• The Plant Pathology Journal
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• v.35 no.6
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• pp.654-661
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• 2019

The soybean cyst nematode, Heterodera glycines, is a major plant-parasitic nematode that has caused important economic losses to Korea's soybean production. Four species of cyst nematodes, H. schachtii, H. glycines, H. trifolii, and H. sojae, all belong to schachtii group are coexist in field soil in Korea. The rapid identification of the nematode is crucial for preventing crop damage and in decision making for controlling this nematode. This study aimed to develop a species-specific primer set for quantitative PCR (qPCR) assay of H. glycines. The specific primer set (HGF1 and HGR1) for H. glycines was designed based on the cytochrome c oxidase subunit I (COI) sequence of mitochondrial DNA. After optimization, it is possible to identify the H. glycines using a qPCR assay with DNA extracted from a single cyst and single second-stage juvenile (J2). The specificity was confirmed by the absence of SYBR fluorescent signals of three other Heterodera species. A serial dilution of DNA extracted from a single cyst was obtained for the sensitivity test. The result showed that the standard curve of the test had a highly significant linearity between DNA concentration and Ct value (R² = 0.996, slope = -3.49) and that the detection limit concentration of DNA of the primer set was 10 pg of DNA per reaction. Our findings suggested that H. glycines could be distinguished from H. sojae and other Heterodera species when a qPCR assay is used with a specific primer set.

• Microbiology and Biotechnology Letters
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• v.34 no.2
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• pp.101-108
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• 2006

YNB54 strain which shows inhibitory activities specific to the plant pathogenic Phytophthora sp. on potato dextrose agar medium was screened among lots of strains isolated from Korean soils. To identify taxonomy of the Phytophthora specific antagonistic bacteria YNB54, 165 rDNA sequence, MIDI fatty acid composition, DNA-DNA hybridization, GC content, and commercial multitest systems such as API 20E and Biolog GN were performed. Results of commercial kits including lots of biochemical and physiological reactions showed that this strain was closely related to taxa including Enterobacter cloacae and Enterobacter cancerogenus species than other genera(Citerobacter Klebsiella, Leclercia). Also, analysis of its MIDI, G+C contents, and DNA-DNA hybridization suggests that this strain was more similiar to the Genus Enterobacter than other genera (Citerobacter Klebsiella, Leclercia). This strain was potentially identified as Enterobacter sp. by these results. But our 16S ribosomal DNA sequences (rDNA) analysis confirmed that it was more closely related to the cluster of Citerobacter freundii ATCC 29935 than any other Enterobacter species. In the absence of defined phylogenetic critia for delineating genera, the results observed with Citrobacter and Enterobacter species suggest that further studies are needed to clarify their relationships. This investigation demonstrates that YNB54 strain is genetically diverse and potentially more taxonomically complex than hitherto realized. Further study is necessary to confirm their taxonomic positions.

• Journal of Ecology and Environment
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• v.31 no.2
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• pp.131-137
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• 2008

This study investigated the population densities and diversity of heterotrophic bacteria, and the rhizosphere-to-soil ratios (R/S) in the rhizosphere soil of halophyte Phragmites communis at the western coastal mudflats of Korea. The population densities of aerobic heterotrophic bacteria on the rhizosphere soil of P. communis were in the range of $3.3\;{\pm}\;0.9\;{\times}\;10^7\;{\sim}\;1.2\;{\pm}\;0.5\;{\times}\;10^8\;cfu\;g^{-1}$ dry weight (d. wt.). Population densities of amylolytic bacteria ranged from $1.1\;{\pm}\;0.2\;{\times}\;10^6$ to $3.0\;{\pm}\;1.2\;{\times}\;10^6\;cfu\;g^{-1}\;d.\;wt.$, while those of cellulolytic bacteria and proteolytic bacteria ranged from $5.6\;{\pm}\;2.3\;{\times}\;10^6$ to $1.5\;{\pm}\;0.3\;{\times}\;10^7\;cfu\;g^{-1}\;d.\;wt.$ and from $1.4\;{\pm}\;0.3\;{\times}\;10^6$ to $3.5\;{\pm}\;2.3\;{\times}\;10^7 \;cfu\;g^{-1}\;d.\;wt.$, respectively. The R/S ratios ranged from 2.26 to 6.89. Genetic (16S DNA) analysis of fifty-one isolates from the roots of P. communis suggested that the dominant species were closely related to the ${\gamma}$-proteobacteria group (18 clones) and the ${\alpha}$-proteobacteria group (14 clones). We found that halophyte species and mudflat environment both affected the rhizosphere bacterial communities.

