• The Journal of Engineering Geology
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• v.23 no.1
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• pp.37-46
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• 2013

Leakage of leachate from animal carcass disposal is a significant issue because disease can easily spread to humans and other livestock. In this study, we analyzed the physicochemical properties of leachate and tested for the presence of aerobic bacteria in leachate using molecular biology methods, for 16 animal carcass disposals in the first stage (after burial for 5 months). Leachate physicochemical analysis revealed higher total coliforms, TOC, $NH^{4+}$, and $NO^{3-}$ concentrations compared with previously published data. In most leachate samples, the concentrations of $NH^{4+}$ and $NO^{3-}$ exceeded the Korean guideline values for drinking water. In 16S rRNA sequence analysis of the distribution of leachate under aerobic conditions, Bacillus pumilus, Lysinibacillus sphaericus, and B. sphaericus were observed with high frequency, whereas no food-poisoning-related bacteria such as B. cereus or Salmonella were detected. The present findings improve our knowledge of the transport of leachate from animal carcass disposal sites through geologic media, and are useful in risk analysis and for subsequent studies.

• Korean Journal of Soil Science and Fertilizer
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• v.39 no.4
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• pp.195-203
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• 2006

An antagonistic strain, Burkholderia MP-1, showed antimicrobial activity against various filamentous plant pathogenic fungi, yeasts and food borne bacteria (Gram-positive and Gram-negative). The nucleotide sequence of the 16S rRNA gene (1491 pb) of strain MP-1 exhibited close similarity (99-100%) with other Burkholderia 16S rRNA genes. Isolation of the antibiotic substances from culture broth was fractionated by ethyl acetate (EtOAc) solvent and EtOAc-soluble acidic fraction. The antibiotic substances were purified through a silica gel, Sephadex LH-20, ODS column chromatography, and high performance liquid chromatography, respectively. Four active substances were identified as phenylacetic acid, hydrocinnamic acid, 4-hydroxyphenylacetic acid and 4-hydroxyphenylacetate methyl ester by gas chromatographic-mass spectrum analysis. The minimum inhibition of concentration (MIC) of each active compound inhibited the growth of the microorganisms tested at 250 to $2500{\mu}g\;ml^{-1}$. The antimicrobial activity of crude acidic fraction at 1 mg of dry weight per 6 mm paper disc was more effective than authentic standard mixture (four active substances were mixed with the same ratio as acidic fraction) over a wide range of bacterial test.

• Korean Journal of Microbiology
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• v.50 no.2
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• pp.119-127
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• 2014

The affiliations and physiological characteristics of culturable bacteria isolated from the sediments of Ross Sea, Antarctica were investigated. Sixty-three isolates obtained by cultivation were grouped into 21 phylotypes affiliated with the phyla Actinobacteria and Bacteroidetes and with the classes Alphaproteobacteria and Gammaproteobacteria by phylogenetic analysis of 16S rRNA gene sequences. Based on phylogenetic analysis (<98.65% sequence similarity), approximately 49% of total isolates represented potentially novel species or genus. Among them, extracellular protease, lipase, and exopolysaccharide activities at $10^{\circ}C$ or $20^{\circ}C$ were detected in approximately 46%, 25%, and 32% of the strains, respectively. Forty-three isolates produced at least one type of extracellular material and 21 of them produced at least two extracellular protease, lipase, and/or exopolysaccharides. Our findings indicate that culturable bacterial diversity present within the marine sediments of Ross Sea, Antarctica may contribute to the hydrolysis of the major organic constituents which is closely related with carbon and nitrogen cycling in this environment.

• Korean Journal of Food Science and Technology
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• v.47 no.1
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• pp.126-131
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• 2015

Pathogenic Escherichia coli is recognized as an important cause of diarrhea, hemorrhagic colitis and hemolytic-uremic syndrome worldwide. This study was conducted to investigate the prevalence E. coli contamination in the Korean traditional food bibimbap. E. coli were isolated from 84 of 1142 (7.3%) bibimbap investigated from 2005 to 2011. Antibiotic resistance profiling demonstrated that 6 of the 84 isolates (7.2%) showed multiple drug resistance. Fifteen virulence genes specific for pathogenic E. coli such as Shiga toxin-producing E. coli (STEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC), and enteroaggregative E. coli (EAEC) were examined by multiplex PCR for mixed bacterial cultures derived from bibimbap samples. The EPEC virulence gene (ent) was detected in 5 strains (5.9%), while ETEC, EAEC, and EIEC were not detected. STEC serotypes O103 (1.2%), O91 (1.2%), and O128 (6.0%) were found, but other serogroups such as O26, O157, O145, O111 and O121 were not detecded. Automated Repetitive-Sequence-Based PCR analysis showed different patterns.

