• Journal of Species Research
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• v.7 no.1
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• pp.24-35
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• 2018

During a series of extensive surveys of prokaryotic species diversity in Korea, bacterial strains belonging to Gammaproteobacteria were isolated from various sources of aquatic and terrestrial environments. A total of 39 isolates were obtained, which represented 39 unrecorded species in Korea belonging to 20 genera in 12 families. Enterobacteriaceae was the largest family, as eight species were assigned, which was followed by Moraxellaceae (6 species) and Pseudomonadaceae (5 species). At the genus level, Marinobacter (6 species), and Pseudomonas (5 species) were the main genera, and at least two species were obtained for Acinetobacter (3 species), Psychrobacter (3 species), Shewanella (2 species), Dickeya (2 species), Salinivibrio (2 species), Vibrio (2 species) and Rhodanobacter(2 species). The detailed description of each unrecorded species is provided.

• Journal of Periodontal and Implant Science
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• v.29 no.4
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• pp.963-979
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• 1999

This study examined ribotypes of 36 P. gingivalis strains isolated from 10 rapidly progressive periodontitis patients in Korean and revealed the presence of genetic heterogeneity among the patients. Ribotyping was performed by using a oligonucleotide probes based on 16S rRNA after whole genomic DNA had been digested with the restriction endonuclease enzyme Kpn I and Pst I. In addition, the antigenic heterogeneity of fimbrillin and protease activity was analysed to observe the virulency of P. gingivalis. The results were as follows. 1. Using KpnI, 6 ribotypes were detected, whereas 7 ribotypes were identified by using PstI. When combined two enzymes, a total of 8 ribotypes was subgrouped. 2. Ribotype I/e was the most common and detected in 4 among 10 patients. 3. The fimbrillin expressed from P. gingivalis isolates had the molecular size of 41kDa, 43kDa, 49kDa. It was observed that the size of fimbrillin with the same ribotypes could be identical. 4. All the P. gingivalis strains showed strong proteolytic activity and had the molecular size more than 120kDa. In summary, total 8 ribotypes were observed for isolates from rapidly progressive periodontitis patients. Forty percent of the patients harbored isolates exhibiting the same ribotype I/e, and it was observed that more than one ribotype can coexist in an individual patient.

• Journal of Microbiology and Biotechnology
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• v.22 no.1
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• pp.1-12
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• 2012

The present study examines the effects of 30 mg/kg butachlor on the cyanobacterial diversity of rice fields in Eastern Uttar Pradesh and Western Bihar in India. A total of 40 samples were grouped into three classes [(i) acidic, (ii) neutral, and (iii) alkaline soils], based on physicochemical and principle component analyses. Acidic soils mainly harbored Westillopsis, Trichormus, Anabaenopsis, and unicellular cyanobacteria; whereas Nostoc, Anabaena, Calothrix, Tolypothrix, and Aulosira were found in neutral and alkaline soils. Molecular characterization using 16S rRNA PCR and DGGE revealed the presence of 13 different phylotypes of cyanobacteria in these samples. Butachlor treatment of the soil samples led to the disappearance of 5 and the emergence of 2 additional phylotypes. A total of 40 DGGE bands showed significant reproducible changes upon treatment with butachlor. Phylogenetic analyses divided the phylotypes into five major clusters exhibiting interesting links with soil pH. Aulosira, Anabaena, Trichormus, and Anabaenopsis were sensitive to butachlor treatment, whereas uncultured cyanobacteria, a chroococcalean member, Westillopsis, Nostoc, Calothrix, Tolypothrix, Rivularia, Gloeotrichia, Fischerella, Leptolyngbya, and Cylindrospermum, appeared to be tolerant against butachlor at their native soil pH. Butachlor-induced inhibition of nitrogen fixation was found to be 65% (maximum) and 33% (minimum) in the soil samples of pH 9.23 and 5.20, respectively. In conclusion, low butachlor doses may prove beneficial in paddy fields having a neutral to alkaline soil pH.

• Journal of Microbiology and Biotechnology
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• v.22 no.4
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• pp.448-456
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• 2012

Thirty-seven carbofuran-degrading bacteria were isolated from agricultural soils, and their genetic and phenotypic characteristics were investigated. The isolates were able to utilize carbofuran as a sole source of carbon and energy. Analysis of the 16S rRNA gene sequence indicated that the isolates were related to members of the genera Rhodococcus, Sphingomonas, and Sphingobium, including new types of carbofuran-degrading bacteria, Bosea and Microbacterium. Among the 37 isolates, 15 different chromosomal DNA patterns were obtained by polymerase chain reaction (PCR) amplification of repetitive extragenic palindromic (REP) sequences. Five of the 15 representative isolates were able to degrade carbofuran phenol, fenoxycarb, and carbaryl, in addition to carbofuran. Ten of the 15 representative isolates had 1 to 8 plasmids. Among the 10 plasmid-containing isolates, plasmid-cured strains were obtained from 5 strains. The cured strains could not degrade carbofuran and other pesticides anymore, suggesting that the carbofuran degradative genes were on the plasmid DNAs in these strains. When analyzed with PCR amplification and dot-blot hybridization using the primers targeting for the previously reported carbofuran hydrolase gene (mcd), all of the isolates did not show any positive signals, suggesting that their carbofuran hydrolase genes had no significant sequence homology with the mcd gene.