• Journal of Life Science
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• v.16 no.2 s.75
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• pp.360-364
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• 2006

Fibrin clots of blood vessels are one of the serious factor caused cardiovascular disease. The development of a antithrombotic and thrombolysis solvent is necessary to prevent and treat these diseases. It has been reported that a strong fibrin-specific fibrinolytic enzyme was produced from a Korean fermented soybean paste similar to Japanese miso. We have been screened the known or novel fibrinolytic enzymes by activity-based and sequence-based screening from soil DNA metagenome library containing all kinds of environmental genomic DNA. The activity-based screening was determined the protease activity on 0.5% skim milk. For sequence-based screening, we designed a set of primer expanding gene sequence of fibrinolytic enzyme, performed PCR and selected clones showing the expected size of amplicons from metagenome library. Transformation of the gene encoding fibrinolytic enzyme was carried out with commercial vectors and their transformants were selected. Finally, we found 15 positive clones from metagenome library. Then each of sequences were analyzed and identified as similar or known the clones of nattokinase. We are going to perform full sequence of each clones, ligate with expression vector, transform into competent cells and then determine activity of expressed enzymes.

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.169-178
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• 2010

The microbial community structure in Thailand soils contaminated with low and high levels of arsenic was determined by denaturing gradient gel electrophoresis. Band pattern analysis indicated that the bacterial community was not significantly different in the two soils. Phylogenetic analysis obtained by excising and sequencing six bands indicated that the soils were dominated by Arthrobacter koreensis and $\beta$-Proteobacteria. Two hundred and sixty-two bacterial isolates were obtained from arsenic-contaminated soils. The majority of the As-resistant isolates were Gramnegative bacteria. MIC studies indicated that all of the tested bacteria had greater resistance to arsenate than arsenite. Some strains were capable of growing in medium containing up to 1,500 mg/l arsenite and arsenate. Correlations analysis of resistance patterns of arsenite resistance indicated that the isolated bacteria could be categorized into 13 groups, with a maximum similarity value of 100%. All strains were also evaluated for resistance to eight antibiotics. The antibiotic resistance patterns divided the strains into 100 unique groups, indicating that the strains were very diverse. Isolates from each antibiotic resistance group were characterized in more detail by using the repetitive extragenic palindromic-PCR (rep-PCR) DNA fingerprinting technique with ERIC primers. The PCR products were analyzed by agarose gel electrophoresis. The genetic relatedness of 100 bacterial fingerprints, determined by using the Pearson product-moment similarity coefficient, showed that the isolates could be divided into four clusters, with similarity values ranging from 5-99%. Although many isolates were genetically diverse, others were clonal in nature. Additionally, the arsenic-resistant isolates were examined for the presence of arsenic resistance (ars) genes by using PCR, and 30% of the isolates were found to carry an arsenate reductase encoded by the arsC gene.

• Journal of Microbiology and Biotechnology
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• v.16 no.5
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• pp.704-715
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• 2006

Oil spill was found in 1999 from a diesel storage facility located near the top of Baekun Mountain in Uiwang City. Application of bioremediation techniques was very relevant in removing oil spills in this site, because the geological condition was not amenable for other onsite remediation techniques. For efficient bioremediation, bacterial communities of the contaminated site and the uncontaminated control site were compared using both molecular and cultivation techniques. Soil bacterial populations were observed to be stimulated to grow in the soils contaminated with diesel hydrocarbon, whereas fungal and actinomycetes populations were decreased by diesel contamination. Most of the dieseldegrading bacteria isolated from contaminated forest soils were strains of Pseudomonas, Ralstonia, and Rhodococcus species. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that the profiles were different among the three contaminated sites, whereas those of the control sites were identical to each other. Analysis of 16S rDNA sequences of dominant isolates and clones showed that the bacterial community was less diverse in the oil-contaminated site than at the control site. Sequence analysis of the alkane hydroxylase genes cloned from soil microbial DNAs indicated that their diversity and distribution were different between the contaminated site and the control site. The results indicated that diesel contamination exerted a strong selection on the indigenous microbial community in the contaminated site, leading to predominance of well-adapted microorganisms in concurrence with decrease of microbial diversity.

• Korean Journal of Environmental Agriculture
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• v.29 no.4
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• pp.388-395
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• 2010

In order to decrease level of an organophosphorus fungicide, tolclofos-methyl, from in situ ginseng cultivating soil, we isolated a tolclofos-methyl degrading bacteria from ginseng cultivating soil samples. The bacterial strain removed tolclofos-methyl around 95% after 3 days incubation with complete liquid media. The strain was identified as Sphingomonas sp. by 16S rDNA sequence comparison, and designated as Sphingomonas sp. 224. Through the GC-MS analysis, Sphingomonas sp. 224 was proposed to have an initiative degradation pathway generating the metabolite such as 2,6-dichloro-4-methyl phenol compound from tolclofos-methyl. In addition, Sphingomonas sp. 224 was confirmed representing the effective degrading capability to tolclofosmethyl in situ soil.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2000.04a
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• pp.150-156
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• 2000