• Microbiology and Biotechnology Letters
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• v.44 no.2
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• pp.156-162
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• 2016

In this study, we isolated a new agar-degrading marine bacterium and characterized its agarase. An agardegrading marine bacterium SH-1 was isolated from seawater, collected from the seashore of Namhae in Gyeongnam province, Korea, and cultured in marine agar 2216 media. It was identified as Maribacter. sp. SH-1 by phylogenetic analyses, based on 16S rRNA gene sequence. The extracellular agarase was extracted from culture media of Maribacter sp. SH-1 and characterized. Its relative activities were 56, 62, 94, 100, and 8% at 20, 30, 40, 50, and 60℃, respectively, whereas 15, 100, 60, and 21% relative activities were observed at pH 5, 6, 7, and 8, respectively. Its extracellular agarase exhibited maximum activity (231 units/l) at pH 6.0 and 50℃, in 20 mM Tris-HCl buffer. Therefore, this agarase would be applicable as it showed the maximum activity at the temperature at which the agar is in a sol state. Furthermore, the agarase activities remained over 90% at 20, 30, and 40℃ after 0.5 h exposure at these temperatures. Thin layer chromatography analysis suggested that Maribacter sp. SH-1 produces extracellular β-agarase, as it hydrolyzes agarose to produce neoagarooligosaccharides, such as neoagarohexaose (34.8%), neoagarotetraose (52.2%), and neoagarobiose (13.0%). Maribacter sp. SH-1 and its β-agarase would be useful for the production of neoagarooligosaccharides, which shows functional properties, like skin moisturizing, skin whitening, inhibition of bacterial growth, and delay in starch degradation.

• The Journal of the Korean Society for Microbiology
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• v.34 no.6
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• pp.519-532
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• 1999

Helicobacter pylori is a causative agent of type B gastritis and plays a central role in the pathogenesis of gastroduodenal ulcer and gastric cancer. To elucidate the host-parasite relationship of the H. pylori infection on the basis of molecular biology, we tried to evaluate the genomic diversity of H. pylori. An ordered overlapping bacterial artificial chromosome (BAC) library of a Korean isolate, H. pylori 51 was constructed to set up a genomic map. A circular physical map was constructed by aligning ApaI, NotI and SfiI-digested chromosomal DNA. When the physical map of H. pylori 51 was compared to that of unrelated strain, H. pylori 26695, completely different restriction patterns were shown. Fifteen known genes were mapped on the chromosome of H. pylori 51 and the genetic map was compared with those of strain 26695 and J99, of which the entire genomic sequences were reported. There were some variability in the gene location as well as gene order among three strains. For further analysis on the genomic diversity of H. pylori, when comparing the genomic structure of 150 H. pylori Korean isolates with one another, genomic macrodiversity of H. pylori was characterized by several features: whether or not susceptible to restriction digestion of the chromsome, variation in chromosomal restriction fingerprint and/or high frequency of gene rearrangement. We also examined the extent of allelic variation in nucleotide or deduced amino acid sequences at the individual gene level. fucT, cagA and vacA were confirmed to carry regions of high variation in nucleotide sequence among strains. The plasticity zone and strain-specific genes of H. pylori 51 were analyzed and compared with the former two genomic sequences. It should be noted that the H. pylori 51-specific sequences were dispersed on the chromosome, not congregated in the plasticity zone unlike J99- or 26695-specific genes, suggesting the high frequency of gene rearrangement in H. pylori genome. The genome of H. pylori 51 shows differences in the overall genomic organization, gene order, and even in the nucleotide sequences among the H. pylori strains, which are far greater than the differences reported on the genomic diversity of H. pylori.

• Korean Journal of Microbiology
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• v.46 no.1
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• pp.63-67
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• 2010

Proteases catalyze hydrolytic cleavage of a peptide bond between amino acids and occupy pivotal positions in application in physiological and commercial fields. During the screening for novel bacteria producing extracellular protease, two bacterial strains, WD12 and WD32, were isolated from rotten trees and they made clear zone on LB plates supplemented with 1% skim milk. The similarities of 16S rRNA gene sequence of either WD12 or WD32 to GenBank database showed the highest to Pseuoxanthomonas mexicana as 97.8 and 99.8%, respectively. Phylogenetic analysis showed that both isolated was located within the cluster comprising P. mexicana and P. japonesis. WD12 and WD32 were catalase- and oxidase-positive, Gram-negative rod strains. In case of WD12, it could assimilate malate, but could not assimilate D-mannose, which were different characteristics from P. mexicana. Both Pseuoxanthomonas sp. WD12 and WD32 optimally produced extracellular protease at $35-37^{\circ}C$, and maximal activity showed as 656 unit/ml and 267 unit/ml, respectively.

