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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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The Korean Journal of Microbiology
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The Microbiological Society of Korea
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Volume & Issues
Volume 51, Issue 4 - Dec 2015
Volume 51, Issue 3 - Sep 2015
Volume 51, Issue 2 - Jun 2015
Volume 51, Issue 1 - Mar 2015
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Defensive roles of Sdu1, a PPPDE superfamily member with ubiquitin C-terminal hydrolase activity, against thermal stress in Schizosaccharomyces pombe
Han, Hee ; Heo, Tae Young ; Ryu, In Wang ; Kim, Kyunghoon ; Lim, Chang-Jin ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 319~328
DOI : 10.7845/kjm.2015.5042
gene encodes Sdu1, a PPPDE superfamily member of deubiquitinating enzymes (DUBs) in Schizosaccharomyces pombe. Sdu1 was previously shown to contain an actual ubiquitin C-terminal hydrolase (UCH) activity using the recombinant plasmid pYSTP which harbors the
gene. This work was designed to assess a thermotolerant role of Sdu1 against high incubation temperatures. In the temperature-shift experiments, the S. pombe cells harboring pYSTP grew much better after the shifts to
, when compared with the vector control cells. After being shifted to
for 6 h, the S. pombe cells harboring pYSTP contained lower reactive oxygen species (ROS) levels, compared with the vector control cells. The nitric oxide (NO) levels of the S. pombe cells harboring pYSTP were slightly lower than those of the vector control cells in the absence or presence of the temperature shifting. The total glutathione (GSH) levels of the S. pombe cells harboring pYSTP were significantly higher than those of the vector control cells. Total superoxide dismutase (SOD) and GSH peroxidase activities were also higher in the S. pombe cells harboring pYSTP after the temperature shifts than in the vector control cells. In brief, the S. pombe Sdu1 plays a thermotolerant role against high incubation temperature through the down-regulation of ROS and NO and the up-regulation of total GSH content, total SOD and GSH peroxidase activities.
Comparative analysis of core and pan-genomes of order Nitrosomonadales
Lee, Jinhwan ; Kim, Kyoung-Ho ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 329~337
DOI : 10.7845/kjm.2015.5061
All known genomes (N
Participation of protein disulfide isomerase 2 in the tolerance against mercury toxicity in Schizosaccharomyces pombe
Choi, Jiye ; Lim, Chang-Jin ; Kim, Kyunghoon ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 338~346
DOI : 10.7845/kjm.2015.5056
The present work was undertaken to address the role of protein disulfide isomerase 2 (Pdi2) in the mercury-tolerance of Schizosaccharomyces pombe, using the Pdi2-overexpressing recombinant plasmid pYPDI2 and the corresponding vector plasmid pRS316. When exposed to mercuric chloride, the PDI2 overepxression cells grew significantly better than the vector control cells. They revealed the lower levels of intracellular reactive oxygen species (ROS) and nitric oxide (NO), when incubated with mercuric chloride for 6 h, than the vector control cells. The PDI2 overepxression cells contained the higher levels of total glutathione (GSH) and superoxide dismutase (SOD) activity than the vector control cells, after 6 h of incubation in mercuric chloride. However, the PDI2 overepxression cells contained similar levels of glutathione peroxidase (GPx) activities, compared to those of the vector control cells. Taken together, the S. pombe Pdi2 promotes the tolerance against mercury toxicity through up-regulating total GSH and SOD and subsequently attenuating ROS and NO elevations.
Bacterial core community in soybean rhizosphere
Lee, Youngmi ; Ahn, Jae-Hyung ; Choi, Yu-Mi ; Weon, Hang-Yeon ; Yoon, Jung-Hoon ; Song, Jaekyeong ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 347~354
DOI : 10.7845/kjm.2015.5052
Soybean is well known to be originated from Korea and far-east Asian countries, and studies of many root nodule bacteria associated with soybean have mainly-focused on nitrogen fixation, but much less study was carried out on bacterial community in the rhizosphere of soybean. In this study, we analyzed the bacterial community in rhizosphere of Korean soybean, Daepungkong using the pyrosequencing method based on the 16S rRNA gene to characterize the change of the rhizosphere community structure according to the growth stages of soybeans and to elucidate bacterial core community in rhizosphere of soybean. Our results revealed that bacterial community of rhizosphere soil differed from that of bulk soil and was composed of a total of 21 bacterial phyla. The predominant phylum in the rhizosphere of soybean was Proteobacteria (36.6-42.5%) and followed by Acidobacteria (8.6-9.4%), Bacteroidetes (6.1-10.9%), Actinobacteria (6.4-9.8%), and Firmicutes (5.7-6.3%). The bacterial core community in soybean rhizosphere was mainly composed of the operational taxonomic units (OTUs) belonging to the phylum Proteobacteria throughout all growth stages. The OTU00006 belonged to the genus Bradyrhizobium had the highest abundance and Steroidobacter, Streptomyces, Devosia were followed. These results show that bacterial core community in soybean rhizosphere was mainly composed of OTUs associated with plant growth promotion and nutrient cycles.
