• Korean Journal of Environmental Biology
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• v.28 no.4
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• pp.223-230
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• 2010

To investigate the variations of physico-chemical factors in four stations (Hanlim, Aewol, Sinchon, Hamdeok) at Jeju coastal area, Water temperature, Salinity, dissolved oxygen (DO), pH, chemical oxygen demand (COD), suspended solid (SS), ammonia-nitrogen ($NH_4-N$), nitrite-nitrogen ($NO_3-N$), nitrate-nitrogen ($NO_2-N$) were analysed. The ranges of water temperature were from 26.23 to $28.6^{\circ}C$, the salinity were from 31.4 to 32.88‰, the pH were from 8.15 to 8.35, the chemical oxygen were from 0.48 to 0.91 mg $L^{-1}$. A total of 52 strains of marine actinomycetes was isolated from Jeju Island coastal area. They were characterized by determining morphological and physio-biochemical properties, the API kit and confirmed by molecular methods including partial sequencing of 16S rRNA. A neighbor-joining tree of partial 16S rRNA sequences divided the 52 isolates in 2 major groups, 22 strains of Gram positive bacteria/Actinobacteria (division)/Actinomycetales (order)/Streptomycineae (suborder)/Streptomycetaceae (family)/Streptomyces (93.1%) and 2 strains of Streptospotangineae (suborder)/Nocardiopsaceae (family)/Nocardiopsis (6.9%).

• Korean Journal of Organic Agriculture
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• v.23 no.4
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• pp.847-858
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• 2015

Bacillus amyloliquefaciens GR4-5 was isolated from the rhizosphere soil of Korean ginseng and displayed broad-spectrum suppression of ginseng root rot pathogens. The survivability of B. amyloliquefaciens GR4-5 in soil was investigated under three different conditions; indoor, outdoor - of which soil was put in 14 mL tube after treatment - and field environments. Soil samples were collected over a four-week period from three experimental designs, and assessed for 16S rRNA gene copy number by quantitative polymerase chain reaction (qPCR). In outdoor condition, the 16S rRNA gene copy number of Bacillus spp. was 8.35 log copies g $soil^{-1}$ immediately after the GR4-5 treatment. Two weeks later, the 16S rRNA gene copy number of Bacillus spp. (6.70 log copies g $soil^{-1}$) was similar to that of the control (6.38 log copies g $soil^{-1}$). In indoor condition, the 16S rRNA gene copy number of Bacillus spp. maintained in a certain level for a longer period than those in outdoor and field. The 16S rRNA gene copy number of Bacillus spp. in field experiment was reduced faster than that of outdoor condition. Our results show that B. amyloliquefaciens GR4-5 can survive in bulk soil for 1 week, indicating its potential use as a biocontrol agent following 7 day application intervals. This study presents that outdoor microcosm system design could be a useful method to assess easily the survivability of beneficial microorganisms.

• Journal of Microbiology and Biotechnology
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• v.11 no.6
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• pp.1046-1054
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• 2001

Bioleaching is the process in which insoluble metal sulfide is oxidized by specialized iron- and/or sulfur-oxidizing lithotrophic bacteria in acidic, metal-rich environments. Most of these processes are carried out by the genus Thiobacillus. Three novel Thiobacillus strains (Thiobacillus thiooxidans AZ11, Thiobacillus thiooxidans MET, and thiobacillus thiooxidans TAS) associated with bioleaching have been isolated from soil and sludge (Korean patent No. 1999-0073060 for T. thiooxidans AZ11, Korean patent No. 1999-0005798 for T. thiooxidans MET, and Korean patent No. 1999-0073059 for T. thiooxidans TAS). A partial sequence of 16S ribosomal RNA gene (16S rDNA) and the entire sequence of 16S/23S intergenic spacer region (ISR) were determined in the three above novel strains and in Thiobacillus ferrooxidans ATCC19859 as a reference strain. When phylogenetic analysis was performed based on G+C contents and sequence alignments, T. ferroxidans ATCC19859 was found to be closely related to previously registered T. ferrooxidans strains in a monophyletic manner, while the three novel T. thiooxidans strains were classified in a paraphyletic manner. Close examination on the base composition of 16S/23S ISR revealed that the 5\` part (nucleotide residues 21-200) was specific for the genus Thiobacillus. On the other end, the 3\` part (nucleotide residues 201-520) showed specificity in T. ferrooxidans strains, but not in T. thiooxidans strains. These results suggest that the proximal and distal halves of 16S/23S could be used as a genetic marker for the identification of the genus Thiobacillus and the species T. ferrooxidans, respectively.

