• Korean Journal of Microbiology
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• v.32 no.4
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• pp.245-251
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• 1994

Ten strains of 7 species from the genus Ganoderma, G. lucidum ATCC 64251, FP-103561-T, and ES70701, G. applanatum ATCC 44053 and FP-57035-T. G. lobatum ATCC 42985, G. resinaceum ATCC 52416, G. subamboinense var. laevisporum ATCC 52420, G. meredithae ATCC 64492, and G. microsporum ATCC 76024, were studied to discuss their phylogenetic relationships by utilizing restriction fragment length polymorphisms (RFLPs) of mitochondrial DNAs (mtDNAs). Six restriction enzymes, BamHI, BglII, EcoRI, HindIII, PvuII, and XbaI which digested mtDNAs into adequate numbers of restriction fragments for cluster analysis, were used in this study. Restriction profiles of strains for each restriction enzyme were treated as analysis characters to calculate similarity coefficients, which were converted into nucleotide sequence divergence values whose mean values were then arranged in a matrix table. This table was utilized for a phylogenetic analysis using the Neighborjoining method of the PHYLIP package to construct phylogenetic tree. Three strains of G. lucidum and two strains of G. applanatum exhibited different lineages each but one of G. applanatum strains showed a close relationship with G. lobatum, which reflected the species complexity of these species whose strains were phenotypically indistinguishable but genetically distinct. The present results suggest that the natural classification of Ganoderma needs to be considered from the viewpoints of molecular biology-based systematics as well as morphological classifications and cultural identifications for better phylogenetic conclusions.

• Journal of the Korean association of regional geographers
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• v.13 no.2
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• pp.129-142
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• 2007

The Purpose of this study is to evaluate the value of abandoned paddy fields as wetland ecosystems and their suitability as habitats for various species. Physical and chemical characteristics of soils and the change of vegetation in paddy fields were analysed -with the passage of time after cease of cultivation. The results of analyses for soil characteristics, vegetation succession, and functional values of abandoned paddy fields as wetlands were as follows: First, top soils become coarser as years after abandonment increase. Second, as the years of abandonment passed. there were significant differences in organic matter, available phosphorate and calcium, while not in magnesium and cation exchange capacity(CEC). Third, species increased from early stage till middle stage, and decreased in late stage. In similarity analysis of species composition, sites were classified into three groups according to the stage of succession. Upper and lower terraces at Daetgol were classified as early stage of succession. The 1st, 2nd and 3rd terraces at Nonbanggol were in middle stage, while tile 4th and 5th were in late stage. Forth, according to evaluation sheets of MoE and RAM(Rapid Assessment Method) standards, me overall average of functional value of Nonbanggol site were 2.13, classified as "common".

• Korean Journal of Ecology and Environment
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• v.40 no.3
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• pp.459-467
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• 2007

The effects of turbid water on fish community was investigated in a clear reference stream (the Bongsan Steam) and a turbid stream (the Daegi Stream) located in the upstream region of the South Han River, Korea. The stress index (SI) of suspended solids (SS) were calculated during a rain event concentration by the equation SI=LN (SS${\times}$duration). EMC of SS was $1{\sim}13$ mg $L^{-1}$ in the clear stream with a mean SI of 5.2, while SS was $97{\sim}1,150$ mg $L^{-1}$ in the turbid stream with a mean SI of 10.3. Even though the number of species was not much different, the dominant species of the two steams were distinctly different. The reference stream was dominated by upstream species such as Rhynchocypris kumgangensis, Brachymystax lenok tsinlingensis, and Cottus poecilopus which are typical upstream community. Whereas the turbid streams was dominated by Rhynchocypris kumgangensis, Zacco koreanus, and Orthrias nudus which are representatives of middle reache community. Fish density was four times higher in the clear steam than the turbid stream. In the similarity analysis of fish communities the community of the turbid stream showed large dissimilarity with other communities in other streams of similar size. In conclusion, although turbidity might be at the sublethal concentration, fish communities are under stress in some turbid streams of Korea that is strong enough to induce community change. It can be an example of a chronic ecological toxicity of turbidity at the community level.

