• 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 Ecology and Environment
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• v.36 no.4
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• pp.223-233
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• 2013

Acid deposition is one of the most serious environmental problems in ecosystems. The present study surveyed the effects of simulated acid rain on leaf litter mass loss and microbial community in the decomposing leaf litter of Sorbus anifolia in a microcosm at $23^{\circ}C$ and 40% humidity. Microbial biomass was measured by substrate-induced respiration (SIR) and phospholipid fatty acids (PLFAs), and the microbial community structures were determined by composition of PLFAs at each interval of decomposition in litter sample and at each pH treatment. The microbial biomass showed peaks at mid-stage of decomposition, decreasing at the late stage. The leaf litter mass loss of S. anifolia decreased with decreasing pH during early and mid-decomposition stages; however the mass loss becomes similar between pH treatments at late-decomposition stage. The acidification remarkably lowers the microbial biomass of bacteria and fungi; however, microbial diversity was unchanged between pH treatments at each stage of litter decomposition. With changes of decomposition stage and pH treatment there were considerable differences in replacement and compensation of microbial species. Fungi/bacteria ratio was considerably changed by pH treatment. The PLFA profile showed significantly larger fungi/bacteria ratio at pH 5 than pH 3 at the early stage of decomposition, and the difference becomes smaller at the later decomposition stage. At low pH, pH 3 and pH 4, the fungi/bacteria ratios were stable according to the litter decomposition stages. Simulated acid rain caused decreases of 10Me17:0, 16:1${\omega}$7c, 18:1${\omega}$7, 15:0, but increase of 24:0. In addition, litter mass loss showed significant positive correlation with microbial biomass measured by SIR and PLFA on the decomposing leaf litter.

• Journal of Ecology and Environment
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• v.33 no.3
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• pp.261-270
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• 2010

Increasing atmospheric $CO_2$ affects the soil carbon cycle by influencing microbial activity and the carbon pool. In this study, the effects of elevated $CO_2$ on extracellular enzyme activities (EEA; ${\beta}$-glucosidase, N-acetylglucosaminidase, aminopeptidase) in salt marsh sediment vegetated with Suaeda japonica were assessed under ambient atmospheric $CO_2$ concentration (380 ppm) or elevated $CO_2$ concentration (760 ppm) conditions. Additionally, the community structure of sulfate-reducing bacteria (SRB) was analyzed via terminal restriction fragments length polymorphism (T-RFLP). Sediment with S. japonica samples were collected from the Hwangsando intertidal flat in May 2005, and placed in small pots (diameter 6 cm, height 10 cm). The pots were incubated for 60 days in a growth chamber under two different $CO_2$ concentration conditions. Sediment samples for all measurements were subdivided into two parts: surface (0-2 cm) and rhizome (4-6 cm) soils. No significant differences were detected in EEA with different $CO_2$ treatments in the surface and rhizome soils. However, the ratio of ${\beta}$-glucosidase activity to N-acetylglucosaminidase activity in rhizome soil was significantly lower (P < 0.01) at 760 ppm $CO_2$ than at 380 ppm $CO_2$, thereby suggesting that the contribution of fungi to the decomposition of soil organic matter might in some cases prove larger than that of bacteria. Community structures of SRB were separated according to different $CO_2$ treatments, suggesting that elevated $CO_2$ may affect the carbon and sulfur cycle in salt marshes.

• Korean Journal of Soil Science and Fertilizer
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• v.42 no.5
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• pp.341-347
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• 2009

Soil microbial community has been changed after the treatment of anaerobic fermentation using wheat bran or rice bran was applied to the soil. In the dilution plate technique, the number of anaerobic bacteria and fungi was higher in rice bran-treated soil than in non and wheat bran-treated soil, but of yeast was higher in wheat bran-treated soil than in non and rice bran-treated soil. Specially, the fungi were not detected in the wheat bran-treated soil. Identified by 16S rDNA sequencing, the number of aerobic bacteria was similar in all treatments, the dominant bacteria was the genus Bacillus. In the phospholipid fatty acid (PLFA) technique, both Gram-positive and Gram-negative bacteria change slightly in all treatments for 20 days of fermentation process but, after 20day, increased rapidly in wheat or rice bran-treated soil. In conclusion, the microbial communities structure was dramatically changed after the treatment of wheat or rice bran to soil.

