• Korean Journal of Plant Taxonomy
• /
• v.42 no.3
• /
• pp.215-221
• /
• 2012

Five Korean Calanthe species, C. discolor, C. bicolor, C. sieboldii, C. reflexa, and C. aristulifera, were studied using amplified fragment length polymorphism (AFLP) to assess their taxonomic and genetic relationships. Sixteen accessions belonging to five native Calanthe spp. and mutants with yellow tepal and white lip (YW mutants) were studied. We identified 50 putative markers using AFLP analysis. The results of AMOVA showed that genetic variance was higher between species than within species. Genetic dissimilarity when compared with the rest of the species was the lowest for individuals of the YW mutants and the highest for individuals of C. reflexa. The mutants clustered outside the major group. Calanthe bicolor clustered with C. discolor, suggesting that its genetic composition is closer to that of C. discolor. Though it is suggested to have originated as a result of natural hybridization between C. sieboldii and C. discolor, introgression is likely to have occurred in the direction of C. discolor based on the data of molecular marker, clustering and genetic dissimilarity. Calanthe reflexa and C. aristulifera were genetically the most diverse of the species studied. In conclusion, the results showed that there is genetic diversity in Korean Calanthe species, that C. bicolor introgressed in the direction of C. discolor and that the YW mutants are genetically closer to C. sieboldii.

• Korean Journal of Environmental Biology
• /
• v.29 no.3
• /
• pp.212-224
• /
• 2011

The Yeongsan River estuary, located in the south west coast, was a typical estuary before a dike was constructed in December 1981. After the construction, the water quality and plankton communities are expected to change. We investigated the change of phytoplankton community and environmental properties in the Yeongsan River estuary by comparing the data collected recently with the results reported before and/or shortly after the construction. Concentrations of $NH_4$-N were significantly increased in the freshwater zone. Concentrations of DO at the surface, $NO_2+NO_3$ and $NH_4$-N were increased while the concentrations of $PO_4$ at the surface were decreased in the seawater zone. The number of green algae species was decreased in the freshwater zone. The number of diatom species was decreased while the numbers of green algae and dinoflagellates were increased in the seawater zone. This study can provide information for better management of the Yeongsan River estuary since no comparison study has been documented between the phytoplankton community before and after the construction of the dike in the estuary.

• Korean Journal of Soil Science and Fertilizer
• /
• v.20 no.1
• /
• pp.77-84
• /
• 1987

The population of actinomycetes in paddy soils, with hay compost and inorganic fertilizer had been applied respectively was investigated. Actinomycetes were isolated by using selective medium and the population densities of actinomycetes in paddy soil was examined. The population of actinomycetes were reached at a range from $2.1{\times}10^6$ to $7.4{\times}10^7$ per gram of the soil. The composition of actinomycetes flora changed considerably after hay compost applied. The significant positive correlations between the organic matter content in paddy soil and the actinomycetes populations were given at 1.38 to 2.69 level. According to the result of several morphological observation, similar strains isolated were classified into 21 groups. More detailed taxonomic characterization were carried out on the isolated strains. Therefore, 15 groups of Streptomyces and 6 groups of non-Streptomyces were classified into actinomycetes isolates, percentage of streptomyces and non-Streptomyces strains were 87.2% and 12.8% in the isolated 250 actinomycetes strains respectively. Streptomyces with sporophore of the spiral chain form accounted for 80% of all the Streptomyces isolates. Surface morphology of spores were determined with the electron microscope, three species have a spiny surface, and 13 strains have a smooth spore surface.

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

• Tuberculosis and Respiratory Diseases
• /
• v.79 no.3
• /
• pp.165-178
• /
• 2016

