• Korean Journal of Organic Agriculture
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• v.28 no.2
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• pp.235-250
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• 2020

Agricultural practices are known to have a crucial influence not only on soil physico-chemical properties but also on microbial communities. To investigate the effect of farming practices on soil microbial communities, a total of 10 soil samples were collected, including five conventional and five organic farming soils cultivated with peppers in plastic greenhouse. We conducted barcorded-pyrosequencing of V1-V3 regions of 16S rRNA genes to examine soil microbial communities of two different farming practices. Taxonomic classification of the microbial communities at the phylum level indicated that a total of 22 bacterial phyla were present across all samples. Among them, seven abundant phyla (>3%) including Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria, Bacteroidetes, Chloroflexi, and Gemmatimonadetes were found, and Proteobacteria (33.0 ± 5.7%), Actinobacteria (19.9 ± 9.7%), and Firmicutes (13.6 ± 5.0%) comprised more than 66% of the relative abundance of the microbial communities. Organic farming soils showed higher relative abundances of Proteobacteria and Firmicutes, while Actinobacteria and Chloroflexi were more abundant in conventional farming soils. Notably, the genera Bacillus (higher in organic farming soils) and Streptomyces (higher in conventional farming soils) exhibited significant variation in relative abundance between organic and conventional farming soils. Finally, correlation analysis identified significant relationships (p<0.05) between soil chemical properties, in particular, pH and organic matter content and microbial communities. Taken together, this study demonstrated that the changes of soil physico-chemical properties by agricultural farming practices effected significantly (p<0.05) on soil microbial communities.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.3 no.2
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• pp.94-102
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• 1998

Temporal changes, density, calcimass, mode of occurrence, size-frequency histogram and survivorship curves were studied for the molluscan death assemblages on a macrotidal flat, Inchon, Korea. The living and death assemblages were compared on the basis of the taxonomic compositions and their numerical abundances. A total of 28 species (16 taxa in gastropods and 12 in bivalves) were identified. Most of the dead shells were the species inhabiting that intertidal mud flat. Species diversity was higher in gastropods than in bivalves. Seasonal variation of the calcimass was influenced by the mactrid bivalve, Mactra veneriformis. Shell-boring naticid gastropods preferred selecting the umbo areas of various valves. Size-frequency distribution and size-specific survivorship curves were analyzed for the dominant species. Survivorship curve of the tellinid bivalve, Morella rutila was convex-up in shape, which is congruent with the expected equilibrium condition but indicates higher mortality in winter. Whereas the survivorship curves of Mactra veneriformis and Reticunassa festiva were semi convex-up with dual modes, suggesting a disequilibrium due to the changes in recruitment and seasonal mortality. This study suggests that the dead shell assemblages may be useful in getting population information like live molluscan assemblages, if solved for several problems related to taphonomic processes.

• Parasites, Hosts and Diseases
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• v.53 no.3
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• pp.299-305
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• 2015

Tapeworms of the genus Spirometra are pseudophyllidean cestodes endemic in Korea. At present, it is unclear which Spirometra species are responsible for causing human infections, and little information is available on the epidemiological profiles of Spirometra species infecting humans in Korea. Between 1979 and 2009, a total of 50 spargana from human patients and 2 adult specimens obtained from experimentally infected carnivorous animals were analyzed according to genetic and taxonomic criteria and classified as Spirometra erinaceieuropaei or Spirometra decipiens depending on the morphology. Morphologically, S. erinaceieuropaei and S. decipiens are different in that the spirally coiled uterus in S. erinaceieuropaei has 5-7 complete coils, while in S. decipiens it has only 4.5 coils. In addition, there is a 9.3% (146/1,566) sequence different between S. erinaceieuropaei and S. decipiens in the cox1 gene. Partial cox1 sequences (390 bp) from 35 Korean isolates showed 99.4% (388/390) similarity with the reference sequence of S. erinaceieuropaei from Korea (G1724; GenBank KJ599680) and an additional 15 Korean isolates revealed 99.2% (387/390) similarity with the reference sequences of S. decipiens from Korea (G1657; GenBank KJ599679). Based on morphologic and molecular databases, the estimated population ratio of S. erinaceieuropaei to S. decipiens was 35: 15. Our results indicate that both S. erinaceieuropaei and S. decipiens found in Korea infect humans, with S. erinaceieuropaei being 2 times more prevalent than S. decipiens. This study is the first to report human sparganosis caused by S. decipiens in humans in Korea.