Growth kinetics and chlorine resistance of heterotrophic bacteria isolated from young biofilms formed on a model drinking water distribution system
Park, Se-Keun ; Kim, Yeong-Kwan ; Oh, Young-Sook ; Choi, Sung-Chan ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 355~363
DOI : 10.7845/kjm.2015.5050
The present work quantified the growth of young biofilm in a model distribution system that was fed with chlorinated drinking water at a hydraulic retention time of 2 h. Bacterial biofilms grew on the surface of polyvinyl chloride (PVC) slides at a specific growth rate of
for total bacteria and
for heterotrophic bacteria, reaching
after 10 days, respectively. The specific growth rates of biofilm-forming bacteria were found to be much higher than those of bulk-phase bacteria, suggesting that biofilm bacteria account for a major part of the bacterial production in this model system. Biofilm isolates exhibited characteristic kinetic properties, as determined by
values using the Monod model, in a defined growth medium containing various amounts of acetate. The lowest
value was observed in bacterial species belonging to the genus Methylobacterium, and their slow growth seemed to confer high resistance to chlorine treatment (0.5 mg/L for 10 min).
values (inversely related to substrate affinity) of Sphingomonas were two orders of magnitude lower for acetate carbon than those of other isolates. The Sphingomonas isolates may have obligate-oligotrophic characteristics, since the lower
values allow them to thrive under nutrient-deficient conditions. These results provide a better understanding and control of multi-species bacterial biofilms that develop within days in a drinking water distribution system.
Isolation and characterization of marine bacteria with alginate degrading activity
Yoon, Young-Jun ; Kim, Jung-Wan ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 364~373
DOI : 10.7845/kjm.2015.5034
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
. 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
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.
Eco-friendly remediation and reuse for coastal dredged materials using a bioaugmentation technology
Kim, In-Soo ; Ha, Shin-Young ; Koh, Sung-Cheol ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 374~381
DOI : 10.7845/kjm.2015.5066
Occurrences of coastal dredged materials are ever increasing due to port construction, navigational course maintenance and dredging of polluted coastal sediments. Ocean dumping of the coastal dredged materials has become virtually prohibited as London Treaty will be enacted as of the year 2012. It will be necessary to treat and recycle the dredged materials that may carry organic pollutants and heavy metals in a reasonable and effective process: collection of the dredged materials, liquid and solid separation, and treatment of organic compounds and heavy metals. In this study we have developed a continuous bioreactor system that can treat a mixture of silt and particulate organic matter using a microbial consortium (BM-S-1). The steady-state operation conditions were: pH (7.4-7.5), temperature (
), DO (7.5-7.9), and salt concentration (3.4-3.7%). The treatment efficiencies of SCOD, T-N and T-P of the mixture were 95-96%, 92-99%, and 79-97%. The system was also effective in removal of heavy metals such as Zn, Ni, and Cr. Levels of MLSS during three months operation period were 11,000-19,000 mg/L. Interestingly, there was little sludge generated during this period of operation. The augmented microbial consortium seemed to be quite active in the removal of the organic component (30%) present in the dredged material in association with indigenous bacteria. The dominant phyla in the treatment processes were Proteobacteria and Bacteroidetes while dominant genii were Marinobacterium, Flaviramulus, Formosa, Alteromonadaceae_uc, Flavobacteriaceae_uc. These results will contribute to a development of a successful bioremediation technology for various coastal and river sediments with a high content of organic matter, inorganic nutrients and heavy metals, leading to a successful reuse of the polluted dredged sediments.
