but non-culturable bacteria in the Pine and Quercus forest soil by improved direct viable count (DVC) and plate count (PC) methods. The number of living bacteria of Pine and Quercus forest soil by PC method were less then 1% of DVC method. This result showed that viable but non-culturable (VBNC) bacteria existed in the forest soil with high percentage. Diversity and structure of VBNC bacterial populations in forest soil were analyzed by direct extracting of DNA and 16S rDNA-ARDRA from Pine and Quercus forest soil. Each of them obtained 111 clones and 108 clones from Pine and Quercus forest soil. Thirty different RFLP types were detected from Pine forest soil and twenty-six different RFLP types were detected from Quercus forest soil by HeaIII. From ARDRA groups, dominant clones were selected for determining their phylogenetic characteristics based on 16S rDNA sequence. Based on the 16S rDNA sequences, dominant clones from ARDRA groups of Pine forest soil were classified into 7 major phylogenetic groups ${\alpha}$-proteobacteria (12 clones), ${\gamma}$-proteobacteria (3 clones), ${\delta}$-proteobacteria (1 clone), Flexibacter/Cytophaga (1 clone), Actinobacteria (4 clones), Acidobacteria (4 clones), Planctomycetes (5 clones). Also, dominant clones from ARDRA groups of Quercus forest soil were classified into 6 major phylogenetic groups : ${\alpha}$-proteobacte,ia (4clones), ${\gamma}$-proteobacteria (2 clones), Actinobacteria (10 clones), Acidobacteria (8 clones), Planctomycetes (1 clone), and Verrucomicobia (1 clone). Result of phylogeneric analysis of microbial community from Pine and Quercus forest soils were mostly confirmed at uncultured or unidentified bacteria, VBNC bacteria of over 99% existent in forest soil were confirmed variable composition of unknown micro-organism.

Biodiversity and Isolation of Gut Microbes from Digestive Organs of Harmonia axyridis (무당벌레 소화기관으로부터 장내세균의 분리 및 계통학적 다양성)

  • Kim, Ki-Kwang;Han, Song-Ih;Moon, Chung-Won;Yu, Yong-Man;Whang, Kyung-Sook
    • Korean Journal of Microbiology
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    • v.47 no.1
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    • pp.66-73
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    • 2011
  • Bacterial density distributions of gut microbes in the digestive organs of Harmonia axyridis collected from three different sources (JK, CK, and CJ) were $6.0{\times}10^4$ CFU/gut under aerobic culture condition and $8.0{\times}10^6$ CFU/gut under anaerobic culture condition. Seven colony types were observed under aerobic condition and three types of similarity were detected under anaerobic condition. In total, 116 strains, including 34 strains under aerobic condition, were isolated from the digestive organs of H. axyridis. Based on the analysis of the 16S rRNA gene sequence, aerobic gut microbes were assigned to the Proteobacteria, Actinobacteria, Firmicutes, and Deinococcus-Thermus. A large number of isolates belonged to the genus Bacillus and Staphylococcus of the Firmicutes commonly found in H. axyridis from different sites. Anaerobic gut microbes were found to be similar according to colony morphological, phylogenetic analysis using ARDRA. Eighty-two anaerobic gut microbes were clustered into 17 different ARDRA types according to HaeIII. Representative anaerobic gut microbes in each ARDRA group were divided into five species of ${\gamma}$-Proteobacteria based on 16S rRNA gene sequence analysis; Hafnia alvei, Enterobacter ludwigii, Enterobacter kobei, Pseudomonas oryzihabitans and Pseudomonas koreensis. Phylogenetic analysis indicated that about 70% of the isolates belonged to ${\gamma}$-Proteobacteria, suggesting predominance of gut microbes.

