• ALGAE
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• v.21 no.4
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• pp.349-375
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• 2006

The application of modern ecological, ultrastructural and molecular methods, aided by the cultivation of numerous cyanobacterial morphotypes, has substantially changed our knowledge of these organisms. It has led to major advances in cyanobacterial taxonomy and criteria for their phylogenetic classification. Molecular data provide basic criteria for cyanobacterial taxonomy; however, a correct phylogenetic system cannot be constructed without combining genetic data with knowledge from the previous 150 years research of cyanobacterial diversity. Thus, studies of morphological variation in nature, and modern morphological, ultrastructural, ecophysiological and biochemical characters need to be combined in a “polyphasic” approach. Taxonomic concepts for generic and infrageneric ranks are re-evaluated in light of combined phenotypic and molecular criteria. Despite their usefulness in experimental studies, the limitations of using strains from culture collections for systematic and nomenclatural purposes is highlighted. The need for a continual revision of strain identification and proper nomenclatural practice associated with either the bacteriological or botanical codes is emphasized. Recent advances in taxonomy are highlighted in the context of prospects for understanding cyanobacterial diversity from natural habitats, and the evolutionary and adaptational processes that cyanobacteria undergo.

• YAKHAK HOEJI
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• v.48 no.1
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• pp.20-26
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• 2004

Twelve strains of Bifidobacterium spp. were isolated from the feces of healthy Korean 20∼30 years. The identification of genera from isolates were performed by the microscopic observation and fructose-6-phosphate phosphoketolase (F6PPK) activity which is the key enzyme to distinguish the Bifidobacterium spp. from other anaerobic bacteria. To determine the antibacterial resistance patterns, minimum inhibitory concentration (MIC) of several antibiotics (including anti-tuberculosis agents) was determined. Five of the isolate!, showed the high degree of resistance to vancomycin. To investigate the genetic diversity between isolates and type strain of Bifidobacterium spp. from KCTC, we peformed the RAPD-fingerprinting. Using a total set of four primers, it is possible to distinguish the isolates and Bifidobacterium spp. from KCTC. Thus, Bifidobacterium strains isolated from our samples may be a new species or strains of Bifidobacteriurn genera, and have the potential as a probiotics.

• Journal of Microbiology
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• v.41 no.1
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• pp.7-15
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• 2003

Nine dichlorprop-degrading bacteria and three pairs of bacteria showing syntrophic metabolism of the herbicide were isolated from soils, and their genetic and phenotypic characteristics were investigated. Analysis of 16S rDNA sequences indicated that the isolates were related to members of the genera, Sphingomonas, Herbaspirillum, and Bradyrhizobium. Twelve different chromosomal DNA patterns were obtained by polymerase-chain-reaction (PCR) amplification of repetitive extragenic palindromic (REP) sequences from the 15 isolates. The isolates were able to utilize the herbicide dichlorprop as a sole source of carbon and energy and their dichlorprop derogative pathways were induced by the presence of dichlorprop. Most of the isolates and syntrophic pairs were able to degrade both (R)- and (S)-dichlorprop, but strain DP522 exhibited enantioselective degradation of (S)-dichlorprop. The isolates degraded 2,4-dichlorophenoxyacetic acid, 2-methyl-4-chlorophenoxyacetic acid , and mecoprop, in addition to dichlorprop. Oxygen uptake experiments indicated that most of the isolates degraded dichlorprop through 2,4-dichlorophenol.

• Food Science and Biotechnology
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• v.27 no.6
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• pp.1755-1760
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• 2018

The objective of this study was to perform genetic diversity analysis of 13 strains isolated from South Korean foods by multilocus sequence typing (MLST). For typing, seven housekeeping loci (atpA, dnaA, dnaK, gyrB, pheS, pyrG, and rpoA) were selected, amplified and analyzed. Fifty-one polymorphic sites varying from 1 to 22 in each species were identified. Thirteen sequence types were generated with allele numbers ranged from 2 to 10. The overall relationship between strains was assessed by unweighted pair group method with arithmetic mean dendrogram and minimum spanning tree. In addition, combined spits tree analysis revealed intragenic recombination. No clear relationship was observed between the isolation sources and strains. The developed MLST scheme enhanced our knowledge of the population diversity of Leu. citreum strains and will be used further for the selection of industrially important strain.

