• Title/Summary/Keyword: 16S rDNA analysis

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Characteristics of Algicide Produced by Micrococcus luteus SY-13 Inhibiting Cochlodinium polykrikoides and the Effects on Marine Organisms (적조생물 Cochlodinium polykrikoides를 저해하는 Micrococcus luteus SY-13이 생산하는 살조물질의 특성과 해양생물에 미치는 영향)

  • Kim, Min-Ju;Jeong, Seong-Yun;Cha, Mi-Sun;Lee, Sang-Joon
    • Journal of Environmental Science International
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    • v.17 no.4
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    • pp.439-449
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    • 2008
  • Algicidal bacterium was isolated from sea water during the declining period of Cochlodinium polykrikoides blooms and this bacterium had a significant algicidal activity against C. polykrikoides. In this study, algicidal bacterium was identified on the basis of biochemical and chemotaxonomic characteristics, and analysis of 16S rDNA sequences. The algicidal bacterium showed 98.6% homology with Micrococcus luteus ATCC $381^T$. Therefore, this bacterium was designated Micrococcus luteus SY-13. The optimal culture conditions of the algicidal bacterium was $25^{\circ}C$, initial pH 8.0, and 3.0% NaCl concentration. M. luteus SY-13 is assumed to produce secondary metabolites which have algicidal activity. When 10% culture filtrate of this strain was applied to C. polykrikoides ($1.0\;{\times}\;10^4\;cells/ml$) cultures, over 98% of C, polykrikoides cells were destroyed within 6 hours. The culture filtrate of M. luteus SY-13 exhibited similar algicidal activity after heat-treatment at $121^{\circ}C$ for 15 min. While algicidal activity remained in filtrates with pH adjusted to 8.0, loss of algicidal activity occurred when the pHs of filtrates were adjusted to over 9.0 or heat-treated at $121{\times}180^{\circ}C$ for 1 hour. M. luteus SY-13 showed significant algicidal activities against C. polykrikoides (98.9%) and a wide algicidal range against various harmful algal bloom (HAB) species. However, there was no algicidal effect on diatom and marine livefood organisms except Isocrysis galbana. These results suggest that M. luteus SY-13 could be a candidate for use in the control of HABs.

Isolation and Diversity of Wild Yeasts from the Waters and Bank Soils of Daejeoncheon, Gapcheon, and Yudeungcheon in Daejeon Metropolitan City, Korea (대전광역시 대전천과 갑천 및 유등천의 물과 주변 토양들로부터 야생효모들의 분리 및 분포 특성)

  • Han, Sang-Min;Lee, Sang-Yeop;Kim, Ha-Kun;Lee, Jong-Soo
    • The Korean Journal of Mycology
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    • v.45 no.4
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    • pp.259-269
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    • 2017
  • In order to investigate the diversity of yeasts from major rivers (the Daejeoncheon, Gapcheon and Yudeungcheon) located in Daejeon city, we isolated wild yeasts by plating diluents of samples collected during the summer and winter of 2016 onto yeast extract-peptone-dextrose (YPD) medium, then identified them using Basic Local Alignment Search Tool (BLAST) analysis to compare the nucleotide sequences of the PCR amplicons for the D1/D2 domain of 26S rDNA. In total, we isolated 191 yeast strains belonging to 104 species from 148 soil or water samples from the rivers and their junctions. Candida spp. (45 strains) including Candida tropicalis (22 strains) were the most abundantly isolated strains from the Daejeoncheon. Candida spp. (16 strains) including Candida vartiovaarae (8 strains) and Candida spp. (18 strains) such as Candida sake (4 strains) were also the dominant isolates from the Gapcheon and Yudeungcheon, respectively. In conclusion, Candida spp. and Cryptococcus spp. were the most dominant strains, corresponding to 42% and 7% of the 191 yeast strains isolated in this study, respectively.

Proteomic Analysis of Proteins Increased or Reduced by Ethanol of Lactobacillus plantarum ST4 Isolated from Makgeolli, Traditional Korean Rice Wine

  • Lee, Seung-Gyu;Lee, Kang-Wook;Park, Tae-Heung;Park, Ji-Yeong;Han, Nam-Soo;Kim, Jeong-Hwan
    • Journal of Microbiology and Biotechnology
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    • v.22 no.4
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    • pp.516-525
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    • 2012
  • LAB were isolated from makgeolli locally produced around Jinju, Gyeongnam, S. Korea during spring of 2011. Randomly selected 11 isolates from MRS agar plates were identified first by API CHL 50 kits and then 16S rRNA gene sequencing. All 11 isolates were identified as Lactobacillus plantarum. Among them, ST4 grew in MRS broth with ethanol up to 10%, showing the highest alcohol resistance. L. plantarum ST4 was moderately resistant against acid and bile salts. When cellular proteins of L. plantarum ST4 under ethanol stress were analyzed by two-dimensional gel electrophoresis (2DE), the intensities of 6 spots increased, whereas 22 spots decreased at least 2-fold. Those 28 spots were identified by peptide mass fingerprinting (PMF). FusA2 (elongation factor G) increased 18.8-fold (6% ethanol) compared with control. Other proteins were AtpD (ATP synthase subunit beta), DnaK, GroEL, Tuf (elongation factor Tu), and Npr2 (NADH peroxidase), respectively. Among the 22 proteins decreased in intensities, lactate dehydrogenases (LdhD and LdhL1) were included.

