• Korean Journal of Microbiology
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• v.34 no.3
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• pp.169-174
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• 1998

To define the structure and diversity of bacterial communities in the aqutic ecosystem, Lake Soyang, the largest artificial reservoir in Korea, a new method, fluorescent in situ hybridization was applied. This technique relies on the specific hybridization of the nucleic acid probes to the naturally amplified intracellular rRNA. By this method, the bacterial community composition of Lake Soyang and bacterial numbers belong to eubacteria, proteobacteria and Cytophaga-Flavobacterium group were estimated. Total bacterial numbers ranged from $0.3{\times}10^6{\sim}2.0{\times}10^6cells{\cdot}ml^{-1}$, and vertical profile of total bacteria showed the peak at 2 and 5 m depths. The ratio of eubacteria to total bacteria were 22~100% and varied with depth and season. The percentage of Proteobacteria ${\alpha}$-group ranged 2.6~66.7%, ${\beta}$-group 4.5~53.5%, ${\gamma}$-group 4.6~76.7% and Cytophaga-Flavobacterium group 2.1~35.9%. Also, bacteria] community had spatial and temporal characteristics. The dominant groups were ${\beta}$-group in winter, ${\gamma}$-group in spring and early summer and ${\alpha}$-group in summer.

• Journal of Life Science
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• v.23 no.3
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• pp.406-414
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• 2013

The influence of a gradual increase in salinity on the diversity of aquatic bacterial in rivers was demonstrated. The denaturing gradient gel electrophoresis (DGGE) was used to analyze the bacterial community shift downstream in the Hyeongsan River until it joins the open ocean. Four water samples were taken from the river showing the salinity gradients of 0.02%, 1.48%, 2.63%, and 3.62%. The samples were collected from four arbitrary stations in 2.91 km intervals on average, and a DGGE analysis was performed. Based on the results of this analysis, phylogenetic similarity identification, tree analysis, and a comparison of each station were performed. The results strongly suggested that the response of the bacterial community response was concomitant to gradual changes in salinity, which implies that salt concentration is a major factor in shifting the microbiota in aquatic habitats. The results also imply a huge diversity in a relatively small area upstream from the river mouth, compared to that in open oceans or coastal regions. Therefore, areas downstream towards a river mouth or delta are could be good starting points in the search for new bacterial species and strains ("biotypes").

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2000.10a
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• pp.109-117
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• 2000

Bacterial community structure composing enhanced biological phosphorus removal (EBPR) activated sludge was analyzed phylogenetically by cloning 165 rDNA after direct DNA extraction. Then, this result was compared with 165 rDNA sequences of randomly isolated bacterial species. The results clearly showed that there are no coincidence between the sequences retrieved directly from activated sludge and those of isolated strains, suggesting that many important bacteria are hidden in activated sludge because of the difficulty in isolation and culture of them.

• Korean Journal of Microbiology
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• v.38 no.4
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• pp.287-292
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• 2002

The composition of bacterial communities was detected in surface water of Cheonho Reservoir dominated by cyanobacteria, using fluorescent in situ hybridization (FISH) method. Total bacterial numbers were very high ranging from 0.6～$1.3{\times}10^7 \cells{\cdot}ml^-1$, whereas the ratio of Eubacteria to total bacteria was 29.8~45.8%, which was lower than that in other freshwater ecosystems. On average only 2.1% of DAPI-stained bacteria were detected by FISH with probes for $\alpha$, $\beta$, and $\gamma$-groups, respectively. Unknown eubacteria which was not bound to any probes except EUB 338, was relatively high. On the other hand, the Cytophaga-Flavobacterium group increased following the change of dominant species from Anabaena sp. to Microcystis sp. This result showed that bacterial communities could be affected by phytoplanktons, especially cyanobacteria.

