• Journal of Microbiology
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• v.43 no.5
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• pp.383-390
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• 2005

The diversity of the denitrifying bacterial populations in Daejeon Sewage Treatment Plant was examined using a culture-dependent approach. Of the three hundred and seventy six bacterial colonies selected randomly from agar plates, thirty-nine strains that showed denitrifying activity were selected and subjected to further analysis. According to the morphological and biochemical properties, the thirty nine isolates were divided into seven groups. This grouping was supported by an unweighted pair group method, using an arithmetic mean (UPGMA) analysis with fatty acid profiles. Restriction pattern analysis of 16S rDNA with four endonucleases (AluI, BstUI, MspI and RsaI) again revealed seven distinct groups, consistent with those defined from the morphological and biochemical properties and fatty acid profiles. Through the phylogenetic analysis using the 16S rDNA partial sequences, the main denitrifying microbial populations were found to be members of the phylum, Proteobacteria; in particular, classes Gammaproteobacteria (Aeromonas, Klebsiella and Enterobacter) and Betaproteobacteria (Acidovorax, Burkholderia and Comamonas), with Firmicutes, represented by Bacillus, also comprised a major group.

• ALGAE
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• v.35 no.1
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• pp.17-32
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• 2020

Asterochloris is one of the most common genera of lichen phycobionts in Trebouxiophyceae. Asterochloris phycobionts associated with the lichenized fungi Cladonia and Stereocaulon in King George Island (Antarctica) and Morro Chico (Chile), were isolated and then used to establish clonal cultures. To understand the phylogenetic relationships and species diversity of Antarctic Asterochloris species, molecular and morphological data were analyzed by using three microscopy techniques (light, confocal laser and transmission electron) and a multi-locus phylogeny with data from the nuclear-encoded internal transcribed spacer (ITS) rDNA and the actin and plastid-encoded ribulose bisphosphate carboxylase large chain (rbcL) coding genes. Morphological data of three Antarctic strains showed significant species-specific features in chloroplast while molecular data segregated the taxa into distinct three clades as well. Each species had unique molecular signatures that could be found in secondary structures of the ITS1 and ITS2. The species diversity of Antarctic Asterochloris was represented by six taxa, namely, A. glomerata, A. italiana, A. sejongensis, and three new species (A. antarctica, A. pseudoirregularis, A. stereocaulonicola).

• Journal of Forest and Environmental Science
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• v.35 no.2
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• pp.90-101
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• 2019

Biodiversity refers to the total number and variation among species of flora and fauna of an area. Due to tremendous biotic especially anthropogenic pressure these natural resources are being vanishing. In present study genetic diversity among accessions of Thamnocalamus spathiflorus was evaluated. A total of 51 vegetative characters and 42 primers (10-mer) were screened. Out of 42 screened primers, 28 polymorphic primers were selected for further analysis. A total of 263 bands were recorded as polymorphic whereas 48 bands were monomorphic. The resolving power (Rp) of 28 Randomly Amplified Polymorphic DNA (RAPD) primers ranged from 4.6 (OPE08) to 17.6 (OPA11). The polymorphic information content (PIC) value ranged from 0.21 (OPAH09) to 0.44 (OPG02). The result revealed high degree of genetic relatedness (56 to 80%). Cluster analysis revealed two major clusters both for morphology as well as RAPD. Unlike morphological characterization, the accession (D5) from Bahli, Rampur, Shimla (H.P.) was clustered separately from the others in RAPD cluster analysis. Accessions with closed locality grouped together through RAPD marker system however analogy was recorded for morphological traits. The study conducted reflects the utility of RAPD technique for species identification and phylogenetic studies in bamboo for conducting bamboo breeding program.

