• Journal of the Korean Wood Science and Technology
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• v.34 no.1
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• pp.68-78
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• 2006

The purpose of this study was to estimate the identification of thermophilic hacterial with fermentation of pig manure. To identify the characters of thermophilic bacteria related to fermentation at a high temperature condition, we selected 28 different kinds of original settling thermophilic bacteria that were sampled at different 23 areas. They were distributed 1$1{\times}10^5{\sim}10^8CFU$ at medium and the enzyme activity at $55^{\circ}C$ incubation condition, especially cellulase and a-amylase, were higher than those of $30^{\circ}C$. Partial sequencing data for 165 rDNA region were obtained from 28 samples representing 15 different genera. Bacillus subcilis, one of those bacteria, has endodermic spores at high fermented condition.

• Journal of Korean Society of Water and Wastewater
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• v.20 no.1
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• pp.44-52
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• 2006

Bio-filtration processes using honeycomb tubes (process 1) and aeration and manganese-sand filtration (process 2) were evaluated for the biological manganese removal efficiency. The concentration of manganese at effluent was stabilized after 20days operation in process 1. It was estimated the required time for attaching and growing microorganisms to honeycomb tubes. In long term of operation periods, manganese removal efficiency was dropped for the excessively attached biofilm and manganese dioxide to honeycomb tubes. It took several days for normal operation in process 2, after that manganese removal efficiency was increased to 98% and stabilized for 1.5 years. Microorganisms in process 1 and 2 were isolated and cultured to characterize manganese-oxidizing bacteria. Among the four types of colony, light brown colony was turned blue color by leuco crystal violet spot test. Stenotropomonas genus, known as manganese-oxidizing bacteria, was identified by 16S rDNA partial sequencing analysis which was isolated in process 1 and 2. For the biological treatment to remove manganese, these two considerations are important. One is to choose the proper media attaching manganese oxidant, another one is to define the cultural condition of isolated manganese-oxidizing bacteria.

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.307-311
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• 2005

Marine microorganisms to produce functional biopolymers were isolated from the seashore of the Kyungsang province. Microorganisms to hydrolyze carboxy-methyl cellulose(CMC) were cultured in marin broth and the other liquid medium that contained 2.0% (w/v) glucose, 0.25% yeast extract, 0.5% $K_2HPO_4$, 1% NaCl, 0.02% $MgSO_4{\cdot}7H_2O$ and 0.06% $(NH_4)_2SO_4$ to investigate the ability to produce carboxymethyl cellululase (CMCase) under aerobic conditions. Twelve microorganisms among them showed higher activities of CMCase than B. amyloliquefaciens DL-3, which was known as a cellulase-producing strain. The microorganism showing highest activity of CMCase in this study was identified as Bacillus subtilis subsp. subtilis with 16S rDNA partial sequencing and gyrase A partial sequencing and named as B. subtilis subsp. subtilis A-53.

• Korean Journal of Microbiology
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• v.39 no.1
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• pp.45-50
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• 2003

The diversity and change of microbial communities during kimchi fermentation at $4^{\circ}C$ were analyzed by denaturing gradient gel electrophoresis (DGGE). Kimchi samples were taken every 5 days over the fermentation periods (for 60 days) to extract total DNA for DGGE analysis. Touchdown polymerase chain reaction was performed to amplify the V3 region of 16S rRNA gene. Sequencing results of partial 16S rDNA amplicons from DGGE profiles revealed that lactic acid bacteria (LAB), especially Weissella koreensis, Lactobacillus sakei and Leuconostoc gelidum were dominants in kimchi fermentation at $4^{\circ}C$. And we knew that W. koreensis steadily existed throughout the whole fermentation period, also Lb. sakei and Leuc. gelidum appeared from 10th day and 30th day of fermentation time, respectively and then these species were to be dominant microorganisms.

• The Plant Pathology Journal
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• v.40 no.2
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• pp.171-191
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• 2024

Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.

• The Korean Journal of Ecology
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• v.28 no.3
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• pp.129-134
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• 2005

The monthly variations of physico-chemical and microbiological water quality were investigate in the artificial Lake Geumgang near estuary barrage. Sixty heterotrophic bacteria were isolated and identified by amplification and sequencing of 16S rDNA. Water temperature, pH, and inorganic nutrients($NH_4$-N, $NO_2$-N, $NO_3$-N, $PO_4$-P) were measured. Concentrations of DO, BOD, and inorganic nutrients were lower than in the middle-stream of Geum river The population densities of heterotrophic bacteria and total coliforms varied from $4.1{\pm}1.0\times10^2$ to $6.7{\pm}1.1{\times}10^3\;cfu\;ml^{-1}$, and 0 to $2.3{\pm}0.6{\times}10^2\;cfu\;ml^{-1}$, respectively. Among the measured numbers of physiological groups of bacteria, cellulolytic bacteria showed higher population densities than those of other physiological groups. Bacterial community structure was analysed based on 16S rDNA partial sequencing. Among 60 isolates, dominant genus was Pseudomones (20 strains).

• Microbiology and Biotechnology Letters
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• v.39 no.3
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• pp.287-293
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• 2011

The purpose of this study was to isolate and characterize fungal deteriogens, which induce discoloration of the cement tunnel, and calcite forming bacteria (CFBs), which have antifungal activity against fungal deteriogens. Isolation of mold, bacteria and yeast was performed using several solid media and partially identified using internal transcribed spacer (ITS); 5.8S rRNA gene sequencing and 16s rDNA sequencing. A total of 19 microbial strains were identified with the most widely distributed fungal strain being Cladospirum sphaerospermum. In addition, five bacteria derived from the tunnel were identified as CFBs. Amongst the latter, Bacillus aryabhatti KNUC205 exhibited antifungal activity against Cladospirum sphaerospermum KNUC253 and Aspergillus niger KCTC6906 as concentrated filtered supernatants.

