• Korean Journal of Microbiology
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• v.46 no.1
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• pp.1-8
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• 2010

New technologies are providing unprecedented knowledge into microbial community structure and functions. Even though nucleic acid based approaches provide a lot of information, metaproteomics could provide a high-resolution representation of genotypic and phenotypic traits of distinct microbial communities. Analyzing the metagenome from different microbial ecosystems, metaproteomics has been applied to seawater, human guts, activated sludge, acid mine drainage biofilm, and soil. Although these studies employed different approaches, they elucidated that metaproteomics could provide a link among microbial community structure, function, physiology, interaction, ecology, and evolution. These approaches are reviewed here to help gain insights into the function of microbial community in ecosystems.

• Korean Journal of Soil Science and Fertilizer
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• v.44 no.5
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• pp.814-818
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• 2011

The seasonal changes were evaluated in the soil microbial populations by selected media in an organic farming system (OFS) with no-till management compared to those in a conventional farming system (CFS) with tillage and synthetic amendments in a flooded paddy from 2009 to 2010. The populations of aerobic bacteria and fungi in the OFS were significantly higher than those in the CFS at the harvesting stages, whereas those of Gram-negative bacteria was significantly higher in the OFS than in the CFS before the submerging stages. In addition, populations of aerobic bacteria, Gram-negative bacteria, and fungi tended to rapidly decreased after the submerging stages may be due to insufficient oxygen. Gram-negative bacteria should be considered as potential factor responsible for the microbial population differentiation observed between the OFS and the CFS in flooded paddy fields.

• Korean Journal of Microbiology
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• v.42 no.2
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• pp.116-124
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• 2006

In this study was performed to analyze quantitatively the number of viable but non-culturable bacteria in the Pine and Quercus forest soil by improved direct viable count (DVC) and plate count (PC) methods. The number of living bacteria of Pine and Quercus forest soil by PC method were less then 1% of DVC method. This result showed that viable but non-culturable (VBNC) bacteria existed in the forest soil with high percentage. Diversity and structure of VBNC bacterial populations in forest soil were analyzed by direct extracting of DNA and 16S rDNA-ARDRA from Pine and Quercus forest soil. Each of them obtained 111 clones and 108 clones from Pine and Quercus forest soil. Thirty different RFLP types were detected from Pine forest soil and twenty-six different RFLP types were detected from Quercus forest soil by HeaIII. From ARDRA groups, dominant clones were selected for determining their phylogenetic characteristics based on 16S rDNA sequence. Based on the 16S rDNA sequences, dominant clones from ARDRA groups of Pine forest soil were classified into 7 major phylogenetic groups ${\alpha}$-proteobacteria (12 clones), ${\gamma}$-proteobacteria (3 clones), ${\delta}$-proteobacteria (1 clone), Flexibacter/Cytophaga (1 clone), Actinobacteria (4 clones), Acidobacteria (4 clones), Planctomycetes (5 clones). Also, dominant clones from ARDRA groups of Quercus forest soil were classified into 6 major phylogenetic groups : ${\alpha}$-proteobacte,ia (4clones), ${\gamma}$-proteobacteria (2 clones), Actinobacteria (10 clones), Acidobacteria (8 clones), Planctomycetes (1 clone), and Verrucomicobia (1 clone). Result of phylogeneric analysis of microbial community from Pine and Quercus forest soils were mostly confirmed at uncultured or unidentified bacteria, VBNC bacteria of over 99% existent in forest soil were confirmed variable composition of unknown micro-organism.

• Microbiology and Biotechnology Letters
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• v.48 no.4
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• pp.515-524
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• 2020

With the increasing demand for enzymes in industrial applications there is a growing need to easily produce industrially important microbial enzymes. This study was carried out to screen the indigenous refinery bacterial isolates for their production of two industrially important enzymes i.e. lipase and protease. A total of 15 bacterial strains were isolated using Soil Extract Agar media from the oil-contaminated environment and one was shown to produce high quality lipase and protease enzymes. The culture conditions (culture duration, temperature, source of nitrogen, carbon, and pH) were optimized to produce the optimum amount of both the lipase (37.6 ± 0.2 Uml-1) and the protease (41 ± 0.4 Uml-1) from this isolate. Productivity of both enzymes was shown to be maximized at pH 7.5 in a medium containing yeast extract and peptone as nitrogen sources and sucrose and galactose as carbon sources when incubated at 35 ± 1℃ for 48 h. Bacterial strain SAB06 was identified as Bacillus licheniformis (MT250345) based on biochemical, morphological, and molecular characteristics. Further studies are required to evaluate and optimize the purification and characterization of these enzymes before they can be recommended for industrial or environmental applications.

