• Korean Journal of Microbiology
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• v.51 no.4
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• pp.347-354
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• 2015

Soybean is well known to be originated from Korea and far-east Asian countries, and studies of many root nodule bacteria associated with soybean have mainly-focused on nitrogen fixation, but much less study was carried out on bacterial community in the rhizosphere of soybean. In this study, we analyzed the bacterial community in rhizosphere of Korean soybean, Daepungkong using the pyrosequencing method based on the 16S rRNA gene to characterize the change of the rhizosphere community structure according to the growth stages of soybeans and to elucidate bacterial core community in rhizosphere of soybean. Our results revealed that bacterial community of rhizosphere soil differed from that of bulk soil and was composed of a total of 21 bacterial phyla. The predominant phylum in the rhizosphere of soybean was Proteobacteria (36.6-42.5%) and followed by Acidobacteria (8.6-9.4%), Bacteroidetes (6.1-10.9%), Actinobacteria (6.4-9.8%), and Firmicutes (5.7-6.3%). The bacterial core community in soybean rhizosphere was mainly composed of the operational taxonomic units (OTUs) belonging to the phylum Proteobacteria throughout all growth stages. The OTU00006 belonged to the genus Bradyrhizobium had the highest abundance and Steroidobacter, Streptomyces, Devosia were followed. These results show that bacterial core community in soybean rhizosphere was mainly composed of OTUs associated with plant growth promotion and nutrient cycles.

• Journal of Korean Society of Forest Science
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• v.106 no.2
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• pp.121-129
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• 2017

The soil microbiome plays important roles in material cycling and plant growth in forest ecosystem. Although a lot of researches on forest soil fungi in Korea have been performed, the studies on forest soil bacterial communities have been limited. In this study, we conducted next generation sequencing (NGS) targeting 16S rRNA gene to investigate the soil bacterial communities from natural red pine (Pinus densiflora) forest in Mt. Janggunbong, Bonghwa-gun, Gyeongbuk, Korea. Our results showed that the entire bacterial communities in the study sites include the phyla Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, which have been typically observed in forest soils. The composition ratio of Proteobacteria was the highest in the soil bacteria community. The results reflect that Proteobacteria is copiotroph, which generally favors relatively nutrient-rich conditions with abundant organic matter. Some rhizobia species such as Burkholderia, Bradyrhizobium, Rhizobium, which are known to contribute to soil nitrogen-fixation, exist in the study sites. As a result of correlation analysis between soil physicochemical characteristics and bacteria communities, the soil pH was significantly correlated with the soil bacteria compositions.

• Applied Biological Chemistry
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• v.40 no.2
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• pp.134-138
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• 1997

The objective of this study was to examine the effect of phosphorus deficiency on nitrogen fixation and photosynthesis of nitrogen fixing soybean plant under $CO_2$ enrichment condition. The soybean plants(Glycine max [L.] Merr.) inoculated with Bradyrhizobium japonicum MN 110 were grown with P-stressed(0.05 mM-P) and control(1 mM-P) treatment under control$(400\;{\mu}l/L\;CO_2)$ and enrichment$(800\;{\mu}l/L\;CO_2)$ enviromental condition in the phytotron equipped with high density lamp$(1000\;{\mu}Em^{-2}S^{-1})$ and $28/22^{\circ}C$ temperature cycle for 35 days after transplanting(DAT). At 35 DAT, phosphorus deficiency decreased total dry mass by 64% in $CO_2$ enrichment condition, and 51% in control $CO_2$ condition. Total leaf area was reduced significantly by phosphorus deficiency in control and enriched $CO_2$ condition but specific leaf weight was increased by P deficiency. Phosphorus deficiency significantly reduced photosynthetic rate(carbon exchange rate) and internal $CO_2$ concentration in leaf in both $CO_2$ treatments, but the degree of stress was more severe under $CO_2$ enrichment condition than under control $CO_2$ environmental condition. In phosphorus sufficient plants, $CO_2$ enrichment increased nodule fresh weight and total nitrogenase activity(acetylene reduction) of nodule by 30% and 41% respectively, but specific nitrogenase activity of nodule and nodule fresh weight was not affected by $CO_2$ enrichment in phosphorus deficient plant at 35 DAT. Total nitrogen concentrations in stem, root and nodule tissue were significantly higher in phosphorus sufficient plant grown under $CO_2$ enrichment, but nitrogen concentration in leaf was reduced by 30% under $CO_2$ enrichment. These results indicate that increasing $CO_2$ concentration does not affect plant growth under phosphorus deficient condition and phosphorus stress might inhibit carbohydrate utilization in whole plant and that $CO_2$ enrichment could not increase nodule formation and functioning under phosphorus deficient conditions and phosphorus has more important roles in nodule growth and functioning under $CO_2$ enrichment environments than under ambient condition.

