• Fisheries and Aquatic Sciences
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• v.16 no.2
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• pp.109-116
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• 2013

Eighteen specimens of juvenile Mugilidae were collected in October 2012 from the southern coastal waters of Jeju Island, and identified based on analysis of their mitochondrial DNA16S rRNA sequences. Seventeen specimens of Oedalechilus labiosus and a single specimen of Ellochelon vaigiensis were found, constituting a new record for these species among Korean ichthyofauna. O. labiosus is identified by the angle at the posterior end of its mouth, which contains a round notch, a darkish dorsal margin of the pectoral fin, the presence of 33-36 lateral line scales, and 23-24 vertebrae. E. vaigiensis is identified by dark dorsal and pectoral fins, the presence of 26 lateral line scales, and 25 vertebrae. The proposed Korean name for Oedalechilus is 'Sol-ip-sung-eo-sok' and that for Ellochelon is 'Nup-jeok-ggo-ri-sung-eo-sok'. The proposed Korean names for the species are 'Sol-ip-sung-eo' and 'Nup-jeok-ggo-ri-sung-eo' for O. labiosus and E. vaigiensis, respectively. We present a key for identification of the Mugilidae family of species from Korea, and include these two newly recorded species.

• Korean Journal of Environmental Biology
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• v.37 no.3
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• pp.260-267
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• 2019

Two aerophytic cyanobacteria from the rockwall of Haje port located in Geum river, Korea, were isolated in unialgal cultures and submitted to polyphasic evaluation. The filaments of the populations presented solitary or several to many parallel arranged. The straight trichomes were not attenuated with rounded apical cell. Phylogenetic analyses based on 16S rDNA sequences indicated that these populations formed the same clade with Wilmottia murrayi and had 99% or greater DNA similarity. Through the ultrastructure of the TEM, these populations showed parietal thylakoid arrangement, which coincides with family Coleofasciculaceae. From the above results, we reported the newly recorded genus Wilmottia, and species W. murrayi in Korea.

• Journal of Photoscience
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• v.8 no.3_4
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• pp.93-97
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• 2001

Heterosigma akashiwo has been reported as red-tide causing phytoplankton in the Korean coastal area during summer when they are exposed to high light. It also shows photosynthetic adaptability to strong light during culture in the laboratory. On the basis of these observations, we tried to find out some genes specifically expressed in Heterosimga akashiwo during exposure to high light, assuming that they might have some resistant mechanisms associated with light adaptation. For this purpose, we carried out DD-PCR to detect differentially expressed mRNAs from cells that had been illuminated under high light for 3 days. We found eight cDNA clones that had been expressed specificically for high light. When they were further screened by reverse Northern hybridization, three of them were identified to be positive cDNA clones. When these cDNA fragments were subjected to DNA sequencing and then their base sequences were compared to GenBank database, one of them showed sequence homology 86% identical to the partial sequence of 16S rRNA gene of eubacterium CRO-18.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.12
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• pp.1887-1894
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• 2007

In this paper, a rapid and reliable gene-targeted species-specific polymerase chain reaction (PCR) technique based on a two-step process was established to identify bifidobacteria in dairy products. The first step was the PCR assay for genus Bifidobacterium with genus specific primers followed by the second step, which identified the species level with species-specific primer mixtures. Ten specific primer pairs, designed from nucleotide sequences of the 16-23S rRNA region, were developed for the Bifidobacterium species including B. angulatum, B. animalis, B. bifidum, B. breve, B. catenulatum, B. infantis, B. longum, B. minimum, B. subtile, and B. thermophilum. This technique was applied to the identification of Bifidobacterium species isolated from 6 probiotic products, and four different Bifidobacterium spp. (B. bifidum, B. longum, B. infantis, and B. breve) were identified. The findings indicated that the 16S-23S rDNA gene-targeted species-specific PCR technique is a simple and reliable method for identification of bifidobacteria in probiotic products. PCR combined with Denaturing Gradient Gel Electrophoresis (DGGE) for identification of the bifidobacteria was also evaluated and compared with the gene-targeted species-specific technique. Results indicated that for fermented milk products consistency was found for both species-specific PCR and PCR-DGGE in detecting species. However, in some lyophilized products, the bands corresponding to these species were not visualized in the DGGE profile but the specific PCR gave a positive result.

