• Proceedings of the Korean Aquaculture Society Conference
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• 2003.10a
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• pp.35-35
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• 2003

We, for the first time, reported molecular sequences of large subunit ribosomal DNA Dl-D3 region of A. hiranoi, A. leei and A. satoanum hitherto unreported. In addition, this study presented the full-length sequences of A. affine, A. fraterculus, A. catenella and A. tamarense occurring in Korean coastal waters. In total, 17 Alexandrium morphospecies were subjected to the phylogenetic analysis using the Maximum-likelihood (ML) method. The alignment result of sequences of A. hiranoi and A. pseudogonyaulax showed that there were only two substitutions without length heterogeneity implying their genetic affiliation. In ML tree, A. leei formed a deeply diverging branch probably because of the accelerated evolutionary rate, and its phylogenetic position was so ambiguous to resolve the phylogenetic relationship to the residual taxa. An A. satoanum culture showing morphological variation in the sulcal plate formed an independent divergent branch with consistent sister relationship to A. hiranoi/A. pseudogonyaulax clade supported by the high posterior probability (PP) value. Blast search in GenBank showed the sequence data of A. affine, A. fraterculus, A. catenella and A. tamarense corresponded to their morphological species designation. In ML tree, Alexandrium species were commonly split into four main clades. The inter-clade relationships were not clear and usually supported by the week PP values. In general, the sulcal plate of Alexandrium species seemed to reflect the true phylogeny at the main clade level, and the connection between the 1 and the apical pore complex seemed to reflect the phylogeny at the subclade level.

• Journal of Species Research
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• v.5 no.1
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• pp.179-187
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• 2016

As a subset investigation to discover indigenous prokaryotic species in Korea, a total of 21 bacterial strains assigned to the class Betaproteobacteria were isolated from a wide range of environmental samples which collected from fresh water, roots of plants, mineral water and soil from ginseng farm. Phylogenetic analysis based on 16S rRNA gene sequences indicated that 21 isolated strains were most closely related to the class Betaproteobacteria, with high 16S rRNA gene sequence similarity (>99.1%) and constructed a robust phylogenetic clade with the closest species in the class Betaproteobacteria. These isolated species have no previous report or publication in Korea; therefore 17 species in 14 genera of 6 families in the order Burkholderiales, 1 species in the order Methylophilales, 2 species in 2 genera of 1 family in the order Neisseriales are reported for betaproteobacterial 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 and as an image.

• Journal of Species Research
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• v.7 no.2
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• pp.97-103
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• 2018

In 2016, as a subset study to discover indigenous prokaryotic species in Korea, a total of 15 bacterial strains were isolated and assigned to the class Betaproteobacteria. From the high 16S rRNA gene sequence similarity (>98.8%) 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 15 species have been described in Korea; therefore, 1 strain of the Aquitalea, 5 strains of the Paraburkholderia, 2 strains of the Comamonas, 1 strain of the Cupriavidus, 1 strain of the Diaphorobacter, 2 strains of the Hydrogenophaga, 1 strain of the Iodobacter, 1 strain of the Massilia and 1 strain of the Rhodoferax within the Betaproteobacteria are described for unreported bacterial species in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, and isolation sources are also described in the species description section.

• The Plant Pathology Journal
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• v.32 no.6
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• pp.500-507
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• 2016

Single-molecule real-time (SMRT) sequencing allows identification of methylated DNA bases and methylation patterns/motifs at the genome level. Using SMRT sequencing, diverse bacterial methylomes including those of Helicobacter pylori, Lactobacillus spp., and Escherichia coli have been determined, and previously unreported DNA methylation motifs have been identified. However, the methylomes of Xanthomonas species, which belong to the most important plant pathogenic bacterial genus, have not been documented. Here, we report the methylomes of Xanthomonas axonopodis pv. glycines (Xag) strain 8ra and X. campestris pv. vesicatoria (Xcv) strain 85-10. We identified $N^6$-methyladenine (6mA) and $N^4$-methylcytosine (4mC) modification in both genomes. In addition, we assigned putative DNA methylation motifs including previously unreported methylation motifs via REBASE and MotifMaker, and compared methylation patterns in both species. Although Xag and Xcv belong to the same genus, their methylation patterns were dramatically different. The number of 4mC DNA bases in Xag (66,682) was significantly higher (29 fold) than in Xcv (2,321). In contrast, the number of 6mA DNA bases (4,147) in Xag was comparable to the number in Xcv (5,491). Strikingly, there were no common or shared motifs in the 10 most frequently methylated motifs of both strains, indicating they possess unique species- or strain-specific methylation motifs. Among the 20 most frequent motifs from both strains, for 9 motifs at least 1% of the methylated bases were located in putative promoter regions. Methylome analysis by SMRT sequencing technology is the first step toward understanding the biology and functions of DNA methylation in this genus.