Isolation and identification of protease-producing bacteria from the intertidal zone in Jeju Island, Korea
Moon, Young-Gun ; Dharaneedharan, Subramanian ; Kim, Dong-Hwi ; Park, So-Hyun ; Heo, Moon Soo ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 382~388
DOI : 10.7845/kjm.2015.5053
Eleven protease-producing bacteria were isolated from the organisms` external shells and the inorganic materials collected from intertidal zone of Jeju Island, Republic of Korea. The samples were diluted serially, inoculated on Zobell agar plates with 1% skim milk and incubated at
. Clear zone forming colonies were selected as protease-producing bacteria and each strain was identified based on the phylogenetic analysis with their 16S rDNA sequences. Strains JJM125, JJM129, YG47 and YG49 belong to the marine bacterial genus Pseudoalteromonas; strain JJM122 belong to the genus Microbulbifer; strains YG51, YG52, YG62 and YG63 belong to the genus Vibrio; and strain YG65 belong to genus Bacillus. Hence, the present study suggests that these protease producing bacteria could be further used to develop new varieties of protease with various biotechnological applications.
Eco-friendly remediation and odor control of a contaminated urban stream using beneficial microorganisms
Chang, Jae-Soo ; Song, Jikyung ; Kim, In-Soo ; Yoo, Jangyeon ; Koh, Sung-Cheol ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 389~397
DOI : 10.7845/kjm.2015.5065
Dongchun, one of the representative streams in urban area, is a downstream that is connected to Hogyechun, Bujeonchun, Jeonpochun, Danggamchun, and Gayachun as its upstream. Hogyechun has been mostly covered with concrete structures for decades, causing sewage pollution from the upstream, overflow of the downstream region and other serious pollution that gave rise to many civil complaints from the residents nearby. In this study, we analyzed 3 stations, including control station for water quality and malodor changes of Hogyechun after applying the microbial augmentation (BM-2) for a few months including the rainy season. Amounts (g/h) of DO in the middle site (Middle) and the downstream site (Borim) increased by 1.7 times compared with the upstream site (Chuhae) after augmentation for about 2 months. Amounts (g/h) of COD and
decreased by 2 and 1.7 times, respectively, in the middle and downstream sites while SS increased by 7.5 and 22 times in the middle and downstream sites, respectively. Moreover, odor removal efficiencies at the middle and downstream sites were 65% and 19%, respectively, indicating the microbial activity in reduction of malodor in the polluted stream. The dominant microbial species of the sampling sites were Hydrogenophaga caeni, Sphaerotilus natans, Acidovorax radicis, Acidovorax delafieldii, and Cloacibacterium rupense. Densities of the two species Sphaerotilus natans and Acidovorax delafieldii were significantly increased in the middle site after augmentation which possessed potential odor removal and denitrification activity, respectively. Potential pathogens (e.g., Arcobacter cryaerophilus) were also removed from the middle site after the implementation.
Bacterial diversity of the Marine Sponge, Halichondria panicea by ARDRA and DGGE
Park, Jin-Sook ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 398~406
DOI : 10.7845/kjm.2015.5069
Culture-dependent ARDRA and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Halichondria panicea collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and Marine agar media. PCR amplicons of the 16S rRNA gene from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rRNA gene sequences derived from ARDRA patterns showed more than 96% similarities compared with known bacterial species, and the isolates belonged to four classes, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Firmicutes, of which Alphaproteobacteria was dominant. DGGE fingerprinting of 16S rRNA genes amplified from the sponge-derived total gDNA showed 14 DGGE bands, and their sequences showed 100% similarities compared with the sequences available in GenBank. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven classes, including Alphaproteobacteria, Gammaproteobacteria, Acidobacteria, Actinobacteira, Bacteroidetes, Cyanobacteria, and Chloroflexi. According to both the ARDRA and DGGE methods, three classes, Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, were commonly found in H. panicea. However, overall bacterial community in the sponge differed depending on the analysis methods. Sponge showed more various bacterial community structures in culture independent method than in culture-dependent method.