• Journal of Microbiology
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• v.43 no.4
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• pp.345-353
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• 2005

The complex ecosystem of intestinal micro flora is estimated to harbor approximately 400 different microbial species, mostly bacteria. However, studies on bacterial colonization have mostly been based on culturing methods, which only detect a small fraction of the whole microbiotic ecosystem of the gut. To clarify the initial acquisition and subsequent colonization of bacteria in an infant within the few days after birth, phylogenetic analysis was performed using 16S rDNA sequences from the DNA iso-lated from feces on the 1st, 3rd, and 6th day. 16S rDNA libraries were constructed with the amplicons of PCR conditions at 30 cycles and $50^{\circ}C$ annealing temperature. Nine independent libraries were produced by the application of three sets of primers (set A, set B, and set C) combined with three fecal samples for day 1, day 3, and day 6 of life. Approximately 220 clones ($76.7\%$) of all 325 isolated clones were characterized as known species, while other 105 clones ($32.3\%$) were characterized as unknown species. The library clone with set A universal primers amplifying 350 bp displayed increased diversity by days. Thus, set A primers were better suited for this type of molecular ecological analysis. On the first day of the life of the infant, Enterobacter, Lactococcus lactis, Leuconostoc citreum, and Streptococcus mitis were present. The largest taxonomic group was L. lactis. On the third day of the life of the infant, Enterobacter, Enterococcus faecalis, Escherichia coli, S. mitis, and Streptococcus salivarius were present. On the sixth day of the life of the infant, Citrobacter, Clostridium difficile, Enterobacter sp., Enterobacter cloacae, and E. coli were present. The largest taxonomic group was E. coli. These results showed that microbiotic diversity changes very rapidly in the few days after birth, and the acquisition of unculturable bacteria expanded rapidly after the third day.

• Journal of Life Science
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• v.12 no.2
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• pp.200-207
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• 2002

This study was carried out to isolate of antagonistic bacterium against Pythium ultimum and Rhizoctonia solani AG-4, causal pathogens of vegetables damping-off. Total of 600 strains were isolated from soil and plait roots. The isolates were screened for antagonism against Pythium ultimum and Rhizoctonia solani AG-4. One strain, named YJ-37, was sellected for detained study among those microoganisms screened. It was identified as Bacillus ehimensis based on morphological and physiological characterisitics according to the Bergey's mannual of systematic bacteriology, Sherlock system of Microbial ID Inc. and 16S rDNA sequences methods. Furthermore Bacillus ehimensis YJ-37 showed antifungal activities against Alternaria altrata, Collectotrichum gloeosporioides, Didymella bryoniae, Fusarium moniliforme, Fusarium oxysporum, F. oxysporum cucumerinum, F. oxysporum niveum, Gloeosporium sp., Glomerella sp., G. cingulata, G. lagenaria, Penicillium digitatum, P. italicum, Phytophthora capsici, Sclerotinia sclerotiorum, and Stemprhylium solani.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.5
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• pp.631-639
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• 2016

