• Ocean and Polar Research
• /
• v.26 no.1
• /
• pp.51-58
• /
• 2004

We isolated and identified culturable Arctic bacteria that had inhabited soils around the Korean Arctic Research Station Dasan located at Ny-Alsund, Svalbard, Norway $(79^{\circ}N,\;12^{\circ}E)$. The collected soils were diluted in distilled water; the diluted soil-water was spread on 3M petri-films at Dasan Station. The petri-films were transported to the laboratory at KORDI, and cultured at $4^{\circ}C$. Colonies grown on the petri-films were subsequently cultured on nutrient agar plates at $4^{\circ}C$ every 7 days. The pure colonies were inoculated into nutrient liquid media, genomic DNA was extracted, and phylogenetic analysis was performed on the basis of 165 rDNA sequences. A total of 227 strains of bacteria were isolated. Among them, 16S rDNA sequences of 185 strains were identical with those of known strains isolated in this study, and 42 strains were finally identified. Phylogenetic analysis using 16S rDNA indicated that the 30 strains belonged to Pseudomonas, 7 strains to Arthrobacter, two strains to Flavobacterium, and the remaining to Achromobacter, Pedobacter, and Psychrobacter. Among the 42 strains, 14 bacteria produced protease: they were 6 strains of Pseudomonax, 4 strains of Arthrobater, an Achromobacter strain, 2 strains of Flavobacterium, and a Pedohacter strain. We expect these Arctic bacteria can be used for screening to develop new industrial enzymes that are active at low temperatures.

• Korean Journal of Microbiology
• /
• v.37 no.1
• /
• pp.85-91
• /
• 2001

Biological treatment of benzene and toluene contaminated soil was investigated in laboratory microcosm of 16 different types for degrading benzene and toluene by indigenous bacteria. At the experimental conditions of the microcosms fast degrading benzene and toluene, moisture contents were 30% and 60% in a soil gap and content of powdered-activated carbon(PCA) for adhesion of benzene and toluene-degrading bacteria was 1% in total soil mass. At the conclusion of the shifted bacteria community, Case 6 and case 7 were operated until 10 days, and then the total cell number and the number of benzene and toluene degrading bacteria were investigated. The total cell number of Case 6 and Case 7 increased 488 fold and 308 fold of total indigenous cell, respectively. The number of benzene and toluene degrading bacteria increased and maintained the percentages occupied in pre-operating microcosm. Species of benzene and toluene degrading bacteria in microcosm changed from species of Gram negative bacteria to Gram positive bacterial species after soil exposed to benzene and toluene.

• Microbiology and Biotechnology Letters
• /
• v.43 no.2
• /
• pp.142-149
• /
• 2015

Bioaerosols are comprised of particles 0.02-100 μm in size that originate in natural and artificial environments, and as a result of human activities. They consist of microorganisms including viruses, bacteria, fungi, and protozoa; fungal spores; microbial toxins; pollen; plant or animal material; expectorated liquid from humans; and glucans (peptidoglycan and β-glucan). Bioaerosols can cause respiratory and other diseases in humans and animals. In this study, bioaerosol samples acquired from agricultural sources, livestock, a sewage treatment plant, a beach, and a pristine area were analyzed to identify and phylogenetically characterize culturable microorganisms. The isolated bacteria exhibited regional differences, with different species dominating. However, Bacillus cereus was isolated in all samples, with a total of 31 strains isolated from all areas, and Acinetobacter baumannii was isolated from an indoor poultry farm. In addition, bacteria determined to be of novel genus or species of the genera Domibacillus, Chryceobacterium, Nocardioides and family Comamonadaceae were isolated from the agricultural, livestock and beach environments.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.5
• /
• pp.995-1004
• /
• 2017