• Korean Journal of Weed Science
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• v.31 no.4
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• pp.323-329
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• 2011

We investigated photodynamic stress-induced antioxidant responses in transgenic rice overexpressing Bradyrhizobium japonicum 5-aminolevulinic acid synthase (ALA-S) coding sequence lacking plastidal transit sequence. High light of $350{\mu}mol\;m^{-2}\;s^{-1}$ decreased the quantum yield in the transgenic lines, C4 and C5, compared to that of wild-type line. By contrast, non-photochemical quenching (NPQ) levels of C4 and C5 under high light were higher than those of the transgenic lines under low light of $150{\mu}mol\;m^{-2}\;s^{-1}$ as well as wild-type line under low and high light. Greater levels of NPQ in the transgenic lines exposed to high light were in a close correlation with increases in the xanthophyll pigment, zeaxanthin. Under high light, levels of neoxanthin, violaxanthin, lutein, and ${\beta}$-carotene in the transgenic lines were lower than those in wild-type line. Taken together, nonphotochemical energy dissipation and photoprotectant xanthophyll pigments play a critical role to deal with the severe photodynamic damage in the transgenic rice plants, although they could not overcome the photodynamic stress, leading to severe photobleaching symptoms.

• Journal of Life Science
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• v.29 no.1
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• pp.123-128
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• 2019

The use of 16S rDNA is commonplace in the determination of prokaryotic species. However, it has limitations, and there are few studies at the genus level. We investigated conserved genes and metabolic pathways at the genus level in 28 strains of 13 genera of prokaryotes using the COG database (conserved genes) and MetaCyc database (metabolic pathways). Conserved genes compared to total genes (core genome) at the genus level ranged from 27.62%(Nostoc genus) to 71.76%(Spiribacter genus), with an average of 46.72%. The lower ratio of core genome meant the higher ratio of peculiar genes of a prokaryote, namely specific biological activities or the habitat may be varied. The ratio of common metabolic pathways at the genus level was higher than the ratio of core genomes, from 58.79% (Clostridium genus) to 96.31%(Mycoplasma genus), with an average of 75.86%. When compared among other genera, members of the same genus were positioned in the closest nodes to each other. Interestingly, Bacillus and Clostridium genera were positioned in closer nodes than those of the other genera. Archaebacterial genera were grouped together in the ortholog and metabolic pathway nodes in a phylogenetic tree. The genera Granulicella, Nostoc, and Bradyrhizobium of the Acidobacteria, Cyanobacteria, and Proteobacteria phyla, respectively, were grouped in an ortholog content tree. The results of this study can be used for (i) the identification of common genes and metabolic pathways at each phylogenetic level and (ii) the improvement of strains through horizontal gene transfer or site-directed mutagenesis.

• 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.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.51 no.4
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• pp.356-361
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• 2006

The present study was conducted to determine plant growth and physiological responses of corn, barnyardgrass, and soybean to ALA (5-aminolevulinic acid). ALA effect on early seedling growth of test plants was greatly concentration dependant, suggesting that it inhibits at higher concentrations. No significant difference in herbicidal activity of two types of ALA on plant height and weight of test plants was observed. Barnyardgrass was the most sensitive to ALA and followed by corn and soybean, indicating that both crop plants were less affected by ALA concentration as well as different growth stages than barnyardgrass. Greatly reduced chlorophyll contents from leaves of three plant species were observed with increasing of ALA concentration. Compared with untreated controls, higher amounts of three tetrapyrroles were detected from three crop plants, indicating more accumulation in ALA-treated plants. The differential selectivity among plant species would be explained with the differences in tetrapyrrole accumulating capabilities, the susceptibility of various greening groups of plant species to the accumulation of various tetrapyrroles, and their metabolism in various plant tissues. The results indicate that negative biological potential of ALA exhibited differently on plant species, and that the photodynamic herbicidal activity against susceptible plants highly correlated with the extent of tetrapyrrole accumulation by the species.