Background: Although recent metagenomic approaches have characterized the distinguished microbial compositions in airways of asthmatics, these results did not reach a consensus due to the small sample size, non-standardization of specimens and medication status. We conducted a metagenomics approach by using terminal restriction fragment length polymorphism (T-RFLP) analysis of the induced whole sputum representing both the cellular and fluid phases in a relative large number of steroid $na{\ddot{i}}ve$ asthmatics. Methods: Induced whole sputum samples obtained from 36 healthy subjects and 89 steroid-$na{\ddot{i}}ve$ asthma patients were analyzed through T-RFLP analysis. Results: In contrast to previous reports about microbiota in the asthmatic airways, the diversity of microbial composition was not significantly different between the controls and asthma patients (p=0.937). In an analysis of similarities, the global R-value showed a statistically significant difference but a very low separation (0.148, p=0.002). The dissimilarity in the bacterial communities between groups was 28.74%, and operational taxonomic units (OTUs) contributing to this difference were as follows: OTU 789 (Lachnospiraceae), 517 (Comamonadaceae, Acetobacteraceae, and Chloroplast), 633 (Prevotella), 645 (Actinobacteria and Propionibacterium acnes), 607 (Lactobacillus buchneri, Lactobacillus otakiensis, Lactobacillus sunkii, and Rhodobacteraceae), and 661 (Acinetobacter, Pseudomonas, and Leptotrichiaceae), and they were significantly more prevalent in the sputum of asthma patients than in the sputum of the controls. Conclusion: Before starting anti-asthmatic treatment, the microbiota in the whole sputum of patients with asthma showed a marginal difference from the microbiota in the whole sputum of the controls.

• Korean Journal of Plant Resources
• /
• v.27 no.5
• /
• pp.576-587
• /
• 2014

The purpose of this research is to classify various plants written in the Korean Buddhist scriptures and assign scientific name to them in accordance with the Hangul Tripitaca as standard scriptures, thereby establishing the foundation of the plants in Buddhist scriptures. As a natural resource, we also assessed the value of the plants written in the Buddhist scriptures that distributed from other countries. To this end, we inferred the route of introduction to Korea of the plants and investigated their function and usage. Taxonomic classification of the plants written in Buddhist scriptures identified a total of 331 taxa belonging to 107 families, 244 genera, 313 species, 1 subspecies, 16 varieties, 1 forms. Species composition of the 331 taxa of plants consisted of two taxa of pteridophyte, 15 taxa of gymnosperm, 261 taxa of dicotyledon, and 53 taxa of monocotyledon. Among them, 183 and 148 were woody and herbaceous plants, respectively. Analysis of the distribution of 331 kinds of plants that India's portion of origin of place is 8.9% which holds a low rank compared with those of Korea (10.5%), China (10.9%), and Japan (10.0%). This explains why many taxa of plants distributed from the three countries appeared in the Hangul Tripitaca. Accordingly, we hypothesized that the majority of the plants were added and replaced at some point in past while Buddhist scriptures were propagated from India to China and from China to Korea. Our analysis indicated that 119 out of the 331 taxa (36 %) were distributed from Korea.

• Korean Journal of Microbiology
• /
• v.37 no.4
• /
• pp.265-272
• /
• 2001

The diversity of acid-tolerant epiphytic bacterial communities on deciduous oak tree (Quercus dentate Thunb.) leaves was examined both in the natural forest area with a clean air and in the industrial estate to assess effects of acidic depositions to the phyllosphere using 16S rDNA sequence data. A total of 444 acid-tolerant epiphytic bacterial clones were obtained, resulting in 17 phylotypes by performing a analysis of restriction fragment length polymorphism (RFLP) for PCR-amplified 16S rDNA products. A very low diversity of dominating acid tolerant bacterial communities in both areas was found, just 2 subphyla groups, $\gamma$-Proteobacteria and low-G+C gram-positive bacteria. As tree leaves grow older, diversities of acid-tolerant bacteria on them significantly increased. The community structure of acid-tolerant epiphytic bacteria consisted of Pseudomonas and Enterobacteriaceae groups in the $\gamma$-Proteobacteria subphylum, and Streptococcaceae and Staphylococcus groups in the low-G+C gram-positive bacteria subphylum. The direct influence of acidic depositions on bacterial phylogenetic composition could not be detected especially when higher taxonomic levels such as subphylum, but at narrower or finer levels it could be observed by a detection of Xanthomonadales group belonged to the $\gamma$-Proteobacteria only in the industrial area and of Acetobacteraceae group belonged to the $\alpha$-Proteobacteria. There remains that these specific acid-tolerant epiphytic bacterial groups could be used as indicators for assessing effects of acidic depositions on the phyllosphere.

