• Journal of Environmental Science International
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• v.16 no.12
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• pp.1337-1343
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• 2007

The aim of this study was to isolate chicken feather-degrading bacteria with high keratinolytic activity and to investigate cultural conditions affecting keratinolytic enzyme production by a selected isolate. A chicken feather-degrading bacterial strain CH3 was isolated from poultry wastes. Isolate CH3 degraded whole chicken feather completely within 3 days. On the basis of phenotypical and 16S rDNA studies, isolate CH3 was identified as Bacillus thuringiensis CH3. This strain is the first B. thuringiensis described as a feather degrader. The bacterium grew with an optimum at pH 8.0 and $37^{\circ}C$, where maximum keratinolytic activity was also observed. The composition of optimal medium for keratinolytic enzyme production was feather 0.1%, sucrose 0.7%, casein 0.3%, $K_2HPO_4$ 0.03%, $KH_2PO_4$ 0.04%, $MgCl_2$ 0.01% and NaCl 0.05%, respectively. The keratinolytic enzyme had a pH and temperature optima 9.0 and $45^{\circ}C$, respectively. The keratinolytic activity was inhibited ethylenediaminetetraacetic acid, phenylmethylsulfonyl fluoride, and metal ions like $Hg^{2+},\;Cu^{2+}\;and\;Zn^{2+}$. The enzyme activated by $Fe^{2+}$, dithiothreitol and 2-mercaptoethanol.

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.450-455
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• 2005

To treat wastewater efficiently by a one-step process of nitrogen removal, a new strain of $N_2-producing$ bacteria from $NH{_4}{^+}$ under an aerobic condition was isolated and identified. By 16S-rDNA analysis, the isolate was identified as Enterobacter asburiae with 96% similarity. The isolate shows that the capacity of $N_2$ production under an oxic condition was approximately three times higher than that under an anoxic condition. The optimal conditions (pH, temperature and C/N ratio) of the immobilized isolate for $N_2$ production were found to be 7.0, $30^{\circ}C$ and 5, respectively. Under all the optimum reaction conditions, the removal efficiency of $COD_{Cr}$ and TN reached 56.1 and 60.9%, respectively. The removal rates of $COD_{Cr}$ and TN were highest for the first 2.5 hrs (with the removal $COD_{Cr}$ ratios of 32.1), and afterwards the rates decreased as reaction proceeded. For application of the immobilized isolate to a practical process of ammonium removal, a continuous bioreactor system exhibited a satisfactory performance at HRT of 12.1 hr, in which the effluent concentrations of $NH{_4}{^+}-N$ was measured to be 15.4 mg/L with its removal efficiency of 56.0%. The maximum removal rate of $NH{_4}{^+}-N$ reached 1.6 mg $NH{_4}{^+}-N/L/hr$ at HRT of 12.1 hr (with N loading rate of 0.08 $Kg-N/m^3-carrier/d)$. As a result, the application of the immobilized isolate appears a viable alternative to the nitrification-denitrification processes.

• Journal of Microbiology and Biotechnology
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• v.20 no.12
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• pp.1744-1749
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• 2010

The role of endophytic fungi in plant growth and development is well documented. However, endophytic fungi with growth promotion capacity have never been isolated from weeds previously. In the current study, we isolated 8 fungal endophytes from the roots of Monochoria vaginalis, a serious weed of rice paddy in Korea. These isolates were screened on Waito-C, in order to identify plant growth promoting metabolites. Two fungal isolates (M5.A & M1.5) significantly promoted the plant height and shoot length of Waito-C during preliminary screening experiments. The culture filtrates (CFs) of M5.A and M1.5 also promoted the shoot length of Echinocloa crusgalli. Gibberellins (GAs) analysis of the CFs of M5.A and M1.5 showed that these endophytic fungi secrete higher quantities of GAs as compared with wild-type G. fujikuroi KCCM12329. The CF of M5.A contained bioactive GAs ($GA_3$, 2.8 ng/ml; $GA_4$, 2.6 ng/ml, and $GA_7$, 6.68 ng/ml) in conjunction with physiologically inactive $GA_9$ (1.61 ng/ml) and $GA_{24}$ (0.18 ng/ml). The CF of M1.5 contained physiologically active GAs ($GA_3$, 1.64 ng/ml; $GA_4$, 1.37 ng/ml and $GA_7$, 6.29 ng/ml) in conjunction with physiologically inactive $GA_9$ (3.44 ng/ml), $GA_{12}$ (0.3 ng/ml), and $GA_{24}$ (0.59 ng/ml). M5.A and M1.5 were identified as new strains of Penicillium sp. and Aspergillus sp., respectively, based on their 18S rDNA sequence homology and phylogenetic analysis.