• Journal of Microbiology and Biotechnology
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• v.20 no.3
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• pp.602-608
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• 2010

An atrazine-degrading bacterium, strain KU001, was obtained from a sugarcane field at the Cane and Sugar Research and Development Center at the Kasetsart University, Kamphaeng Saen Campus, Thailand. Strain KU001 had a rod-to-coccus morphological cycle during growth. Biolog carbon source analysis indicated that the isolated bacterium was Arthrobacter histidinolovorans. Sequence analysis of the PCR product indicated that the 16S rRNA gene in strain KU001 was 99% identical to the same region in Arthrobacter sp. The atrazine degradation pathway in strain KU001 consisted of the catabolic genes trzN, atzB, and atzC. Strain KU001 was able to use atrazine as a sole nitrogen source for growth, and surprisingly, atrazine degradation was not inhibited in cells grown on ammonium, nitrate, or urea, as compared with cells cultivated on growth-limiting nitrogen sources. During the atrazine degradation process, the supplementation of nitrate completely inhibited atrazine degradation activity in strain KU001, whereas ammonium and urea had no effect on atrazine degradation activity. The addition of strain KU001 to sterile or nonsterile soils resulted in the disappearance of atrazine at a rate that was 4- to 5-fold more than that achieved by the indigenous microbial community. The addition of citrate to soils resulted in enhanced atrazine degradation, where 80% of atrazine disappeared within one day following nutrient supplementation.

• Journal of Microbiology and Biotechnology
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• v.28 no.7
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• pp.1156-1167
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• 2018

The aim of this study was to isolate and characterize lead (Pb)-solubilizing bacteria from heavy metal-contaminated mine soils and to evaluate their inoculation effects on the growth and Pb absorption of Brassica juncea. The isolates were also evaluated for their plant growth-promoting characteristics as well as heavy metal and salt tolerance. A total of 171 Pb-tolerant isolates were identified, of which only 15 bacterial strains were able to produce clear haloes in solid medium containing PbO or $PbCO_3$, indicating Pb solubilization. All of these 15 strains were also able to dissolve the Pb minerals in a liquid medium, which was accompanied by significant decreases in pH values of the medium. Based on 16S rRNA gene sequence analysis, the Pb-solubilizing strains belonged to genera Bacillus, Paenibacillus, Brevibacterium, and Staphylococcus. A majority of the Pb-solubilizing strains were able to produce indole acetic acid and siderophores to different extents. Two of the Pb-solubilizing isolates were able to solubilize inorganic phosphate as well. Some of the strains displayed tolerance to different heavy metals and to salt stress and were able to grow in a wide pH range. Inoculation with two selected Pb-solubilizing and plant growth-promoting strains, (i.e., Brevibacterium frigoritolerans YSP40 and Bacillus paralicheniformis YSP151) and their consortium enhanced the growth and Pb uptake of B. juncea plants grown in a metal-contaminated soil. The bacterial strains isolated in this study are promising candidates to develop novel microbe-assisted phytoremediation strategies for metal-contaminated soils.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.50 no.4
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• pp.378-387
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• 2017

This study was performed to isolate bacteria that could control the nitrite levels in a biofloc technology (BFT) culture tank. Nitrite-eliminating bacteria were isolated from a BFT culture tank rearing goldfish, and the isolated bacterium exhibiting the most potent nitrite eliminating ability was labeled as the "NOBSB1" strain. Sequencing the 16S rRNA revealed that NOBSB1 is a species in the genera Bosea. NOBSB1 had the following characteristics with regard to nitrite removal: (1) it removed nitrite by functioning heterotrophically in the presence of a carbon source (sugars); (2) it eliminated nitrite most effectively within a temperature range of $20-30^{\circ}C$, but its activity decreased at temperatures above $35^{\circ}C$ and below $20^{\circ}C$; (3) it had optimum nitrite removal ability within a pH range of 6.0-8.0; (4) it removed nitrite more effectively under hypoxic than aerobic conditions. NOBSB1 inoculation did not decrease ammonia or nitrate levels, but eliminated nitrite in a BFT culture tank rearing common carp (Cyprinus carpio). After inoculating the NOBSB1 strain in a BFT culture tank, NOBSB1 controlled and sufficiently reduced the nitrite concentration in the tank.