• Journal of Korean society of Dental Hygiene
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• v.5 no.2
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• pp.131-145
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• 2005

There are normal inhabitants doing medically useful functions in the body. There are many kinds of bacteria performing specific functions in the oral cavity. Two strains of lactic add bacteria were isolated from normal inhabitants of children's oral cavity, which inhibited the production of volatile sulfur compounds by anaerobic bacteria. The authors identified the isolates by 16S rDNA partial sequencing. 1. Two isolates were Gram-positive bacilli and produced hydrogen peroxide. 2. When Streptococcus mutans was cultured in the media, the mean weight of formed artificial plaque on the orthodontic wires was $124.4{\pm}30.4$ mg, whereas being reduced to $5.2{\pm}2.0$ mg and $10.6{\pm}6.6$ mg in the media cultured with Streptococcus mutans and each isolate, respectively(p<0.05). 3. The number of viable cells of Streptococcus mutans was $3.4{\times}10^9$ per ml in the cultured solution, whereas those of Streptococcus mutans in the combined culture with each of isolates were $4.6{\times}10^8$ and $2.4{\times}10^8$ per ml. 4. The optical density was 1.286 in the supernatant of Fusoacterium nucleatum after vortexing for 30 minutes, whereas in the supernatant of combined Fusoacterium nucleatum and each isolate, they were reduced to 0.628 and 00497, which the percentages of coaggregation between them were 2904% and 57.8%, respectively. 5. The optical density of Fusoacterium nucleatum precipitate was 1.794 in the culture media containing cysteine and $FeSO_4$ being reduced to 1.144 and 0.915 in the coaggregated precipitates of Fusoacterium nucleatum and each isolate. 6. The similarity values of 16S rDNA sequence between each of isolates and Lactobacillus salivarius subsp. salicinius were 99.60% and 99.73%, respectively, meaning that isolates were Lactobacillus salivarius subsp. salicinius. These results indicated that two strains isolated from children's saliva, which inhibited the formation of plaque and the production of volatile sulfur compounds, were identified as Lactobacillus salivarius subsp. salicinius.

• Korean Journal of Microbiology
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• v.42 no.2
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• pp.103-110
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• 2006

T-RFLP analysis and clone sequencing analysis based on bacterial 16S rDNA were conducted to assess bacterial community structure and diversity in Zoysia japonica soil treated with liquid fertilizer containing amino acids(LFcAA) after spray with herbicide. The results of T-RFLP (terminal restriction fragment length poly-morphism) analysis using restriction enzyme Hae III showed that the T-RFs of various size appeared evenly in the 32 clones of KD3 and 38 clones of KD4 respectively that had been treated with liquid fertilizer containing amino acid(LFcAA) compared to 23 clones of KD2 hat had not been treated with LFcAA. The microbial com- munity structure in KD2 appeared less diverse than those in KD3 and KD4. Analysis of partial sequences for 110 clones from KDI (control), KD2 (non-treated), KD3 (LFcAA 1X), KD4 (LFcAA 2X), respectively, revealed that most bacteria were related with uncultured bacteria in a 16S rDNA sequence similarity range of 91-99% through blast search. Otherwise, the other clones were members of proteobacteria, Acidobacteria, Act-inobacteria, Sphingobacteria and Planctomyces groups. Especially in KD4, members of Alpha Proteobacteria, Rhizobiales, Sphigomonadales, Caulobacterales, Gamma Proteobacteria, the genus Pseudomonas, Betapro-teobacteria, Nitrosomonadales and genus Nitrosospira appeared to be dominant. In addition, Acidobacteria group, Actinobacteria group, Planctomycetacia and Sphingobacteria were also shown. The microbial com-munity structure in Z. japonica soil sprayed with herbicide was affected by LFcAA.

• Korean Journal of Microbiology
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• v.40 no.3
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• pp.189-198
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• 2004

T-RFLP analysis and clone sequencing analysis based on bacterial 16S rDNA were conducted to assess bacterial community structure and diversity in two layers (0-1cm, 6-7cm depth) of the sediment from Janghwari intertidal flat in Ganghwa Island. The results of T-RFLP (terminal-restriction fragment length polymorphism) analysis using restriction enzyme HhaI showed that the T-RFs of various size ($60{\pm}2$) bp-($667{\pm}2$) bp) appeared evenly at the surface sediments but two T-RFs with 60(${\pm}2$)bp and 93 (${\pm}2$)bp predominated at 6-7cm depth. Analysis of partial sequences for 172 clones revealed that 98% of the clones were not matched with the sequences of cultured bacteria strains in the GenBank (${\geq}similarity$ 98%), and approximately 86% of them were classified as different phylotypes. Most clones belonged to $\alpha$-, $\gamma$-, and $\delta$-Proteobacteria, Acidobacteria/Holophaga and green nonsulfur bacteria group. Proteobacteria group occupied the highest proportion in both layers (69% at 0-1cm depth and 46% at 6-7cm depth). $\gamma$-Proteobacteria and $\delta$-Proteobacteria that are associated with oxidation and reduction of sulfur compounds were appeared to be dominant, and comprised 21.5% and 15.7% of total clones, respectively. Overall results indicated that extremely diverse bacterial groups were inhabiting in the sediment of Ganghwa intertidal flat, and bacterial communities associated with the behaviour of sulfur seemed to playa significant role in the biogeochemical environment in this anoxic sediment.