• The Plant Pathology Journal
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• v.35 no.4
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• pp.389-392
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• 2019

The studies on detection of the Strawberry mottle virus (SMoV) have been conducted in Poland for breeding programme purpose and for producers of strawberry plant material. Leaf samples collected from infected strawberry plants were grafted on Fragaria sp. Indicators which were maintained in greenhouse for further study. Seven Fragaria vesca var. semperflorens 'Alpine' indicators infected by SMoV were used for the study aimed on molecular characterization of virus isolates. Partial RNA2 was amplified from total nucleic acids using the RT-PCR method. The obtained amplicons separately digested with BfaI, FauI, HaeIII, HincI, and TaqI enzymes showed different restriction profiles. The nucleotide sequences analysis of RNA2 fragment confirmed the genetic diversity of the SMoV isolates as their similarity ranged from 94.7 to 100%. Polish isolates shared 75.7-99.2% identity with sequence of the virus strains from the Czech Republic, the Netherlands, and Canada. Phylogenetic analysis resulted in grouping of the isolates found in Poland together with one of the Czech strain whereas two other from the Czech and the strains from the Netherlands and Canada created the separate cluster.

• Korean Journal of Microbiology
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• v.45 no.2
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• pp.105-111
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• 2009

Norovirus (NV) with a variety of genotypes, a member of the family Caliciviridae, causes acute nonbacterial gastroenteritis in humans. We determined the nucleotide sequence of three open reading frames (ORFs) of a NV Korean strain and characterized the genetic relationship with others. The Korean strain designated Hu/NLV/Gunpo/2006/KO was isolated from the stool specimen of a 2-year-old female suffering from gastroenteritis. By performing reverse transcription and PCR amplification, three overlapping cDNAs were synthesized and used for direct sequencing. We found that like other NVs, this strain contains three ORFs: ORF1, 5,100 bp; ORF2, 1,647 bp; ORF3, 765 bp. Of 35 NVs, ORF1 had a level of genetic diversity lower than ORF2 and ORF3, of which the C-termini of the ORF2 and ORF3 showed a relatively high degree of genetic diversity. Phylogenetic analyses indicated that the Korean strain belonged to genogroup II, with Saitama U1, Gifu'96, Mc37, and Vietnam 026 being formed a single genetic cluster. The nucleotide sequence information of three ORFs of a NV Korean isolate will be useful not only for the development of a diagnostic tool and understanding of genetic relationship, but also provide important basic information for the functional analysis of their gene products.

• Korean Journal of Ecology and Environment
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• v.53 no.4
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• pp.344-354
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• 2020

Identification of the target species of 2-MIB (2-methyllisoborneol) production is crucial in the management of off-flavor problem in the freshwater system. This study was conducted to identify 2-MIB-producing Pseudanabaena strains occurring in the North Han River system using molecular genetic method. Eleven phenotypes of Pseudanabaena were isolated from several mainstream sites of the North Han River, including Sambong-ri, Joam-myun, and Lake Uiam areas. Despite of morphological similarity of the strains, the phylogenetic analysis using 16S rDNA classified them into different species with low genetic similarity (40~55%). Isolated Pseudanabaena strains were converged to four species; Pseudanabaena cinerea, P. yagii, P. mucicola, and P. redekei. Among them, the 2-MIB synthesizing gene (mibC) was detected in P. cinerea, P. yagii, and P. redekei. However, actual 2-MIB production was detected only in P. cinerea and P. redekei based on gas chromatography analysis. This study is the first report of the molecular identification of Pseudanabaena strains and their 2-MIB production potential in Korea. The results of this study provides an evidence of species diversity of Pseudanabaena occurring in the North Han River.

