• Journal of Microbiology and Biotechnology
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• v.26 no.4
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• pp.757-762
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• 2016

The group of Fe(III) oxide-reducing bacteria includes exoelectrogenic bacteria, and they possess similar properties of transferring electrons to extracellular insoluble-electron acceptors. The exoelectrogenic bacteria can use the anode in microbial fuel cells (MFCs) as the terminal electron acceptor in anaerobic acetate oxidation. In the present study, the anodic community was compared with the community using Fe(III) oxide (ferrihydrite) as the electron acceptor coupled with acetate oxidation. To precisely analyze the structures, the community was established by enrichment cultures using the same inoculum used for the MFCs. High-throughput sequencing of the 16S rRNA gene revealed considerable differences between the structure of the anodic communities and that of the Fe(III) oxide-reducing community. Geobacter species were predominantly detected (>46%) in the anodic communities. In contrast, Pseudomonas (70%) and Desulfosporosinus (16%) were predominant in the Fe(III) oxide-reducing community. These results demonstrated that Geobacter species are the most specialized among Fe(III)-reducing bacteria for electron transfer to the anode in MFCs. In addition, the present study indicates the presence of a novel lineage of bacteria in the genus Pseudomonas that highly prefers ferrihydrite as the terminal electron acceptor in acetate oxidation.

• Ocean Science Journal
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• v.40 no.3
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• pp.145-153
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• 2005

Variation in the microbial biomass and community structure found in sediment of heavily polluted bays and the adjacent unpolluted areas were examined using phospholipid fatty acid analysis. Total microbial biomass and microbial community structure were responding to environmental determinants, sediment grain size, depth of sediment, and pollution due to petroleum hydrocarbons. The marker fatty acids of microeukaryotes and prokaryotes - aerobic, anaerobic, and sulfate-reducing bacteria - were detected in sediments of the areas studied. Analysis of the fatty acid profiles revealed wide variations in the community structure in sediments, depending on the extent of pollution, sediment depth, and sediment grain size. The abundance of specific bacterial fatty acids points to the dominance of prokaryotic organisms, whose composition differed among the stations. Fatty acid distributions in sediments suggest the high contribution of aerobic bacteria. Sediments of polluted sites were significantly enriched with anaerobic bacteria in comparison with clean areas. The contribution of this bacterial group increased with the depth of sediments. Anaerobic bacteria were predominantly present in muddy sediments, as evidenced from the fatty acid profiles. Relatively high concentrations of marker fatty acids of sulfate-reducing bacteria were associated with organic pollution in this site. Specific fatty acids of microeukaryotes were more abundant in surface sediments than in deeper sediment layers. Among the microeukaryotes, diatoms were an important component. Significant amounts of bacterial biomass, the predominance of bacterial biomarker fatty acids with abundance of anaerobic and sulfate-reducing bacteria are indicative of a prokaryotic consortium responsive to organic pollution.

• The Plant Pathology Journal
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• v.32 no.2
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• pp.136-144
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• 2016

Pseudomonas fluorescens pc78 is an effective biocontrol agent for soil-borne fungal diseases. We previously constructed a P43-gfp tagged biocontrol bacteria P. fluorescens pc78-48 to investigate bacterial traits in natural ecosystem and the environmental risk of genetically modified biocontrol bacteria in tomato rhizosphere. Fluctuation of culturable bacteria profile, microbial community structure, and potential horizontal gene transfer was investigated over time after the bacteria treatment to the tomato rhizosphere. Tagged gene transfer to other organisms such as tomato plants and bacteria cultured on various media was examined by polymerase chain reaction, using gene specific primers. Transfer of chromosomally integrated P43-gfp from pc78 to other organisms was not apparent. Population and colony types of culturable bacteria were not significantly affected by the introduction of P. fluorescens pc78 or pc78-48 into tomato rhizosphere. Additionally, terminal restriction fragment length polymorphism profiles were investigated to estimate the influence on the microbial community structure in tomato rhizosphere between non-treated and pc78-48-treated samples. Interestingly, rhizosphere soil treated with strain pc78-48 exhibited a significantly different bacterial community structure compared to that of non-treated rhizosphere soil. Our results suggest that biocontrol bacteria treatment influences microbial community in tomato rhizosphere, while the chromosomally modified biocontrol bacteria may not pose any specific environmental risk in terms of gene transfer.