Antilisterial activity of fresh cheese fermented by Lactobacillus paracasei BK57
Lim, Eun-Seo ; Lee, Eun-Woo ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 407~418
DOI : 10.7845/kjm.2015.5059
This study is focused on establishing the optimal conditions to enhance the production of antilisterial substances by Lactobacillus paracasei BK57 isolated from Baikkimchi. In addition, the growth and in situ lactic acid and bacteriocin production of this strain were investigated during the manufacture of fresh cheese. And then the efficacy of using Lactobacillus starter as a protective culture to improve the safety of fresh cheese against Listeria monocytogenes KCTC 3569 was estimated. Maximum growth rate and activity of antibacterial substances were obtained in Lactobacilli MRS broth at
with controlled pH 6.0 after 30 h of incubation under aerobic condition. However, the growth rate and antimicrobial activity of bacteriocin produced in whole milk supplemented with yeast extract (2.0%) as a substrate were lower than those obtained in MRS broth. Live cells and cell-free culture supernatant of BK57 strain were effective in the suppression of L. monocytogenes in milk, whereas the inhibitory of the bacteriocin obtained from BK57 strain was higher in BHI broth than in milk. During storage at
for 6 days, no significant difference was found in the cell viability and antimicrobial activity of BK 57 strain in fresh cheese. In samples held at two temperatures, there was at least a 15% reduction in the numbers of the pathogen in fresh cheese artificially contaminated with approximately
of L. monocytogenes within 6 days. Our results demonstrated the usefulness of L. paracasei BK57 having antilisterial activity as a biopreservative in the cheese making process.
Isolation and characterization of a Bacillus spp. for manufacturing the feed additives in livestock
Park, Hae Suk ; Jo, Seung Wha ; Yim, Eun Jung ; Kim, Yun Sun ; Moon, Sung Hyun ; Cho, Ho Seong ; Kim, Hyun-Young ; Cho, Yong Sik ; Cho, Sung Ho ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 419~426
DOI : 10.7845/kjm.2015.5060
The aims of this study were to isolate spore-forming Bacillus strains that exhibit high digestibility and anti-pathogenic bacteria toward feed for calves. Total 136 spore-forming strains were isolated from finished feeds and their ingredients. Among them, 93 strains were identified as Bacillus species when analyzed by 16S rRNA sequencing. For industrial use, three strains named as Bacillus licheniformis SHS14, B. subtilis LCB7, B. amyloliquefaciens LCB10 were selected after evaluating the industrial standards that are related with heat and acid resistance, enzyme activities, and anti-pathogenic activities against Samonella dublin ATCC15480 and E. coli K99. After each culture, 3 selected strains were mixed together at 1:1:1 (v/v/v) ratio and then prepared as the mixed starter culture for feeding. The changes in microbial community were analyzed via 16S rRNA metagenomics. The initial community ratio among three strains was maintained even after manufacturing into final products. Also, in vitro, enzymatic and anti-pathogenic activities were almost same as those when cultured in single culture, and results of anti-pathogenic activities conducted with calves showed 90% activities against lincomycin, which would be indicative of a promising feed starter.
Isolation and characterization analysis of the halophilic archaea isolated from solar saltern, Gomso
Koh, Hyeon-Woo ; Kim, So-Jeong ; Rhee, Sung-Keun ; Park, Soo-Je ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 427~434
DOI : 10.7845/kjm.2015.5041
Most of halophilic archaea are found in the various hypersaline environments including solar saltern, salt lake with very high salt concentration. The present study is about isolation and characterization of halphilic archaea from Gomso solar saltern known as a representative high salt environment in Korea. In order to isolate the halophilic archaea, we prepared and used high salt medium. Finally, total 7 strains obtained were tentatively identified based on comparative similarity analysis for 16S rRNA gene sequence and physiological traits. All halophilic archaea belonged to Haloruburm, Halogeometriucm, Halobacterium, and Haloarcula genera. These isolates were all Gram-staining negative, and growth was not observed using nitrate as an alternative electron acceptor under anaerobic conditions. In addition, all isolates required about 12-30% (w/v, NaCl) salt. This case study might provide basic information on microbial isolation technologies and related research in halophilic microorganisms from domestic halophilic environments, and contribute to obtaining useful indigenous halophilic archaea in a variety of extreme environmental conditions.