• Korean Journal of Microbiology
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• v.45 no.2
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• pp.170-176
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• 2009

Culture-independent 16S rDNA-DGGE profiling and phylogenetic analysis were used to examine the predominant bacterial communities associated with the two sponges, Dictyonella sp. and Spirastrella abata from Jeju island. The culture-independent approach involved extraction of total bacterial DNA, PCR amplification of the 16S ribosomal DNA using primer pair 341f-GC and 518r, and separation of the amplicons on a denaturing gradient gel. Denaturing gradient gel electrophoresis banding patterns indicated 8 and 7 bands from the two sponge species, Dictyonella sp. and Spirastrella abata, respectively. There were not common major bands in two different sponges. Comparative sequence analysis of variable DGGE bands revealed from 93% to 98% similarity to the known published sequences. The dominant bacterial group of Dictyonella sp. belonged to uncultured Gammaproteobacteria, while, that of Spirastrella abata belonged to uncultured Alphaproeobacteria and Firmicutes. DGGE analysis indicated predominant communities of the sponge-associated bacteria differ in the two sponges from the same geographical location. This result revealed that bacterial community profiles of the sponges were host species-specific.

• Korean Journal of Microbiology
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• v.38 no.3
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• pp.192-197
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• 2002

Fluorescent in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes was used to compare the community structures of free-living and aggregated bacteria at thawing period in Lake Baikal. Targeted groups were Eubacteria, $\alpha$-, $\beta$-, $\gamma$- proteobacteria groups, Cytophaga-Flavobacterium group and Planctomycetales. Total bacterial numbers of free-living bacteria were ranged from $0.2{\times}10^6\cells{\cdot}ml^-1$ to $3.2{\times}10^6\cells{\cdot}ml^-1$, which were decreasing with depth, while the aggregated bacterial numbers were dramatically increasing from $0.4{\times}10^4 to 3.3{\times}10^4 \cells{\cdot}ml^-1$ with depth. The ratios of EUB probe binding cells to DAPI counts were ranged from 52.3 to 74.1% in free-living bacteria, and from 39.6 to 66.7% in the aggregated bacteria, respectively. Community structures of the aggregated bacteria were very different from each free-living bacteria at every depth. At 25 m depth, where the chlorophyll a concentration was highest, both structures were quite different from those of surface layers, rendering the fact that the community structures might be affected by phytoplankton. The vertical profile of community structure of aggregated bacteria is particular. The proportion of $\beta$-proteobacteria group was increasing with depth and it was 51.8% at 100 m, but the dominant group was $\gamma$-pro-teobacteria group at 250 m. Taken together, the biodiversity and succession of aggregated bacteria are quite different from free-living bacteria.

• Journal of Microbiology and Biotechnology
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• v.19 no.9
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• pp.858-868
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• 2009

The abundance, biomass, size distribution, and taxonomic composition of bacterial and protistan (heterotrophic and autotrophic nanoflagellates and ciliates) communities were investigated in six lakes of Masurian Lake District (north-eastern Poland) differing in trophic state. Samples were taken from the trophogenic water layer during summer stratification periods. Image analysis techniques with fluorescent in situ hybridization (FISH) as well as [$^3H$]-methyl-thymidine incorporation methods were applied to analyze differences in the composition and activity of bacterial communities. The greatest differences in trophic parameters were found between the humic lake and remaining non-humic ones. The same bacterial and heterotrophic nanoflagellate (HNF) cell size classes dominated in all the studied lakes. However, distinct increases in the contributions of large bacterial (>$1.0{\mu}m$) and HNF (>$10{\mu}m$) cells were observed in eutrophic lakes. The bacterial community was dominated by the ${\beta}$-Proteohacteria group, which accounted for 27% of total DAPI counts. Ciliate communities were largely composed of Oligotrichida. Positive correlations between bacteria and protists, as well as between nanoflagellates (both heterotrophic and autotrophic) and ciliates, suggest that concentrations of food sources may be important in determining the abundance of protists in the studied lakes.

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.169-178
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• 2010

