• 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].

• Korean Journal of Environmental Biology
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• v.21 no.1
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• pp.45-51
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• 2003

Genetic diversity of local populations among geologically isolated groups of Rana amurensis was refined by sequence comparison of the mitochondrial (mt) 165 rDNA genes. Each 401 base pairs of DNA sequences, which was determined from four local populations of Rana amurensis, two local populations of R. nigromacutata, and three species of the genus Rana were used in this analysis. Despite morphological similarity of Rana amurensis, Korean populations were well distinguished from the other groups on the basis of 105 rDNA gene difference. Further analyses for additional local populations belonging to R. amurensis will be necessary to clarify the taxonomic status.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.18 no.12
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• pp.466-472
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• 2017

This study was designed to examine the diversity census of fungi in rumen microbiome via meta-analysis of fungal 28S rDNA sequences. Both terms, "rumen" and "ruminal," were searched to retrieve the sequences of rumen fungi. As of September 2016, these sequences (n=165) of ruminal origin were retrieved from the Ribosomal Database Project (RDP; http://rdp.cme.msu.edu), an archive of all 28S rDNA sequences and were assigned to the phyla Ascomycota, Neocallimastigomycota, and Basidiomycota, which accounted for 109, 48, and 8 of the 165 sequences, respectively. Ascomycota sequences were assigned to the genera Pseudonectria, Magnaporthe, Alternaria, Cochliobolus, Cladosporium, and Davidiella, including fungal plant pathogens or mycotoxigenic species. Moreover, Basidiomycota sequences were assigned to the genera Thanatephorus and Cryptococcus, including fungal plant pathogens. Furthermore, Neocallimastigomycota sequences were assigned to the genera Cyllamyces, Neocallimastix, Anaeromyces, Caecomyces, Orpinomyces, and Piromyces, which may degrade the major structural carbohydrates of the ingested plant material. This study provided a collective view of the rumen fungal diversity using a meta-analysis of 28S rDNA sequences. The present results will provide a direction for further studies on ruminal fungi and be applicable to the development of new analytic tools.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2000.10a
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• pp.109-117
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• 2000

Bacterial community structure composing enhanced biological phosphorus removal (EBPR) activated sludge was analyzed phylogenetically by cloning 165 rDNA after direct DNA extraction. Then, this result was compared with 165 rDNA sequences of randomly isolated bacterial species. The results clearly showed that there are no coincidence between the sequences retrieved directly from activated sludge and those of isolated strains, suggesting that many important bacteria are hidden in activated sludge because of the difficulty in isolation and culture of them.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.136.2-137
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• 2003

In order to diagnose and differentiate jujube witches' broom (JWB) phytoplasma rapidly, oligonucleotide primer pair, 16Sr(V) F/R, for polymerase chain reactions (PCRs) was designed on the basis of 165 rRNA sequences of JWB phytoplasma. The PCR employing phytoplasma universal primer pair P1/P7 consistently amplified DNA in all tested phytoplasma isolates. But no phytoplasma DNA was detected in healthy jujube seedlings. The nested PCR, the primer pair 16S(V) F/R, about 460 bp fragment, amplified DNA in all tested JWB and related phytoplasmas including LiWB phytoplasma of the 165 rRNA group V, but no DNA amplification was detected from other phytoplasma strains such as group 16SrI (Aster yellows) and group 16SrⅩII (Stolbur group) phytoplasmas in which mulberry dwarf phytoplasma and chrysanthemum witches broom phytoplasma are belonged to, respectively The same results were obtained from both Korean- and Chinese-isolates of JWB. Nested-PCR using phytoplasma universal primer pair P1/P7 and 16S rRNA group V specific primer pair 16S(V) F/R could detect group V phytoplasma rapidly and easily, in particular JWB phytoplasma.