• Journal of Life Science
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• v.30 no.12
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• pp.1063-1069
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• 2020

Two crucian carp species (Carassius auratus and C. cuvieri) inhabit Lake Yedang in South Korea, and C. auratus is known to be native to Korea. Classification of these two freshwater fish species is often confused because of their morphological similarity. To distinguish the two species, we conducted phylogenetic and population genetic analyses of C. auratus and C. cuvieri based on their mitochondrial DNA sequences of the cytochrome b gene (CYTB). We also compared our partial CYTB sequence (<1,056 bp) with 10 Chinese, nine Japanese, and two Russian crucian carp fishes. The results of our phylogenetic analysis showed that C. auratus and C. cuvieri were clearly divided into two phylogroups. The nucleotide diversity (π) of C. auratus from Korea, China, and Japan showed a range of 0.146%~0.421%, while the range of π of C. cuvieri from Korea and Japan was lower than those of C. auratus (0.0%~0.054%). Moreover, the comparison of CYTB divergence among crucian carp fishes in China, Japan, and Korea indicated that Korean Carassius fishes were distantly related to those from China and Japan, with two exceptions: the pairwise Fst value between Korean C. auratus and northern Chinese C. auratus was not significantly different. In addition, no significant genetic divergence between Korean and Japanese C. cuvieri was detected. We conclude that, despite the morphological similarities, C. auratus and C. cuvieri should be considered as separate freshwater fish resources in conservation efforts for genetic diversity.

• Korean Journal of Environmental Biology
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• v.41 no.1
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• pp.60-88
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• 2023

This study was conducted to investigate the vertical distribution and vascular plants in the Gakho mountain. Form the results of three field surveys from May 2022 to September 2022, a total of 478 total taxa, representing 426 species, 11 subspecies, 35 varieties, four forms, and two hybrids were identified, which were categorized in 282 genera and 94 families. We identified the elevational distribution ranges of 398 taxa of vascular plants. Among them, 19 taxa were endemic to Korea, one taxon was identified as a rare plant. The floristic target plants amounted to 72 taxa, specifically two taxa of grade V, two taxa of grade IV, 16 taxa of grade III, 27 taxa of grade II, and 25 taxa of grade I. Further, 71 taxa were identified as northern lineage plants. A total of 19 taxa of alien plants were identified, with a Naturalized Index of 4.0%, an Urbanization Index of 6.6%, and three plants that disturbed the ecosystem. The result of analyzing the pattern of species richness showed a reversed hump shape with minimum richness at mid-high elevation. A cluster analysis showed a high degree of similarity between adjacent elevation sections that are geographically adjacent with similar habitat environments. Warmth index in the Gakho mountain ranged from 57.2℃·month to 84.2℃·month. Our results provide basic data on vascular plants and valuable information on elevational distribution ranges of current plant species in the Gakho mountain, which could serve as a baseline for comparison of the shifts in elevation under future climate change.

• Journal of Microbiology and Biotechnology
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• v.33 no.10
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• pp.1292-1298
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• 2023