• Journal of Ecology and Environment
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• v.46 no.4
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• pp.282-291
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• 2022

Background: The Arctic permafrost stores enormous amount of carbon (C), about one third of global C stocks. However, drastically increasing temperature in the Arctic makes the stable frozen C stock vulnerable to microbial decomposition. The released carbon dioxide from permafrost can cause accelerating C feedback to the atmosphere. Soil organic matter (SOM) composition would be the basic information to project the trajectory of C under rapidly changing climate. However, not many studies on SOM characterization have been done compared to quantification of SOM stocks. Thus, the purpose of our study is to determine soil properties and molecular compositions of SOM in four different Arctic regions. We collected soils in different soil layers from 1) Cambridge Bay, Canada, 2) Council, Alaska, USA, 3) Svalbard, Norway, and 4) Zackenberg, Greenland. The basic soil properties were measured, and the molecular composition of SOM was analyzed through pyrolysis-gas chromatography/mass spectrometry (py-GC/MS). Results: The Oi layer of soil in Council, Alaska showed the lowest soil pH and the highest electrical conductivity (EC) and SOM content. All soils in each site showed increasing pH and decreasing SOC and EC values with soil depth. Since the Council site was moist acidic tundra compared to other three dry tundra sites, soil properties were distinct from the others: high SOM and EC, and low pH. Through the py-GC/MS analysis, a total of 117 pyrolysis products were detected from 32 soil samples of four different Arctic soils. The first two-axis of the PCA explained 38% of sample variation. While short- and mid-hydrocarbons were associated with mineral layers, lignins and polysaccharides were linked to organic layers of Alaska and Cambridge Bay soil. Conclusions: We conclude that the py-GC/MS results separated soil samples mainly based on the origin of SOM (plants- or microbially-derived). This molecular characteristics of SOM can play a role of controlling SOM degradation to warming. Thus, it should be further investigated how the SOM molecular characteristics have impacts on SOM dynamics through additional laboratory incubation studies and microbial decomposition measurements in the field.

• Korean Journal of Microbiology
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• v.41 no.4
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• pp.293-299
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• 2005

Many isolates from soil of Korean ginseng rhizosphere did not show remarkable growth on full strength of the conventional nutrient broth (NB medium) but grew on its 100-fold dilution (DNB medium). Six hundred-forty strains were isolated as oligotrophic bacteria. In the course of screening for new bioactive compounds from oligotrophic bacteria from soil, 8 strains which had appeared to form of clear zone on a medium containing colloidal chitin as a sole carbon source were selected for further studies. Strain CR42 hydrolyzed a fluorogenic analogue of chitin, 4-methylumbelliferyl-D-glucosaminide (MUF-NAG) . Mo st of the culture supernatant of these isolates hydrolyzed 4-methylumbelliferyl-D-N,N'-diacetylchitobioside (MUF-diNAG). The isolates were heterogeneous and categorized to gamma- and beta-proteobacteria, Bacillaceae, Actinobactepia, and Bacteroides by 16S rRNA analysis. Two strains, WR164 and CR18, had a 16S rRNA sequence of $95-96\%$ identical to uncultured bacteria. It was observed that CR2 and CR75 could inhibit the growth of Colletotrichum gloeosporioides with hyphal extention-inhibition assay on PDA plate supplemented with $1\%$ colloidal chitin.

• Molecular & Cellular Toxicology
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• v.2 no.1
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• pp.11-14
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• 2006

In this study we attempted to develop a novel genomic method to selectively isolate target functional microbial genomes from environmental samples. For this purpose, stable isotope probing (SIP) was applied in selectively isolating organic pollutant-assimilating populations. When soil microbes were fed with $^{13}C-labeled $ biphenyl, biphenyl-utilizing cells were incorporated with the heavy carbon isotope. The heavy DNA portion was successfully separated by CsCl equilibrium density gradient. And the diversity in the heavy DNA was sufficiently reduced, being suitable for the current DNA microarray techniques to detect biphenyl-utilizing populations in the soil. In addition, we proposed a new way to get more genetic information by combining this SIP method with selective metagenomic approach. The increased selective power of these new DNA isolation methods will be expected to provide a good quality of new genetic information, which, in turn, will result in development of a variety of biomarkers that may be used in assessing ecotoxicology issues including the impacts of organic hazards, and antibiotic-resistant pathogens on human and ecological systems.