• Journal of Microbiology and Biotechnology
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• v.25 no.9
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• pp.1467-1475
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• 2015

The use of microbial extracts containing plant hormones is a promising technique to improve crop growth. Little is known about the effect of bacterial cell-free extracts on plant growth promotion. This study, based on phytohormonal analyses, aimed at exploring the potential mechanisms by which Enterococcus faecium LKE12 enhances plant growth in oriental melon. A bacterial strain, LKE12, was isolated from soil, and further identified as E. faecium by 16S rDNA sequencing and phylogenetic analysis. The plant growth-promoting ability of an LKE12 bacterial culture was tested in a gibberellin (GA)-deficient rice dwarf mutant (waito-C) and a normal GA biosynthesis rice cultivar (Hwayongbyeo). E. faecium LKE12 significantly improved the length and biomass of rice shoots in both normal and dwarf cultivars through the secretion of an array of gibberellins (GA₁, GA₃, GA₇, GA₈, GA₉, GA₁₂, GA₁₉, GA₂₀, GA₂₄, and GA₅₃), as well as indole-3-acetic acid (IAA). To the best of our knowledge, this is the first study indicating that E. faecium can produce GAs. Increases in shoot and root lengths, plant fresh weight, and chlorophyll content promoted by E. faecium LKE12 and its cell-free extract inoculated in oriental melon plants revealed a favorable interaction of E. faecium LKE12 with plants. Higher plant growth rates and nutrient contents of magnesium, calcium, sodium, iron, manganese, silicon, zinc, and nitrogen were found in cell-free extract-treated plants than in control plants. The results of the current study suggest that E. faecium LKE12 promotes plant growth by producing GAs and IAA; interestingly, the exogenous application of its cell-free culture extract can be a potential strategy to accelerate plant growth.

• Journal of Microbiology and Biotechnology
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• v.30 no.4
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• pp.526-532
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• 2020

A bacterial strain, designated B301^T and isolated from raw chicken meat obtained from a local market in Korea, was characterized and identified using a polyphasic taxonomic approach. Cells were gram-negative, non-motile, obligate-aerobic coccobacilli that were catalase-positive and oxidase-negative. The optimum growth conditions were 30℃, pH 7.0, and 0% NaCl in tryptic soy broth. Colonies were round, convex, smooth, and cream-colored on tryptic soy agar. Strain B301^T has a genome size of 3,102,684 bp, with 2,840 protein-coding genes and 102 RNA genes. The 16S rRNA gene analysis revealed that strain B301^T belongs to the genus Acinetobacter and shares highest sequence similarity (97.12%) with A. celticus ANC 4603^T and A. sichuanensis WCHAc060041^T. The average nucleotide identity and digital DNA-DNA hybridization values for closely related species were below the cutoff values for species delineation (95-96% and 70%, respectively). The DNA G+C content of strain B301^T was 37.0%. The major respiratory quinone was Q-9, and the cellular fatty acids were primarily summed feature 3 (C_16:1 ω6c/C_16:1 ω7c), C_16:0, and C_18:1 ω9c. The major polar lipids were phosphatidylethanolamine, diphosphatidyl-glycerol, phosphatidylglycerol, and phosphatidyl-serine. The antimicrobial resistance profile of strain B301^T revealed the absence of antibiotic-resistance genes. Susceptibility to a wide range of antimicrobials, including imipenem, minocycline, ampicillin, and tetracycline, was also observed. The results of the phenotypic, chemotaxonomic, and phylogenetic analyses indicate that strain B301^T represents a novel species of the genus Acinetobacter, for which the name Acinetobacter pullorum sp. nov. is proposed. The type strain is B301^T (=KACC 21653^T = JCM 33942^T).

