• Journal of Marine Bioscience and Biotechnology
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• v.7 no.2
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• pp.42-51
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• 2015

The community structure of cultivable bacteria associated with the marine sponge, Petrosia corticata, collected from Jeju Island in summer (September) of 2012 and winter (January) of 2013, were compared by the PCR-ARDRA method. Bacterial strains were cultured for 4 days at $26^{\circ}C$ on Zobell medium and marine agar medium. After PCR amplification of 16S rRNA gene of individual strains, the restriction enzymes MspI and HaeIII were used to make restriction patterns. As a result, 24 ARDRA patterns from the summer sponge and 20 ARDRA patterns from the winter sponge were obtained. The sequencing result of 1-3 selected strains from each pattern showed over 98% similarities with the known sequences from the public database. At the phylum level, the bacterial community structures of both sponges (summer and winter) were identical qualitatively and composed of 4 phyla : Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Alphaproteobacteria accounted for 42.5% of total in summer sponge and 25.2% in winter, decreasing in the winter sample. Gammaproteobacteria accounted for 27.5% of total in summer sponge and 35.2% in winter, increasing in the winter sample. At the genus and species level, summer sponge had more diverse bacterial communities than winter sponge. Actinobacteria, Bacteroidetes, and Firmicutes increased in the winter sample.

• Korean Journal of Environmental Biology
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• v.38 no.2
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• pp.289-298
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• 2020

As part of the research program "2018 Rapid screening and identification of freshwater microorganisms using MALDI-TOF/MS library" freshwater samples were collected from a branch of the Nakdong River. Almost 300 antibiotic-resistant bacterial strains were isolated from freshwater samples and subsequently identified by 16S rRNA gene sequencing. Seventeen strains among the isolates shared high 16S rRNA gene sequence similarity (>99.0%) with known species that were not previously recorded in Korea, and each of the isolates also formed a robust phylogenetic clade with the closest species. These species were phylogenetically diverse, belonging to four phyla, seven classes, 10 orders, and 13 genera. At the genus and class level, the previously unrecorded species belonged to Rhodovarius, Xanthobacter, and Shinella of the class Alphaproteobacteria; Ottowia, Simplicispira, and Zoogloea of Betaproteobacteria; Pseudomonas, Acinetobacter, and Shewanella of Gammaproteobacteria; Arcobacter of Epsilonproteobacteria; Sphingobacterium of Sphingobacteriia; Trichococcus of Bacilli; and Leucobacter of Actinobacteria. The previously unrecorded species were further characterized by examining their gram-staining, colony and cell morphology, biochemical properties, and phylogenetic position.

• Journal of Species Research
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• v.7 no.1
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• pp.60-72
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• 2018

Our study aimed to discover indigenous prokaryotic species in Korea. A total of 29 bacterial species in the phylum Proteobacteria were isolated from freshwater and sediment of rivers and brackish zones in Korea. From the high 16S rRNA gene sequence similarity (${\geq}98.8%$) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to an independent and predefined bacterial species. To our knowledge, there is no official report or publication that has previously described these 29 species in Korea. Specifically, we identified 10, 12, and seven species of eight, 12, and seven genera that belong to classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, respectively; all are reported as previously unrecorded bacterial species in Korea. The Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs for each are also described.

• Journal of Microbiology
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• v.45 no.1
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• pp.1-5
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• 2007

The bacterial compositions between the dental unit water system and human saliva were characterized and compared by direct sequence analysis of 16S rDNA clone libraries. Based on the species richness estimation, bacterial diversity in the dental unit water system (DUW) was more diverse than that of the human saliva (HS). The Chaol estimates of species richness in HS and DUW samples were 12.0 and 72.4, respectively. The total numbers of OTUs observed in the combined libraries accounted for 83% (HS) and 59% (DUW) of the Chaol diversity estimate as defined at the 80% similarity threshold. Based on the sequence analysis, the phylum Proteobacteria was the major group in both clone libraries at phylum level. DUW clone library contained 80.0% Proteobacteria, 8.0% Bacteroides, 4.0% Nitrospira, 4.0% Firmicutes, 2.0% Planctomycetes and 2.0% Acidobacteria. On the other hand, human saliva (HS) clone library contained 55.5% Proteobacteria, 36.1% Firmicutes and 8.4% Bacteroides. The majority of bacteria identified belonged to phylum Proteobacteria in both samples. In dental unit water system (DUW), Alphaproteobacteria was detected as the major group. There was no evidence of the bacterial contamination due to a dental treatment. Most sequences were related to microorganisms derived from biofilm in oligotrophic environments.