• Journal of Applied Biological Chemistry
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• v.62 no.4
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• pp.333-337
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• 2019

In this study, we investigated the effects of fasting on gut microbiota of mice fed normal (CTL) or high-fat diets (HF). Mice were raised for 16 weeks and fasted for a day at the end of the experiment. Fecal samples were collected one day before and after fasting, which were analyzed using MiSeq. Our results showed that the species richness and evenness were decreased in fasted HF group, whereas no difference was observed for CTL groups. Moreover, HF fed mice gut microbiota showed different microbial communities after fasting, while CTL groups did not show microbiota shifts. Differential abundance analysis showed that fasting CTL group mice increased and decreased one operational taxonomic unit (OTU) in S24_7 and one OTU in Ruminococcaceae, respectively. On the other hand, fasting HF group mice decreased 10 OTUs and increased 3 OTUs most of which were classified to Ruminococcaceae. Our results suggest that fasting mice may affect the abundance of Ruminococcaceae species and effects of fasting seem to be more obvious for HF-fed mice compared to those of mice fed CTL-diet.

• Korean Journal of Environmental Biology
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• v.32 no.4
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• pp.353-362
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• 2014

In this study, we investigated the effect of geographical variations on Sargassum thunbergii morphology to make a taxonomic reconsideration about infraspecific taxa in this species. In order to examine the morphological characteristics of S. thunbergii, total 27 matured and morphologically intact thalli were collected from the east, west and south coast in spring 2011. Interestingly, it was observed that the species populations on the west coast were characterized by short, thin and coarse thallus, and soft texture. However, the populations on the east coast showed thicker thallus, larger leaf and vesicle, and tougher texture. Thallus height of S. thunbergii was found to be similar at both east and west coast. Further, the height of the thallus and lateral branch of the species populations residing south coast were highest whereas the size of leaf and vesicle are shortest, in comparison with east and west coast species. Although morphological characteristics of the north east coast populations corresponded to the original description of S. thunbergii f. latifolium, we could not find exact morphological features and diagnostic characters to distinguish form in S. thunbergii. These results indicated that it is not the optimal characteristics to identify infraspecific form in this species. In contrast, morphological variations may signify the adaptation of this species to local environmental factors. Thus, we recommend that intraspecific morphological variation of S. thunbergii should be carefully used to identify infraspecific taxa.

• Applied Microscopy
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• v.42 no.2
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• pp.61-66
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• 2012

Ultrastructural characteristics of blacktip grouper, Epinephelus fasciatus spermatozoa were investigated using transmission and scanning electron microscopy. The spermatozoa of E. fasciatus consisted of a spherical head part, a midpiece with cytoplasmic canal entrance and a flagellum with lateral fins. Internal ultrastructurally, the nucleus contains high electron dense chromatin having granular particles and has no acrosome. The centriolar complex lies outside of the nuclear fossa and it is connected by the osmophilic filaments. Also the osmophilic filaments connect between the centriolar complex and the nuclear membrane. The midpiece contains eight to nine spherical mitochondria, cytoplasmic canal and necklaces. The flagellum has a typical 9+2 axonemal structure. The lateral fins contain vesicles and a typical 9+2 axonemal structure. Consequently this study contributes to comparative grouper spermatology and provide useful systematic taxonomic characters.

• Journal of Periodontal and Implant Science
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• v.50 no.3
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• pp.171-182
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• 2020

Purpose: The aims of this study were to examine the salivary microbiota in conditions of periodontal health and disease and to explore microbial changes following nonsurgical periodontal treatment. Methods: Non-stimulated saliva samples were collected from 4 periodontally healthy participants at baseline and from 8 patients with chronic periodontitis at baseline and 3 months following nonsurgical periodontal therapy. The V3 and V4 regions of the 16S rRNA gene from the DNA of saliva samples were amplified and sequenced. The salivary microbial compositions of the healthy participants and patients with periodontitis prior to and following nonsurgical treatment of periodontitis were compared based on the relative abundance of various taxa. Results: On average, 299 operational taxonomic units were identified in each sample. The phylogenetic diversity in patients with periodontitis was higher than that in healthy participants and decreased following treatment. The abundance of the phylum Spirochaetes and the genus Treponema in patients with periodontitis was 143- and 134-fold higher than in the healthy control group, respectively, but decreased significantly following treatment. The species that were overabundant in the saliva of patients with periodontitis included the Peptostreptococcus stomatis group, Porphyromonas gingivalis, the Fusobacterium nucleatum group, Parvimonas micra, Porphyromonas endodontalis, Filifactor alocis, and Tannerella forsythia. The phylum Actinobacteria, the genus Streptococcaceae_uc, and the species Streptococcus salivarius group were more abundant in healthy participants than in those with periodontitis. There was a trend toward a decrease in disease-associated taxa and an increase in health-associated taxa following treatment. Conclusions: Our results revealed differences in the taxa of salivary microbiota between conditions of periodontal health and disease. The taxa found to be associated with health or disease have potential for use as salivary biomarkers for periodontal health or disease.

