• Korean Journal of Soil Science and Fertilizer
• /
• v.44 no.1
• /
• pp.127-145
• /
• 2011

Various environmental ecosystems are valuable sources for microbial ecology studies, and their analyses using recently developed molecular ecological approaches have drawn significant attention within the scientific community. Changes in the microbial community structures due to various anthropogenic activities can be evaluated by various culture-independent methods e.g. ARISA, DGGE, SSCP, T-RFLP, clone library, pyrosequencing, etc. Direct amplification of total community DNA and amplification of most conserved region (16S rRNA) are common initial steps, followed by either fingerprinting or sequencing analysis. Fingerprinting methods are relatively quicker than sequencing analysis in evaluating the changes in the microbial community. Being an efficient, sensitive and time- and cost effective method, T-RFLP is regularly used by many researchers to access the microbial diversity. Among various fingerprinting methods T-RFLP became an important tool in studying the microbial community structure because of its sensitivity and reproducibility. In this present review, we will discuss the important developments in T-RFLP methodology to distinguish the total microbial diversity and community composition in the various ecosystems.

• Korean Journal of Environmental Biology
• /
• v.41 no.3
• /
• pp.308-324
• /
• 2023

This study investigated unrecorded freshwater bacterial species in Korea. Water and sediment samples were collected from the Nakdong River basin from 2020-2022. Bacterial isolates obtained through the conventional culture method with commercial media were subjected to 16S rRNA gene sequencing to identify unrecorded bacterial species. Results of 16S rRNA gene sequencing of the bacterial isolates revealed that a total of 44 bacterial isolates shared 16S rRNA gene sequence similarities of more than 98.65%, with validly published bacterial species not reported in Korea yet. These isolates were phylogenetically assigned to 4 phyla, 7 classes, 21 orders, 33 families, and 42 genera. A total of 2, 6, 12, and 24 species belonged to phyla Bacillota, Bacteroidota, Actinomycetota, and Pseudomonadota, respectively. Here, we provide details of these 44 unrecorded bacterial species, including Gram staining, colony and cellular morphologies, biochemical properties, and phylogenetic position.

• Journal of Microbiology and Biotechnology
• /
• v.22 no.9
• /
• pp.1218-1223
• /
• 2012

${\varepsilon}$-Poly-$_L$-lysine (${\varepsilon}$-PL), produced by Streptomyces or Kitasatospora strains, is a homo-poly-amino acid of $_L$-lysine, which is used as a safe food preservative. The present study investigates the combined use of cell immobilization and in situ adsorption (ISA) to produce ${\varepsilon}$-PL in shaken flasks. Loofah sponge-immobilized Streptomyces ahygroscopicus GIM8 produced slightly more ${\varepsilon}$-PL than those immobilized on synthetic sponge, and sugarcane bagasse. Moreover, loofah sponge supported the maximum biomass. Hence, loofah sponge was chosen for cell immobilization. Meanwhile, the ion-exchange resin D152 was employed for ISA. The loofah sponge-immobilized cells produced $0.54{\pm}0.1g/l$ ${\varepsilon}$-PL, which significantly increased to $3.64{\pm}0.32g/l$ after combining with ISA through the addition of resin bags. The free cells with ISA using the dispersed resin yielded $2.73{\pm}0.26g/l$ of ${\varepsilon}$-PL, an increase from $0.82{\pm}0.08g/l$. These data illustrate that the proposed combination method improved production most significantly compared with either immobilization or ISA only. Moreover, the immobilized cells could be repeatedly used and an ${\varepsilon}$-PL total amount of $8.05{\pm}0.84g/l$ was obtained. The proposed combination method offers promising perspectives for ${\varepsilon}$-PL production.

• Journal of Dairy Science and Biotechnology
• /
• v.34 no.1
• /
• pp.9-20
• /
• 2016

Various microflora, including lactic acid bacteria, are important and necessary components of various cheeses and have significant roles in cheese manufacturing and ripening. In general, the starter culture and secondary microflora could affect the physicochemical properties of various cheeses and could contribute to modifications during manufacturing and ripening. Therefore, during cheese manufacturing and ripening, microbial diversity may depend on continuous interactions among microflora and various environmental conditions. The microbial diversity of cheese is very complex and difficult to control using the classical microbiological techniques. However, recent culture-independent methods have been rapidly developed for microflora in cheese, which could be directly detected using DNA (and/or RNA) in combination with culture-dependent methods. Therefore, this review summarizes state-of-the-art molecular methods to analyze microbial communities in order to understand the properties that affect quality and ripening as well as the complex microbial diversity of various raw-milk, long-ripened cheeses.

• Journal of Microbiology and Biotechnology
• /
• v.33 no.2
• /
• pp.260-267
• /
• 2023

In this study, we sought to improve lutein and zeaxanthin production in Mychonastes sp. 247 and investigated the effect of environmental factors on lutein and zeaxanthin productivity in Mychonastes sp. The basic medium selection and N:P ratio were adjusted to maximize cell growth in one-stage culture, and lutein and zeaxanthin production conditions were optimized using a central composite design for two-stage culture. The maximum lutein production was observed at a light intensity of 60 μE/m²/s and salinity of 0.49%, and the maximum zeaxanthin production was observed at a light intensity of 532 μE/m²/s and salinity of 0.78%. Lutein and zeaxanthin production in the optimized medium increased by up to 2 and 2.6 folds, respectively, compared to that in the basic medium. Based on these results, we concluded that the optimal conditions for lutein and zeaxanthin production are different and that optimization of light intensity and culture salinity conditions may help increase carotenoid production. This study presents a useful and potential strategy for optimizing microalgal culture conditions to improve the productivity of lutein and zeaxanthin, which has applications in the functional food field.