• Journal of Microbiology and Biotechnology
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• v.13 no.2
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• pp.243-250
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• 2003

Eight numerically dominant 4-(2,4-dichlorophenoxy) butyric acid (2,4-DB)-degrading bacteria and three pairs of bacteria showing syntrophic metabolism of 2,4-DB were isolated from soils, and their phylogenetic and phenotypic characteristics were investigated. The isolates were able to utilize 2,4-DB as a sole source of carbon and energy, and their 2.4-DB degradative enzymes were induced by the presence of 2.4-DB. Analysis of 16S rDNA sequences indicated that the isolates were related to members of the genera, Variovorax, Sphingomonas, Bradyrhizobium, and Pseudomonas. The chromosomal DNA patterns of the isolates obtained by polymerase-chain-reaction (PCR) amplification of repetitive extragenic palindromic (REP) sequences were distinct from each other. Four of the isolates had plasmids, but only one strain, DB 1, rad a transmissible 2,4-D degradative plasmid. When analyzed with PCR using primers targeted to the tfdA, B, and C genes, only strains DB2 and DB9a produced DNA bands of the expected sizes with the tfdA and C primers, respectively. All of the isolates were able to degrade 2,4-D as well as 2,4-DB, suggesting that the degradation pathways of these compounds were closely related to each other, but respiratory activities of many isolates adapted to 2,4-DB metabolism were quite low with 2,4-D.

• The Plant Pathology Journal
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• v.15 no.2
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• pp.127-130
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• 1999

Cytological changes of cowpea root at the early stage of root nodule formation (within 5 days after inoculation) were viewed by light and electron microscopy. The root region affected by the rhizobial infection, which was composed of a redial array of cortical cells, had prominent cell divisions, mostly anticlinal in the inner cortical cells and in addition oblique and periclinal in the outer cells. An infected root hair cell (or root hair-producing epidermal cell) had numerous infection threads and degenerated cytoplasm. Module meristem was formed adjacent to the infected root hair cell, and characterized by dense cytoplasm, prominent nucleus, numerous small vacuoles, and increased plastids, containing infection threads as well. Bacterial cells were dividing inside the infection thread, the wall materials of which appeared to be dissolved ad accumulated in small vacuoles. inner cortical cells contiguous to the nodule meristem appeared to be actively dividing and dedifferentiating; however, they were not infected by the rhizobia. These structural characteristics are similar to those in the Bradyrhizobium-soybean association previously reported, and may reflect the similar cytological process in cowpea in the early nodule formation.

• Microbiology and Biotechnology Letters
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• v.47 no.3
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• pp.423-433
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• 2019

Midgut microbiota is known to play a fundamental role in the biology and physiology of the agricultural pest, Spodoptera litura. This study reports the difference in the larval midgut microbiota of field-caught and laboratory-reared populations of S. litura by performing 16S rDNA amplicon pyrosequencing. Field populations for the study were collected from castor crops, whereas laboratory-reared larvae were fed on a regular chickpea based diet. In total, 23 bacterial phylotypes were observed from both laboratory-reared and field-caught caterpillars. Fisher's exact test with Storey's FDR multiple test correction demonstrated that bacterial genus, Clostridium was significantly abundant (p < 0.05) in field-caught larvae of S. litura as compared to that in the laboratory-reared larvae. Similarly, bacterial genera, such as Bradyrhizobium, Burkholderia, and Fibrisoma were identified (p < 0.05) predominantly in the laboratory-reared population. The Bray-Curtis dissimilarity matrix depicted a value of 0.986, which exhibited the maximum deviation between the midgut microbiota of the laboratory-reared and field-caught populations. No significant yeast diversity was seen in the laboratory-reared caterpillars. However, two yeast strains, namely Candida rugosa and Cyberlindnera fabianii were identified by PCR amplification and molecular cloning of the internal transcribed space region in the field-caught caterpillars. These results emphasize the differential colonization of gut residents based on environmental factors and diet.