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

• Korean Journal of Soil Science and Fertilizer
• /
• v.16 no.3
• /
• pp.286-293
• /
• 1983

The glucose application remarkably increased the heterotrophic acetylene reducing activities during one month incubation. The amount of the increases varied between the soils. Application of rice straw brought about the significant increases during incubation time. Compost contained the largest amount of available-N among the C-sources, and thereby brought the smallest increase in all soils. The cumulative fixed nitrogen with application of rice straw at 30 days incubation in the three experimented soils were highest in Hwadong clay soil, i.e, $2.2mg^N/100g$, intermediate in Ratchaburi soil $0.85mg^N$, and least in Konosu soil $0.80mg^N/100g$. On the other hand, nitrogen fixing heterotrophic, bacteria, such as Clostridia, aerobes and anaerobes, were remarkably increased by application of rice straw while Azotobacter and Beijerinkia were not. The cumulative fixed nitrogen was more pronounced in the clay soil than in the coarse loamy soil. More pronounced nitrogen fixing activities in light condition(heterotrophic + photosynthetic) than that in dark(heterotrophic) condition have been observed both in the coarse loamy and clay soils. The nitrogen fixing ability of photosynthetic microbes in paddy soil is probably higher in coarse loamy soil than in clay soil.

• Journal of the Korean GEO-environmental Society
• /
• v.19 no.10
• /
• pp.21-26
• /
• 2018

Soil-water characteristic curve, which is called soil retention curve, is required to explore water flows in unsaturated soils, relative permeability of water in multi-phase fluids flow, and change to stiffness and volume of soils. Thus, the understanding of soil-water characteristic curves of soils help us explore the behavior of soils inclduing fluids. Biopolymers are environmental-friendly materials, which can be completely degraded by microbes and have been believed not to affect the nature. Thus, various biopolymers such as deacetylated power, polyethylene oxide, xanthan gum, alginic acid sodium salt, and polyacrylic acid have been studies for the application to soil remediation, soil improvement, and enhanced oil recovery. PAA (polyacrylic acid) is one of biopolymers, which have shown a great effect in enhanced oil recovery as well as soil remediation because of the improvement of water-flood performance by mobility control. The study on soil-water characteristic curves of sandy soils containing PAA (polyacrylic acid) has been conducted through experimentations and theoretical models. The results show that both capillary entry pressure and residual water saturation dramatically increase according to the increased concentration of PAA (polyacrylic acid). Also, soil-water characteristic curves by theoretical models are quite well consistent with the results by experimental studies. Thus, soil-water characteristic curves of sandy soils containing biopolymers such as PAA (polyacrylic acid) can be estimated using fitting parameters for the theoretical model.

• Korean Journal of Soil Science and Fertilizer
• /
• v.30 no.2
• /
• pp.200-207
• /
• 1997

In order to evaluate the soil microbiological characteristics of paddy fields in Korea, surface soils were sampled from 63 sites in different agroclimatic zones before submersion of the fields. The distribution of microorganisms and the microbial diversity indices were examined. Soil microbial populations were generally higher in southern area than in northern area. The colony forming units(cfus) of fluorescence Pseudomonas sp. showed the greatest regional differences, among the microbes investigated. On the topographical differences, the cfus of aerobic bacteria, fluorescence Pseudomonas sp. and Azotobacter sp. maintained high level in coastal plains; and on the sail textural difference, fungus was the highest in clay soil, but Bacillus sp., Azotobacter sp and denitrifiers were the highest in silty clay loam soil at 0.05 probability level based on the multiple range test. The numbers of ammonium oxidizers and Azotobacter sp. were increased with soil pH. Microbial diversity indices of paddy fields which calculated from the percentages of Bacillus sp. fluorescence Pseudomonas sp. Azotobacter sp. denitrifiers, ammonium oxidizers, nitrite oxidizers, actinomycetes and fungus to these total microbial numbers were between 0.109 and 0.661. On the soil textures, the microbial diversity indices of sandy, sandy loam, silty clay loam, clay loam and clay soil were 0.443, 0.427, 0.414, 0.405 and 0.362 respectively.

• The Plant Pathology Journal
• /
• v.25 no.1
• /
• pp.70-76
• /
• 2009

The rhizobacteria of Panax notoginseng were isolated from six sites in Yanshan, Maguan and Wenshan Counties, Yunnan Province of China, and their antagonistic activity against P. notoginseng root-rot fungal pathogens was determined. Of the 574 rhizobacteria isolated, 5.8% isolates were antagonistic in vitro to at least one of the five pathogens, Cylindrocarpon didynum, Fusarium solani, Phytophthora cactorum, Phoma herbarum, and Rhizoctonia solani. The number of rhizo bacteria and the number that inhibited fungi differed depending on sampling sites and isolation methods. Rhizobacteria isolated from the site in Yanshan and Maguan showed more antagonistic effect than them in Wenshan. Heat treatment of rhizosphere soil at $80^{\circ}C$ for 20 min scaled the antagonists up to 14.0%. Antagonistic bacteria in the roots proportioned 3.9% of the total isolates. The most antagonistic isolates 79-9 and 81-4 are Bacillus subtilis based on their 168 rDNA sequence and biochemical and physiological characteristics. Identification and evaluation of antagonistic bacteria against P. notoginseng root-rot pathogens in the main planting areas improved our understanding of their distribution in rhizosphere soil. Furthermore these results indicated that the interactions between biocontrol agent and soil microbes should be seriously considered for the successful survival and biocontrol efficacy of the agents in soil.