• Journal of Species Research
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• v.5 no.2
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• pp.241-253
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• 2016

In 2014, as a subset study to discover indigenous prokaryotic species in Korea, a total of 33 bacterial strains assigned to the class Gammaproteobacteria were isolated from diverse environmental samples collected from soil, tidal flat, freshwater, seawater, oil-contaminated soil, and guts of animal. From the high 16S rRNA gene sequence similarity (>98.5%) 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 33 species have been described in Korea; therefore, 1 strain of the Aeromonadales, 6 strains of the Alteromonadales, 3 strains of the Chromatiales, 5 strains of the Enterobacteriales, 4 strains of the Oceanospirillales, 11 strains of the Pseudomonadales, and 3 strains of the Xanthomonadales within the Gammaproteobacteria are described for unreported bacterial species in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, and isolation sources are also described in the species description section.

• Journal of Species Research
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• v.9 no.2
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• pp.85-104
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• 2020

In 2019, after a comprehensive investigation of indigenous prokaryotic species in Korea, a total of 12 bacterial strains assigned to the phylum Proteobacteria were isolated from soil. With the high 16S rRNA gene sequence similarity (>98.8%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to independent, predefined bacterial species. This study identified two species in the family Burkholderiaceae, one species in the family Comamonadaceae, two species in the family Oxalobacteraceae, one species in the family Micrococcaceae, one species in the family Bradyrhizobiaceae, one species in the family Methylobacteriaceae, one species in the family Rhizobiaceae, one species in the family Rhodocyclaceae, and one species in the family Sphingomonadaceae. There is no official report about these 12 species in Korea, so are described as unreported bacterial species in Korea in this study. Gram reaction, basic biochemical characteristics, colony, and cell morphology are also described in the species description section.

• Journal of Species Research
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• v.8 no.3
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• pp.249-258
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• 2019

Owing to a distinct environmental regime and anthropogenic effects, freshwater bacterial communities of urban streams are considered to be different from those of large freshwater lakes and rivers. To obtain unrecorded, freshwater bacterial species in Korea, water and sediment samples were collected from various urban streams of the Han River watershed in 2018. After plating the freshwater samples on R2A agar, approximately 1000 bacterial strains were isolated from the samples as single colonies and identified using 16S rRNA gene sequence analyses. A total of 26 strains, with >98.7% 16S rRNA gene sequence similarity with validly published bacterial species but not reported in Korea, were determined to be unrecorded bacterial species in Korea. The unrecorded bacterial strains were phylogenetically diverse and belonged to four phyla, six classes, 12 orders, 16 families, and 21 genera. At the generic level, the unreported species were assigned to Nocardioides, Streptomyces, Microbacterium, Kitasatospora, Herbiconiux, Corynebacterium, and Microbacterium of the class Actinobacteria; Paenibacillus and Bacillus of the class Bacilli; Caulobacter, Methylobacterium, Novosphingobium, and Porphyrobacter of the class Alphaproteobacteria; Aquabacterium, Comamonas, Hydrogenophaga, Laribacter, Rivicola, Polynucleobacter, and Vogesella of the class Betaproteobacteria; Arcobacter of the class Epsilonproteobacteria; and Flavobacterium of the class Flavobacteriia. The details of the 26 unreported species, including Gram reaction, colony and cell morphology, biochemical properties, and phylogenetic position are also provided in the strain descriptions.