• BMB Reports
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• v.37 no.3
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• pp.351-355
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• 2004

Separate protocols are commonly used to prepare plasmid DNA, chromosomal DNA, or total RNA from E. coli cells. Various methods for the rapid preparation of plasmid DNA have been developed previously, but the preparation of the chromosomal DNA and total RNA are usually laborious. We report here a simple, fast, reliable, and cost-effective method to extract total nucleic acids from E. coli by direct lysis of the cells with phenol. Five distinct and sharp bands, which correspond to chromosomal DNA, plasmid DNA, 23S rRNA, 16S rRNA, and a mixture of small RNA, were observed when analyzing the prepared total nucleic acids on a regular 1-2% agarose gel. The simple and high-quality preparation of the total nucleic acids in a singe tube allowed us to rapidly screen the recombinant plasmid, as well as to simultaneously monitor the change of the plasmid copy number and rRNA levels during the growth of E. coli in the liquid medium.

• Journal of Species Research
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• v.10 no.3
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• pp.191-200
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• 2021

To study the biodiversity of bacterial species, here we report indigenous prokaryotic species of Korea. A total of 23 bacterial strains affiliated to the class Alphaproteobacteria were isolated from various environmental sources including seaweeds, seawater, fresh water, wetland/marsh, tidal sediment, plant roots, sewage and soil. Considering higher than 98.8% 16S rRNA gene sequence similarities and formation of a well-defined phylogenetic clade with named species, it was confirmed that each strain belonged to the predefined bacterial species of the class Alphaproteobacteria. There is no official report of these 23 species in Korea; 20 species of 16 genera (Mameliella, Yangia, Paracoccus, Ruegeria, Loktanella, Phaeobacter, Dinoroseobacter, Tropicimonas, Lutimaribacter, Litoreibacter, Sulfitobacter, Roseivivax, Labrenzia, Hyphomonas, Maricaulis, Thalassospira) in the order Rhodobacterales and 3 species of a single genus (Brevundimonas) in the order Caulobacterales. Gram-staining, cell morphology, basic biochemical characteristics, isolation sources, optimum temperature, growth media, and strain IDs are detailed in the species description as well as Table 1.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.7
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• pp.1057-1065
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• 2002

The antagonistic activities of 30 strains of lactobacilli against Helicobacter pylori were determined and Lactobacillus helveticus CU631 has been selected as the strain which possesses the strongest inhibitory effect in the disc diffusion assay showing inhibition zone diameter of $10{\pm}1.5mm$, whereas those of L. plantarum and L. fermentum have been shown to be $4.0{\pm}0.6mm$. H. pylori G88016 revealed the highest vacuolating toxin producing activity among the 8 strains, the inhibitory activity of L. helveticus CU631 in vacuolating toxin producing activity of H. pylori manifested in the co-culture of two strains and in the 5:5 mixture of supernatant of the two strains. Both L. helveticus CU631 and cell free culture supernatant had a strong inhibitory activities in urease and cytotoxin producing activities of H. pylori NCTC11637 and CJH12. An accelerated proteolytic activity of water soluble peptides by L. helveticus CU631 during the refrigeration storage has been manifested in the cream cheese. DNA seqences of 16S-23S ribosomal RNA spacer region showed typical pattern among the various strains of L. helveticus, which could be used in the identification of L. helveticus CU 631.

• 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.