• Journal of Korean Society on Water Environment
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• v.31 no.4
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• pp.399-406
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• 2015

A sequencing batch reactor was operated under different pH conditions to see the influence of free ammonia (FA) and free nitrous acid (FNA) to microbial community on ammonium partial nitrification. Long-term influences of FA and FNA were evaluated by polymerase chain reaction-denaturing gradient gel electrophoresis and fluorescence in situ hybridization. Nitrite accumulation was successfully achieved at pH 8.2 and 6.3. The shifts in the microbial community were observed when influent ammonia concentration increased to 1 g $NH_4$-N/L at pH 8.2, and then when pH was dropped to 6.3. Both Nitrosomonas and Nitrosospira were selected during the startup of the reactor, and eventually became dominant members as ammonia-oxidizing bacteria. The results of molecular microbiological analysis strongly suggested that the composition of microbial community was changed according to the method used to control nitrite-oxidizing bacteria.

• 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
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• v.37 no.1
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• pp.10-13
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• 1999

The bacterial abundance, proportion of respiring bacteria, and bacterial community of southern Lake Baikal were analyzed at 1 m and 400m depths during winter. The total bacterial numbers were 5.1${\times}$105 cells ml-1 at 1 m and 2.5${\times}$105 cells ml-1 at 400 m depth, which are about half and quarter of the numbers of other lakes. The proportion of respiring bacteria was as low as 2.5% at 1 m and 1.4% at 400 m depth. Considering the amount of organic carbon which need to be degraded and low proportion of respiring bacteria, the bacteria could be assumed to have high activities. The EUB/DAPI ratios were 77 and 89% at 1 m and 400 m depths, respectively. Of the bacterial community, the other group was dominant at both depths, and gamma group of protebacteria followed next. But the beta group of proteobacteria and Cytophaga-Flavobacterium groups occupied very small proportions.

• Journal of Microbiology and Biotechnology
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• v.27 no.10
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• pp.1808-1819
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• 2017

Knowledge on the functional characteristics and temporal variation of anaerobic bacterial populations is important for better understanding of the microbial process of two-stage anaerobic reactors. However, owing to the high diversity of anaerobic bacteria, close attention should be prioritized to the frequently abundant bacteria that were defined as core bacteria and putatively functionally important. In this study, using MiSeq sequencing technology, the core bacterial community of 98 operational taxonomic units (OTUs) was determined in a two-stage upflow blanket filter reactor treating pharmaceutical wastewater. The core bacterial community accounted for 61.66% of the total sequences and accurately predicted the sample location in the principal coordinates analysis scatter plot as the total bacterial OTUs did. The core bacterial community in the first-stage (FS) and second-stage (SS) reactors were generally distinct, in that the FS core bacterial community was indicated to be more related to a higher-level fermentation process, and the SS core bacterial community contained more microbes in syntrophic cooperation with methanogens. Moreover, the different responses of the FS and SS core bacterial communities to the temperature shock and influent disturbance caused by solid contamination were fully investigated. Co-occurring analysis at the Order level implied that Bacteroidales, Selenomonadales, Anaerolineales, Syneristales, and Thermotogales might play key roles in anaerobic digestion due to their high abundance and tight correlation with other microbes. These findings advance our knowledge about the core bacterial community and its temporal variability for future comparative research and improvement of the two-stage anaerobic system operation.