PAMB 00755^T, a bacterial strain, was isolated from Korean fir leaves. The strain exhibits yellow colonies and consists of Gram-negative, non-motile, short rods or ovoid-shaped cells. It displays optimal growth conditions at 20℃, 0% NaCl, and pH 6.0. Results of 16S rRNA gene-based phylogenetic analyses showed that strain PAMB 00755^T was most closely related to Sphingomonas chungangi MAH-6^T (97.7%) and Sphingomonas polyaromaticivorans B2-7^T (97.4%), and ≤96.5% sequence similarity to other members of the genus Sphingomonas. The values of average nucleotide identity (79.9-81.3%), average amino acid identity (73.3-75.9%), and digital DNA-DNA hybridization (73.3-75.9%) were significantly lower than the threshold values for species boundaries; these overall genome-related indexes (OGRI) analyses indicated that the strain represents a novel species. Genomic analysis revealed that the strain has a 4.4-Mbp genome encoding 4,083 functional genes, while the DNA G+C content of the whole genome is 66.1%. The genome of strain PAMB 00755^T showed a putative carotenoid biosynthetic cluster responsible for its antioxidant activity. The respiratory quinone was identified as ubiquinone 10 (Q-10), while the major fatty acids in the profile were identified as C_18:1ω7c and/or C_18:1ω6c (summed feature 8). The major polar lipids of strain PAMB 00755^T were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, and phosphatidylcholine. Based on a comprehensive analysis of genomic, phenotypic, and chemotaxonomic characteristics, we proposed the name Sphingomonas abietis sp. nov. for this novel species, with PAMB 00755^T as the type strain (= KCTC 92781^T = GDMCC 1.3779^T).

• Journal of Korean Society of Forest Science
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• v.113 no.1
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• pp.51-65
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• 2024

Phyto-sociological methods were used in this study to assess the vegetation structure of a forest stand at Mt. Goehwa in Sejong-Si with the aim of providing vegetation information for urban forest utilization and management plans. The actual forest vegetation was classified into two types of community groups (Quercus serrata-Lindera obtusiloba and Coreopsis lanceolata community groups) at the highest hierarchical level. The Q. serrata-L. obtusiloba community group was classified into six units, which included artificial forest and natural forest vegetation. Artificial forests were classified into three communities (Pinus rigida, Castanea crenata, and Robinia pseudoacacia), whereas natural forests were classified into three communities (Quercus variabilis, Quercus acutissimaa, and Pinus densiflora). The Coreopsis lanceolata community group, which exhibited vegetative characteristics of urban forest edge areas, was categorized into four units. The urban forest edges were classified into four communities (Indigofera bungeana, Lespedeza bicolor, Amorpha fruticosa, and Lespedeza cuneata). Accordingly, the vegetation structure of Mt. Goehwa was categorized into 10 vegetation unit systems. An importance value analysis showed the highest importance value for C. crenata at 6.7%, followed by P. rigida at 6.4%, and R. pseudoacacia at 6.3%, indicating that the ecological impact of plantation species can be significant on Mt. Goehwa. A community coefficient of similarity analysis revealed that the artificial and natural forests had similar species compositions; however, both forests differed from the urban forest edge. This variation was further confirmed by Detrended correspondence analysis(DCA), with similar results. Canonical correspondence analysis(CCA) showed that the artificial forest and natural forest community types were positively correlated with altitude, bare rock, and the present species. By contrast, the urban forest edge community types were negatively correlated with these factors.

• Korean Journal of Environment and Ecology
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• v.27 no.3
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• pp.327-343
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• 2013

The aim of this study is to perform community analysis and biological assessment of water quality using benthic macroinvertebrate from Wangpi-cheon watershed which is defined as conservation areas of ecosystem and landscape by ministry of environment in Korea. Field survey of the study area was carried out 2 times from June to September in 2012. As a result of the field survey, total 155 species of benthic macroinvertebrates in 74 families, 15 orders, 7 classes and 5 phyla were collected. The findings of community analysis using the classified species and individuals showed relatively low DI(Dominant Index) value of 0.22 and very high value of average H'(Diversity index) as 4.24. And the analyzed results of SI(Similarity Index) according to habitat types using functional feeding groups showed higher values of 94.51% and 93.19% respectively to tributary and main stream after the designation of conservation areas of ecosystem and landscape. These results infer that various species and lots of individual are widely distributed at Wangpi-cheon watershed and stream ecosystem of the study area is healthy and well maintained after the designation of conservation areas. And also, the calculated EPT value was 62.9% as high enough to explain the cleanness of Wangpi-cheon watershed. We evaluated environmental condition and biological water quality by using ESB(Ecological Score of Benthic macroinvertebrate community) and KSI(Korean Saprobic Index). The average evaluated ESB shows very high value of 208.2, therefore Wangpi-cheon watershed is designated as 'First priority protection waters' area and the value of KSI is 0.32 which meets the saprobic water quality standard as 'First class'.