Identification and Molecular Analysis of Ixodid Ticks (Acari: Ixodidae) Infesting Domestic Animals and Tick-Borne Pathogens at the Tarim Basin of Southern Xinjiang, China

  • Zhao, Li;Lv, Jizhou;Li, Fei;Li, Kairui;He, Bo;Zhang, Luyao;Han, Xueqing;Wang, Huiyu;Johnson, Nicholas;Lin, Xiangmei;Wu, Shaoqiang;Liu, Yonghong
    • Parasites, Hosts and Diseases
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    • v.58 no.1
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    • pp.37-46
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    • 2020
  • Livestock husbandry is vital to economy of the Tarim Basin, Xinjiang Autonomous Region, China. However, there have been few surveys of the distribution of ixodid ticks (Acari: Ixodidae) and tick-borne pathogens affecting domestic animals at these locations. In this study, 3,916 adult ixodid ticks infesting domestic animals were collected from 23 sampling sites during 2012-2016. Ticks were identified to species based on morphology, and the identification was confirmed based on mitochondrial 16S and 12S rRNA sequences. Ten tick species belonging to 4 genera were identified, including Rhipicephalus turanicus, Hyalomma anatolicum, Rh. bursa, H. asiaticum asiaticum, and Rh. sanguineus. DNA sequences of Rickettsia spp. (spotted fever group) and Anaplasma spp. were detected in these ticks. Phylogenetic analyses revealed possible existence of undescribed Babesia spp. and Borrelia spp. This study illustrates potential threat to domestic animals and humans from tick-borne pathogens.

Isolation of a New Agar Degrading Bacterium, Maribacter sp. SH-1 and Characterization of its Agarase (신규 한천분해세균 Maribacter sp. SH-1의 분리 및 효소 특성조사)

  • Lee, Chang-Eun;Lee, Sol-Ji;Lee, Dong-Geun;Lee, Sang-Hyeon
    • 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.

Isolation and characterization of marine bacteria with alginate degrading activity (알긴산 분해능을 갖는 Pseudoalteromonas 및 Vibrio 속 해양세균들의 분리 및 특성분석)

  • Yoon, Young-Jun;Kim, Jung-Wan
    • Korean Journal of Microbiology
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    • v.51 no.4
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    • pp.364-373
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    • 2015
  • As an effort to utilize alginate, 103 bacterial isolates that were positive for the alginate lyase activity were isolated from various clams and seawater samples collected in Incheon coastal area. Among them, 3 strains (M1-2-1, M6-1, and C8-15) were finally selected for further analysis based on their activities at higher levels than others. These isolates were all Gram-negative and rod shaped halophilic bacteria with motility. According to their physiological and biochemical properties as well as DNA sequence of their 16S rRNA genes, M1-2-1 and M6-1 were identified as a member of genus Pseudoalteromonas and C8-15 belonged to genus Vibrio. They exhibited the alginate degrading activity at the maximal level when they were cultured in APY broth for 6-8 h at $25^{\circ}C$. Both their growth and the enzyme activity were greatly enhanced when NaCl was added to the growth medium. The crude alginate lyases from the supernatants of the bacterial cultures showed the highest activity at $45^{\circ}C$ and pH 7.0-8.0. M1-2-1 and M6-1 produced 2.723 and 1.976 g/L of reducing sugar from alginate, respectively, suggesting that they have potential for commercial application.

Isolation of Pseudoalteromonas sp. HJ 47 from Deep Sea Water of East Sea and Characterization of its Extracellular Protease (동해 심층수로부터 Pseudoalteromonas sp. HJ 47의 분리 및 체외단백질분해효소 특성)

  • Cha, In-Tae;Lim, Hayung-Joon;Roh, Dong-Hyun
    • Journal of Life Science
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    • v.17 no.2 s.82
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    • pp.272-278
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    • 2007
  • Proteases are enzymes that break peptide bonds between amino acids of other proteins and occupy a crucial position with respect to their applications in both physiological and commercial fields. In order to screen new source of protease, bacteria producing extracellular proteases at low temperature were isolated from deep sea water of East Sea, Korea. A bacterium showing the best growth rate and production of an extracellular protease at low temperature was designated HJ 47. The DNA sequence analysis of the 16S rRNA gene, phenotypic tests and morphology led to the placement of this organism in the genus Pseudoalteromonas. Although maximal growth was observed at $37^{\circ}C$, enzyme production per culture time was maximum at $20^{\circ}C$. At this temperature, extracellluar protease production was detected from the end of the exponential phage to stationary phase, and maximal at 15 hours after initial production. The optimum temperature and pH of the protease were found to be $35^{\circ}C$ and 8.