• The Korean Journal of Mycology
• /
• v.13 no.2
• /
• pp.89-97
• /
• 1985

To find antibacterial strains of the soil microorganisms in Korea, they were isolated from the soil samples of different locations and screened for antibacterial activity against several standard microorganisms. An isolate among them had antibacterial activities against gram-positive and gram-negative bacteria. The examination of its morphological, biochemical, cultural and physiological characteristics according to the International Streptomyces Project methods showed that it belongs to the genus Streptomyces. This strain appears to be a novel strain when it was compared with those species of the genus which have been so far reported. The antibiotic metabolite was produced in the submerged culture of the strain. This metabolite was extracted from the culture filtrate and purified by ion-exchange column chromatography. Physico-chemical properties of the antibacterial metabolite were characterized.

• Journal of Soil and Groundwater Environment
• /
• v.11 no.3
• /
• pp.66-77
• /
• 2006

This review inquired the recently applied molecular biological and biochemical methods analyzing the microbial community structure of groundwater and, as a result, summarized the functional or taxonomic groups of active microorganisms with major contaminants in groundwater. The development of gene amplification through PCR has been possible to figure out microbial population and identification. Active microbial community structures have been analyzed using a variety of fingerprinting techniques such as DGGE, SSCP, RISA, and microarray and fatty acid analyses such as PLFA and FAME, and the activity of a specific strain has been examined using FISH. Also, this review included the dominant microflora in groundwater contaminated with fuel components such as n-alkanes, BTEX, MTBE, and ethanol and chlorinated compounds such as TCE, PCE, PCB, CE, carbon tetrachloride, and chlorobenzene.

• Journal of Microbiology
• /
• v.44 no.2
• /
• pp.155-161
• /
• 2006

Comparative analysis of microbial communities in a sequencing batch reactor which performed enhanced biological phosphorus removal (EBPR) was carried out using a cultivation-based technique and 16S rRNA gene clone libraries. A standard PCR protocol and a modified PCR protocol with low PCR cycle was applied to the two clone libraries of the 16S rRNA gene sequences obtained from EBPR sludge, respectively, and the resulting 424 clones were analyzed using restriction fragment length polymorphisms (RFLPs) on 16S rRNA gene inserts. Comparison of two clone libraries showed that the modified PCR protocol decreased the incidence of distinct fragment patterns from about 63 % (137 of 217) in the standard PCR method to about 34 % (70 of 207) under the modified protocol, suggesting that just a low level of PCR cycling (5 cycles after 15 cycles) can significantly reduce the formation of chimeric DNA in the final PCR products. Phylogenetic analysis of 81 groups with distinct RFLP patterns that were obtained using the modified PCR method revealed that the clones were affiliated with at least 11 phyla or classes of the domain Bacteria. However, the analyses of 327 colonies, which were grouped into just 41 distinct types by RFLP analysis, showed that they could be classified into five major bacterial lineages: ${\alpha},\;{\beta},\;{\gamma}-$ Proteobacteria, Actinobacteria, and the phylum Bacteroidetes, which indicated that the microbial community yielded from the cultivation-based method was still much simpler than that yielded from the PCR-based molecular method. In this study, the discrepancy observed between the communities obtained from PCR-based and cultivation-based methods seems to result from low culturabilities of bacteria or PCR bias even though modified culture and PCR methods were used. Therefore, continuous development of PCR protocol and cultivation techniques is needed to reduce this discrepancy.

• Archives of Pharmacal Research
• /
• v.28 no.4
• /
• pp.433-437
• /
• 2005

Human cytochromes P450 (GYP) 2A6 and 2E1 are of great interest because of their important roles in the oxidation of numerous drugs and carcinogens. Bacterial expression systems, especially Escherichia coli cells, have been widely used for the production of various GYP enzymes in order to obtain high yield of proteins. The expression methods usually employ longer culture time (30-72 h) at lower temperature (usually under $30^{\circ}C$). Expression levels of GYPs 2A6 and 2E1 at $37^{\circ}C$ were compared to those at $28^{\circ}C$, which is a usual temperature used in most bacterial expression systems for human GYP expression. Within 18 h the expression levels of GYPs 2A6 and 2E1 reached up to 360 and 560 nmol per liter culture at $37^{\circ}C$, respectively, which are compatible with those of 36 h culture at $28^{\circ}C$. The activities of GYPs expressed at $37^{\circ}C$ were also comparable to those expressed at $28^{\circ}C$. The present over-expression system can be useful for rapid production of large amounts of active human GYPs 2A6 and 2E1 in E. coli.

• Environmental Engineering Research
• /
• v.25 no.1
• /
• pp.29-35
• /
• 2020

The aim of this study was to estimate the microbial metabolic activity of indigenous soil microbes under the radon exposure with different intensity and times in the secured laboratory radon chamber. For this purpose, the soil microbes were collected from radon-contaminated site located in the G county, Korea. Thereafter, their metabolic activity was determined after the radon exposure of varying radon concentrations of 185, 1,400 and 14,000 Bq/㎥. The average depth variable concentrations of soil radon in the radon-contaminated site were 707, 860 and 1,185 Bq/㎥ from 0, 15, and 30 cm in deep, respectively. Simultaneously, the soil microbial culture was mainly composed of Bacillus sp., Brevibacillus sp., Lysinibacillus sp., and Paenibacillus sp. From the radon exposure test, higher or lower radiation intensities compared to the threshold level attributed the metabolic activity of mixed microbial consortium to be reduced, whereas the moderate radiation intensity (i.e. threshold level) induced it to the pinnacle point. It was decided that radon radiation could instigate the microbial metabolic activity depending on the radon levels while they were exposed, which could consequently address that the certain extent of threshold concentration present in the ecosystem relevant to microbial diversity and population density to be more proliferated.