• Korean Journal of Microbiology
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• v.34 no.4
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• pp.194-199
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• 1998

Bacterial diversity was determined by amplification and sequencing of 16S rDNA at Tancheon and Jungrang in Han river. Twenty-seven clones constructed were divided 7 groups using RFLP. Fifteen clones were classified 4 groups in Tancheon and the group (HT-1 clone) including many clones was affiliated a high similarity with Aerobacter cryaerophilus (the class Proteobacteria including members of the delta subdivisions). The other two groups (HT-6 and HT-9 clone) including several clones were classified with the class Cytophagales in Tancheon. Twelve clones were classified 3 groups in Jungrang and the group (HJ-1 clone) including many clones was affiliated a high similarity with Sphingomonas sp. (the class Proteobacteria including members of the alpha subdivisions). As a whole results, the class Proteobacteria (alpha, beta and delta subdivision), the order Cytophagales, and the order Actinomycetales were detected.

• Korean Journal of Microbiology
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• v.43 no.3
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• pp.210-216
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• 2007

The principal objective of this study was to analyze 16S rDNA-ARDRA of the humus forest soil via an improved manual method and an ISOIL kit on the basis of the UPGMA clustering of the 16S rDNA combined profile, 44 ARDRA clusters of 76 clones via the ISOIL kit method and 45 ARDRA clusters of 136 clones via the improved manual method. On the basis of the 16S rDNA sequences, 44 clones from the ARDRA clusters by the ISOIL kit were classified into 3 phyla : ${\alpha}-,\;{\beta}-,\;{\gamma}-,\;{\delta}-Proteobacteria$, Acidobacteria and Actinobacteria. Using the improved manual method, the specimens were classified into 6 phyla : the ${\alpha}-,\;{\beta}-,\;{\gamma}-,\;{\delta}-Proteobacteria$, Acidobacteria, Bacteroides, Verrucomicrobia, Planctomycetes and Gemmatomonadetes. As a result, the modified manual method indicated greater phylogenetic diversity than was detected by the ISOIL kit. Approximately 40 percent of the total clones were identified as ${\alpha}-Proteobacteria$ and 30 percent of the total clones were ${\gamma}-Proteobacteria$ and assigned to dominant phylogenetic groups using the ISOIL kit. Using the modified manual method, 41 percent of the total clones were identified as Acidobacteria and 28 percent of total clones were identified as ${\alpha}-proteobacteria$ and assigned to dominant phylogenetic groups.

• Korean Journal of Microbiology
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• v.40 no.3
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• pp.189-198
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• 2004

T-RFLP analysis and clone sequencing analysis based on bacterial 16S rDNA were conducted to assess bacterial community structure and diversity in two layers (0-1cm, 6-7cm depth) of the sediment from Janghwari intertidal flat in Ganghwa Island. The results of T-RFLP (terminal-restriction fragment length polymorphism) analysis using restriction enzyme HhaI showed that the T-RFs of various size ($60{\pm}2$) bp-($667{\pm}2$) bp) appeared evenly at the surface sediments but two T-RFs with 60(${\pm}2$)bp and 93 (${\pm}2$)bp predominated at 6-7cm depth. Analysis of partial sequences for 172 clones revealed that 98% of the clones were not matched with the sequences of cultured bacteria strains in the GenBank (${\geq}similarity$ 98%), and approximately 86% of them were classified as different phylotypes. Most clones belonged to $\alpha$-, $\gamma$-, and $\delta$-Proteobacteria, Acidobacteria/Holophaga and green nonsulfur bacteria group. Proteobacteria group occupied the highest proportion in both layers (69% at 0-1cm depth and 46% at 6-7cm depth). $\gamma$-Proteobacteria and $\delta$-Proteobacteria that are associated with oxidation and reduction of sulfur compounds were appeared to be dominant, and comprised 21.5% and 15.7% of total clones, respectively. Overall results indicated that extremely diverse bacterial groups were inhabiting in the sediment of Ganghwa intertidal flat, and bacterial communities associated with the behaviour of sulfur seemed to playa significant role in the biogeochemical environment in this anoxic sediment.

