• Journal of Species Research
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• v.5 no.2
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• pp.206-219
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• 2016

As a subset study to discover indigenous prokaryotic species in Korea, a total of 42 bacterial strains assigned to the class Alphaproteobacteria were isolated from diverse environmental habitats including plant roots, ginseng soil, forest soil, marsh, mud flat, freshwater, and seawater. From the high 16S rRNA gene sequence similarity (>99.1%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 42 species have been described in Korea; therefore 4 species of 1 genera in the order Caulobacterales, 18 species of 10 genera in the order Rhizobiales, 7 species of 5 genera in the order Sphingomonadales and 13 species of 11 genera in the order Rhodobacterales within the Alphaproteobacteria are reported for alphaproteobacterial species found in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are also described in the species description section.

• Journal of Microbiology and Biotechnology
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• v.22 no.3
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• pp.301-310
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• 2012

Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

• Journal of Microbiology and Biotechnology
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• v.22 no.5
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• pp.699-707
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• 2012

Since the 2009 pandemic human H1N1 influenza A virus emerged in April 2009, novel reassortant strains have been identified throughout the world. This paper describes the detection and isolation of reassortant strains associated with human pandemic influenza H1N1 and swine influenza H1N2 (SIV) viruses in swine populations in South Korea. Two influenza H1N2 reassortants were detected, and subtyped by PCR. The strains were isolated using Madin-Darby canine kidney (MDCK) cells, and genetically characterized by phylogenetic analysis for genetic diversity. They consisted of human, avian, and swine virus genes that were originated from the 2009 pandemic H1N1 virus and a neuraminidase (NA) gene from H1N2 SIV previously isolated in North America. This identification of reassortment events in swine farms raises concern that reassortant strains may continuously circulate within swine populations, calling for the further study and surveillance of pandemic H1N1 among swine.

• Journal of Microbiology and Biotechnology
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• v.22 no.5
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• pp.575-584
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• 2012

Listeria monocytogenes is an important foodborne pathogen that comprises four genetic lineages: I, II, III, and IV. Of these, lineage II is frequently recovered from foods and environments and responsible for the increasing incidence of human listeriosis. In this study, the phylogenetic structure of lineage II was determined through sequencing analysis of the ascB-dapE internalin cluster. Fifteen sequence types proposed by multilocus sequence typing based on nine housekeeping genes were grouped into three distinct sublineages, IIA, IIB, and IIC. Organization of the ascB-dapE internalin cluster could serve as a molecular marker for these sublineages, with inlGHE, inlGC2DE, and inlC2DE for IIA, IIB, and IIC, respectively. These sublineages displayed specific genetic and phenotypic characteristics. IIA and IIC showed a higher frequency of recombination (${\rho}/{\theta}$). However, recombination events had greater effect (r/m) on IIB, leading to its high nucleotide diversity. Moreover, IIA and IIB harbored a wider range of internalin and stress-response genes, and possessed higher nisin tolerance, whereas IIC contained the largest portion of low-virulent strains owing to premature stop codons in inlA. The results of this study indicate that IIA, IIB, and IIC might occupy different ecological niches, and IIB might have a better adaptation to a broad range of environmental niches.

• Journal of Microbiology and Biotechnology
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• v.24 no.7
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• pp.888-897
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• 2014

A bacterial community analysis of the gut of Tenebrio molitor larvae was performed using pyrosequencing of the 16S rRNA gene. A predominance of genus Spiroplasma species in phylum Tenericutes was observed in the gut samples, but there was variation found in the community composition between T. molitor individuals. The gut bacteria community structure was not significantly affected by the presence of antibiotics or by the exposure of T. molitor larvae to a highly diverse soil bacteria community. A negative relationship was identified between bacterial diversity and ampicillin concentration; however, no negative relationship was identified with the addition of kanamycin. Ampicillin treatment resulted in a reduction in the bacterial community size, estimated using the 16S rRNA gene copy number. A detailed phylogenetic analysis indicated that the Spiroplasma-associated sequences originating from the T. molitor larvae were distinct from previously identified Spiroplasma type species, implying the presence of novel Spiroplasma species. Some Spiroplasma species are known to be insect pathogens; however, the T. molitor larvae did not experience any harmful effects arising from the presence of Spiroplasma species, indicating that Spiroplasma in the gut of T. molitor larvae do not act as a pathogen to the host. A comparison with the bacterial communities found in other insects (Apis and Solenopsis) showed that the Spiroplasma species found in this study were specific to T. molitor.

• International Journal of Industrial Entomology and Biomaterials
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• v.28 no.2
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• pp.39-50
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• 2014

In order to understand the diversity and genetic relationships of silkworm strains preserved in Korea, we genotyped 78 Bombyx mori strains (Bombycidae: Lepidoptera) originating from Japan, using eight polymorphic microsatellite loci. We obtained per-locus allele numbers ranging from 5 to 16 (with an average value of 9.1), per-locus observed heterozygosity ranging from 0.13 to 1.00, and per-locus polymorphic information content ranging from 0.36 to 0.77, indicating that some loci are highly variable. Phylogenetic analysis with the eight concatenated microsatellite loci showed no clustering based on known strain characteristics and origin. Nineteen strain-specific apomorphic alleles, which discriminated 16 of the 78 silkworm strains, were obtained from eight loci. These strain-specific alleles can thus be utilized for routine discrimination of strains from Japan, without any further typing of other loci. Homozygotes were also observed at some loci (27 of 118 genotypes), which can also be used to discriminate several strains by typing a few loci. These results showed that eight microsatellite loci described herein were sufficiently variable to discriminate among the 78 silkworm strains we examined, and may be useful for future investigations of this economically important species.

