• Korean Journal of Microbiology
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• v.49 no.3
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• pp.282-285
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• 2013

Microbial diversities in the 300 m and 500 m deep seawaters near Goseong, Gangwon Province (South Korea), were investigated. Pyrosequencing of 16S rRNA genes of marine microbes resulted in 19,474 reads from the 300 m deep seawaters, which consisted of Alphaproteobacteria (57.41%) and Gammaproteobacteria (38.85%), and 82,806 reads from the 500 m deep seawaters, which consisted of Gammaproteobacteria (99.64%) mostly. Rhodobacterales (57.31%) were dominant in the 300 m deep seawaters, but Alteromonadales (45.65%) and Oceanospirillales (34.61%) were dominant in the 500 m deep seawaters. On the bases of operational taxonomic units and diversity indexes (Shannon and Simpson), biodiversity of marine bacteria in the 500 m deep seawaters was shown to be higher than that in the 300 m deep seawaters.

• Journal of Species Research
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• v.9 no.2
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• pp.105-116
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• 2020

A total of 37 anaerobic bacteria strains within the classes Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidia, Flavobacteriia, Bacilli, Clostridia, and Fusobacteriia were isolated from freshwater and sediment of the Geum River in Korea. The unreported species were related with Rhizobium and Oleomonas of the class Alphaproteobacteria; Acidovorax, Pseudogulbenkiania, and Aromatoleum of the class Betaproteobacteria; Tolumonas, Aeromonas, Cronobacter, Lonsdalea, and Phytobacter of the class Gammaproteobacteria; Bacteroides, Dysgonomonas, Macellibacteroides, and Parabacteroides of the class Bacteroidia; Flavobacterium of the class Flavobacteriia; Bacillus and Paenibacillus of the class Bacilli; Clostridium, Clostridioides, Paraclostridium, Romboutsia, Sporacetigenium, and Terrisporobacter of the class Clostridia; and Cetobacterium and Ilyobacter of the class Fusobacteriia. A total of 37 strains, with >98.7% 16S rRNA gene sequence similarity with validly published bacterial species, but not reported in Korea, were determined to be unrecorded anaerobic bacterial species in Korea.

• Korean Journal of Microbiology
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• v.51 no.3
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• pp.312-317
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• 2015

Pyrosequencing of 16S rDNA tags was used to obtain the bacterial diversity and community structure in the uncultured seawaters as well as in the cultured seawaters, which were collected from the 7 ports (Cheonbu, Hyunpo, Taeha, Namyang, Sadong, Dodong, and Jeodong) and 1 seashore (Guam) around the Ulleng island, Korea. Alphaproteobacteria were the most abundant group in the clean seawaters such as seawaters of Taeha and Sadong ports. Gammaproteobacteria proportion increased depending upon the wastewater amounts mixed with the seawaters such as seawaters of Namyang, Dodong, and Jeodong ports. The genuses of Alteromonas (from samples of Cheonbu, Taeha, Guam, Namyang, Sadong), Shewanella (from sample of Jeodong), and Vibrio (from samples of Hyunpo and Dodong) were dominant group in each of the cultured seawaters incubated in marine broth (Difoco). The results suggest that the incoming wastewaters to the port seawaters contribute to the dynamic change of the marine bacterial community around the Ulleng island.

• Korean Journal of Microbiology
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• v.49 no.4
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• pp.377-382
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• 2013

The bacterial community structures of the marine sponge, Dactylospongia metachromia, collected from Chuuk of Micronesia on February 2012, were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints of two individuals of D. metachromia, CH607 and CH840 showed the same band patterns. The sequences derived from DGGE bands revealed 93~100% similarities with known bacterial species in the public database and high similarity with uncultured bacterial clones. The bacterial community structures of both D. metachromia sponges (CH607, CH840) were composed of 6 phyla, 8 classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, Spirochaetes. DGGE fingerprint - based phylogenetic analysis revealed that the bacterial community profiles were identical in two individuals of the same sponge species collected from the same geographical location.

• Korean Journal of Microbiology
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• v.50 no.2
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• pp.152-157
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• 2014

The aim of this study was to investigate the bacterial community inhabited in Callyspongia elegans. Marine bacteria were isolated from the marine sponge C. elegans using marine agar. The resulting 112 isolated pure cultures were then used for further study. They were characterized by determining morphological characteristics through Gram's staining and morphological observation. The colony pigments of bacterial isolates were characterized as yellow, brown, ivory, and white. Thirty-seven strains were found to be Gram-positive and 75 strains were Gram-negative. Seventy-nine strains were coccus-shaped, while 16 strains were rod-shaped. On the basis of the results of the comparative analyses of 16S rDNA gene sequences, the 112 isolated bacteria were divided into 5 major groups: Alphaproteobacteria (39%), Gammaproteobacteria (22%), Actinobacteria (14%), Fimicutes (9%), and Bacteroidetes (6%). It is strongly suggested that fifteen isolates are candidates for a new genera or species, based on the analyses of 16S rDNA gene sequences.