The microbial community structure in Thailand soils contaminated with low and high levels of arsenic was determined by denaturing gradient gel electrophoresis. Band pattern analysis indicated that the bacterial community was not significantly different in the two soils. Phylogenetic analysis obtained by excising and sequencing six bands indicated that the soils were dominated by Arthrobacter koreensis and $\beta$-Proteobacteria. Two hundred and sixty-two bacterial isolates were obtained from arsenic-contaminated soils. The majority of the As-resistant isolates were Gramnegative bacteria. MIC studies indicated that all of the tested bacteria had greater resistance to arsenate than arsenite. Some strains were capable of growing in medium containing up to 1,500 mg/l arsenite and arsenate. Correlations analysis of resistance patterns of arsenite resistance indicated that the isolated bacteria could be categorized into 13 groups, with a maximum similarity value of 100%. All strains were also evaluated for resistance to eight antibiotics. The antibiotic resistance patterns divided the strains into 100 unique groups, indicating that the strains were very diverse. Isolates from each antibiotic resistance group were characterized in more detail by using the repetitive extragenic palindromic-PCR (rep-PCR) DNA fingerprinting technique with ERIC primers. The PCR products were analyzed by agarose gel electrophoresis. The genetic relatedness of 100 bacterial fingerprints, determined by using the Pearson product-moment similarity coefficient, showed that the isolates could be divided into four clusters, with similarity values ranging from 5-99%. Although many isolates were genetically diverse, others were clonal in nature. Additionally, the arsenic-resistant isolates were examined for the presence of arsenic resistance (ars) genes by using PCR, and 30% of the isolates were found to carry an arsenate reductase encoded by the arsC gene.

• The Korean Journal of Pesticide Science
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• v.21 no.1
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• pp.1-8
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• 2017

Although a global ban on the use of endosulfan, an organochloline insecticide, has taken effect in mid-2012, it has been still used in several countries, including India and China, and detected in diverse environments in the world due to its relative persistence and semi-volatility. In this study, the effect of endosulfan on soil bacterial community was investigated using 16S rRNA gene pyrosequencing method. When endosulfan was applied to an upland soil at a rate of 100 mg/kg soil (ES soil), the number of operational taxonomic units (OTU) and diversity indices for bacteria initially decreased and gradually recovered to the level of the non-treated soil (NT soil) during an eight-week incubation period. At bacterial phylum level, relative abundances of Proteobacteria and Verrucomicrobia were higher while those of Chloroflexi and Spirochaetes were lower in the ES soil than in the NT soil, suggesting that an endosulfan application affects the bacterial community structure in soil. In the ES soil, the relative abundances of the OTUs affiliated to the genera Sphingomonas and Burkholderia increased in the initial period of incubation while those affiliated to the genera Pseudonocardia and Opitutus increased in the late period of incubation. Because the first three genera contain bacterial strains reported to degrade endosulfan, they are expected to be involved in the degradation of endosulfan, probably one after another.

• Animal Bioscience
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• v.37 no.2
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• pp.261-273
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• 2024

Objective: The objective of this study was to evaluate the growth performance, rumen fermentation parameters and bacterial community of post-weaning dairy calves in response to five diets varying in corn silage (CS) inclusion. Methods: A total of forty Holstein weaned bull calves (80±3 days of age;128.2±5.03 kg at study initiation) were randomized into five groups (8 calves/group) with each receiving one of five dietary treatments offered as total mixed ration in a 123-d feeding study. Dietary treatments were control diet (CON; 0% CS dry matter [DM]); Treatment 1 (T1; 27.2% CS DM); Treatment 2 (T2; 46.5% CS DM); Treatment 3 (T3; 54.8% CS DM); and Treatment 4 (T4; 67.2% CS DM) with all diets balanced for similar protein and energy concentration. Results: Results showed that calves offered CS had greater average daily gain, body length and chest depth growth, meanwhile altered rumen fermentation indicated by decreased rumen acetate concentrations. Principal coordinate analysis showed the rumen bacterial community structure was affected by varying CS inclusion diets. Bacteroidetes and Firmicutes were the predominant bacterial phyla in the calf rumens across all treatments. At the genus level, the abundance of Bacteroidales_RF16_group was increased, whereas Unclassified_Lachnospiraceae was decreased for calves fed CS. Furthermore, Spearman's correlation test between the rumen bacteria and rumen fermentation parameters indicated that Bacteroidales_RF16_group and Unclassified Lachnospiraceae were positively correlated with propionate and acetate, respectively. Conclusion: The results of the current study suggested that diet CS inclusion was beneficial for post-weaning dairy calf growth, with 27.2% to 46.5% CS of diet DM recommended to achieve improved growth performance. Bacteroidales_RF16_group and Unclassified Lachnospiraceae play an important role in the rumen fermentation pattern for post-weaning calves fed CS.