• Microbiology and Biotechnology Letters
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• v.33 no.4
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• pp.295-301
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• 2005

About seven hundred bacterial strains were collected from Jeot-Kal, a Korean traditional fermented fishes, in various Korean districts. One of the strains designated JKK238 has its ability to antagonize in vitro the growth of a wide variety of plant pathogenic fungi responsible for diseases of economical importance. The JKK238 strain was isolated from Oh-Jeot, a kind of fermented shrimps, of Kangkyeung in Korea, and was identified as Bacillus subtilis based on its physiological characteristics, fatty acids compositions of cellular wall, and 16S rDNA sequence analysis. We isolated simply antimicrobial lipopeptides (AMLP) by $25\%$ ammonium sulfate precipitation of 3 days-old tryptic soy broth cultures of the JKK238 strain. Further analysis of AMLP revealed that B. subtilis JKK238 produces a wide variety of antifungal lipopeptide isomers from the iturin, fengycin and surfactin families simultaneously. Above results indicate that the JKK238 strain can be added to the limited number B. subtilis strains reported to co-produce the three kinds of lipopeptide families.

• Journal of Microbiology and Biotechnology
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• v.13 no.6
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• pp.960-968
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• 2003

A bacterial isolate showing a strong endochitosanase activity was isolated from soil and then characterized. The isolate was identified and designated as Bacillus cereus P16, based on morphological and biochemical properties, assimilation tests, cellular fatty acids pattern, along with 16S rRNA gene sequence. The optimized medium for producing extracellular chitosanase in a batch culture contained 1% tryptone, 0.5% chitosan, and 1% NaCl (pH 7.0). Powder chitosan and tryptone served the best as carbon and nitrogen sources, respectively, for the chitosanase production. Chitosanase activity was the highest when culture was completed at $37^{\circ}C$ among various temperatures ($20-42^{\circ}C$) tested in a shaking incubator (200 rpm). The levels of chitosanase activity in the culture fluid were 2.0 U/ml and 3.8 U/ml, respectively, when incubated in a flask for 60 h and in a jar fermenter for 24 h. The culture supernatant showed a strong liquefying activity on the soluble chitosan. The viscosity of 1% chitosan solution, that was incubated with the culture supernatant, was rapidly decreased, suggesting the secretion of endochitosanolytic enzymes by P16. The culture fluid revealed six endo-type chitosanase isozymes, two major (38 and 45 kD), and four minor (54, 65, 82, and 96 kD) forms by staining profile. The crude enzymes were very stable, and full activity was maintained for 4 weeks at $4^{\circ}C\;or\;-20^{\circ}C$ in the culture supernatant, suggesting a highly desirable stability rate for making an industrial application of the crude enzymes. The supernatant also cleaved the insoluble chitosan powder, but the hydrolysis rate was much lower. The enzymic degradation products of chitosan contained $(GlcN)_n$ (n=2-8). The concentration of chitosan in the reaction mixture of the crude enzyme affected the chitooligosaccharides composition of the hydrolysis products. When the higher concentration of chitosan was used, the higher degree of polymerized chitooligosaccharides were produced. By comparison with other commercial chitosanase preparations, P16 was indeed found to be a valuable enzyme source for industrial production of chitooligosaccharides from chitosan.

• Journal of Microbiology and Biotechnology
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• v.13 no.6
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• pp.881-891
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• 2003

Paenibacillus polymyxa is a plant growth-promoting rhizobacterium (PGPR) which can be used for biological control of plant diseases. Several bacterial strains were isolated from rotten roots of Korean ginseng (Panax ginseng C. A. Meyer) that were in storage. These strains were identified as P. polymyxa, based on a RAPD analysis using a P. polymyxa-specific primer, cultural and physiological characteristics, an analysis utilizing the Biolog system, gas chromatography of fatty acid methyl esters (GC-FAME), and the 16S rDNA sequence analysis. These strains were found to cause the rot in stored ginseng roots. Twenty-six P. polymyxa strains, including twenty GBR strains, were phylogenetically classified into two groups according to the ERIC and BOX-PCR analyses and 16S rDNA sequencing, and the resulting groupings systematized to the degrees of virulence of each strain in causing root rot. In particular, highly virulent GBR strains clustered together, and this group may be considered as subspecies or biovar. The virulence of the strains seemed to be related to their starch hydrolysis enzyme activity, but not their cellulase or hemicellulase activity, since strains with reduced or no starch-hydrolytic activity showed little or no virulence. Artificial inoculation of the highly virulent strain GBR-1 onto the root surfaces of Korean ginseng resulted in small brown lesions which were sunken and confined to the outer portion of the root. Ginseng root discs inoculated in vitro or two-year-old roots grown in soil drenched with the inoculum developed significant rot only when the inoculum density was $10^{6}-10^{7}$ or more colony-forming units (CFU) per ml. These results suggest that P. polymyxa might induce ginseng root rot if their population levels are high. Based on these results, it is recommended that the concentration of P. polymyxa should be monitored, when it is used as a biocontrol agent of ginseng, especially in the treatment of stored roots.