• Journal of Microbiology and Biotechnology
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• v.19 no.4
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• pp.339-345
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• 2009

We evaluated the activity and abundance of the crude-oil-degrading bacterium Nocardia sp. H17-1 during bioremediation of oil-contaminated soil, using real-time PCR. The total petroleum hydrocarbon(TPH) degradation rate constants(k) of the soils treated with and without H17-1 were $0.103\;d^{-1}$ and $0.028\;d^{-1}$ respectively. The degradation rate constant was 3.6 times higher in the soil with H17-1 than in the soil without H17-1. In order to detect and quantify the Nocardia sp. H17-1 in soil samples, we quantified the genes encoding 16S ribosomal RNA(16S rRNA), alkane monooxygenase(alkB4), and catechol 2,3-dioxygenase(23CAT) with real-time PCR using SYBR green. The amounts of H17-1 16S rRNA and alkB4 detected increased rapidly up to 1,000-folds for the first 10 days, and then continued to increase only slightly or leveled off. However, the abundance of the 23CAT gene detected in H17-1-treated soil, where H17-1 had neither the 23CAT gene for the degradation of aromatic hydrocarbons nor the catechol 2,3-dioxygenase activity, did not differ significantly from that of the untreated soil($\alpha$=0.05,p>0.22). These results indicated that H17-1 is a potential candidate for the bioaugmentation of alkane-contaminated soil. Overall, we evaluated the abundance and metabolic activity of the bioremediation strain H17-1 using real-time PCR, independent of cultivation.

• Korean Journal of Ichthyology
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• v.22 no.3
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• pp.201-205
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• 2010

One specimen of a natural hybrid of an Oplegnathus (Oplegnathus fasciatus $\times$ Oplegnathus punctatus) was found in Tongyeong, Korea in August 2008. We, herein, describe its morphological and genetic characteristics and compare them with those of O. fasciatus and O. punctatus. In morphology, the hybrid showed many distinctive black rounded blotches on body sides and four faint vertical bars, being in those features similar to O. punctatus. Although the counts and measurements of the hybrid mostly overlapped between O. fasciatus and O. punctatus, the Oplegnathus hybrid resembled O. punctatus in the ratio of pelvic-fin length in standard length: Oplegnathus hybrid (26.7%) was closer to O. punctatus (26.4%) than to O. fasciatus (17.2~23.6%). In genetics, as a result of analysis of 510 base pair sequences of mitochondrial DNA 16S rRNA, the hybrid was closer to O. fasciatus (d=0.000~0.010) than to O. punctatus (d=0.020). Our results suggest that the natural hybridization represented by the subject specimen occurred between an O. fasciatus female and an O. punctatus male.

• ALGAE
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• v.38 no.2
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• pp.93-110
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• 2023

Progress in phylogenomic analysis has led to a considerable re-evaluation of former cyanobacterial system, with many new taxa being established at different nomenclatural levels. The family Geminocystaceae is among cyanobacterial taxa recently described on the basis of polyphasic approach. Within this family, there are six genera: Geminocystis, Cyanobacterium, Geminobacterium, Annamia, Picocyanobacterium, and Microcrocis. The genus Geminocystis previously encompassed two species: G. herdmanii and G. papuanica. Herein, a new species G. urbisnovae was proposed under the provision of the International Code of Nomenclature for algae, fungi, and plants (ICN). Polyphasic analysis was performed for five strains from the CALU culture collection (St. Petersburg State University, Russian Federation), and they were assigned to the genus Geminocystis in accordance with high 16S rRNA gene similarity to existing species, as well as because of proximity to these species on the phylogenetic trees reconstructed with RaxML and Bayes methods. Plausibility of their assignment to a separate species of the genus Geminocystis was substantiated with smaller cell size; stenohaline freshwater ecotype; capability to complementary chromatic adaptation of second type (CA2); distinct 16S rRNA gene clustering; sequences and folding of D1-D1' and B box domains of the 16S-23S internal transcribed spacer region. The second objective pursued by this communication was to provide a survey of the family Geminocystaceae. The overall assessment was that, despite attention of many researchers, this cyanobacterial family has been understudied and, especially in the case of the crucially important genus Cyanobacterium, taxonomically problematic.