• Journal of Ecology and Environment
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• v.47 no.2
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• pp.14-26
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• 2023

Background: An important consideration for the risk assessment of transgenic plants is their overwintering potential in a natural ecosystem, which allows the survival of the seed bank and may lead to seed reproduction. Here, we investigated the overwintering of sunflower (Helianthus annuus L.) seeds in the laboratory (temperatures: -5, -1, 5, and 10℃) and in the field (burial depth: 0, 5, 15, and 30 cm) as a case study to examine the invasiveness of transgenic crops. Results: Sunflower seeds germinated when incubated at 5℃ and 10℃ for 2, 4, 6, and 12 weeks but not when incubated at -5℃ or -1℃. However, the seeds incubated at -5℃ or -1℃ germinated when they were transferred to the optimal germination temperature (25℃). Up to 16.5% and 15.0% of seeds were dormant when cultured at sub-zero temperatures in a Petri dish containing filter paper and soil, respectively. In the field trial, soil temperature, moisture, and microbial communities differed significantly between soil depths. Germination-related microorganisms were more distributed on the soil surface. Seeds buried on the surface decayed rapidly from 4 weeks after burial, whereas those buried at depths of 15 cm and 30 cm germinated even 16 weeks after burial. No dormancy was detected for seeds buried at any depth. Conclusions: Although sunflower seeds did not overwinter in situ in this study, we cannot exclude the possibility that these seeds lie dormant at sub-zero temperatures and then germinate at optimal temperatures in nature.

• The Korean Journal of Ecology
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• v.21 no.5_3
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• pp.695-702
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• 1998

This study was carried out to investigate to determine seasonal variation of dehydrogenase activity, phosphatase activity, adenosine tri-phosphate content and some physicochemical properties, such as soil pH, moisture content, organic matter and several heavy metal concentrations from Apr. 1997 to jan. 1998 in Pinus densiflora and Quercus mongolica forest in Mt. Nam, to explain a relationship between enzyme activity and the soil factors. There were ranges of 4.03-4.65 in soil pH, 18.65-51.09% in moisture content and 6.69-95.95% in orgainc matter. The organic matter content decreased with soil horizon, showing the higher values in Q. mongolica forest. In comparison to the results of Kawngneung site as control area, there were slightly differences due to a development level of forest ecosystem and microbial degradation of organic matter. The heavy metal concentrations showed 32.50-75.55 ${\mu}g/g$ in Cu, 69.33-134.84 ${\mu}g/g$ in Zn, 57.02-150.32 ${\mu}g/g$ in Pb, and 0.36-1.00 ${\mu}g/g$ in Mt. Nam. These values are higher than in Kwangneung site because of long-term exposure to air pollutants from central city. On the other hand, ATP contents in Mt. Nam were lower than in Kawngneung site in relation to soil organic matter, moisture content and relatively high heavy metal concentrations. ATP contents per soil weight was largest in F+H layer and in spring time of other seasons. Dehydrogenase activity as an index of soil microbial activity had a ranges of 170.67-1,221.66 ${\mu}g$ TPF/g that showed lower values than in Kawngneung site. However, phophatase activity had a contray tendency due to P fertilization for a continuous management. Those values increased through spring to a maximum in the summer and fall in autumn. This is basically caused by metabolic state of soil on the biological activity and several and several factors, such as aeration, soil temperature, vegetation and microflora.

• Applied Biological Chemistry
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• v.49 no.3
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• pp.170-174
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• 2006

For the purpose of developing a high quality agricultural microbial inoculant, methods and materials for improving encapsulation were investigated. Preparation of capsule was conducted by improving extrusion system with micro-nozzle and peristaltic pump. The sodium alginate was selected because of its cheapness, stability of cells, and gel formation ability. The yields, physical properties and gel formation abilities of extractable alginate from sea tangle were investigated by hot water extractable and alkali soluble methods. The extraction yields of hot water extractable alginate (HWEA) and alkali soluble alginate (ASA) from sea tangle were 8 and 20%, respectively. The HWEA was almost not viscous even in 1.5% of the sample solution, whereas the ASA was very highly viscous in above 3% sample solution. The gel formation ability of each samples varied from 1.5% to 5% and the ASA showed a good gel formation ability at 3% solution as commercial alginate (CA). The soil microbial inoculant, Bacillus thuringiensis, Bacillus subtilis, Lactobacillus plantarum and Geotrichum candidum encapsulated sodium alginate with starch and zeolite for stabilizer. The survivability of encapsulated soil microbial inoculant using alginate without stabilizer appeared to be 66, 52, 70 and 50%, respectively. Inclusion of starch and zeolite with alginate bead increased viabilities in Bacillus sp. and Geotrichum candidum by 81-83% and 89%, respectively.