• Korean Journal of Plant Taxonomy
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• v.45 no.4
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• pp.306-317
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• 2015

This study was conducted to address the taxonomic status of the Korean endemic species Saxifraga octopetala, which is sometimes considered conspecific to Micranthes manchuriensis. Extensive molecular phylogenetic analysis using nrITS sequences as well as morphological examination of type specimens of the two species were undertaken to ascertain the phylogenetic position and species delimitation of S. octopetala. In the resulting nrITS trees, a total of 65 accessions representing S. octopetala grouped together and nested within the Micranthes clade, exhibiting a close relationship with M. nelsoniana and M. manchuriensis. Multiple accessions of M. manchuriensis collected from China and Russia also formed a clade, showing a sister group relationship with M. nelsoniana var. pacifica and M. fusca. The ambiguous species entity of S. octopetala is thought to have originated from Nakai's misinterpretation of Wilford's collection (type specimens of M. manchuriensis), which is a complex collection including an inflorescence of M. nelsoniana. In spite of apparent morphological similarity between S. octopetala and M. manchuriensis, they differ in the presence and absence of underground stolons. The distinct position of S. octopetala within the Micranthes clade on the nrITS tree suggests that it should retain species status in Micranthes. Thus a new combination (Micranthes octopetala) is proposed.

• Korean Journal of Plant Taxonomy
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• v.45 no.4
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• pp.332-352
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• 2015

The tribe Neillieae, a small group of about 18 species in the Rosaceae, comprises three taxonomically difficult genera, Neillia, Physocarpus, and Stephanandra. The tribe, characterized by lobed leaves with persistent or deciduous stipules and ovoid, shiny seeds with copious endosperm, is strongly supported as a monophyletic group by a variety of lines of molecular evidence. Due to the high amount of morphological variation across the three genera and the species in tribe Neillieae, conflicting classification schemes and numerous species have been proposed over the past three centuries. However, no comprehensive systematic study of the group, including all species across their geographic ranges, has ever been undertaken. As part of a taxonomic revision of tribe Neillieae, a revision of Physocarpus based on the morphological examination of herbarium specimens, including types, and field observation is presented. Artificial keys, comprehensive nomenclatural treatments, descriptions, distribution maps, and lists of specimens examined are provided. Six species in Physocarpus are recognized. A lectotype is here designated for the following species: Opulaster pubescens, Opulaster ramaleyi, Spiraea opulifolia var. parvifolia, Spiraea opulifolia var. tomentella, Physocarpus michiganensis, and Physocarpus missouriensis.

• Journal of Life Science
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• v.25 no.3
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• pp.323-328
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• 2015

The study of microbial diversity and richness in soil samples from a volcanic island named Ulleungdo, located east of South Korea. The soil bacterial communities on the Ulleungdo were analyzed using pyrosequencing method based on 16S rRNA gene. There were 1,613 operational taxonomic units (OUT) form soil sample. From results of a BLASTN search against the EzTaxon-e database, the validated reads (obtained after sequence preprocessing) were almost all classified at the phylum level. Proteobacteria was the most dominant phylum with 48.28%, followed by acidobacteria (26.30%), actionbacteria (6.89%), Chloroflexi (4.58), Planctomycetes (4.56%), Nitrospirae (1.83%), Bacteroidetes (1.51%), Verrucomicrobia (1.48%), and Gemmatimonadetes (1.11%). α-proteobacteria was the most dominant class with 36.07% followed by Acidobacteria_c (10.65%), Solibacteres (10.64%), δ-proteobacteria (4.42%), γ-proteobacteria (4.29%), Planctomycetacia (4.16%), Actinobacteria_c (4.00%), Betaproteobacteria (3.50%), EU686603_c (2.97%), Ktedonobacteria (2.91%), Acidimicrobiia (1.32%), Verrucomicrobiae (1.27%), Gemmatimonadetes_c (1.11%), Sphingobacteria (1.09%), and GU444092_c (1.06%). Bradyrhizobiaceae was the most dominant family with 22.83% followed by Acidobacteriaceae (10.62%), EU445199_f (5.72%), Planctomycetaceae (4.03%), Solibacteraceae (3.63%), FM209092_f (3.58%), Steroidobacter_f (2.81%), EU686603_f (2.73%), Hyphomicrobiaceae (2.33%), Ktedonobacteraceae (1.75%), AF498716_f (1.46%), Rhizomicrobium_f (1.03%), and Mycobacteriaceae (1.01%). Differences in the diversity of bacterial communities have more to do with geography than the impact on environmental factors and also the type of vegetation seems to affect the diversity of bacterial communities.