• The Plant Pathology Journal
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• v.31 no.2
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• pp.152-164
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• 2015

Biological control of major rice diseases has been attempted in several rice-growing countries in Asia during the last few decades and its application using antagonistic bacteria has proved to be somewhat successful for controlling various fungal diseases in field trials. Two novel endophytic Bacillus species, designated strains YC7007 and $YC7010^T$, with antimicrobial, plant growth-promoting, and systemic resistance-inducing activities were isolated from the roots of rice in paddy fields at Jinju, Korea, and their multifunctional activities were analyzed. Strain YC7007 inhibited mycelial growth of major rice fungal pathogens strongly in vitro. Bacterial blight and panicle blight caused by Xanthomonas oryzae pv. oryzae (KACC 10208) and Burkholderia glumae (KACC 44022), respectively, were also suppressed effectively by drenching a bacterial suspension ($10^7cfu/ml$) of strain YC7007 on the rhizosphere of rice. Additionally, strain YC7007 promoted the growth of rice seedlings with higher germination rates and more tillers than the untreated control. The taxonomic position of the strains was also investigated. Phylogenetic analyses based on 16S rRNA gene sequences indicated that both strains belong to the genus Bacillus, with high similarity to the closely related strains, Bacillus siamensis KACC $15859^T$ (99.67%), Bacillus methylotrophicus KACC $13105^T$ (99.65%), Bacillus amyloliquefaciens subsp. plantarum KACC $17177^T$ (99.60%), and Bacillus tequilensis KACC $15944^T$ (99.45%). The DNA-DNA relatedness value between strain $YC7010^T$ and the most closely related strain, B. siamensis KACC $15859^T$ was $50.4{\pm}3.5%$, but it was $91.5{\pm}11.0%$ between two strains YC7007 and $YC7010^T$, indicating the same species. The major fatty acids of two strains were anteiso-$C_{15:0}$ and iso $C_{15:0}$. Both strains contained MK-7 as a major respiratory quinone system. The G+C contents of the genomic DNA of two strains were 50.5 mol% and 51.2 mol%, respectively. Based on these polyphasic studies, the two strains YC7007 and $YC7010^T$ represent novel species of the genus Bacillus, for which the name Bacillus oryzicola sp. nov. is proposed. The type strain is $YC7010^T$ (= KACC $18228^T$). Taken together, our findings suggest that novel endophytic Bacillus strains can be used for the biological control of rice diseases.

• Experimental and Molecular Medicine
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• v.50 no.12
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• pp.1.1-1.14
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• 2018

DNA methylation is a regulatory mechanism in epigenetics that is frequently altered during human carcinogenesis. To detect critical methylation events associated with gastric cancer (GC), we compared three DNA methylomes from gastric mucosa (GM), intestinal metaplasia (IM), and gastric tumor (GT) cells that were microscopically dissected from an intestinal-type early gastric cancer (EGC) using methylated DNA binding domain sequencing (MBD-seq) and reduced representation bisulfite sequencing (RRBS) analysis. In this study, we focused on differentially methylated promoters (DMPs) that could be directly associated with gene expression. We detected 2,761 and 677 DMPs between the GT and GM by MBD-seq and RRBS, respectively, and for a total of 3,035 DMPs. Then, 514 (17%) of all DMPs were detected in the IM genome, which is a precancer of GC, supporting that some DMPs might represent an early event in gastric carcinogenesis. A pathway analysis of all DMPs demonstrated that 59 G protein-coupled receptor (GPCR) genes linked to the hypermethylated DMPs were significantly enriched in a neuroactive ligand-receptor interaction pathway. Furthermore, among the 59 GPCRs, six GI hormone receptor genes (NPY1R, PPYR1, PTGDR, PTGER2, PTGER3, and SSTR2) that play an inhibitory role in the secretion of gastrin or gastric acid were selected and validated as potential biomarkers for the diagnosis or prognosis of GC patients in two cohorts. These data suggest that the loss of function of gastrointestinal (GI) hormone receptors by promoter methylation may lead to gastric carcinogenesis because gastrin and gastric acid have been known to play a role in cell differentiation and carcinogenesis in the GI tract.

