• Journal of Microbiology and Biotechnology
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• v.23 no.5
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• pp.602-613
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• 2013

This paper aims at an investigation of the features of bacterial communities in surface sediments of the South China Sea (SCS). In particular, biogeographical distribution patterns and the phylogenetic diversity of bacteria found in sediments collected from a coral reef platform, a continental slope, and a deep-sea basin were determined. Bacterial diversity was measured by an observation of 16S rRNA genes, and 18 phylogenetic groups were identified in the bacterial clone library. Planctomycetes, Deltaproteobacteria, candidate division OP11, and Alphaproteobacteria made up the majority of the bacteria in the samples, with their mean bacterial clones being 16%, 15%, 12%, and 9%, respectively. By comparison, the bacterial communities found in the SCS surface sediments were significantly different from other previously observed deep-sea bacterial communities. This research also emphasizes the fact that geographical factors have an impact on the biogeographical distribution patterns of bacterial communities. For instance, canonical correspondence analyses illustrated that the percentage of sand weight and water depth are important factors affecting the bacterial community composition. Therefore, this study highlights the importance of adequately determining the relationship between geographical factors and the distribution of bacteria in the world's seas and oceans.

• Journal of Microbiology and Biotechnology
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• v.16 no.5
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• pp.740-747
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• 2006

Amplification by universal consensus sequences in pathogenic bacterial DNA would allow rapid identification of pathogenic bacteria, and amplification of genus-specific and species-specific sequences of pathogenic bacterial DNA might be used for genotyping at the genus and species levels. For design of probes for molecular diagnostics, several tools are available as stand-alone programs or as Web application. However, since most programs can design only a few probe sets at one time, they are not suitable for large-scale and automatic probes design. Therefore, for high-throughput design of specific probes in diagnostic array development, an automated design tool is necessary. Thus, we developed a Web-based automatic system for design of genus-specific and species-specific probes for pathogen detection. The system is available at http://www.miprobe.com.

• Journal of Microbiology
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• v.43 no.1
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• pp.1-10
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• 2005

We isolated and cultured bacteria inhabiting solar saltern ponds in Taean-Gun, Chungnam Province, Korea. All of the isolated 64 strains were found to be moderately halophilic bacteria, growing in a salt range of 2-20 %, with an optimal concentration of 5% salt. Bacterial diversity among the isolated halophiles was evaluated via RFLP analyses of PCR-amplified 16S rDNAs, followed by phylogenetic analysis of the partial 16S rDNA sequences. The combination of restriction enzyme digestions with HaeIII, CfoI, MspI and RsaI generated 54 distinct patterns. A neighbor-joining tree of the partial 16S rDNA sequences resulted in the division of the 64 strains into 2 major groups, 45 strains of ${\gamma}-Proteobacteria$ (70.3%) and 19 strains of Firmicutes (29.7%). The ${\alpha}-Proteobacteria$ and Cytophaga-Flavobacterium-Bacterioides groups, which were repeatedly found to exist in thalassohaline environments, were not represented in our isolates. The ${\gamma}-Proteobacteria$ group consisted of several subgroups of the Vibrionaceae (37.5%), Pseudoalteromonadaceae (10.9%), Halomonadaceae (7.8%), Alteromonadaceae (7.8%), and Idiomarinaceae (6.3%). Members of Salinivibrio costicola (29.7%) were the most predominant species among all of the isolates, followed by Halobacillus treperi (12.5%). Additionally, three new species candidates were found, based on similarities of the 16S rDNA sequences to those of previously published species.

• The Korea Genome Conference
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• 2006.09a
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• pp.36-36
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• 2006

• The Korea Genome Conference
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• 2005.09a
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• pp.66-66
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• 2005

• Journal of Microbiology and Biotechnology
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• v.21 no.6
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• pp.590-598
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• 2011

Bacterial assimilation of $CO_2$ into stable biomolecules using electrochemical reducing power may be an effective method to reduce atmospheric $CO_2$ without fossil fuel combustion. For the enrichment of the $CO_2$-fixing bacteria using electrochemical reducing power as an energy source, a cylinder-type electrochemical bioreactor with a built-in anode compartment was developed. A graphite felt cathode modified with neutral red (NR-graphite cathode) was used as a solid electron mediator to induce bacterial cells to fix $CO_2$ using electrochemical reducing power. Bacterial $CO_2$ consumption was calculated based on the variation in the ratio of $CO_2$ to $N_2$ in the gas reservoir. $CO_2$ consumed by the bacteria grown in the electrochemical bioreactor (2,000 ml) reached a maximum of approximately 1,500 ml per week. Time-coursed variations in the bacterial community grown with the electrochemical reducing power and $CO_2$ in the mineral-based medium were analyzed via temperature gradient gel electrophoresis (TGGE) of the 16S rDNA variable region. Some of the bacterial community constituents noted at the initial time disappeared completely, but some of them observed as DNA signs at the initial time were clearly enriched in the electrochemical bioreactor during 24 weeks of incubation. Finally, Alcaligenes sp. and Achromobacter sp., which are capable of autotrophically fixing $CO_2$, were enriched to major constituents of the bacterial community in the electrochemical bioreactor.