• Journal of Species Research
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• v.9 no.4
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• pp.339-345
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• 2020

The Earth contains billions of microbial species, although the vast majority cannot be cultured in laboratories and are thus considered unidentified and uncharacterized. Extremophiles are microorganisms that thrive in extreme conditions, including temperature, salinity, and pH. Extremophilic microorganisms have provided important insights for biological, metabolic, and evolutionary studies. Between 2017 and 2019, as part of a comprehensive investigation to identify bacterial species in Korea, eight bacterial strains were isolated from marine and non-marine environments in Jeju Island. These strains were cultured under extreme salinity or pH conditions. Phylogenetic analysis using 16S ribosomal RNA(rRNA) gene sequencing indicated that all eight strains belonged to the phyla Gammaproteobacteria, Bacilli, and Alphaproteobacteria. Based on their high 16S rRNA gene sequence similarities(>98.7%) and the formation of strong monophyletic clades with their closest related species, all isolated strains were considered as an unrecorded strain, previously unidentified species. Gram stain reaction, culture conditions, colony and cell morphology, biochemical characteristics, isolation source, and National Institute of Biological Resources(NIBR) IDs are described in this article. The characterization of these unrecorded strains provides information on microorganisms living in Korea.

• Journal of Microbiology
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• v.44 no.2
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• pp.171-176
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• 2006

A strictly aerobic, non-motile, ovoid-shaped Alphaproteobacteria, designated strain $JC2049^T$ was isolated from a tidal flat sediment sample. The results of 16S rRNA gene sequence analysis indicated that this isolate belonged to the genus Thalassobius, with a sequence similarity of 96.9-97.3% to other valid Thalassobius spp. The cells required 1-7% NaCl for growth (optimum 2%) and accumulated $poly-\beta-hydroxybutyrate$. Nitrite was reduced to nitrogen, but nitrate was not reduced to nitrite. No genetic potential for aerobic anoxygenic photosynthesis was detected. The primary isoprenoid quinone (Ubiquinone-10), predominant cellular fatty acids $(C_{18:1}{\omega}7c,\;11\;methyl\;C_{18:1}\omega7c\;and\;C_{16:0})$ and DNA G+C content (61 mol %) were all consistent with the assignment of this isolate to the genus Thalassobius. Several phenotypic characteristics clearly distinguished our isolate from other Thalassobius species. The degree of genomic relatedness between strain $JC2049^T$ and other Thalassobius species was in a range of 20-43 %. The polyphasic data presented in this study indicates that our isolate should be classified as a novel species within the genus Thalassobius. The name Thalassobius aestuarii sp. novo is therefore proposed for this isolate; the type strain is $JC2049^T(=IMSNU\;14011^T=KCTC\;12049^T=DSM\;15283^T)$.

• Journal of Microbiology and Biotechnology
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• v.26 no.2
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• pp.373-384
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• 2016

The membrane-aerated biofilm reactor (MABR) is a promising municipal wastewater treatment process. In this study, two cross-flow MABRs were constructed to explore the carbon and nitrogen removal performance and bacterial succession, along with changes of influent loading shock comprising flow velocity, COD, and NH₄-N concentrations. Redundancy analysis revealed that the function of high flow velocity was mainly embodied in facilitating contaminants diffusion and biosorption rather than the success of overall bacterial populations (p > 0.05). In contrast, the influent NH₄-N concentration contributed most to the variance of reactor efficiency and community structure (p < 0.05). Pyrosequencing results showed that Anaerolineae, and Beta- and Alphaproteobacteria were the dominant groups in biofilms for COD and NH₄-N removal. Among the identified genera, Nitrosomonas and Nitrospira were the main nitrifiers, and Hyphomicrobium, Hydrogenophaga, and Rhodobacter were the key denitrifiers. Meanwhile, principal component analysis indicated that bacterial shift in MABR was probably the combination of stochastic and deterministic processes.

