• Research in Plant Disease
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• v.23 no.3
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• pp.212-227
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• 2017

Pseudomonas chlororaphis O6, isolated from the roots of dryland, field-grown commercial wheat in the USA, enhances plant health and therefore it is used in agriculture as a biofertilizer and biocontrol agent. The metabolites produced by this pseudomonad stimulate plant growth through direct antagonism of pathogens and by inducing systemic resistance in the plant. Studies upon P. chlororaphis O6 identify the pathways through which defined bacterial metabolites generate protection against pathogenic microbes, insects, and nematodes. P. chlororaphis O6 also triggers plant resistance to drought and salinity stresses. The beneficial determinants are produced from bacterial cells as they form biofilms during root colonization. Molecular control these processes in P. chlororaphis O6 involves the global regulatory Gac/Rsm signaling cascade with cross-talk between other global regulatory pathways. The Gac/Rsm regulon allows for coordinate phasing of expression of the genes that encode these beneficial traits among a community of cells. This review provides insights on the Gac/Rsm regulon in expression of beneficial traits of the P. chlororaphis O6 which can contribute to help yield enhancement and quality in agricultural production.

• Journal of Korean Society of Water and Wastewater
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• v.24 no.6
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• pp.723-734
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• 2010

With a belief of high water quality production and less chemical usage, membrane technology including Microfiltration (MF), Ultrafiltration (UF), and Nanofiltration(NF) is being employed more and more in drinking water treatment process. However, due to higher energy consumption of UF and NF, MF is normally used for drinking water treatment especially in a plant of large scale. In this investigation, performance ofsand filtration and membrane filtration was compared regarding removal of various water quality parameters, such as TOC, DOC, KMnO4 consumption, THMFP, and HAAFP. Two lines of pilot plant have been operated, one of which line is a traditional advanced water treatment process which includes sedimentation, sand filtration, ozonation, and activated carbon, and the other line is an alternative treatment process which includes sedimentation with inclined plate, MF membrane, ozonation, and activated carbon. For the first about 4months of period, MF filtration showed similar or little bit higher performance than sand filtration. However, after about 4month later, sand filtration showed much higher performance in removing all parameters monitored in the investigation. It was found that sand filtration is a better option than MF filtration as far as microbial community is fully activated in sand filter bed.

• Journal of Ecology and Environment
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• v.33 no.4
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• pp.317-323
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• 2010

Nutrient availability is a critical component of agroecosystems, and is relevant to both above- and below- ground interactions. The principal objective of this study was to determine how the cessation of fertilization affects the communities of weeds and soil organisms in a corn/wheat field. Changes in dominant weed species, substrate-induced respiration, and the population density of nematodes and microarthropods were evaluated. Microbial substrate-induced respiration (SIR) and the population density of microarthropods decreased following the cessation of fertilization and were partly correlated with the aboveground weed biomass. The cessation of organic fertilizer application but continuing application of inorganic fertilizer reduced the population density of nematodes. In response to the cessation of fertilization, weed communities were dominated by species with little dependency on fertilization. Amaranthus retroflexus was identified as the most dominant species in the corn field; however, it was replaced by Digitaria ciliaris after the cessation of fertilization. In the wheat field, the cessation of fertilization led to a rapid reduction in the biomass of most weeds, except for Vicia angustifolia, supposedly as the result of symbiotic nitrogen fixation. Additionally, the fact that weed biomass was partially correlated with SIR or the population density of microarthropods may reflect a mutual feedback between soil organisms and weeds. The results indicate that the cessation of fertilization alters communities of weeds and soil organisms through changes in weed biomass and interactions with symbiotic microorganisms.

• Journal of Environmental Science International
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• v.25 no.4
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• pp.525-534
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• 2016

The biological wastewater treatment plant, which uses microbial community to remove organic matter and nutrients in wastewater, is known as its nonlinear behavior and uncertainty to operate. Therefore, operation of the biological wastewater treatment process much depends on observation and knowledge of operators. The manual inspection of human operators is essential to manage the process properly, however, it is impossible to detect a fault promptly so that the process can be exposed to improper condition not securing safe effluent quality. Among various process faults, equipment malfunction is critical to maintain normal operational state. To detect equipment faults automatically, the dynamic time warping was tested using on-line oxidation-reduction potential (ORP) and dissolved oxygen (DO) profiles in a sequencing batch reactor (SBR), which is a type of wastewater treatment process. After one cycle profiles of ORP and DO were measured and stored, they were warped to the template profiles which were prepared already and the distance result, accumulated distance (D) values were calculated. If the D values were increased significantly, some kinds of faults could be detected and an alarm could be sent to the operator. By this way, it seems to be possible to make an early detecting of process faults.