• Korean Journal of Microbiology
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• v.45 no.2
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• pp.163-169
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• 2009

This study was performed to investigate the type of extended-spectrum $\beta$-lactamases (ESBL) produced by bacteria isolated from the sewage of wastewater treatment plant at Minragdong, Suyong-gu in Busan. The facility is located at sushi restaurants and guides its drain water to the wastewater treatment plant at Yonghodong, Nam-gu in Busan. Samples were collected on January, 2009. A total of 19 strains were selected as potential ESBL positive strains through a double disk synergy test. On the basis of the results from biochemical tests including indole, methyl-red, Voges-Proskauer, Simmon's citrate, decarboxylase-dihydrolase and sugar-fermentation tests, the 19 strains were identified with 16 strains of Escherichia coli and 3 strains of Klebsiella pneumoniae. Out of 19 strains, 4 transconjugants against Escherichia coli J53, which is sodium azide resistant recipient strain, were obtained. The plasmids isolated from transconjugants were used for PCR analysis. The type of each extended-spectrum $\beta$-lactamase (ESBL) produced by the strains was determined on the basis of isoelectric focusing analysis and DNA sequencing. The results indicated that the types of ESBL from Klebsiella pneumoniae were SHV-12 (3 strains), and Escherichia coli was SHV-12/TEM-1 (1 strain), respectively.

• The Korean Journal of Mycology
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• v.25 no.1 s.80
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• pp.46-67
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• 1997

From 1985 to 1993, we collected 20 isolates throughout Kangwon and obtained 6 isolates from other sources. A. mellea formed rhizomorph actively, and some of A. osroyae were poor in the formation of rhizomorph and some without formation of rhizomorph. A. tabescens was active in the growth of aerial mycelium and poor in the development of rhizomorph. In A. gallica, the mycelium development among the isolates were variable greatly, and especially in isolate A8(KNU-250), the mycelial development was similar to that of A. osroyae, but A8(KNU-250) showed the feature of A. gallica to change medium into brown color. In PCR-RFLP analysis of the IGS region in rDNA, the homology between each isolate in the A. mellea and A. ostoyae showed 100% homology. A. tabescens showed $0.919{\sim}0.974$ homology, and A. gallica showed $0.619{\sim}1.000$ homology. A19 and A12 showed 100% homology as the same group, but compared with other subgroups they showed less than 10% homology as $0.051{\sim}0.108$ value. In RAPD analyses, the isolates of A. mellea showed high homology among themselves as $0.983{\sim}1.000$, and A. ostoyae also showed high similarity. The homology between isolates of A. tabescens showed $0.594{\sim}0.953$ value because A. gallica showed $0.280{\sim}0.733$ value, and the variations between isolates were greater than other species. Especially, A19 and A22 were identified as new novel group which were remoted from other groups, and the homology between these two isolates showed 0.921 value, and the genetic similarity between these groups and other 4 groups showed less than 7% as $0.012{\sim}0.069$ value. Of 5 species identified in this study, 4 species were identified as A. mellea, A. ostoyae, A. tabescens, and A. gallica that were already reported ones and 1 species was suggested as a new specie in Korea.

• The Korean Journal of Mycology
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• v.41 no.2
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• pp.67-73
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• 2013

Microbial diversity of soil samples from ancient stone-lined tombs was investigated. The tombs, discovered at Eoryung Ocheon-Ri site, Korea, were estimated to be belonged to middle class people from an ancient country, Gaya, which existed till AD 559 at the southern part of Korea. Nine fungal stains and 70 bacterial strains were isolated from the twelve soil samples, which were collected from the tomb Nos. 5 and 6. Ribosomal DNA sequence analysis discovered 5 fungal and 22 bacterial strains belonged to 10 genus groups from the tomb No. 5 while 1 fungal and 28 bacterial strains belonged to 6 genus from the tomb No. 6. The higher microbial diversity suggests that the tomb No. 5 was constructed warmer season than the tomb No. 6. Moreover, the discovery of Staphylococcus warneri, which is found as part of the skin flora on human and animals, and Bacillus aquimaris, which is a marine bacterium and can be discovered from tidal flat, from the surface of large dagger suggests that the ancient people may use meat and seafood at the burial ceremony.