• Korean Journal of Microbiology
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• v.51 no.1
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• pp.31-38
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• 2015

The bacterial community structures of two marine sponges, Cinachyrella sp. and Plakortis sp., collected from Chuuk in the South Pacific in February 2012 were analyzed by PCR-DGGE (Denaturing Gradient Gel Electrophoresis) fingerprinting. After isolation of the total genomic DNAs from the sponges, the V3 regions of the 16S rRNA genes were amplified and subjected to DGGE profiling. The two species of sponges displayed different DGGE band patterns. The sequences derived from the DGGE bands revealed 85-100% similarities to known bacterial species in the public database. The bacterial community of Cinachyrella sp. was composed of 6 classes: Actinobacteria, Bacteroidetes, Chloroflexi, and Proteobacteria (Alpha-, Gamma-, Delta-). The bacterial community of Plakortis sp. included 7 classes: Actinobacteria, Chloroflexi, Firmicutes, Spirochaetes, and Proteobacteria (Alpha-, Gamma-, Delta-). Though Actinobacteria, Chloroflexi and Proteobacteria were commonly found in both sponges, the predominant bacterial communities differed between the two. Namely, the predominant bacterial groups in Cinachyrella sp. and Plakortis sp. were Proteobacteria and Chloroflexi, respectively. The sponge-associated bacteria are sponge host-specific, as each of the tested sponges from the same geographical location had different predominant bacterial diversity.

• Korean Journal of Microbiology
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• v.39 no.4
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• pp.260-266
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• 2003

In this study bacterial community was analyzed to evaluate the impacts of long-term use of agricultural chemicals on a soil ecosystem as well as to obtain fundamental data on the relationship. Sequences of 16S rRNA clones from a non-agricultural site and a tangerine orchard soil which has a history of long-term use of agricultural chemicals over 30 years were analyzed. This revealed that bacterial community containing 5 divisions and 18 genera was distributed in a tangerine orchard soil, while bacterial community containing 9 divisions and 44 genera was distributed. In a tangerine orchard soil site, the most abundant bacteria in subdivision level were placed into Proteobacteria γ group which occupied 56% of total clones. The other bacterial clones from the ocrhcard soil exposed to agricultural chemicals over 30 years were Acidobacteria group (25%), Fimicutes group (5%), Planctomycetes group (2%), Proteobacteria α (1%), δ group (1%), and Cyanobacteria group (1%). Whereas, the clones were from the non-agricultural site were distributed among the division or subdivision Acidobacteria group (14%), Planctomycetes group (13%), Proteobacteria α (10%), β (9%), δ (9%), Fimicutes group (8%), Verrucomicrobia group (8%), Actinobacteria group (6%), Proteobacteria γ group (3%), Bacteroidetes group (3%), Gemmatimonadetes group (3%), and Cyanobacteria group (1%). This finding suggests the possibility that long-term application of agricultural chemicals or fertilizers on a tangerine orchard might result in drastic reduction or alteration in the composition of the bacterial community in the contaminated soil site.

• Korean Journal of Microbiology
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• v.37 no.2
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• pp.137-144
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• 2001

In order to investigate the diversity of bacterial community in the mud flat of Sunchon Bay, Chunnam province, diversity of amplified 16S rDNA was examined. Total DNA was extracted from sediment soils and 16S rDNAs were amplified using PCR primers based on the universally conserved sequences in bacteria. Clonal libraries were constructed and 111 clones were examined by amplified rDNA restriction analysis (ARDRA) using HaeIII. Clones were clustered based on restriction patterns using computer program, GelCompar II. One hundred different RFLP types were detected from 111 clones. The 20 clones were selected and sequenced according to dendrograms derived from ARDRA, to cover most of the bacterial diversity in the clone libraries. None of the clones were identical to any representatives in the Ribosomal Database Project small subunit RNA databases and GenBank. All sequences showed between 77 and 96.8% similarity to the known 16s rRNA sequence from cultured organisms. The 20 clones sequenced fell into seven major lineages of the domain Bacteria: alpha-, delta-, gamma-Proteobacteria, low G+C Gram positive bacteria, high G+C Gram positive bacteria, Sphingobacteria (Cytophaga) and Cyanobacteria (chloroplast). Among the clones, the Proteobacteria were dominant.

