• The Plant Pathology Journal
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• v.37 no.3
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• pp.280-290
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• 2021

Population genetic studies of Hemileia vastatrix have been conducted in order to describe the evolutionary dynamics of the pathogen and the disease epidemiology as consequence of changes in disease management and host distribution occurred in Peru after the 2013 epidemic. These analyses were performed by sequencing the internal transcribed spacers of the nuclear ribosomal DNA (rDNA-ITS) of H. vastatrix collected from two coffee growing areas in 2014 and 2018. H. vastatrix population showed high haplotype diversity (Hd = 0.9373 ± 0.0115) with a low nucleotide diversity (π = 0.00322 ± 0.00018). Likewise, AMOVA indicated that fungus population has behaved as a large population without structuring by geographical origin and sampling years (F_ST = 0.00180, P = 0.20053 and F_ST = 0.00241, P = 0.19693, respectively). Additionally, the haplotype network based on intraspecific phylogenetic analysis of H. vastatrix using Peruvian and NCBI sequences revealed that Peruvian ancestral haplotypes, which were maintained in time and space, would correspond to the reported sequences of the races II and XXII. This result suggests that no substantial changes have occurred through time in Peruvian Hemileia vastatrix population.

• Journal of Forest and Environmental Science
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• v.39 no.1
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• pp.1-12
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• 2023

To understand the health conditions and growth patterns of forest estate for environmental resilience and climate change mitigation, assessment of structure and species diversity is paramount. This study aimed at assessing the structure, alpha, and beta diversities of tree species in three ecological zones in Taraba, Nigeria for management purposes. In recent time, no research has been reported on the structure and beta diversity of the study areas. A systematic sampling design was used for data collection. Five sample plots of 50×50 m were laid in each of the six natural forest areas. The result showed a mean DBH (42.5 cm) and a tree height (15.0 m) from the forests. The forests have a structure of an inverse "J-shape," which is typical of natural forests in the tropics. The southern Guinea savanna zone had the highest mean Shannon-Weiner diversity index (2.8). The least beta diversity index (0.02) was between Baissa and Jen Gininya forest areas. Baissa and Bakin Dutse Protected Forest Areas (PFAs) contained 76.5% of the tree species. There is a high chance of all tree species to be found in these 2 forest areas. Proximity to a location influences how similar two tree species are, according to the least beta diversity index (0.02) recorded. The Federal Government's method of management for the forest, known as Gashaka Gumti National Park, may be responsible for the high beta diversity index in the Montane ecozone. Therefore, it should be strongly encouraged to practice strict oversight of natural areas, as their contributions to reducing climate change in Taraba State, Nigeria, cannot be overstated.

• Journal of Oral Medicine and Pain
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• v.47 no.1
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• pp.10-26
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• 2022

Purpose: The purpose of this study was to investigate whether various saliva collection methods affect the observed salivary microbiome and whether microbiomes of stimulated and unstimulated saliva and plaque differ in richness and diversity. Methods: Seven sampling methods for unstimulated saliva, stimulated saliva, and plaque samples were applied to six orally and systemically healthy participants. Bacterial 16S ribosomal RNA genes of 10 major oral bacterial species, namely, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum, Prevotella intermedia, Prevotella nigrescens, Streptococcus mitis, Streptococcus sobrinus, and Lactobacillus casei, were analyzed by real-time polymerase chain reaction. We comprehensively examined the dependence of the amount of bacterial ribosomal DNA (rDNA), bacterial-community composition, and relative abundance of each species on sample collection methods. Results: There were significant differences in the bacterial rDNA copy number depending on the collection method in three species: F. nucleatum, P. nigrescens, and S. mitis. The species with the highest richness was S. mitis, with the range from 89.31% to 100.00%, followed by F. nucleatum, P. nigrescens, T. denticola, T. forsythia, and P. intermedia, and the sum of the proportions of the remaining five species was less than 1%. The species with the lowest observed richness was P. gingivalis (<0.1%). The Shannon diversity index was the highest in unstimulated saliva collected with a funnel (4.449). The Shannon diversity index was higher in plaque samples (3.623) than in unstimulated (3.171) and stimulated (3.129) saliva and in mouthwash saliva samples (2.061). Conclusions: The oral microbial profile of saliva samples can be affected by sample collection methods, and saliva differs from plaque in the microbiome. An easy and rapid technique for saliva collection is desirable; however, observed microbial-community composition may more accurately reflect the actual microbiome when unstimulated saliva is assayed.