China has a long history of sheep (Ovis aries [O. aries]) breeding and an abundance of sheep genetic resources. Knowledge of the complete O. aries mitogenome should facilitate the study of the evolutionary history of the species. Therefore, the complete mitogenome of O. aries was sequenced and annotated. In order to characterize the mitogenomes of 3 Chinese sheep breeds (Altay sheep [AL], Shandong large-tailed sheep [SD], and small-tailed Hulun Buir sheep [sHL]), 19 sets of primers were employed to amplify contiguous, overlapping segments of the complete mitochondrial DNA (mtDNA) sequence of each breed. The sizes of the complete mitochondrial genomes of the sHL, AL, and SD breeds were 16,617 bp, 16,613 bp, and 16,613 bp, respectively. The mitochondrial genomes were deposited in the GenBank database with accession numbers KP702285 (AL sheep), KP981378 (SD sheep), and KP981380 (sHL sheep) respectively. The organization of the 3 analyzed sheep mitochondrial genomes was similar, with each consisting of 22 tRNA genes, 2 rRNA genes (12S rRNA and 16S rRNA), 13 protein-coding genes, and 1 control region (D-loop). The NADH dehydrogenase subunit 6 (ND6) and 8 tRNA genes were encoded on the light strand, whereas the rest of the mitochondrial genes were encoded on the heavy strand. The nucleotide skewness of the coding strands of the 3 analyzed mitogenomes was biased toward A and T. We constructed a phylogenetic tree using the complete mitogenomes of each type of sheep to allow us to understand the genetic relationships between Chinese breeds of O. aries and those developed and utilized in other countries. Our findings provide important information regarding the O. aries mitogenome and the evolutionary history of O. aries inside and outside China. In addition, our results provide a foundation for further exploration of the taxonomic status of O. aries.

• Korean Journal of Microbiology
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• v.39 no.2
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• pp.102-107
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• 2003

With the enrichment culture technique, bacterial strains which degrade diesel oil were isolated from soil contaminated with diesel oil. One of the isolates named GENECO 1 showed the highest activity for emulsification of diesel oil as well as the highest growth rate. This strain, GENECO 1, was identified as a Pseudomonas sp. based on its biochemical, physiological characteristics and 16S rDNA sequences. The optimal cultural conditions for cell growth and oil emulsifying activity of its culture were as follow; $30^{\circ}C$ for temperature, 7.0 for pH. Diesel oil degradation was analysed by the gas chromatography. More than 95% of 1% treated diesel oil were converted into a form no longer extractable by mixed organic solvents after 96 hours incubation.

• Journal of Microbiology and Biotechnology
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• v.16 no.5
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• pp.704-715
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• 2006

Oil spill was found in 1999 from a diesel storage facility located near the top of Baekun Mountain in Uiwang City. Application of bioremediation techniques was very relevant in removing oil spills in this site, because the geological condition was not amenable for other onsite remediation techniques. For efficient bioremediation, bacterial communities of the contaminated site and the uncontaminated control site were compared using both molecular and cultivation techniques. Soil bacterial populations were observed to be stimulated to grow in the soils contaminated with diesel hydrocarbon, whereas fungal and actinomycetes populations were decreased by diesel contamination. Most of the dieseldegrading bacteria isolated from contaminated forest soils were strains of Pseudomonas, Ralstonia, and Rhodococcus species. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that the profiles were different among the three contaminated sites, whereas those of the control sites were identical to each other. Analysis of 16S rDNA sequences of dominant isolates and clones showed that the bacterial community was less diverse in the oil-contaminated site than at the control site. Sequence analysis of the alkane hydroxylase genes cloned from soil microbial DNAs indicated that their diversity and distribution were different between the contaminated site and the control site. The results indicated that diesel contamination exerted a strong selection on the indigenous microbial community in the contaminated site, leading to predominance of well-adapted microorganisms in concurrence with decrease of microbial diversity.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.7
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• pp.1045-1054
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• 2012

The phylogenetic diversity of the bacteria in hot composting samples collected from three spatial locations was investigated by molecular tools in order to determine the influence of gradient effect on bacterial communities during the thermophilic phase of composting swine manure with rice straw. Total microbial DNA was extracted and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, restriction fragment length polymorphism-screened and sequenced. The superstratum sample had the highest microbial diversity among the three samples which was possibly related to the surrounding conditions of the sample resulting from the location. The results showed that the sequences related to Bacillus sp. were most common in the composts. In superstratum sample, 45 clones (33%) and 36 clones (27%) were affiliated with the Bacillus sp. and Clostridium sp., respectively; 74 clones (58%) were affiliated with the Clostridium sp. in the middle-level sample; 52 clones (40%) and 29 clones (23%) were affiliated with the Clostridium sp. and Bacillus sp. in substrate sample, respectively. It indicated that the microbial diversity and community in the samples were different for each sampling site, and different locations of the same pile often contained distinct and different microbial communities.