• Journal of Soil and Groundwater Environment
• /
• v.25 no.2_spc
• /
• pp.86-100
• /
• 2020

Analyzing and monitoring environmental contaminants based on geophysical exploration techniques have become important and it is now widely applied to delineate spatial distribution geophysical characteristics in wide area. Among the techniques, induced polarization (IP) method, which measures polarization effects on electrical potential distribution, has drawn much attention as an effective tool for environmental monitoring since IP is sensitive to changes in biochemical reactions. However, various reactions stemming from the presence of multiple contaminants have greatly enhanced heterogeneity of polluted sites to result in highly variable electrical characteristics of the site. Those contaminants influence chemical and physical state of soil and groundwater to alter electrical double layer, which in turn influences polarization of the media. Since biochemical reactions between microbes and contaminants result in various IP effects, IP laboratory experiments were conducted to investigate IP responses of the contaminated soil samples under various conditions. Field IP surveys can delineate the spatial distribution of contamination, while providing additional information about electrical properties of a target medium, together with DC resistivity. Reviewing IP effects of contaminants as well as IP surveys can serve as a good starting point for the application of IP survey in site assessment for environmental remediation.

• Genomics & Informatics
• /
• v.10 no.4
• /
• pp.249-255
• /
• 2012

In this study, fosmid cloning strategies were used to assess the microbial populations in water from the International Space Station (ISS) drinking water system (henceforth referred to as Prebiocide and Tank A water samples). The goals of this study were: to compare the sensitivity of the fosmid cloning strategy with that of traditional culture-based and 16S rRNA-based approaches and to detect the widest possible spectrum of microbial populations during the water purification process. Initially, microbes could not be cultivated, and conventional PCR failed to amplify 16S rDNA fragments from these low biomass samples. Therefore, randomly primed rolling-circle amplification was used to amplify any DNA that might be present in the samples, followed by size selection by using pulsed-field gel electrophoresis. The amplified high-molecular- weight DNA from both samples was cloned into fosmid vectors. Several hundred clones were randomly selected for sequencing, followed by Blastn/Blastx searches. Sequences encoding specific genes from Burkholderia, a species abundant in the soil and groundwater, were found in both samples. Bradyrhizobium and Mesorhizobium, which belong to rhizobia, a large community of nitrogen fixers often found in association with plant roots, were present in the Prebiocide samples. Ralstonia, which is prevalent in soils with a high heavy metal content, was detected in the Tank A samples. The detection of many unidentified sequences suggests the presence of potentially novel microbial fingerprints. The bacterial diversity detected in this pilot study using a fosmid vector approach was higher than that detected by conventional 16S rRNA gene sequencing.

• The Plant Pathology Journal
• /
• v.28 no.1
• /
• pp.68-74
• /
• 2012

Biocontrol microbes have mainly been screened among large collections of microorganisms $via.$ nutrient-rich $in$ $vitro$ assays to identify novel and effective isolates. However, thus far, isolates from only a few genera, mainly spore-forming bacilli, have been commercially developed. In order to isolate field-effective biocontrol microbes, we screened for more than 200 oligotrophic bacterial strains, isolated from rhizospheres of various soil samples in Korea, which induced systemic resistance against the soft-rot disease caused by $Pectobacterium$ $carotovorum$ SCC1; we subsequently conducted in $planta$ bioassay screening. Two oligotrophic bacterial strains were selected for induced systemic disease resistance against the $Tobacco$ $Mosaic$ $Virus$ and the gray mold disease caused by $Botrytis$ $cinerea$. The oligotrophic bacterial strains were identified as $Pseudomonas$ $manteilii$ B001 and $Bacillus$ $cereus$ C003 by biochemical analysis and the phylogenetic analysis of the 16S rRNA sequence. These bacterial strains did not exhibit any antifungal activities against plant pathogenic fungi but evidenced several other beneficial biocontrol traits, including phosphate solubilization and gelatin utilization. Collectively, our results indicate that the isolated oligotrophic bacterial strains possessing induced systemic disease resistance could provide useful tools as effective biopesticides and might be successfully used as cost-effective and preventive biocontrol agents in the field.

• Journal of Animal Science and Technology
• /
• v.51 no.5
• /
• pp.427-432
• /
• 2009

This study was undertaken to screen a high xylanase and mannanase producing microbes. In the first experiment, screening was undertaken against 50 samples of microorganisms having xylanase and mannanase activities from soil and fallen leaves. The screening process has focused on picking out fungi having high xylanase and mannanase activities under the solid-state fermentation. The xylanase and mannanase activities of 6 screened microbes were 0.9~1.6 unit/mL and 0.2~0.4 unit/mL, respectively, under the submerged fermentation condition. However, under the solid-state fermentation, xylanase and mannanase activities were 103.7~220.0 unit/g and 20.1~40.3 unit/g, respectively. Finally one microbe (E-3) was selected and its xylanase and mannanase activities were 197.3 unit/g and 39.9 unit/g, respectively. The morphological and molecular biological classification of E-3 showed 99% homology with the Aspergillus niger.

• Journal of Korean Society on Water Environment
• /
• v.22 no.6
• /
• pp.1031-1037
• /
• 2006

In order to improve water quality of the Juam Lake, a constructed wetland was implemented and operated for 2 years with the effluent of sewage treatment plant and diffuse pollutant discharged from agricultural area. During the summer season, average removal efficiencies for BOD and SS were 15.8% and 39.4%, respectively. Due to the mixed effect of vegetation, soil microbes and sediments, the higher nutrient removal efficiencies were obtained: average T-N and T-P removal efficiencies were 64.2% and 71.7%, respectively. The concentration of sediment was increased initially, and maintained constant throughout monitoring period. The highest nitrogen and phosphorus uptake were observed in Phragmites japonica. The nitrogen uptake was estimated as 0.235 DW mg/g while phosphorus uptake was estimated as 2.059 DW mg/g.