• Journal of Microbiology and Biotechnology
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• v.21 no.4
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• pp.333-340
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• 2011

Herbicide-tolerant Zoysia grass has been previously developed through Agrobacterium-mediated transformation. We investigated the effects of genetically modified (GM) Zoysia grass and the associated herbicide application on bacterial community structure by using culture-independent approaches. To assess the possible horizontal gene transfer (HGT) of transgenic DNA to soil microorganisms, total soil DNAs were amplified by PCR with two primer sets for the bar and hpt genes, which were introduced into the GM Zoysia grass by a callus-type transformation. The transgenic genes were not detected from the total genomic DNAs extracted from 1.5 g of each rhizosphere soils of GM and non-GM Zoysia grasses. The structures and diversities of the bacterial communities in rhizosphere soils of GM and non-GM Zoysia grasses were investigated by constructing 16S rDNA clone libraries. Classifier, provided in the RDP II, assigned 100 clones in the 16S rRNA gene sequences library into 11 bacterial phyla. The most abundant phyla in both clone libraries were Acidobacteria and Proteobacteria. The bacterial diversity of the GM clone library was lower than that of the non- GM library. The former contained four phyla, whereas the latter had seven phyla. Phylogenetic trees were constructed to confirm these results. Phylogenetic analyses of the two clone libraries revealed considerable difference from each other. The significance of difference between clone libraries was examined with LIBSHUFF statistics. LIBSHUFF analysis revealed that the two clone libraries differed significantly (P<0.025), suggesting alterations in the composition of the microbial community associated with GM Zoysia grass.

• Research in Plant Disease
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• v.16 no.1
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• pp.35-40
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• 2010

Suppression effect of the 12 bacterial isolates from plant rhizosphere against late blight caused by Phytophthora citrophthora were investigated on citrus fruits. Among the bacterial isolates, THJ609-3, TRH423-3, BRH433-2, Lyso-chit and KRY505-3 presented disease suppression after wound inoculation with the fungal pathogen in vivo. The anti-fungal activity was evaluated by measuring the length of inhibition zone of the mycelium P. citrophthora adjacent to the effective bacterial isolates in which all of the 5 bacterial isolates showed antagonistic effects. However, there was no positive correlations between the efficacy of disease suppression and the antagonistic effect. On the other hand, Lyso-chit and KRY505-3 were identified as Bacillus cereus, BRH433-2 as B. circulans and TRH423-3 as Burkholderia gladioli, respectively, by analysis of rDNA sequence on the internal transcript spaces. It is suggested that the effective bacterial isolates may be useful for finding biological control agents against late blight especially on environment-friendly farm where the application of fungicide is limited.

• Parasites, Hosts and Diseases
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• v.45 no.1 s.141
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• pp.1-9
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• 2007

The endosymbionts of 4 strains of Acanthamoeba(KA/E9, KA/E21, KA/E22, and KA/E23) isolated from the infected corneas of Korean patients were characterized via orcein stain, transmission electron microscopic examination, and 16S rDNA sequence analysis. Double membrane-bound, rod-shaped endosymbionts were distributed randomly throughout both the trophozoites and cysts of each of Acanthamoeba isolates. The endosymbionts of KA/E9, KA/E22, and KA/E23 were surrounded by electron-translucent areas. No lacunae-like structures were observed in the endosymbionts of KA/E21, the bacterial cell walls of which were studded with host ribosomes. Comparative analyses of the 16S rDNA sequences showed that the endosymbionts of KA/E9, KA/E22 and KA/E23 were closely related to Caedibacter caryophilus, whereas the KA/E21 endosymbiont was assigned to the Cytophaga-Flavobacterium-Bacteroides(CFB) phylum. In the 4 strains of Acanthamoeba, the hosts of the endosymbionts were identified as belonging to the Acanthamoeba castellanii complex, which corresponds to the T4 genotype. Acanthamoeba KA/E21 evidenced characteristics almost identical to those of KA/E6, with the exception of the existence of endosymbionts. The discovery of these endosymbionts from Acanthamoeba may prove essential to future studies focusing on interactions between the endosymbionts and the amoebic hosts.

• Journal of Microbiology and Biotechnology
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• v.18 no.5
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• pp.815-820
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• 2008

Two culture-independent methods, namely ribosomal DNA libraries and denaturing gradient gel electrophoresis (DGGE), were adopted to examine the microbial community of a Malaysian light crude oil. In this study, both 16S and 18S rDNAs were PCR-amplified from bulk DNA of crude oil samples, cloned, and sequenced. Analyses of restriction fragment length polymorphism (RFLP) and phylogenetics clustered the 16S and 18S rDNA sequences into seven and six groups, respectively. The ribosomal DNA sequences obtained showed sequence similarity between 90 to 100% to those available in the GenBank database. The closest relatives documented for the 16S rDNAs include member species of Thermoincola and Rhodopseudomonas, whereas the closest fungal relatives include Acremonium, Ceriporiopsis, Xeromyces, Lecythophora, and Candida. Others were affiliated to uncultured bacteria and uncultured ascomycete. The 16S rDNA library demonstrated predomination by a single uncultured bacterial type by >80% relative abundance. The predomination was confirmed by DGGE analysis.