• The Korean Journal of Mycology
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• v.51 no.1
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• pp.7-24
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• 2023

More than five hundreds of yeast species (including 9 variants) encompassing 142 genera and 48 classes of 2 phyla exist in Korea. However, only 173 species have been cataloged in the National Species List of Korea (NSLK), the backbone reference to claim sovereign rights over biological resources, as of December 2021, due to the lack of taxonomic descriptions, although some of these species are extensively used in industry. The present pilot study investigated the taxonomy of strains belonging to the six most widely used or frequently isolated yeast species (Meyeromyma guilliermondii, Saccharomyces cerevisiae, Saccharomycopsis fibuligera, Wickerhamomyces anomalus, Candida tropicalis, and Papiliotrema flavescens) to include these species in the NSLK. Strains with diverse habitats and geographic origins were retrieved from the National Institute of Biological Resources culture collection. These strains clustered in the same clade as the type strains of the designated species according to phylogenetic analysis of the D1/D2 sequences. Moreover, we described the cell morphology and physiological characteristics of representative strains of each species. This study suggests that these six species are indigenous to Korea and can be accordingly listed in the NSLK.

• Journal of Species Research
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• v.12 no.spc2
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• pp.1-6
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• 2023

During an investigation into the indigenous prokaryotic species diversity in Korea, a total of five bacterial strains were isolated from various environments in Korea. The isolated bacterial strains were identified by analyzing their 16S rRNA gene sequences, and those with a minimum of 98.7% sequence similarity with known bacterial species but not reported in Korea were designated as unrecorded species. These isolates were assigned to three phyla, five orders, five families, and five different genera. The isolates were identified as Cumulibacter manganitolerans (99.1%) and Myolicibacterium tusciae (98.7%) of the class Actinomycetes; Bacillus marasmi (99.9%) of the class Bacilli; and Novosphingobium mathurense (100%) and Microvirga ossetica (98.8%) of the class Alphaproteobacteria. Gram reaction, colony and cellular morphology, basic biochemical characteristics, and phylogenetic position of theses isolates are also described.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.215-215
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• 2022

Starch synthase proteins (SSI, SSII and SSIII) in rice are mainly involved in amylopectin synthesis mediating its chain elongation, and the functional loss of SSII can increase amylose accumulation through decreasing of amylopectin chain proportions. For purposes of identifying functional haplotypes and evolutionary analyses of this gene, SSII-1, we investigated 374 rice accessions belonging to different subgroups of origins. We subsequently performed bioinformatic analyses on their variations through haplotyping, resequencing and structuring based on different classified populations. Haplotyping of cultivated rice accessions using genetic variations within SSII-1 genomic region of chromosome 10 revealed a total of 8 haplotypes, representing 6 functional haplotypes by 4 non-synonymous SNPs of three different exons (1, 4 and 10), which effect on protein structure. Higher nucleotide diversity value was found in wild group (0.0055) compared to any of cultivated subpopulations, of which aus showed the most reduction of diversity value (0.0003). Tajima's D analysis exhibits the most Tajima's D value only in admixture group (0.3600) which appears to be the cause of a sudden population contraction by rare alleles scarcity. A clear separation of some wild accessions from the admixed cultivated subpopulations was observed in PCA and phylogenetic analysis. Similar admixed pattern of population structure was estimated with an increased K values of 2 to 8 where genetic components of almost all cultivated subpopulations were shared with the wild which can also be subsequently estimated by very low F_ST-values by -0.011 (wild-aromatic) and -0.003 (wild-admixture).

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.216-216
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• 2022

The starch-branching enzymes (BEs) are responsible for synthesizing the amylopectin, which plays an important role in determining the structural and physical properties of starch granules. BE has two differently functioning isoforms (BEI and BEIIa/b) based on their difference in the chain-length pattern by the degree of polymerization (DP), which mainly contributes to the amylopectin chain length distribution in starch biosynthesis. In this study, we investigated functional haplotypes and evolutionary analyses of SBE1 in 374 rice accessions (320 Korean bred and 54 wild). The analyses were performed based on the classified subpopulations. Haplotype analysis generates a total of 8 haplotypes, of which only four haplotypes were functional carrying four functional SNPs in four different exons of SBE1 on chromosome 6. Nucleotide diversity analysis showed a highest pi-value in aromatic group (0.0029), while the lowest diversity value was in temperate japonica (0.0002), indicating the signal of this gene evolution origin. Different directional selections could be estimated by negative Tajima's D value of temperate japonica (-1.1285) and positive Tajima's D value of tropical japonica (0.9456), where the selective sweeps were undergone by both positive purifying and balancing selections. Phylogenetic analysis indicates a closer relationship of the wild with most of the cultivated subgroups indicating a common ancestor for SBE1 gene. FST-values indicate distant genetic relationships of temperate japonica from all other classified groups. PCA and population structure analysis show an admixed structure of wild and cultivated subpopulations in some proportions.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.217-217
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• 2022