• Korean Journal of Microbiology
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• v.52 no.3
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• pp.319-326
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• 2016

An antimicrobial bacterium to pathogenic microorganisms, strain $W5-1^T$ was isolated from Korean fermented-food Kimchi. The isolate was Gram-staining-variable, strictly aerobic, rod-shaped, endospore-forming, and motile with peritrichous flagella. It grew at $15-40^{\circ}C$, at pH 6.0-10.0, and in the presence of 0-4% NaCl. Strain $W5-1^T$ could hydrolyze esculin and xylan, and assimilate $\small{D}$-mannose, but not $\small{D}$-mannitol. Strain $W5-1^T$ showed antimicrobial activity against Listeria monocytogens, Pseudomonas aeruginosa, Staphylococcus aureus, and Salmonella typhi. The G+C content of the DNA of strains $W5-1^T$ was 52.6 mol%. The predominant respiratory quinone was menaquinone-7 (MK-7) and the major cellular fatty acids were $C_{16:0}$, antieiso-$C_{15:0}$, $C_{18:0}$, and $C_{12:0}$. The strain contained meso-diaminopimelic acid in cell-wall peptidoglycan. On the basis of 16S rRNA gene sequence and phylogenetic analysis, the strain W5-1 was shown to belong to the family Paenibacillaceae and was most closely related to Paenibacillus pinihumi $S23^T$ (98.4% similarity) and Paenibacillus tarimensis $SA-7-6^T$ (96.4%). The DNA-DNA relatedness between the isolate and Paenibacillus pinihumi $S23^T$ was 8.5%, indicating that strain $W5-1^T$ represented a species in the genus Paenibacillus. On the basis of the evidence from this polyphasic study, it is proposed that strain $W5-1^T$ is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus kimchicus sp. nov. is proposed. The type strain is $W5-1^T$ (=KACC $15046^T$ = $LMG 25970^T$).

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.8 no.3
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• pp.285-294
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• 2003

To select an appropriate sampler for the environmental monitoring survey in coastal waters of Saemangeum, Jeollabuk-do, a macrobenthic sampling was conducted in April 2002. Employed samplers were dredge (type Charcot), a semi-quantitative sampler and Smith-McIntyre (SM) and van Veen grab (VV) as quantitative ones. One haul was tried for dredge and 3 replicates (0.1 ㎡${\times}$3) for SM and W at each of 11 stations. Comparisons of sediment volume in sampler bucket and of precision of biological parameters (i.e., density, biomass, species number and diversity index, H') were made between SM and VV. Sediment volume was significantly different (SM > VV) at p-value of 0.0050 (paired t-test) and, in average, 3 replicate samples of SM and VV satisfied a precision level of 0.2 by applying 4th root transformation. Patterns of observed and expected species numbers and H' were compared. Dredge-VV samples showed higher affinity than any other pair. Several dominant species in the area were underestimated in dredge samples (e.g., polychaete Heteromastus filiformis. Aricidea assimilis etc.). Quantifying the agreement pattern of multi-species responses was accomplished by estimating correlations between similarity matrices. Correlation between dredge and VV was slightly higher, but near-per-fect matches were found in general. Different ranks and composition among principal species lists were presumably linked to the effect of penetration depth that differs among samplers. Lower level of some species' abundance in VV samples (ca. 50％ compared with those of SM) was explained in this context. It seem appropriate to regard the effect as a probable cause of relatively higher correlations in dredge-VV, Overall bio-logica1 features indicated that a better choice could be SM in situations of requiring high data quality. The others work well, however, on observing and defining faunal characteristics and their capability cannot be questionted if we do not expect a first-order quality.