• Weed & Turfgrass Science
• /
• v.4 no.2
• /
• pp.124-128
• /
• 2015

Large patch, caused by Rhizoctonia solani AG2-2 IV, is a soil-born disease that is the most important of warm season turfgrass such as zoysia and Bermuda grass. This study was conducted to analysis of the soil microbial community structure on large patch. Center of the large patch (CLC), edge (CLE) and healthy (CLH) part of microbial communities were examined using metagenomics in Phylum level. Distribution trends of the rhizosphere microorganisms were similar to the order Proteobacteria, Acidobacteria, Chloroflexi, Firmicutes, Planctomycetes, Gemmatimonadetes, Nitrospira, Cyanobactria and Verrucomicrobia in soil collections. Contrastively Actinobacteria was more 56% abundant in healthy part soil (16%) than in the center (9.28%) or edge (10.84%) parts. Taxonomic distributions were compared among the CLC, CLE and CLH, total 6,948 OTUs were detected in the CLC, 6,505 OTUs for the CLE and 5,537 OTUs were detected in the CLE. Distributions of Actinobacteria OTUs were appeared 615 OTUs in the CLC, 709 OTUs in the CLE and 891 OTUs in the CLH. Among Actinobacteria, 382 OTUs were overlapped in the all soils. Not matched OTUs of CLH (286 OTUs) was detected 23 times higher than CLC (91 OTUs) and CLE (126 OTUs).

• Journal of Microbiology and Biotechnology
• /
• v.25 no.8
• /
• pp.1195-1204
• /
• 2015

Increasing evidence suggests that gut microbiota underpin the development of health and longevity. However, our understanding of what influences the composition of this community of the longevous has not been adequately described. Therefore, illumina sequencing analysis was performed on the gut microbiota of centenarians (aged 100-108 years; RC) and younger elderlies (aged 85-99 years; RE) living in Bama County, Guangxi, China and the elderlies (aged 80-92 years; CE) living in Nanning City, Guangxi, China. In addition, their diet was monitored using a semiquantitative dietary questionary (FFQ 23). The results revealed the abundance of Roseburia and Escherichia was significantly greater, whereas that of Lactobacillus, Faecalibacterium, Parabacteroides, Butyricimonas, Coprococcus, Megamonas, Mitsuokella, Sutterella, and Akkermansia was significantly less in centenarians at the genus level. Both clustering analysis and UniFraq distance analysis showed structural segregation with age and diet among the three populations. Using partial least square discriminate analysis and redundancy analysis, we identified 33 and 34 operational taxonomic units (OTUs) as key OTUs that were significantly associated with age and diet, respectively. Age-related OTUs were characterized as Ruminococcaceae, Clostridiaceae, and Lachnospiraceae, and the former two were increased in the centenarians; diet-related OTUs were classified as Bacteroidales, Lachnospiraceae, and Ruminococcaceae. The former two were deceased, whereas the later one was increased, in the high-fiber diet. The age and high-fiber diet were concomitant with changes in the gut microbiota of centenarians, suggesting that age and high-fiber diet can establish a new structurally balanced architecture of gut microbiota that may benefit the health of centenarians.

• The Korean Journal of Mycology
• /
• v.49 no.2
• /
• pp.199-209
• /
• 2021

The present study was performed to improve the technique used for fermenting the mushroom growth medium. Taxonomic analysis of 16S rDNA sequence from the predominant Bacillus strain CY-24 isolated during the fermentation phase of the rice straw medium identified it as Bacillus licheniformis. In addition, the growth environment of B. licheniformis was also examined in this study, which revealed the optimal growth temperature and pH to be 30 ℃ and 6.0, respectively. This study also revealed that carboxymethyl cellulase (CMCase) and polygalacturonase (PGase) enzymes isolated from B. licheniformis achieved their maximal activities at 50 ℃ and 60 ℃ respectively. Furthermore, the study confirmed that the two enzymes, i.e., CMCase and PGase in B. licheniformis are stable at temperatures above 60 ℃. The present study thus demonstrates that B. licheniformis CY-24 possesses excellent enzymatic properties. It also reveals that the action of enzymes during the production of growth mediums used for the cultivation of mushrooms is closely associated with the promotion of fermentation and softening of the rice straw. Overall, this study provides elementary information regarding the role of B. licheniformis enzymes during growth medium fermentation for Agaricus bisporus cultivation.