• Journal of Species Research
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• v.7 no.1
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• pp.13-23
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• 2018

In 2016, as a part of the research program 'Survey of Korean Indigenous Species', diverse environmental samples were collected from various sources of freshwater, seawater, soil, wetland, reclaimed land, sand, pine forest, plant root, ginseng field, solar saltern, and caves. Thousands of bacterial strains were isolated from the diverse samples and identified based on 16S rRNA gene sequence analyses. The present study, as a phylogenetic subset of the primary research program, reports 24 unrecorded bacterial species in Korea that belong to the orders Rhizobiales and Sphingomonadales in the class Alphaproteobacteria. Based on the high 16S rRNA gene sequence similarities (>98.8%) and formation of a robust phylogenetic clade with the closest type species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 24 bacterial species have been described in Korea; therefore, 10 species of nine genera in the order Rhizobiales and 14 species of seven genera in the order Sphingomonadales are described for unreported alphaproteobacterial species in Korea. Gram reaction, colony and cell morphology, biochemical properties, and isolation sources are also provided in the species description section.

• Journal of Microbiology and Biotechnology
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• v.20 no.12
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• pp.1717-1723
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• 2010

The integrated fixed-film activated sludge (IFAS) system is a variation of the activated sludge wastewater treatment process, in which hybrid suspended and attached biomass is used to treat wastewater. Although the function and performance of the IFAS system are well studied, little is known about its microbial community structure. In this study, the composition and diversity of the bacterial community of suspended and attached biomass samples were investigated in a full-scale IFAS system using a high-throughput pyrosequencing technology. Distinct bacterial community compositions were examined for each sample and appeared to be important for its features different from conventional activated sludge processes. The abundant bacterial groups were Betaproteobacteria (59.3%), Gammaproteobacteria (8.1%), Bacteroidetes (5.2%), Alphaproteobacteria (3.9%), and Actinobacteria (3.2%) in the suspended sample, whereas Actinobacteria (14.6%), Firmicutes (13.6%), Bacteroidetes (11.6%), Betaproteobacteria (9.9%), Gammaproteobacteria (9.25%), and Alphaproteobacteria (7.4%) were major bacterial groups in the attached sample. Regarding the diversity, totals of 3,034 and 1,451 operational taxonomic units were identified at the 3% cutoff for the suspended and attached samples, respectively. Rank abundance and community analyses demonstrated that most of the diversity was originated from rare species in the samples. Taken together, the information obtained in this study will be a base for further studies relating to the microbial community structure and function of the IFAS system.

• Journal of Microbiology and Biotechnology
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• v.24 no.3
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• pp.313-323
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• 2014

Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coal-mining reclamation areas was suggested.

• Korean Journal of Microbiology
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• v.53 no.4
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• pp.309-315
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• 2017

Most of acidophiles are found in the various low pH environments and affect to metal cycle through oxidation and reduction reactions. The present study was carried out above 50 strains as acidophiles isolated from acidic soils of exhausted mine and Jeju Gotjawal. Finally, total 19 strains obtained and were tentatively identified based on comparative similarity analysis for 16S rRNA gene sequence and physiological characterizations. These isolates belonged to Gammaproteobacteria (6 strains), Actinobacteria (5 strains), Betaproteobacteria (4 strains), Alphaproteobacteria (2 strains), and Bacilli (2 strains). We observed that these isolates can grow under low pH culture condition. This case study for analysis physiological characterizations of indigenous microorganisms in acidic soil might provide basic information on useful application.

• Korean Journal of Food Science and Technology
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• v.53 no.3
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• pp.334-343
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• 2021

Various vegetables, including cucumbers, have a high probability of foodborne illness because they are usually eaten raw. In this study, we analyzed the 16S rRNA gene sequences of the cucumber (Cucumis sativus L.) microbiota. The diversity indices of cucumber cultivated in May were higher than in cucumber cultivated in November. At the phylum level, Proteobacteria, Firmicutes, and Actinobacteria were predominant. The classes generally comprised Gammaproteobacteria, Bacilli, Alphaproteobacteria, and Actinobacteria. At the genus level, the proportions of Aureimonas, Escherichia, and Microbacterium in samples from May were relatively high, whereas Enterococcus, Pseudomonas, and Rhizobium accounted for a higher proportion in samples from November. Moreover, it is noteworthy that potential pathogenic genera such as Acinetobacter, Aerococcus, Aureimonas, Enterobacter, Enterococcus, Escherichia, Pantoea, Pseudomonas, and Staphylococcus were detected. Although further studies on the characteristics of potential pathogens are required, our results can be used to improve the food safety of vegetables.