Culture Conditions for Improving Extracellular Lipolytic Enzyme Production by a Novel Thermophilic Geobacillus sp. AR1 (신규 고온성 Geobacillus sp. AR1의 extracellular 지질분해효소 생산을 위한 배양조건)

  • Park, Su-Jin;Jeon, Sung-Jong
    • Journal of Life Science
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    • v.23 no.1
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    • pp.110-115
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    • 2013
  • A microorganism (strain AR1) producing an extracellular lipolytic enzyme was isolated from hot springs located in Beppu, Japan. Phylogenetic analysis based on the 16S rDNA sequence and biochemical studies indicated that AR1 belongs to the genus Geobacillus. This study focused on novel strategies to increase extracellular lipolytic enzyme production by this novel Geobacillus sp. AR1. Cultures of the AR1 strain grew within a wide temperature range (from 35 to $75^{\circ}C$); the optimum temperature was $65^{\circ}C$. The pH for optimal growth was 6.5, whereas the optimum pH for lipolytic enzyme production was 8.5. The presence of oils in the culture medium led to improvements in lipolytic enzyme activity. Soybean oil was the most efficient inducer, and it yielded better results when added in the exponential phase. On the other hand, the addition of chemical surfactants led to lipolytic enzyme production. Their addition to the culture could affect the location of the enzyme activity. The addition of Tween 20 in the stationary phase significantly increased the proportion of the extracellular enzyme activity. According to the results, following the addition of soybean oil and Tween 20 in the exponential and stationary phases, the extracellular lipolytic activity was increased 2.4-fold compared with that of a control.

The Characteristics of Tetrachloroethylene (PCE) Degradation by Pseudomonas putida BJ10 (Pseudomonas putida BJ10의 Tetrachloroethylene (PCE) 분해 특성)

  • Choi, Myung-Hoon;Kim, Jai-Soo;Lee, Sang-Seob
    • Korean Journal of Microbiology
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    • v.44 no.4
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    • pp.311-316
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    • 2008
  • In this study, biological PCE degradation by using a BTEX degrading bacterium, named BJ10, under aerobic conditions in the presence of toluene was examined. According to morphological, physiological characteristics, 16S rDNA sequencing and fatty acid analysis, BJ10 was classified as Pseudomonas putida. As a result of biological PCE degradation at low PCE concentrations (5 mg/L), PCE removal efficiency by P. putida BJ10 was 52.8% for 10 days, and PCE removal rate was 5.9 nmol/hr (toluene concentration 50 mg/L, initial cell density 1.0 g (wet weight)/L, temperature 30, pH 7 and DO $3.0{\sim}4.2\;mg/L$. At high PCE concentration (100 mg/L), PCE removal efficiency by P. putida BJ10 was 20.3% for 10 days, and PCE removal rate was 46.0 nmol/hr under the same conditions. The effects of various toluene concentration (5, 25, 50, 100, 200 mg/L) on PCE degradation were examined under the same incubation conditions. The highest PCE removal efficiency of PCE was 57.0% in the initial PCE concentration of 10 mg/L in the presence of 200 mg/L toluene for 10 days. Furthermore, the additional injection of 5.5 mg/L PCE (total 7.6 mg/L) made 63.0% degradation for 8 days in the presence of 50 mg/L toluene under the same conditions. Its removal rate was 13.5 nmol/hr, which was better than the initial removal rate (8.1 nmol/hr).

Organic acid production and phosphate solubilization by Enterobacter intermedium 60-2G (Enterobacter intermedium 60- 2G의 유기산 생성과 불용성인의 가용화)

  • Kim, Kil-Yong;Hwangbo, Hoon;Kim, Yong-Woong;Kim, Hyo-Jeong;Park, Keun-Hyung;Kim, Young-Cheol;Seong, Ki-Young
    • Korean Journal of Soil Science and Fertilizer
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    • v.35 no.1
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    • pp.59-67
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    • 2002
  • A phosphate solubilizing bacterium. strain 60-2G, possessing a strong ability to solubilize insoluble phosphate was isolated from the rhizosphere of grass. On the basis of GC-FAME profile, carbon utilization pattern, and the DNA sequence of a conserved partial 16S rRNA gene, the 60-2G was identified as Enterobacter intermedium. The analysis by HPLC revealed that the strain 60-2G produced mainly gluconic and 2-ketogluconic acids with small amounts of lactic acid in broth culture medium containing hydroxyapatite. During the incubation period of the strain 60-2G in broth culture, pH of the medium decreased upto 3.8 while the soluble phosphate concentration increased. The reversed correlation between pH and soluble phosphate concentration indicated that the solubility of P was due to the produced organic acids. The sequence homology of the deduced amino acids suggested that E. intermedium 60-2G synthesized PQQ which is essential for the oxidation of glucose by glucose dehydrogenase.