• Journal of Ecology and Environment
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• v.36 no.4
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• pp.371-390
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• 2013

Remarkable diversity of diatom taxa occurs in intertidal sand-flats of the Nakdong River estuary, one of the most dynamic and productive ecosystem in Korea. Benthic diatoms were collected from the sandy sediments to clarify the taxonomic accounts and distribution of the old genus Navicula, i.e., the naviculoid flora. Total 92 taxa belonging to Navicula sensu stricto and 22 genera separated from Navicula sensu lato are reported with brief descriptions and micrographs, and many species remain unidentified. The genera are ranked by the number of diatom species: Navicula of 33 species and varieties, Fallacia of 17 species, Placoneis of five species, Fogedia and Parlibellus of four species, Austariella, Hippodonta and Petroneis of three species, Cosmioneis, Diadesmis, Luticola, Moreneis and Sellaphora of two species and variety, Berkeleya, Chamaepinnularia, Cocconeiopsis, Diademoides, Dickieia, Eolimna, Geissleria, Haslea, Lyrella and Mayamaea of one species. Through 32 samplings of the 12 areas, the important species were identified Navicula perminuta, N. gregaria, N. torneensis, Fallacia cunoniae, F. litoricola, F. subforcipata, F. tenera. The naviculoid diatoms constitute an average of 27% (range: minimum to maximum, 5-75%), of the benthic diatom assemblages. The diatom assemblages are characterized by the colonizing of a few dominant or frequent species and many occasional or rare species. The dominant species were observed to fluctuate with sampling site and time. Among the reported naviculoid diatoms, 46 taxa are newly reported in Korea.

• Fisheries and Aquatic Sciences
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• v.16 no.2
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• pp.125-129
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• 2013

Vibrio ichthyoenteri is a facultatively anaerobic gram-negative bacterium with straight or slightly curved rod morphology. The bacterium is an etiological agent of bacterial enteritis of Olive flounder Paralichthys olivaceus. Only a handful of studies, using a limited number of isolates, have investigated the phenotypic and genetic characteristics of V. ichthyoenteri. We isolated 40 V. ichthyoenteri strains, identified based on the 16S rRNA gene sequence, from the diseased flounder larvae and investigated the API 20E and ZYM profiles. The isolates exhibited highly divergent phenotypic characteristics regardless of sampling time point and location, and fish age. Essential enzymes produced by V. ichthyoenteri seemed to be alkaline phosphatase, leucine arylamidase, and N-acetyl-${\beta}$-glucosaminidase. This study reveals a much greater enzymatic and biochemical phenotype diversity than has been evident to date. These results suggest that a given population of V. ichthyoenteri could be heterogeneous in terms of its phenotypic characteristics.

• Journal of Conservation Science
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• v.38 no.1
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• pp.64-71
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• 2022

Many investigations have been conducted on the biological damage and environmental conditions necessary to preserve the Janggyeong Panjeon and Daejanggyeongpan (woodblocks). We performed a survey on the concentration and diversity of airborne fungi in the Janggyeong Panjeon and compared them with the results of a survey from 2012. The temperature of the Beopbojeon building was slightly lower, while the relative humidity was higher than those found at the Sudarajang building. The concentration of airborne fungi in the Beopbojeon was 1.44-fold that of the Sudarajang. It was confirmed that the concentration and diversity of airborne fungi in the Janggyeong Panjeon differed depending on the sampling site. In total, 23 fungal genera were identified from the air samples, and 11 fungal and 1 bacterial genera were identified from the surface of the woodblocks. Among these, only five types of fungi were commonly distributed in the indoor air and surface of the Daejanggyeongpan; however, 58.3% of the fungi identified on the surface of the woodblocks were not observed in the in the air samples. The surface-dwelling fungi may accumulate dust to form microbial communities over time.