분자생물학적 기법을 사용한 질산화유도 반응기내 군집동태변화

  • Jo, Sun-Ja;Jeong, Yong-Ju;Kim, Jeong-Cheol;Lee, Sang-Jun
    • Proceedings of the Korean Environmental Sciences Society Conference
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    • 2005.05a
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    • pp.247-248
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    • 2005
  • 본 연구는 서로 다른 조건에서 질산화를 유도한 반응기의 군집동태를 살피기 위해 RAPD, ARDRA, DGGE와 같은 기법들을 적용시켜 반응기 초기의 슬러지 구성 군집의 상태 와 질산화 유도후의 군집 변화를 살펴보고자 하였다. 결과적으로 1.5 kb정도의 165 rDNA를 이용한 RAPD와 ARDRA에서는 RAPD에 의한 군집 Patterns변화가 훨씬 다양했으며, 250 bP정도의 PCR산물로 분리를 시도한 DGGE에서도 비교적 예상했던 바와 같이 군집이 단순화되는 양상을 볼 수 있었다.

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Bacterial Diversity in the Mud Flat of Sunchon Bay, Chunnam Provice, by 16S rRNA Gene Analysis (16S rRNA 유전자 분석에 의한 전남 순천만 갯벌의 세균 다양성)

  • 이명숙;홍순규;이동훈;배경숙
    • Korean Journal of Microbiology
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    • v.37 no.2
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    • pp.137-144
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    • 2001
  • In order to investigate the diversity of bacterial community in the mud flat of Sunchon Bay, Chunnam province, diversity of amplified 16S rDNA was examined. Total DNA was extracted from sediment soils and 16S rDNAs were amplified using PCR primers based on the universally conserved sequences in bacteria. Clonal libraries were constructed and 111 clones were examined by amplified rDNA restriction analysis (ARDRA) using HaeIII. Clones were clustered based on restriction patterns using computer program, GelCompar II. One hundred different RFLP types were detected from 111 clones. The 20 clones were selected and sequenced according to dendrograms derived from ARDRA, to cover most of the bacterial diversity in the clone libraries. None of the clones were identical to any representatives in the Ribosomal Database Project small subunit RNA databases and GenBank. All sequences showed between 77 and 96.8% similarity to the known 16s rRNA sequence from cultured organisms. The 20 clones sequenced fell into seven major lineages of the domain Bacteria: alpha-, delta-, gamma-Proteobacteria, low G+C Gram positive bacteria, high G+C Gram positive bacteria, Sphingobacteria (Cytophaga) and Cyanobacteria (chloroplast). Among the clones, the Proteobacteria were dominant.

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A Comparison of Genospecies of Clinical Isolates in the Acinetobacter spp. Complex Obtained from Hospitalized Patients in Busan, Korea

  • Park, Gyu-Nam;Kang, Hye-Sook;Kim, Hye-Ran;Jung, Bo-Kyung;Kim, Do-Hee;Chang, Kyung-Soo
    • Biomedical Science Letters
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    • v.25 no.1
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    • pp.40-53
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    • 2019
  • Of the Acinetobacter spp., A. baumannii (genospecies 2) is the most clinically significant in terms of hospital-acquired infections worldwide. It is difficult to perform Acinetobacter-related taxonomy using phenotypic characteristics and routine laboratory methods owing to clusters of closely related species. The ability to accurately identify Acinetobacter spp. is clinically important because antimicrobial susceptibility and clinical relevance differs significantly among the different genospecies. Based on the medical importance of pathogenic Acinetobacter spp., the distribution and characterization of Acinetobacter spp. isolates from 123 clinical samples was determined in the current study using four typically applied bacterial identification methods; partial rpoB gene sequencing, amplified rRNA gene restriction analysis (ARDRA) of the intergenic transcribed spacer (ITS) region of the 16~23S rRNA, the $VITEK^{(R)}$ 2 system (an automated microbial identification system) and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). A. baumannii isolates (74.8%, 92/123) were the most common species, A. nosocomialis (10.6%, 13/123) and A. pittii isolates (7.5%, 9/123) were second and third most common strains of the A. calcoaceticus-A. baumannii (ACB) complex, respectively. A. soli (5.0%, 6/123) was the most common species of the non-ACB complex. RpoB gene sequencing and ARDRA of the ITS region were demonstrated to lead to more accurate species identification than the other methods of analysis used in this study. These results suggest that the use of rpoB genotyping and ARDRA of the ITS region is useful for the species-level identification of Acinetobacter isolates.