• Korean Journal of Microbiology
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• v.39 no.1
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• pp.36-39
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• 2003

The rapid and reliable 16S rDNA multiplex polymerase chain reaction (PCR) assay was established to characterize bacterial etiologies of middle ear effusion. These etiologies included Haemophilus influenzae, Moraxella catarrhalis and Streptococcus pneumonia, which were detected in middle-ear effusion (MEE) samples taken from patient with otitis media. A total of 39 MEE samples were aspirated from 26 patients. DNA was extracted from MEE samples, and PCR was done with DNA extracts by using the common primers, which is localized at C4 region in the 16S rDNA gene of all bacterial species, and species-specific primers: (i) Haemophilus-specific primer, (ii) Moraxella- specific primer, and (iii) Streptococcus-specific primer. Among 39 samples tested, 24 (61.5%) were positive for H. influenzae, 10 (25.6%) were positive for M. catarrhalis, 3(7.7%) were positive for S. pneumonia, and 11 (28%) were negative for 165 rDNA multiplex PCR reaction. Nine samples (28.6%) exhibited a mixed infection and were positive for both H. infuenzae and M. catarrhalis. We suggested that 16S rDNA multiplex PCR is a useful method to identify rapidly for rapid identification of the pathogenic bacteria and characterization of bacterial etiologies of middle ear effusion.

• Korean Journal of Microbiology
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• v.39 no.3
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• pp.187-191
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• 2003

In an attempt to isolate myxobacteria from soil samples, we isolated swarm and fruiting body forming bacteria that have bacteriolytic activity on Coli-spot agar plate. For the classification of myxobacteria, 16S rDNA RFLP patterns were analyzed. Amplified 16S rDNAs of myxobacteria type strains (Family I, II, III and IV), negative control strains and soil-isolates were restricted with HaeIII, EcoRI and EcoRV, respectively. We found that the soil-isolates belongs to myxobacteria Family I, II, III.

• Research in Plant Disease
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• v.10 no.1
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• pp.63-68
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• 2004

Twenty-three strains of Serratia sp., isolated from surface-sterilized rice roots collected in Chonbuk and Chungnam province, were identified and characterized. They were Gram-negative, rod shaped and red pigmented typically and their endophytism was confirmed by inoculation and reisolation of the strains in planta. Their antifungal activity against 4 rice pathogenic fungi was compared and ranged from 62.4 to 85.2％ against Rhizoctonia solani and 68.0 to 88.5％ against Pyricularia grisea. Among the 23 strains tested, strain Rsm220 showed the strongest inhibition activity against 4 pathogenic fungi. The strain was, therefore, selected as a biocontrol candidate for both the pathogens and its bacteriological characteristics and 165 rDNA sequences were analyzed. Phenotypic and biochemical characteristics of the selected Rsm220 were highly related to the type strain of S. marcescens and 165 rDNA sequencing of Rsm220 showed a homology of 98.2％ to the type strain of S. marcescens. The strain Rsm220 was identified as S. marcescens and the inhibition result of this endophytic strain indicates that it is a potential biocontrol agent for R. solani and R grisea.

• Korean Journal of Microbiology
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• v.38 no.2
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• pp.107-112
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• 2002

To isolate the bacteria lysing cyanobacteria, the sediment samples were collected from Dochang and Pal'tang Reservoir and Seokchon Lake. Each sample was smeared on the Anabaena cylindrica lawn and incubated in light chamber for 11 days. Bacteria having cyanobacteria-Iysing activity were isolated from the samples of Seokchon reservoir. Confirmation of cyanobacteria-Iysing activity was carried out to measure chlorophyll a and bacterial cell counting in mixed culture of Anabaena cylindrica and bacteria. Lysis was detected when extracellular meterials was added to the Anabaena cylindrica culture. The isolate was identified by analysis based on 16S rDNA sequence and morphological and physiological properties. The bacterial strain was taxonomically studied by the phylogenetic analysis based on 165 rDNA sequence. This strain was identified as a member of the genus Bacillus and designated as Bacillus sp. CHS1.

• Journal of Microbiology and Biotechnology
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• v.13 no.2
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• pp.236-242
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• 2003

A culture-independent and -dependent survey of the bacterial community structure in the rhizosphere and soil samples from hot pepper plants was conducted using 16S rDNA clone library and FAME analyses. Out of the 78 clones sequenced, 56% belonged to Proteobacteria, 4% to high G+C Gram- positive group, 3% to Cytophyga-Flexibacter-Bacreroides, and 32% could not be grouped with any known taxonomic division. Among the 127 FAME isolates identified, 66% belonged to low G+C Gram-positive bacteria (Baciilus spp.) and 26% to high G+C Gram-positive bacteria. In a cluster analysis, the results for both methods were found to be strikingly dissimilar. The current study is the first comparative study of FAME and 165 rDNA clonal analyses performed on the same set of soil, rhizosphere soil, and root samples.