• The Korean Journal of Mycology
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• v.37 no.2
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• pp.121-129
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• 2009

In 2007, a total of 77 isolates of Fusarium spp. were obtained from ear rot symptoms of corns collected from 5 locations in Gangwon Province, Korea. The fungal isolates were identified based on their morphological features. Out of the isolates, fifteen isolates were identified as Fusarium verticillioides which formed microconidia in long chains on monophialides. Four isolates were identified as F. subglutinans which formed microconida only on false heads. Six isolates were identified as F. graminearum which produced red pigment in PDA culture. Besides these Fusarium species, F. napiform, F. nygamai, and F. oxysporum were identified from the rest isolates. To assess for genetic diversity of the isolates, a random amplified polymorphic DNA(RAPD) technique was carried out using URP primers. The results from the RAPD analysis showed that the isolates from corn were divided into 6 groups. These RAPD groups of the Fusarium species corresponded to morphological characters of the Fusarium species. The phylogenetic analysis of most isolates by DNA sequencing of EF-1$\alpha$ gene corresponded to morphological characters of the Fusarium species. The results of pathogenicity tests by two inoculation methods revealed that F. verticillioides, F. graminearum and F. subglutinans are strongly pathogenic to corn stalks.

• Mycobiology
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• v.48 no.2
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• pp.95-103
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• 2020

The genus Termitomyces (Lyophyllaceae, Basidiomycota) is often associated with fungus-feeding termites (Macrotermitinae) due to their strong symbiotic relationships. The genus is widely found exclusively in certain regions of Africa and Asia. They are recognized as edible mushroom within Southeast Asia as well. But it is often misidentified based on morphology by the local communities especially in Malaysia for Chlorophyllum molybdites which is a highly poisonous mushroom. Thus, it is necessary to study the genus for Malaysia with the synergy of using both morphological and molecular identification. In this study, we aim to describe another new species as an addition to the genus Termitomyces found within Sabah, Malaysia. We generated two new sequences (nrLSU and mtSSU) for the new species and a total of 28 nrLSU and mtSSU sequences were retrieved from GenBank for the phylogenetic analysis using maximum likelihood and Bayesian inferences. We identified that the new collection from Sabah province is a new species and named as Termitomyces gilvus based on the termites found in the mound. A phylogeny tree made from the concatenated genes of LSU and mtSSU suggests that T. gilvus is closely related to T. bulborhizus from China. According to our results, the combination of molecular and morphology proved to be a robust approach to re-evaluate the taxonomic status of Termitomyces species in Malaysia. Additional surveys are needed to verify the species diversity and clarify their geographic distribution.

• Mycobiology
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• v.48 no.4
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• pp.276-287
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• 2020

An algific talus slope is composed of broken rocks with vents connected to an ice cave, releasing cool air in summer and relatively warmer air in winter to maintain a more stable microclimate all year round. Such geological features create a very unusual and delicate ecosystem. Although there are around 25 major algific talus slopes in Korea, lichen ecology of these areas had not been investigated to date. In this study, we report the first exploration of lichen diversity and ecology at an algific talus slope, Jangyeol-ri, in Korea. A total of 37 specimens were collected over 2017-2018. Morphological and sequencing analysis revealed 27 species belonging to 18 genera present in the area. Of particular interest among these species was Solorina saccata, as it has previously not been reported in Korea and most members of genus Solorina are known to inhabit alpine regions of the Northern Hemisphere. We provide here a taxonomic key for S. saccata alongside molecular phylogenetic analyses and prediction of potential habitats in South Korea. Furthermore, regions in South Korea potentially suitable for Solorina spp. were predicted based on climatic features of known habitats around the globe. Our results showed that the suitable areas are mostly at high altitudes in mountainous areas where the annual temperature range does not exceed 26.6 ℃. Further survey of other environmental conditions determining the suitability of Solorina spp. should lead to a more precise prediction of suitable habitats and trace the origin of Solorina spp. in Korea.

• Journal of Species Research
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• v.7 no.3
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• pp.231-239
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• 2018

While screening indigenous prokaryotic species in Republic of Korea in 2017, a total of 17 bacterial strains assigned to the phylum Bacteroidetes were isolated from a variety of environmental habitats including water of fountain, tidal flat, plant root, soil, the gut of Russian grayling butterfly, ginseng field, seawater, lagoon and seashore sand. From the 16S rRNA gene sequence similarity of more than 98.7% and the formation of a robust phylogenetic clade with the closest species, it was found that the 17 strains belong to independent and recognized bacterial species. There has been no official report that the identified 17 species have been previously isolated in the Republic of Korea. Thus, 15 species in 10 genera of one family in the order Flavobacteriales, one species in one genus of one family in the order Cytophagales, and one species in one genus of one family in the order Sphingobacteriales are proposed as unrecorded species of the phylum Bacteroidetes found in the Republic of Korea. Gram reaction, colony and cell morphology, basic phenotypic characteristics, isolation source, taxonomic status, strain ID and other information are described in the species descriptions.