Pullulanase (PUL), a debranching enzyme, has been utilized in hydrolyzing the a-1,6 glucosidic linkages in starch, amylopectin, pullulan, as well as related oligosaccharides. It has also been indicated that PUL is a novel indicator of inherent RS (Resistant Starch) formation in rice. In this study, we performed haplotype analysis on 320 bred rice accessions, and additional 54 wild accessions were added to study genetic diversity along with other population-based analyses of the PUL gene. Through these investigations, we summarized a total of 10 functional (non-synonymous) SNPs from 7 different exons on chromosome 4. There were 10 haplotypes, of which only six haplotypes were functional, implicating different subpopulations. Diversity reduction was noticed in temperate japonica (0.0005) compared to the highest one (aus, 0.0154), illustrating their higher genetic differentiation by F_ST-value (0.926). The highest Tajima^ D value was observed in indica (3.6613), indicating PUL gene domestication signature under balancing selection, while the lowest Tajima's D value was found in temperate japonica (-2.2191) which might have undergone under positive selection and purified due to the excess of rare alleles. PCA, population structure, and phylogenetic analyses provide information on the genetic relatedness between and or among the cultivated subpopulations and the wild based on PUL genomic region.

• The Korean Journal of Mycology
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• v.51 no.4
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• pp.287-306
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• 2023

According to our previous study, 500 species of yeast exist in Korea, including nine variants comprising 142 genera and 48 classes in two phyla. Additionally, 4,483 fungal species have been documented at the National Institute of Biological Resources (NIBR). However, despite the industrial use of several yeasts, only 173 species formed part of the National Species List of Korea (NSLK) as of December 2021, mainly due to the lack of taxonomic descriptions. This study aimed to investigate the taxonomy of seven newly isolated yeast species (Hyphopichia burtonii, Starmerella sorbosivorans, Cyberlindnera mycetangii, Cutaneotrichosporon oleaginosum, Nakazawaea ernobii, Pichia kudriavzevii, and Schizosaccharomyces japonicus) for inclusion in the NSLK. The strains were clustered for the phylogenetic analysis of fungal rDNA (D1/D2-26S) sequences. This study provides descriptions of their cell morphology and physiological characteristics, the results of which confirm the indigenous origin of these seven species in Korea and recommend their inclusion in the NSLK.

• Journal of Species Research
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• v.13 no.2
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• pp.111-126
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• 2024

Korean bamboo forests encompass 22,067 hectares and are dominated by Phyllostachys species. These forests serve as vital ecosystems, providing nourishment and habitat for diverse flora, fauna, and microorganisms. Among these inhabitants, various fungal species have been documented worldwide, displaying ecological roles as saprobes, parasites, and symbionts within or outside the bamboo host. However, a comprehensive study of bambusicolous fungi within the Korean bamboo ecosystem remains a critical gap in our knowledge. In this study, we conducted an extensive survey of bamboo materials collected from various bamboo forests and subsequently undertook fungal isolation. Primary identification of bambusicolous fungi was achieved through analysis of the internal transcribed spacer (ITS) region. As a result, we identified seven previously unrecorded bambusicolous fungal species (Fusarium bambusarum, Fusicolla violacea, Macroconia gigas, Neopestalotiopsis camelliae-oleiferae, Neopestalotiopsis iberica, Neopestalotiopsis longiappendiculata, and Thyridium punctulatum). Phylogenetic analysis using protein-coding genes appropriate for each taxon and morphological observation were conducted to ensure accurate identification. This study contributes to our understanding of fungal diversity within bamboo forests in Korea.