Effects of fission yeast ortholog of THOC5 on growth and mRNA export in fission yeast
Koh, Eun-Jin ; Yoon, Jin Ho ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 435~439
DOI : 10.7845/kjm.2015.5058
THO/TREX complex plays an important role in transcriptional elongation, mRNA processing, nuclear RNA export, and genome stability. A fission yeast, Schizosaccharomyces pombe, SPBC577.04 gene encoding the ortholog of THOC5, a component of THO/TREX complex, was identified and characterized. The S. pombe thoc5 (spthoc5) is not essential for both growth and mRNA export, but deletion of the spthoc5 gene caused growth defect and slight accumulation of
RNA in the nucleus. And the functional spThoc5-GFP protein is localized mainly in the nucleus. Co-immunoprecipitation analysis showed that the Hpr1(THOC1) protein, an evolutionally well-conserved component of THO/TREX complex, interacted with spThoc5 as well as Tho2(THOC2), another subunit of THO complex. These results suggest that S. pombe Thoc5 as a component of THO/TREX complex is also involved in mRNA export from the nucleus.
Diversity of ampicillin resistant bacteria in domestic streams
Go, Eun Byeul ; Chung, In-Young ; Kim, Hyuk ; Seok, Kwang-Seol ; Kim, Byeori ; Yoo, Yong-Jae ; Jang, Yejin ; Chae, Jong-Chan ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 440~443
DOI : 10.7845/kjm.2015.5067
The widespread emergence of antibiotic resistant microorganisms in clinics and natural environments has attracted public concern. Especially, microorganisms inhabiting natural environment is considered as a source responsible for increasing the abundance of antibiotic resistant genes in ecosystem. In this study, the diversity of culturable bacteria resistant to ampicillin was investigated with water samples collected from seven locations in Korea. The genera belonging to Aeromonas and Acidovorax were dominant among the isolated 498 strains. The 66% of isolates showed multi-drug resistance against more than six antibiotics among tested fourteen ones and isolates resistant to seven antibiotics were the most prevalent with 19.7% abundance. Using the antibiotics susceptibility results, the intrinsic resistance profile was suggested for the most dominant genera, Aeromonas, Acidovorax, Pseudomonas, and Elizabethkingia.
Inhibitory effect of SeO
on cell growth of methicillin-resistant Staphylococcus aureus
Han, Yeong-Hwan ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 444~447
DOI : 10.7845/kjm.2015.5062
This study was carried out to determine the antibacterial activity of
against pathogenic bacteria, methicillin-resistant Staphylococcus aureus (MRSA). Using the disc diffusion method,
showed higher antibacterial activity against Gram-positive bacteria than Gram-negative bacteria used in this study. Coccus-form bacteria showed much susceptible to
, compared to bacillus-form bacteria. Compared to antibiotics-susceptible S. aureus, antibiotics used in this study showed lower antibacterial activity against MRSA. As
was applied, diameters of clear zone for S. aureus and MRSA were 20-32.7 mm and 13.5-17.9 mm, respectively. For MRSA, minimal inhibitory concentration of
was added in culture broth, cell growth of MRSA was inhibited. These results will be applied to determine antibacterial mechanism of MRSA and other pathogenic microorganisms.
Inhibition of yeast Candida growth by protein antibiotic produced from Pseudomonas fluorescens BB2
Ahn, Kyung-Joon ;
The Korean Journal of Microbiology, volume 51, issue 4, 2015, Pages 448~452
DOI : 10.7845/kjm.2015.5055
The bacterial strain that was isolated from chinese cabbage rhizosphere, showed inhibition of yeast growth. This strain was identified as Pseudomonas fluorescens BB2 by API 20NE test and 16S rRNA gene sequence analysis. P. fluorescens BB2 strain produced antibiotics against yeast as a secondary metabolite effectively when the culture was carried out in YM medium with 3% glucose at
. The protein antibiotic of BB2 strain which was concentrated by ammonium sulfate precipitation and n-butanol extraction inhibited the growth of yeast with the minimal inhibitory concentration of
against Candida albicans KCTC 7965, and the growth of yeast was completely inhibited at
. The hydrophilic fraction of n-butanol extraction inhibited the growth of Bacillus cereus ATCC 21366, showed orange halo on chrome azurol S plate, which means the fraction contained iron chelating siderophore. The results of crystal violet uptake through the cell membrane showed that membrane permeability was increased about 9% than control, when the concentration of hydrophobic antibiotic against yeast C. albicans was
. As a result, the antibiotic produced by P. fluorescens BB2 against yeast Candida is considered antimicrobial peptide, and this is the first report in the genus Pseudomonas.