• Journal of Species Research
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• v.7 no.3
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• pp.193-201
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• 2018

Culturable bacterial diversity was investigated using freshwater and sediment samples collected from the North Han River basin in 2017, as a part of the research program 'Survey of freshwater organisms and specimen collection'. Over a thousand bacterial strains were isolated from the samples and identified based on 16S rRNA gene sequences. Among the bacterial isolates, 22 strains showing higher than 98.7% sequence similarity with validly published bacterial species, but not reported in Korea, were classified as unrecorded species in Korea. The 22 bacterial strains were phylogenetically diverse and assigned to 6 classes, 11 orders, 15 families, and 21 different genera. At the generic level, the unreported species were affiliated with Flavobacterium of the class Flavobacteria, Flexibacter of the class Cytophagia, Blastomonas, Brevundimonas, Elstera, Rhizobium, Roseomonas, Sphingomonas, and Xanthobacter of the class Alphaproteobacteria, Albidiferax, Cupriavidus, Curvibacter, Ferribacterium, Hydrogenophaga, Iodobacter, Limnohabitans, Polaromonas, Undibacterium, and Variovorax of the class Betaproteobacteria, Pseudomonas of the class Gammaproteobacteria, and Arcobacter of the class Epsilonproteobacteria. The unreported bacterial species were further characterized by examining Gram reaction, colonial and cellular morphology, and biochemical properties. The detailed descriptions of 22 strains of the unreported bacterial species are also provided.

• Journal of Species Research
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• v.9 no.2
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• pp.77-84
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• 2020

As a part of the research project "Survey of freshwater organisms and specimen collection," freshwater samples were collected from the Nakdong River. Among the bacterial isolates, we selected strains that showed higher than 98.7% 16S rRNA gene sequence similarity with confirmed bacterial species previously unreported in South Korea. The 14 new records to South Korea were phylogenetically diverse and belonged to four phyla, six classes, 11 orders, and 14 genera. At the genus level, these species were found to be affiliated with Reyranella, Ferrovibrio, Brevundimonas, and Aquidulcibacter of the class Alphaproteobacteria; Pseudomonas, Cellvibrio, and Photobacterium of the class Gammaproteobacteria; Paenibacillus and Bacillus of the phylum Firmicutes; Chryseobacterium, Flavobacterium, Pedobacter of the phylum Bacteroidetes; and Actinomadura and Leifsonia of the phylum Actinobacteria. These species were further characterized by examining their Gram reaction, colony and cell morphologies, biochemical properties, and phylogenetic positions. The detailed descriptions of these 14 previously unreported species are provided.

• Journal of Species Research
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• v.11 no.3
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• pp.143-154
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• 2022

To obtain unrecorded bacterial species in Korea, various marine samples were collected from Jeollanam-do Province, Korea in 2021. After plating the samples on marine agar and marine R2A agar, and incubating aerobically and anaerobically, approximately 1200 bacterial strains were isolated and identified using 16S rRNA gene sequences. A total of 30 strains showed ≥98.7% 16S rRNA gene sequence similarity with validly published bacterial species but not reported in Korea, indicating that they are unrecorded bacterial species in Korea. The unrecorded bacterial strains belonged to 4 phyla, 7 classes, 13 orders, 19 families, and 22 genera, which were assigned to Azospirllium, Loktanella, and Pseudovibrio of the class Alphaproteobacteria; Grimontia, Halomonas, Marinobacter, Microbulbifer, Photobacterium, Pseudoalteromonas, Pseudidiomarina, Ferrimonas, Shewanella, Simiduia, Thalassotalea, and Vibrio of the class Gammaproteobacteria; Priestia and Enterococcus of the class Bacilli; Persicobacter of the class Cytophagia; Aureivirga of the class Flavobacteriia; Propionigenium and Psychrilyobacter of the class Fusobacteriia; and Tepidibacter of the class Clostridia. 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.