• Journal of Periodontal and Implant Science
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• v.46 no.3
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• pp.136-151
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• 2016

Peri-implant disease is a serious problem that plagues today's dentistry, both in terms of therapy and epidemiology. With the expansion of the practice of implantology and an increasing number of implants placed annually, the frequency of peri-implant disease has greatly expanded. Its clinical manifestations, in the absence of a globally established classification, are peri-implant mucositis and peri-implantitis, the counterparts of gingivitis and periodontitis, respectively. However, many doubts remain about its features. Official diagnostic criteria, globally recognized by the dental community, have not yet been introduced. The latest studies using metagenomic methods are casting doubt on the assumption of microbial equivalence between periodontal and peri-implant crevices. Research on most of the features of peri-implant disease remains at an early stage; moreover, there is not a commonly accepted treatment for it. In any case, although the evidence so far collected is limited, we need to be aware of the current state of the science regarding this topic to better understand and ultimately prevent this disease.

• The Korean Journal of Food And Nutrition
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• v.23 no.1
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• pp.84-87
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• 2010

Effects of gamma irradiation on microbiological changes of Gorosoe sap were characterized during a post-irradiation storage at $4^{\circ}C$. The aseptically collected sap was irradiated and stored at $4^{\circ}C$ for 0 to 60 days and analysed for standard plate counts and 16S rDNA. There were significant differences in the total number of colony forming units(CFUs) of bacteria between irradiated and non-irradiated control sap. Bacteria of non-irradiated sap were present at levels of $1.5{\times}10^4{\sim}2.3{\times}10^8\;CFU/m{\ell}$, whereas no viable microbial cells were detected in sap after 10 kGy of irradiation during storage. According to the 16S rDNA sequence analysis, bacterial community structures decrease with time and the most abundant strain was Pseudomonas species. Our results suggested that gamma irradiation can be used to enhance the shelf-life of Gorosoe sap.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.81-85
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• 2002

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. At the dendrogram based on cellular fatty acid composition, four clusters(I-IV) were separated at a euclidian distance of about 50. Based on the 16S rDNA sequence analysis, the two representative strains(MH256 and MA828) of cluster 3 showed the close relation to genera, Xathomonas/Stenotrophomonas, but were not included in these genera. 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. We attempted to screening of bioactive compounds from oligotrophs which was isolated from forest soil. The active compounds were analyzed by mass and NMR spectrum, one of them identified as crisamicin A. Another one designated as SAPH is a new compound. The results indicate that there were possibilities for finding new compounds from the rare microorganisms such as oligotrophs.

• Mycobiology
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• v.45 no.3
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• pp.150-159
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• 2017

This study analyzed the distribution of endophytic fungi in 3 coastal environments with different climatic, geographical, and geological characteristics: the volcanic islands of Dokdo, the East Sea, and the West Sea of Korea. The isolated fungal endophytes were characterized and analyzed with respect to the characteristics of their host environments. For this purpose, we selected common native coastal halophyte communities from three regions. Molecular identification of the fungal endophytes showed clear differences among the sampling sites and halophyte host species. Isolates were also characterized by growth at specific salinities or pH gradients, with reference to previous geographical, geological, and climate studies. Unlike the East Sea or West Sea isolates, some Dokdo Islands isolates showed endurable traits with growth in high salinity, and many showed growth under extremely alkaline conditions. A smaller proportion of West Sea coast isolates tolerate compared to the East Sea or Dokdo Islands isolates. These results suggest that these unique fungal biota developed through a close interaction between the host halophyte and their environment, even within the same halophyte species. Therefore, this study proposes the application of specific fungal resources for restoring sand dunes and salt-damaged agricultural lands and industrialization of halophytic plants.

• Journal of Microbiology and Biotechnology
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• v.24 no.1
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• pp.113-118
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• 2014

Environmental microorganisms are emerging as an important source of new enzymes for wide-scale industrial application. In this study, novel phytase genes were identified from a soil microbial community. For this, a function-based screening approach was utilized for the identification of phytase activity in a metagenomic library derived from an agricultural soil. Two novel phytases were identified. Interestingly, one of these phytases is an unusual histidine acid phosphatase family phytase, as the conserved motif of the active site of PhyX possesses an additional amino acid residue. The second phytase belongs to a new type, which is encoded by multiple open reading frames (ORFs) and is different to all phytases known to date, which are encoded by a single ORF.