• Journal of Applied Biological Chemistry
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• v.60 no.3
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• pp.257-263
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• 2017

A cellulolytic strain Y2 was isolated from soil obtained in the Canadian Alpine region. The isolate was identified as Paenibacillus sp. Y2 by 16S rRNA sequencing. When grown in LB medium supplemented with carboxymethyl-cellulose (CMC), CMCase production increased to 122.0% of that observed in LB without CMC. Culture supernatant was concentrated by ultrafiltration and 80% ammonium sulfate precipitates were separated by Hi-Trap Q and CHT-II chromatography. The purified enzyme (EG-PY2) showed a homogeneous single band and the molecular mass was estimated to be 38 kDa by SDS-PAGE. Optimum pH and temperature of the enzyme were 4.5 and $30^{\circ}C$, respectively. The half-life of enzyme activity at 50 was 140.7 min, but the enzyme was drastically inactivated within 5 min at $55^{\circ}C$. The enzyme was highly activated to 135.7 and 126.7% by 5.0 mM of $Cu^{2+}$ or $Mg^{2+}$ ions, respectively, and moderately activated by $Ba^{2+}$ and $Ca^{2+}$ ions, whereas it was inhibited to 76.8% by $Fe^{2+}$, and to ${\leq}50%$ by $Mn^{2+}$, $Co^{2+}$, $Zn^{2+}$, and EDTA. The enzyme was activated to 211.5% in the presence of 0.5 M of NaCl and greatly tolerant to 3.15M of NaCl. The enzyme showed 2.98 times higher ${\beta}$-glucanase activity than CMCase activity. Based on these results, it can be concluded that EG-PY2 is an acidophilic, cold-active, and halotolerant endoglucanase. The authors suggest it is considered to be useful for various industrial applications, such as, fruit juice clarification, acidic deinking processes, high-salt food processing, textile and pulp industries, and for biofuel production from seaweeds.

• Korean Journal of Environmental Agriculture
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• v.35 no.4
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• pp.294-301
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• 2016

BACKGROUND: Recent studies have described the importance of microbes and enzymes that can compost food waste. This study was carried out to improve production of protease of isolated microbes from food waste. METHODS AND RESULTS: Seven bacteria isolated from various sources were screened for protease production by adding skim milk into the agar medium. About 7 microbes producing protease were tested, and strain JH-35 showed the highest protease activity among them. The strain was identified as Bacillus amyloliquefaciens JH-35 based on morphological, cultural, physiological characteristics and 16S rRNA. In the fermentation experiment, the assay B. amyloliquefaciens JH-35 showed the highest protease activity in the condition of 1% glucose, 1.5% yeast extract and 0.2%$ K_2HPO_4$. The optimal condition of culture with temperature $35^{\circ}C$, initial pH of 7 and shaking speed of 200 rpm and 24 hr. CONCLUSION: The protease of the B. amyloliquefaciens JH-35 had its activity at pH 7 and the optimal culture time was 24 hr. Also, B. amyloliquefaciens JH-35 was high salt tolerance. Our results suggest that B. amyloliquefaciens JH-35 from food waste may have the potential to degrade protein and carbohydrate in food waste.

• The Plant Pathology Journal
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• v.30 no.3
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• pp.288-298
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• 2014

We examined the efficacy of a bacterium for biocontrol of the root-knot nematode (RKN) Meloidogyne hapla in carrot (Daucus carota subsp. sativus) and tomato (Solanum lycopersicum). Among 542 bacterial isolates from various soils and plants, the highest nematode mortality was observed for treatments with isolate C1-7, which was identified as Bacillus cereus based on cultural and morphological characteristics, the Biolog program, and 16S rRNA sequencing analyses. The population density and the nematicidal activity of B. cereus C1-7 remained high until the end of culture in brain heart infusion broth, suggesting that it may have sustainable biocontrol potential. In pot experiments, the biocontrol efficacy of B. cereus C1-7 was high, showing complete inhibition of root gall or egg mass formation by RKN in carrot and tomato plants, and subsequently reducing RKN damage and suppressing nematode population growth, respectively. Light microscopy of RKN-infected carrot root tissues treated with C1-7 showed reduced formation of gall cells and fully developed giant cells, while extensive gall cells and fully mature giant cells with prominent cell wall ingrowths formed in the untreated control plants infected with RKNs. These histopathological characteristics may be the result of residual or systemic biocontrol activity of the bacterium, which may coincide with the biocontrol efficacies of nematodes in pots. These results suggest that B. cereus C1-7 can be used as a biocontrol agent for M. hapla.