• Journal of Microbiology and Biotechnology
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• v.27 no.5
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• pp.995-1004
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• 2017

Culture-dependent methods, such as heterotrophic plate counting (HPC), are usually applied to evaluate the bacteriological quality of hemodialysis water. However, these methods cannot detect the uncultured or viable but non-culturable (VBNC) bacteria, both of which may be quantitatively predominant throughout the hemodialysis water treatment system. Therefore, propidium monoazide (PMA)-qPCR associated with HPC was used together to profile the distribution of the total viable bacteria in such a system. Moreover, high-throughput sequencing of 16S rRNA gene amplicons was utilized to analyze the microbial community structure and diversity. The HPC results indicated that the total bacterial counts conformed to the standards, yet the bacteria amounts were abruptly enhanced after carbon filter treatment. Nevertheless, the bacterial counts detected by PMA-qPCR, with the highest levels of $2.14{\times}10^7copies/100ml$ in softener water, were much higher than the corresponding HPC results, which demonstrated the occurrence of numerous uncultured or VBNC bacteria among the entire system before reverse osmosis (RO). In addition, the microbial community structure was very different and the diversity was enhanced after the carbon filter. Although the diversity was minimized after RO treatment, pathogens such as Escherichia could still be detected in the RO effluent. In general, both the amounts of bacteria and the complexity of microbial community in the hemodialysis water treatment system revealed by molecular approaches were much higher than by traditional method. These results suggested the higher health risk potential for hemodialysis patients from the up-to-standard water. The treatment process could also be optimized, based on the results of this study.

• Korean Journal of Soil Science and Fertilizer
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• v.48 no.2
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• pp.81-86
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• 2015

Soil management for orchard depends on the effects of soil microbial activities. The present study evaluated the soil microbial community of 25 orchard (5 sites for sandy loam, 7 sites for silt loam, and 13 sites for loam) in Gyeongnam Province by fatty acid methyl ester (FAME) method. The average values for 25 orchard soil samples were $270nmol\;g^{-1}$ of total FAMEs, $72nmol\;g^{-1}$ of total bacteria, $34nmol\;g^{-1}$ of Gram-negative bacteria, $34nmol\;g^{-1}$ of Gram-positive bacteria, $6nmol\;g^{-1}$ of actinomycetes, $49nmol\;g^{-1}$ of fungi, and $7nmol\;g^{-1}$ of arbuscular mycorrhizal fungi. In addition, silt loam soils had significantly low ratio of cy17:0 to $16:1{\omega}7c$ and cy19:0 to $18:1{\omega}7c$ compared with those of loam soils (p < 0.05), indicating that microbial activity increased. The average soil microbial communities in the orchard soils were 26.7% of bacteria, 17.9% of fungi, 12.6% of Gram-negative bacteria, 12.5% of Gram-positive bacteria, 2.5% of arbuscular mycorrhizal fungi, and 2.2% of actinomycetes. The soil microbial community of Gram-negative bacteria in silt loam soils was significantly higher than those of sandy loam and loam soils (p < 0.05).

• Ocean and Polar Research
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• v.39 no.4
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• pp.245-255
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• 2017

There are a number of pieces of evidences that suggest a link between marine diatoms and microorganisms, but knowledge about related microbial communities is greatly lacking. The present study investigated the microbial community structures related to the growth of the marine diatom Cyclotella meneghiniana. We collected free-living bacteria (FLB) and particle-associated bacteria (PAB) at each growth stage (e.g., lag, exponential, stationary and death) of the diatom, and analyzed their bacterial 16S rDNA using pyrosequencing. Metagenomics analysis showed that community structures of FLB and PAB differed considerably with the progress of growth stages. FLB showed higher diversity than PAB, but variation in the different growth stages of C. meneghiniana was more evident in PAB. The proportion of the genus Hoeflea, belonging to the order Rhizobiales, was dominant in both FLB and PAB, and it gradually increased with the growth of C. meneghiniana. However, Enhydrobacter clade tended to considerably decrease in PAB. In addition, Marinobacter decreased steadily in FLB, but first increased and then decreased in PAB. These results suggest that Hoeflea, Enhydrobacter, and Marinobacter may be closely related to the growth of diatom C. meneghiniana.