• Asian-Australasian Journal of Animal Sciences
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• v.32 no.1
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• pp.92-102
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• 2019

Objective: To investigate changes in rumen fermentation characteristics and bacterial community by a sudden change to a high concentrate diet (HC) in Korean domestic ruminants. Methods: Major Korean domestic ruminants (each of four Hanwoo cows; $545.5{\pm}33.6kg$, Holstein cows; $516.3{\pm}42.7kg$, and Korean native goats; $19.1{\pm}1.4kg$) were used in this experiment. They were housed individually and were fed ad libitum with a same TMR (800 g/kg timothy hay and 200 g/kg concentrate mix) twice daily. After two-week feeding, only the concentrate mix was offered for one week in order to induce rapid rumen acidosis. The rumen fluid was collected from each animals twice (on week 2 and week 3) at 2 h after morning feeding using an oral stomach tube. Each collected rumen fluid was analyzed for pH, volatile fatty acid (VFA), and $NH_3-N$. In addition, differences in microbial community among ruminant species and between normal and an acidosis condition were assessed using two culture-independent 16S polymerase chain reaction (PCR)-based techniques (terminal restriction fragment length polymorphism and quantitative real-time PCR). Results: The HC decreased ruminal pH and altered relative concentrations of ruminal VFA (p<0.01). Total VFA concentration increased in Holstein cows only (p<0.01). Terminal restriction fragment length polymorphism and real-time quantitative PCR analysis using culture-independent 16S PCR-based techniques, revealed rumen bacterial diversity differed by species but not by HC (p<0.01); bacterial diversity was higher in Korean native goats than that in Holstein cows. HC changed the relative populations of rumen bacterial species. Specifically, the abundance of Fibrobacter succinogenes was decreased while Lactobacillus spp. and Megasphaera elsdenii were increased (p<0.01). Conclusion: The HC altered the relative populations, but not diversity, of the ruminal bacterial community, which differed by ruminant species.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.19 no.2
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• pp.147-154
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• 2014

Bacteria play an important role in biogeochemical cycles in marine environments and their functional attributes in ecosystems depend primarily on species composition. In this study, seasonal variation of bacterial diversity was investigated by pyrosequencing of 16S rDNA in surface sediment and overlying seawater collected in the south East Sea, planned for the site of $CO_2$ sequestration by the carbon capture and storage (CCS) project. Gammaproteobacteria was dominant in the sediment in most seasons, whereas Alphaproteobacteria was a most dominant group in the overlying water. Thus, the bacterial diversity greatly differ between sediment and seawater samples. On the genus level, bacterial diversity between two habitats was also different. However, the number of genera found over 5% were less than 10 in both habitats and the bacterial community was composed of a number of diverse minor or rare genera. Elevation of $CO_2$ concentration during a $CO_2$ storage process, could result in change of bacterial diversity. Thus, this study will be very useful to access the effect of $CO_2$ on bacterial diversity and to predict functional change of the ecosystem during the process of CCS project.

• Membrane and Water Treatment
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• v.10 no.1
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• pp.29-38
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• 2019

Microbial community and composition in stormwater runoff from mixed land use land cover (LULC) catchment with ongoing land development was diverse across the hydrological stage due different environmental parameters (hydrometeorological and physicochemical) and source of runoff. However, limited studies have been made for bacterial composition in this catchment. Therefore, this study aims to: (1) quantify the concentration of fecal indicator bacteria (FIB), stormwater quality and bacterial composition and structure according to hydrological stage; and (2) determine their correlation to environmental parameters. The 454 pyrosequencing was used to determine the bacterial community and composition; while Pearson's correlation was used to determine the correlation among parameters-FIB, stormwater quality, bacterial composition and structure-to environmental parameters. Results demonstrated that the initial and peak runoff has the highest concentration of FIB, stormwater quality and bacterial composition and structure. Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were dominant bacteria identified in this catchment. Furthermore, the 20 most abundant genera were correlated with runoff duration, average rainfall intensity, runoff volume, runoff flow, temperature, pH, organic matter, nutrients, TSS and turbidity. An increase of FIB and stormwater quality concentration, diversity and richness of bacterial composition and structure in this study was possibly due to leakage from septic tanks, cesspools and latrines; feces of domestic and wild animals; and runoff from forest, destroyed septic system in land development site and urban LULC. Overall, this study will provide an evidence of hydrological stage impacts on the runoff microbiome environment and public health perspective.

• Environmental Engineering Research
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• v.12 no.2
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• pp.37-45
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• 2007

Phytoremediation has been used effectively for the biodegradation of oil-based contaminants, including diesel, by the stimulation of soil microbes near plant roots (rhizosphere). However, the technique has rarely been assessed for itsinfluence on soil microbial properties such as population, community structure, and diversity. In this study, the removal efficiency and characteristics of rhizobacteria for phytoremediation of diesel-contaminated soils were assessed using barnyard grass (Echinochloa crusgalli). The concentration of spiked diesel for treatments was around $6000\;mg\;kg^{-1}$. Diesel removal efficiencies reached 100% in rhizosphere soils, 76% in planted bulk soils, and 62% in unplanted bulk soils after 3weeks stabilization and 2 months growth(control, no microbial activity: 32%). The highest populations of culturable soil bacteria ($5.89{\times}10^8$ per g soil) and culturable hydrocarbon-degraders($5.65{\times}10^6$ per g soil) were found in diesel-contaminated rhizosphere soil, also yielding the highest microbial dehydrogenase. This suggests that the populations of soil bacteria, including hydrocarbon-degraders, were significantly increased by a synergistic rhizosphere + diesel effect. The diesel treatment alone resulted in negative population growth. In addition, we investigated the bacterial community structures of each soil sample based on DGGE (Denaturing Gel Gradient Electrophoresis) band patterns. Bacterial community structure was most influenced by the presence of diesel contamination (76.92% dissimilarity to the control) and by a diesel + rhizosphere treatment (65.62% dissimilarity), and least influenced by the rhizosphere treatment alone (48.15% dissimilarity). Based on the number of distinct DGGE bands, the bacterial diversity decreased with diesel treatment, but kept constant in the rhizosphere treatment. The rhizosphere thus positively influenced bacterial population density in diesel-contaminated soil, resulting in high removal efficiency of diesel.