• Journal of Microbiology and Biotechnology
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• v.16 no.10
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• pp.1640-1645
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• 2006

We studied the diversity of the halophilic archaea and bacteria in crystallizer ponds of a Korean solar saltern by analyzing 16S rRNA gene libraries. Although diverse halophilic archaeal lineages were detected, the majority (56%) were affiliated with the uncultured and cultured Halorubrum group. Halophilic archaea that have been frequently observed in solar saltern environments previously, such as Halogeometricum, Halococcus, Haloarcula, and Haloferax, were not detected in our samples. The majority of clones (53%) belonged to the Cytophaga-Flavobacterium-Bacteroides and ${\alpha}-,\;{\gamma}-,\;and\;{\delta}-Proteobacteria$ groups, with 47% of the clones being affiliated with ${\gamma}-Proteobacteria$. We also identified new ${\delta}-Proteobacteria$-related bacteria that have not been observed in hypersaline environments previously. Our data show that the diversity of the halophilic archaea and bacteria in our Korean saltern differs from that of solar salterns found in other geographic locations. We also showed by quantitative real-time PCR analysis that bacteria can form a significant component of the microbial community in solar salterns.

• Microbiology and Biotechnology Letters
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• v.44 no.1
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• pp.84-88
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• 2016

In this study, bacterial diversity in the living room and bathroom of a residential environment was analyzed using the pyrosequencing method. There was no difference in the diversity index of bacteria between the 2 rooms; however, differences were noted in the composition of bacteria. The classes ${\beta}$-Proteobacteria and ${\delta}$-Proteobacteria were found in the bathroom at higher abundances than in the living room. The phyla Acidobacteria, Chlorobi, Chloroflexi, Fusobacteria, Nitrospirae, and Planctomycetes were found in the bathroom, but not in the living room, indicating a broader range of bacteria. However, the living room showed a more diverse range of bacterial genera than the bathroom did. In both the living room and the bathroom, the genus Methylobacterium was dominant.

• Journal of Environmental Health Sciences
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• v.34 no.6
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• pp.403-413
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• 2008

Toxic effect of methyl tert-butyl ether (MTBE), tert-butyl alcohol (TBA) and formaldehyde (FA) on microbial activity and diversity was compared in rice field, leek patch, and tidal mud flat soil samples. MTBE, TBA and FA with different concentrations were added into microcosms containing these soil samples, and placed at room temperature for 30 days. Then the microbial activities such as dehydrogenase and viable cell numbers and microbial community using a DGGE (Denaturing gradient gel electrophoresis) fingerprinting method were measured. Among the samples, dehydrogenase activity in rice field was inhibited the most by MTBE, TBA and FA. The toxic effect was higher according to the following orders: FA > MTBE > TBA. Dominant species in the microcosms contaminated with MTBE, TBA and FA were Chloroflex, Bacilli, gamma-proteobacteria in the rice field sample, Sphingobacteria, Flavobacteria, Actinobacteria, Bacilli, gamma-proteobacteria in the leek patch sample, and Sphingobacteria, Flavobacteria, delta-proteobacteria, gamma-proteobacteria in the tidal mud flat sample.

• Journal of Microbiology and Biotechnology
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• v.14 no.1
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• pp.205-211
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• 2004

A 16S rDNA clone library was generated to investigate the bacterial diversity in tidal flat sediment in Ganghwa Island, Republic of Korea. A total of 103 clones were sequenced and analyzed by comprehensive phylogenetic analyses. No clones were identical to any of known 16S rRNA sequences in public databases. Sequenced clones fell into thirteen lineages of the domain Bacteria: the alpha, beta, gamma, delta, and epsilon Proteobacteria, Actinobacteria, CFB group, Chloroflexi, Acidobacteria, Planctomycetes, Verrucomicrobia, and known uncultured candidate divisions (OP11, BRC1, KSB1, and WS1). Two clones were not associated with any known bacterial divisions. The majority of clones belonged to the gamma and delta Proteobacteria (46.7%). Clones of Actinobacteria were distantly related to known taxa. It is evident from 16S rDNA-based community analysis that the bacterial community in tidal flat sediment is remarkably diverse and unique among other marine environments examined so far.