Culture-dependent methods, such as heterotrophic plate counting (HPC), are usually applied to evaluate the bacteriological quality of hemodialysis water. However, these methods cannot detect the uncultured or viable but non-culturable (VBNC) bacteria, both of which may be quantitatively predominant throughout the hemodialysis water treatment system. Therefore, propidium monoazide (PMA)-qPCR associated with HPC was used together to profile the distribution of the total viable bacteria in such a system. Moreover, high-throughput sequencing of 16S rRNA gene amplicons was utilized to analyze the microbial community structure and diversity. The HPC results indicated that the total bacterial counts conformed to the standards, yet the bacteria amounts were abruptly enhanced after carbon filter treatment. Nevertheless, the bacterial counts detected by PMA-qPCR, with the highest levels of $2.14{\times}10^7copies/100ml$ in softener water, were much higher than the corresponding HPC results, which demonstrated the occurrence of numerous uncultured or VBNC bacteria among the entire system before reverse osmosis (RO). In addition, the microbial community structure was very different and the diversity was enhanced after the carbon filter. Although the diversity was minimized after RO treatment, pathogens such as Escherichia could still be detected in the RO effluent. In general, both the amounts of bacteria and the complexity of microbial community in the hemodialysis water treatment system revealed by molecular approaches were much higher than by traditional method. These results suggested the higher health risk potential for hemodialysis patients from the up-to-standard water. The treatment process could also be optimized, based on the results of this study.

• The Plant Pathology Journal
• /
• v.38 no.4
• /
• pp.313-322
• /
• 2022

Seed-borne pathogens in crops reduce the seed germination rate and hamper seedling growth, leading to significant yield loss. Due to the growing concerns about environmental damage and the development of resistance to agrochemicals among pathogen populations, there is a strong demand for eco-friendly alternatives to synthetic chemicals in agriculture. It has been well established during the last few decades that plant seeds harbor diverse microbes, some of which are vertically transmitted and important for plant health and productivity. In this study, we isolated culturable endophytic bacteria and fungi from soybean seeds and evaluated their antagonistic activities against common bacterial and fungal seed-borne pathogens of soybean. A total of 87 bacterial isolates and 66 fungal isolates were obtained. Sequencing of 16S rDNA and internal transcribed spacer amplicon showed that these isolates correspond to 30 and 15 different species of bacteria and fungi, respectively. Our antibacterial and antifungal activity assay showed that four fungal species and nine bacterial species have the potential to suppress the growth of at least one seed-borne pathogen tested in the study. Among them, Pseudomonas koreensis appears to have strong antagonistic activities across all the pathogens. Our collection of soybean seed endophytes would be a valuable resource not only for studying biology and ecology of seed endophytes but also for practical deployment of seed endophytes toward crop protection.

• Journal of Microbiology and Biotechnology
• /
• v.5 no.4
• /
• pp.181-187
• /
• 1995

The cells of Vibrio vulnificus can be induced to the viable but nonculturable (VBNC) state by natural environmental parameters. The V. vulnificus cells in the VBNC state can not be recovered by ordinary laboratory techniques. This nonculturability could often hamper development of effective processing strategies to minimize the number of V. vulnificus in seafoods. Even with V. vulnificus cells in a culturable state, the length of time required to identify the bacteria in contaminated food by phenotyphic characterization may prevent appropriate in-time responses by public health agencies to infections of the bacteria. In the present study, we used polymerase chain reaction (PCR) to develop a rapid and direct detection method for V. vulnificus in small octopus (Octopus variabilis) which is consumed as a raw food in Korea. The region targeted was a 704-base pair (bp) portion of the hemolysin gene, vvhA, of V. vulnificus. The primers designed for PCR amplification were specific for all V. vulnificus sp. tested. Several methods were examined to extract total DNA directly from V. vulnificus seeded into the octopus homogenate and the guanidine isothiocyanate (CITC) method appeared to be most effective. From the octopus homogenate seeded by V. vulnificus at an initial level of $10^2$ CFU/ml of the homogenate and then incubated for 12 h, the targeted sequence was successfully amplified by PCR and the 704-bp DNA fragment was observed by gel electrophoresis. The total completion of this assay requires less than one day.