• Korean Journal of Microbiology
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• v.49 no.4
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• pp.336-342
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• 2013

Trichloroethylene (TCE) is a widely used substance in commercial and industrial applications, yet it must be removed from the contaminated soil and groundwater environment due to its toxic and carcinogenic nature. We investigated bacterial community structure, dominant bacterial strain, and removal efficiency in a TCE contaminated groundwater treatment system using immobilized carrier. The microbial diversity was determined by the nucleotide sequences of 16S rRNA gene library. The major bacterial population of the contaminated groundwater treatment system was belonging to BTEX degradation bacteria. The bacterial community consisted mainly of one genus of Pseudomonas (Pseudomonas putida group). The domination of Pseudomonas putida group may be caused by high concentration of toluene and TCE. Furthermore, we isolated a toluene and TCE degrading bacterium, named Pseudomonas sp. DHC8, from the immobilized carrier in bioreactor which was designed to remove TCE from the contaminated ground water. Based on the results of morphological and physiological characteristics, and 16S rRNA gene sequence analysis, strain DHC8 was identified as a member of Pseudomonas putida group. When TCE (0.83 mg/L) and toluene (60.61 mg/L) were degraded by this strain, removal efficiencies were 72.3% and 100% for 12.5 h, respectively. Toluene removal rate was 2.89 ${\mu}mol/g$-DCW/h and TCE removal rate was 0.02 ${\mu}mol/g$-DCW/h. These findings will be helpful for maintaining maximum TCE removal efficiency of a reactor for bioremediation of TCE.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.11
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• pp.1546-1550
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• 2006

The purpose of this study was to assess the genetic variation and establish the relationship amongst breeds and strains using 15 chicken specific microsatellite markers. A total of 285 unrelated DNA samples from four Korean native chicken strains (Black strain of Korean native chicken; KL, Red Brown strain of Korean native chicken; KR, Ogol strain of Korean native chicken; KS and Yellow Brown strain of Korean native chicken; KY) and three introduced chicken breeds (F strain of White Leghorn; LF, K strain of White Leghorn; LK, Rhode Island Red; RC and Cornish; CN) were genotyped to estimate within and between breed genetic diversity indices. All the loci analyzed in 15 microsatellite markers showed a polymorphic pattern and the number of alleles ranged from 5 to 14. The polymorphism information content (PIC) of UMA1019 was the highest (0.872) and that of ADL0234 was the lowest (0.562). The expected total heterozygosity (He) within breed and mean number of observed alleles ranged from 0.540 (LF) to 0.689 (KY), and from 3.47 (LK) to 6.07 (KR), respectively. The genetic variation of KR and KY were the highest and the lowest within Korean native strains, respectively. The genetic distance results showed that Korean native chicken strains were separated with the three introduced chicken breeds clustered into another group. The lowest distance (0.149) was observed between the KR and KL breeds and the highest distance (0.855) between the KR and LK breeds. The microsatellite polymorphism data were shown to be useful for assessing the genetic relationship between Korean native strains and other foreign breeds.

• Journal of Species Research
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• v.6 no.1
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• pp.15-24
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• 2017

During the extensive survey of the prokaryotic species diversity in Korea, bacterial strains belonging to Betaproteobacteria and Epsilonproteobacteria were isolated from various sources including freshwater, sediment, soil and fish. A total of 23 isolates were obtained, among which 22 strains were assigned to the class Betaproteobacteria and one strain to the class Epsilonproteobacteria. The 22 betaproteobacterial strains were further assigned to Comamonadaceae (11 strains), Burkholderiaceae (6 strains), Oxalobacteraceae (2 strains), Neisseriaceae (1 strain) and unclassified family groups (2 strains). For the strains of Burkholderiaceae, 3 strains were identified as 3 species of Burkholderia, and 2 strains were as 2 species of Cupriavidus. For the strains of Comamonadaceae, 4 strains were identified as 2 species of the genus Hydrogenophaga, 2 strains as 2 species of Acidovorax, 2 strains as 2 species of Limnohabitans, and each of the remaining strains as single species of Comamonas, Curvibacter and Rhodoferax, respectively. For the strains of Oxalobacteraceae, 1 strain was identified as a species of Undibacterium, and the other strain as a species of Herbaspirillum. The strain belonging to Neisseriaceae was identified as a species of Iodobacter. The remaining strains of Betaproteobacteria were identified as species of Sphaerotilus and Methylibium respectively (family unassigned). The epsilonproteobacterial strain was identified as a species of Arcobacter of the family Camplyobacteraceae. The detailed description of each unrecorded species is provided.