• Journal of Forest and Environmental Science
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• v.30 no.1
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• pp.133-144
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• 2014

This study was carried out to review the pattern of forest stand development for six Gangwondo Baekdudaegan Mountains which experienced different type and duration of intensive legal protection. Vegetation data from point sampling method were employed to classify community types by cluster analysis on the basis of the importance values of canopy tree species for the study areas. The names of classified communities were given by the composition of dominant tree species. The communities were also compared one another in terms of stand structure by species diversity index. The results indicated that National Parks (Seoraksan and Odaesan) had greater proportion of mixed mesophytic forest type which was supposed to progress further forest succession process so as to have more complex and diversified stand structure. On the other hand, ordinary forest areas (Seokbyeongsan and Deokhangsan) had greater proportion of the forest types which was dominatively composed of Quercus mongolica and Pinus densiflora. The forest types with large amount of these two species would tend to develop for relatively short period of time of 40-50 years after artificial disturbances. Hyangnobong of Natural Protection Area and Hambaeksan of Natural Ecosystem Conservation Area showed intermediate stand development pattern in between National Parks and ordinary forest areas. The period of intensive legal protection of the forest area was positively correlated with species diversity index (R=0.736), and noted that the forest which received intensive protection regulation for longer period tended to show more complex and diversified stand structure.

• Journal of Microbiology and Biotechnology
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• v.17 no.4
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• pp.560-570
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• 2007

The effective and accurate assessment of the total microbial community diversity is one of the primary challenges in modem microbial ecology, especially for the detection and characterization of unculturable populations and populations with a low abundance. Accordingly, this study was undertaken to investigate the diversity of the microbial community during the biodegradation of cis- and trans-dichloroethenes in soil and wastewater enrichment cultures. Community profiling using PCR targeting the l6S rRNA gene and denaturing gradient gel electrophoresis (PCR-DGGE) revealed an alteration in the bacterial community profiles with time. Exposure to cis- and trans-dichloroethenes led to the disappearance of certain genospecies that were initially observed in the untreated samples. A cluster analysis of the bacterial DGGE community profiles at various sampling times during the degradation process indicated that the community profile became stable after day 10 of the enrichment. DNA sequencing and phylogenetic analysis of selected DGGE bands revealed that the genera Acinetobacter, Pseudomonas, Bacillus, Comamonas, and Arthrobacter, plus several other important uncultured bacterial phylotypes, dominated the enrichment cultures. Thus, the identified dominant phylotypes may play an important role in the degradation of cis- and trans-dichloroethenes.

• Journal of Microbiology and Biotechnology
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• v.18 no.1
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• pp.5-14
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• 2008

The deep subseafloor rock in oil reservoirs represents a unique environment in which a high oil contamination and a very low biomass can be observed. Sampling this environment has been a challenge owing to the techniques used for drilling and coring. In this study, the facilities developed by the Brazilian oil company PETROBRAS for accessing deep subsurface oil reservoirs were used to obtain rock samples at 2,822-2,828 m below the ocean floor surface from a virgin field located in the Atlantic Ocean, Rio de Janeiro. To address the bacterial diversity of these rock samples, PCR amplicons were obtained using the DNA from four core sections and universal primers for 16S rRNA and for APS reductase (aps) genes. Clone libraries were generated from these PCR fragments and 87 clones were sequenced. The phylogenetic analyses of the 16S rDNA clone libraries showed a wide distribution of types in the domain bacteria in the four core samples, and the majority of the clones were identified as belonging to Betaproteobacteria. The sulfate-reducing bacteria community could only be amplified by PCR in one sample, and all clones were identified as belonging to Gammaproteobacteria. For the first time, the bacterial community was assessed in such a deep subsurface environment.

• Korean Journal of Plant Taxonomy
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• v.52 no.4
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• pp.214-218
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• 2022

Eleocharis R. Br. (Cyperaceae) is characterized by unbranched culms, one terminal spikelet, bisexual flowers, and bristly perianths, occurring mainly in circumboreal marshes and wetlands. There are about 250 species worldwide, and 15 taxa in Korea have been recognized. Chromosomes in Cyperaceae are known to be holocentric, missing constricted centromeres during cell division. For the first time, we report the chromosome counts of Eleocharis from Korean populations of E. attenuata f. laeviseta (Nakai) H. Hara (2n = 20); E. parvula (Roem. & Schult.) Link ex Bluff, Nees & Schauer (2n = 10); E. ussuriensis Zinserl. (2n = 16); and E. valleculosa var. setosa Ohwi (2n = 16). The populations exhibit variations in their chromosome sizes from ca.1.7 ㎛ to ca. 6 ㎛, categorized as gradient and bimodal karyotypes. The karyotypes observed are congruent with previous phylogenetic groups proposed. To clarify the traditional and phylogenetic classification of Korean Eleocharis, further taxonomic and chromosomal investigations with additional taxon sampling efforts are required.