• Journal of Microbiology
• /
• v.43 no.3
• /
• pp.219-227
• /
• 2005

Little is known about the bacterial communities associated with the plants inhabiting sand dune ecosystems. In this study, the bacterial populations associated with two major sand dune plant species, Calystegia soldanella (beach morning glory) and Elymus mollis (wild rye), growing along the costal areas in Tae-An, Chungnam Province, were analyzed using a culture-dependent approach. A total of 212 bacteria were isolated from the root and rhizosphere samples of the two plants, and subjected to further analysis. Based on the analysis of the 16S rDNA sequences, all the bacterial isolates were classified into six major phyla of the domain Bacteria. Significant differences were observed between the two plant species, and also between the rhizospheric and root endophytic communities. The isolates from the rhizosphere of the two plant species were assigned to 27 different established genera, and the root endophytic bacteria were assigned to 21. Members of the phylum Gammaproteobacteria, notably the Pseudomonas species, comprised the majority of both the rhizospheric and endophytic bacteria, followed by members of Bacteroidetes and Firmicutes in the rhizosphere and Alphaproteobacteria and Bacteroidetes in the root. A number of isolates were recognized as potentially novel bacterial taxa. Fifteen out of 27 bacterial genera were commonly found in the rhizosphere of both plants, which was comparable to 3 out of 21 common genera in the root, implying the host specificity for endophytic populations. This study of the diversity of culturable rhizospheric and endophytic bacteria has provided the basis for further investigation aimed at the selection of microbes for the facilitation of plant growth.

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

• Food Science and Preservation
• /
• v.22 no.6
• /
• pp.920-925
• /
• 2015

The microbial composition in Nuruk, a Korean cereal fermentation starter, is a critical factor for the quality and organoleptic properties of traditional alcoholic beverages. This study was aimed at monitoring the compositional change and enzyme activity of culturable lactic acid bacteria (LAB) in two types of Nuruk fermented at different temperatures. All culturable LAB were isolated at various time points (0, 3, 6, 10, 20, and 30 days) and identified by 16S rRNA sequencing. In traditional Nuruk type A (TN-A), which was fermented at $36^{\circ}C$, the population of total culturable LAB during the fermentation period was between $10^4$ and $10^5$ log CFU/mL. On the other hand, the LAB population in traditional Nuruk type B (TN-B) fermented at $45^{\circ}C$ (primary fermentation for 10 days) and $35^{\circ}C$ (secondary fermentation for 20 days) was $10^2$ log CFU/mL; however, these bacteria could not be detected after 6 days. Major LAB strains were identified in both Nuruk types: (1) from the MRS-culture of TN-A, Pediococcus pentosaceus at 3-30 days; (2) from MRS-culture of TN-B, P. pentosaceus at 3 days and Enterococcus hirae at 6 days. The protease activities of the dominant LAB isolated from the TN-A and TN-B cultures were within the ranges of 0.64~1.03 mg/mL and 0.74~0.81 mg/mL (tyrosine content), respectively, whereas the ${\alpha}$-amylase activities were 0.75~0.98 mg/mL and 0.78~0.79 mg/mL (amylose content), respectively.

• Journal of Environmental Science International
• /
• v.10 no.3
• /
• pp.239-245
• /
• 2001

This research was performed to investigate the dynamics of microbial community by RBC (Rotating Biological Contactor) using Rhodococcus sp. EL-GT and activated sludge. Cell counts revealed by DAPI were compared with culturable bacterial counts from nutrient agar. Colony counts on nutrient agar gave values 20~25% and 1~15% of cell counts (DAPI). The cell counts for the dynamics of bacterial community were determined by combination of in situ hybridization with fluorescently-labelled oligonyucleotide probes and epifluorescence microscopy. Around 90~80% of total cells visualized DAPI were also detected by the bacteria probe EUB 338. For both reactors proteobacteria belonging to the gamma subclass were dominant in the first stage (1 and 2 stage) and proteobacteria belonging to the gamma subclass were dominant in the last stage (3 and 4 stage).