• Journal of Species Research
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• v.10 no.3
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• pp.227-236
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• 2021

To obtain unrecorded freshwater bacterial species in Korea, water and sediment samples were collected from streams, lakes, and wetland of the Han River watershed in 2020. Approximately 800 bacterial strains were isolated on R2A agar after aerobic or anaerobic incubation, and identified using 16S rRNA gene sequences. A total of 28 strains, with ≥98.7% 16S rRNA gene sequence similarity with validly published bacterial species but not reported in Korea, were determined to be unrecorded bacterial species in Korea. The unrecorded bacterial strains were phylogenetically diverse and belonged to four phyla, eight classes, 13 orders, 19 families, and 25 genera. The unreported species were assigned to Acetobacter, Alsobacter, Mesorhizobium, Prosthecomicrobium, and Microvirga of the class Alphaproteobacteria; Vogesella, Formosimonas, Aquincola, Massilia, Acidovorax, and Brachymonas of the class Betaproteobacteria; Pseudoxanthomonas, Thermomonas, Lysobacter, Enterobacter, Kosakonia, and Acinetobacter of the class Gammaproteobacteria; Sulfuricurvum of the class Epsilonproteobacteria; Mycolicibacterium, Agromyces, Phycicoccus, and Microbacterium of the class Actinobacteria; Paenibacillus of the class Bacilli; Clostridium of the class Clostridia; and Flavobacterium of the class Flavobacteriia. The details of the unreported species, including Gram reaction, colony and cell morphology, biochemical characteristics, and phylogenetic position are also provided in the description of the strains.

• Journal of Species Research
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• v.11 no.3
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• pp.133-142
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• 2022

In 2020, 24 bacterial strains were isolated from algae, kudzu leaf, mud, pine cone, seashore sand, sea water, soil, tidal flat, and wetland from the Republic of Korea. Isolated bacterial strains were identified based on 16S rRNA gene sequences, and those exhibiting at least 98.7% sequence similarity with known bacterial species, but not reported in Korea, were highlighted as unrecorded species. These isolates were allocated to the phyla Bacteroidetes and Proteobacteria as unrecorded species in Korea. The four Bacteroidetes strains were classified into the families Chitinophagaceae, Flavobacteriaceae, and Sphingobacteriaceae (of the orders Chitinophagales, Flavobacteriales, and Sphingobacteriales, respectively). The 20 Proteobacteria strains belonged to the Aeromonadaceae, Marinobacter, Microbulbiferaceae, Enterobacteriaceae, Erwiniaceae, Morganellaceae, Yersiniaceae, Lysobacteraceae, Halomonadaceae, Moraxellaceae, Pseudomonadaceae, Steroidobacteraceae, Xanthomonadaceae, and Myxococcaceae (of the orders Aeromonadales, Alteromonadales, Cellvibrionales, Enterobacterales, Lysobacterales, Oceanospirillales, Pseudomonadales, Steroidobacter, Xanthomonadales, and Myxococcales). This study focused on the description of 24 unreported bacterial species in Korea in the phyla Bacteroidetes and Proteobacteria belonging to six classes.

• Korean Journal of Ecology and Environment
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• v.56 no.1
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• pp.14-35
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• 2023

Freshwater and brackish blue-green algae were collected at 43 freshwater and brackish sites (including lakes, ponds, swamps, streams, and rivers and estuaries) throughout South Korea from March 2017 to October 2018, and were identified using light microscopy. A total 223 taxa in freshwater and 230 taxa in brackish waters in 2017 and 274 taxa in fresh and brackish waters in 2018 were identified and among them, 20 taxa were unreported taxa of blue-green algae in Korea; The new recorded taxa were Aphanocapsa marina, Calothrix fusca f. durabilis, Calothrix littoralis, Calothrix parva, Chamaesiphon minimus, Chroococcidiopsis cubana, Chroococcidiopsis fissurarum, Coelosphaerium aerugineum, Dolichospermum mendotae, Eucapsis alpine, Gomphosphaeria cordiformis, Gomphosphaeria natans, Merismopedia danubiana, Lynbya aestuarii var. gaditana, Tolypothrix tenuis, Pseudocapsa maritima, Pseudocapsa sphaerica, Pseudophormidium tenue, Trichodesmus sp. and Woronichinia elorantae.