• Microbiology and Biotechnology Letters
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• v.38 no.3
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• pp.263-272
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• 2010

One hundred sixty three strains showing different colony morphological characteristics on different concentration of marine agar (MA) plates were isolated from ambient seawater near Dokdo island. Bacterial diversity and distributions were studied by phylogenetic analysis of the partial 16S rRNA gene sequences. One hundred sixty three strains were partially sequenced and analyzed phylogenetically. They were composed of 5 phyla, of which gamma-proteobacteria (58%), alpha-proteobacteria (20%), bacteriodetes (16%) were predominant. They were affiliated with 90 species. The 16S rRNA sequence similarity of the isolates was in 93.3 to 100 % range to reported sequence data. Thirty six isolates of among them were assumed to be novel species candidates based on similarity analysis of the 16S rRNA gene sequences. Overall, Proteobacteria and Bacteriodetes of the Dokdo coastal sea water showed a high diversity.

• 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.

• Journal of Conservation Science
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• v.38 no.1
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• pp.64-71
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• 2022

Many investigations have been conducted on the biological damage and environmental conditions necessary to preserve the Janggyeong Panjeon and Daejanggyeongpan (woodblocks). We performed a survey on the concentration and diversity of airborne fungi in the Janggyeong Panjeon and compared them with the results of a survey from 2012. The temperature of the Beopbojeon building was slightly lower, while the relative humidity was higher than those found at the Sudarajang building. The concentration of airborne fungi in the Beopbojeon was 1.44-fold that of the Sudarajang. It was confirmed that the concentration and diversity of airborne fungi in the Janggyeong Panjeon differed depending on the sampling site. In total, 23 fungal genera were identified from the air samples, and 11 fungal and 1 bacterial genera were identified from the surface of the woodblocks. Among these, only five types of fungi were commonly distributed in the indoor air and surface of the Daejanggyeongpan; however, 58.3% of the fungi identified on the surface of the woodblocks were not observed in the in the air samples. The surface-dwelling fungi may accumulate dust to form microbial communities over time.

• 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").

• Korean Journal of Microbiology
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• v.49 no.4
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• pp.336-342
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• 2013

Trichloroethylene (TCE) is a widely used substance in commercial and industrial applications, yet it must be removed from the contaminated soil and groundwater environment due to its toxic and carcinogenic nature. We investigated bacterial community structure, dominant bacterial strain, and removal efficiency in a TCE contaminated groundwater treatment system using immobilized carrier. The microbial diversity was determined by the nucleotide sequences of 16S rRNA gene library. The major bacterial population of the contaminated groundwater treatment system was belonging to BTEX degradation bacteria. The bacterial community consisted mainly of one genus of Pseudomonas (Pseudomonas putida group). The domination of Pseudomonas putida group may be caused by high concentration of toluene and TCE. Furthermore, we isolated a toluene and TCE degrading bacterium, named Pseudomonas sp. DHC8, from the immobilized carrier in bioreactor which was designed to remove TCE from the contaminated ground water. Based on the results of morphological and physiological characteristics, and 16S rRNA gene sequence analysis, strain DHC8 was identified as a member of Pseudomonas putida group. When TCE (0.83 mg/L) and toluene (60.61 mg/L) were degraded by this strain, removal efficiencies were 72.3% and 100% for 12.5 h, respectively. Toluene removal rate was 2.89 ${\mu}mol/g$-DCW/h and TCE removal rate was 0.02 ${\mu}mol/g$-DCW/h. These findings will be helpful for maintaining maximum TCE removal efficiency of a reactor for bioremediation of TCE.

• Journal of Microbiology and Biotechnology
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• v.22 no.9
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• pp.1264-1270
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• 2012

The ecotoxicological effects of nanomaterials on animal, plant, and soil microorganisms have been widely investigated; however, the nanotoxic effects of plant-soil interactive systems are still largely unknown. In the present study, the effects of ZnO nanoparticles (NPs) on the soil-plant interactive system were estimated. The growth of plant seedlings in the presence of different concentrations of ZnO NPs within microcosm soil (M) and natural soil (NS) was compared. Changes in dehydrogenase activity (DHA) and soil bacterial community diversity were estimated based on the microcosm with plants (M+P) and microcosm without plants (M-P) in different concentrations of ZnO NPs treatment. The shoot growth of M+P and NS+P was significantly inhibited by 24% and 31.5% relative to the control at a ZnO NPs concentration of 1,000 mg/kg. The DHA levels decreased following increased ZnO NPs concentration. Specifically, these levels were significantly reduced from 100 mg/kg in M-P and only 1,000 mg/kg in M+P. Different clustering groups of M+P and M-P were observed in the principal component analysis (PCA). Therefore, the M-P's soil bacterial population may have more toxic effects at a high dose of ZnO NPs than M+P's. The plant and activation of soil bacteria in the M+P may have a less toxic interactive effect on each of the soil bacterial populations and plant growth by the ZnO NPs attachment or absorption of plant roots surface. The soil-plant interactive system might help decrease the toxic effects of ZnO NPs on the rhizobacteria population.