Oligotrophic bacteria isolated from forest soil showed a specific community consisting of various taxonomic groups compared with those in other soil or aquatic habitats. Based on the cell shape, the isolates were divided into four groups: regular rod, curved/spiral rod, irregular rod, and prosthecate bacteria. The cellular fatty acids 60 oligotrophic isolates were analyzed. The 30 fatty acids which were identified or characterized are classified. At the dendrogram based on cellular fatty acid composition, four clusters(I-IV) were separated at a euclidian distance of about 50. Cluster 3 and 4-a strains were containing Q-8, these strains are accommodated in the Proteobacteria gamma and beta subdivision. The chemotaxonomic profiles of the cluster 4-a strains showed good agreement with those of the genus Burkholderia. Cluster 3 was characterized by the presence of branched-chain fatty acids, iso-C15:0, iso-C17:1, and iso-C17:0 as the major components. These chemotaxonomy suggested the close relationship of the isolates with Xathomonas/Sterotrophomonas group. Based on the 16S rDNA sequence analysis, the two representative strains(MH256 and MA828) of cluster 3 showed the close relation to genera, Xathomonas/Sterotrophomonas, but were not included in these genera. These strains were even further away from core Xanthomonas, and clearly were seen to branch outside the cluster formed by the Sterotrophomonas maltophilia. MH256 and MA828 16S rDNA sequence was different enough to put new genus on a separate branch. The isolates with Q-10 were also studied. They are corresponded to the two large groups in Proteobacteria alpha subdivision. One was incorporated in the genus Bradyrhizobium cluster, which also includes Agromonas, a genus for oligotrophic bacteria. The strains of the other group showed high similarity to the genus Agrobacterium.

• Journal of Ecology and Environment
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• v.29 no.4
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• pp.399-404
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• 2006

This study was carried out to investigate the population densities, R/S ratios, and identification of heterotrophic bacteria on the rhizosphere soil of halophyte Suaeda japonica found on the western and southern mudflats of Korea. The population densities of aerobic and anaerobic heterotrophic bacteria on the rhizosphere soil of Suaeda japonica were in the range of $1.3\;{\pm}\;0.3\;{\times}\;10^6\;{\sim}\;6.3\;{\pm}\;3.3\;{\times}\;10^7\;and\;2.8\;{\pm}\;1.3\;{\times}\;10^4\;{\sim}\;1.8\;{\pm}\;0.7\;{\times}\;10^7\;cfu\;g^{-1}\;d.\;wt.$, respectively. In case of physiologically specific bacteria, population densities of amylolytic bacteria on the rhizosphere soil of Suaeda japonica were in the range of $4.4\;{\pm}\;0.6\;{\times}\;10^6\;{\sim}\;2.5\;{\pm}\;1.2\;{\times}\;10^7\;cfu\;g^{-1}\;d.\;wt.$, those of cellulolytic bacteria were from $8.5\;{\pm}\;6.0\;{\times}\;10^4\;{\sim}\;2.3\;{\pm}\;1.6\;{\times}\;10^6\;cfu\;g^{-1}\;d.\;wt.$, and those of proteolytic bacteria were from $3.8\;{\pm}\;1.8\;{\times}\;10^5\;{\sim}\;4.2\;{\pm}\;2.9\;{\times}\;10^6\;cfu\;g^{-1}\;d.\;wt.$, respectively. The R/S ratios were ranged from 2.33 to 2.39. Among eleven isolates from the roots of halophyte Suaeda japonica of Goheung bay by using 16S rDNA analysis, five clones were closely related to ${\gamma}-Proteobacteria$ group and six clones were closely related to ${\alpha}-Proteobacteria$ group. Among four isolates from Suncheon bay, two strains were related to ${\gamma}-Proteobacteria$ group and another two were related to Actinobacteria and Bacilli group, respectively.

• Journal of Mushroom
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• v.21 no.4
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• pp.228-240
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• 2023

To understand microorganism effects on wild mushroom fruiting bodies, we investigated the fungi in hyphosphere soil supporting wild mushroom species Cortinarius violaceus, Amanita hemibapha, Laccaria vinacelavellanea, and Amanita verna found in the Gotjawal area of Jeju Island. Fungal species identification based on morphological traits and molecular analysis of ITS, LSU rDNA, and β-tubulin gene sequences resulted in isolation and identification of eleven fungal species previously unrecorded in Korea. These newly-recorded species are: Arthrinium kogelbergensis, Kalmusia longisporum, Keithomyces carneum, Neopyrenochaeta cercidis, Penicillium ranomafanaense, Phomatodes nebulosa, Pyrenochaeta nobilis, Tolypocladium album, Talaromyces kendrickii, Talaromyces qii, and Umbelopsis gibberispora, and their morphological characteristics and phylogenetic positions are described.