• Journal of Microbiology and Biotechnology
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• v.34 no.4
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• pp.863-870
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• 2024

Meju, a fermented soybean brick, is a key component in soybean foods like doenjang and ganjang, harboring a variety of microorganisms, including bacteria and fungi. These microorganisms significantly contribute to the nutritional and sensory characteristics of doenjang and ganjang. Amplicon-based next-generation sequencing was applied to investigate how the microbial communities of meju fermented at low and high temperatures differ and how this variation affects the microbial communities of doenjang, a subsequently fermented soybean food. Our metagenomic data showed distinct patterns depending on the fermentation temperature. The microbial abundance in the bacterial community was increased under both temperatures during the fermentation of meju and doenjang. Weissella was the most abundant genus before the fermentation of meju, however, it was replaced by Bacillus at high temperature-fermented meju and lactic acid bacteria such as Weissella and Latilactobacillus at low temperature-fermented meju. Leuconostoc, Logiolactobacillus, and Tetragenococcus gradually took over the dominant role during the fermentation process of doenjang, replacing the previous dominant microorganisms. Mucor was dominant in the fungal community before and after meju fermentation, whereas Debaryomyces was dominant under both temperatures during doenjang fermentation. The dominant fungal genus of doenjang was not affected regardless of the fermentation temperature of meju. Strong correlations were shown for specific bacteria and fungi linked to specific fermentation temperatures. This study helps our understanding of meju fermentation process at different fermentation temperatures and highlights different bacteria and fungi associated with specific fermentation periods which may influence the nutritional and organoleptic properties of the final fermented soybean foods doenjang.

• The Korean Journal of Ecology
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• v.22 no.6
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• pp.337-342
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• 1999

Rotifer grazing rates in both species and community levels on bacteria and phytoplankton were determined by using representative models (fluorescent beads: 0.75$\mu m$ for bacteria and 10 $\mu m$ for phytoplankton) at biweekly intervals. One-year study at the lower part of the Nakdong River (Mulgum) indicated that the seasonal pattern of rotifer biomass was similar to that of total zooplankton biomass. Total mean biomass of rotifers was significantly higher than that of other groups (rotifers, 148$\pm $327 $\mu g$C/l; cladoceran. 25$\pm 69$$\mu g$C/l; copepodids. 58$\pm 159$$\mu g$C/l). For laboratory grazing experiments. mean specific filtering rate (SFR: $ml\cdot \; l^{-1}\cdot \; day^{-1}$) for rotifers varied from 0.001 to 0.726, and > 90% individuals of rotifer species took up fluorescent microspheres. The high SFRs were achieved by Brachionus angularis, B. calyciflorus, and Filinia longiseta. Community filtering rates (CFRs, $ml\cdot \; l^{-1}\cdot \; day^{-1}$) varied in the range from 2 ~ 1,670. Rotifer filtering rates on phytoplankton were much higher than bacterial filtering rates, especially in the late growing season (May. June, and November). Rotifers appear to be important in transferring both bacterial and phytoplankton carbon to higher trophic levels at the lower Nakdong River.

• The Plant Pathology Journal
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• v.37 no.4
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• pp.404-412
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• 2021

Despite the plant microbiota plays an important role in plant health, little is known about the potential interactions of the flower microbiota with pathogens. In this study, we investigated the microbial community of apple blossoms when infected with Erwinia amylovora. The long-read sequencing technology, which significantly increased the genome sequence resolution, thus enabling the characterization of fire blight-induced changes in the flower microbial community. Each sample showed a unique microbial community at the species level. Pantoea agglomerans and P. allii were the most predominant bacteria in healthy flowers, whereas E. amylovora comprised more than 90% of the microbial population in diseased flowers. Furthermore, gene function analysis revealed that glucose and xylose metabolism were enriched in diseased flowers. Overall, our results showed that the microbiome of apple blossoms is rich in specific bacteria, and the nutritional composition of flowers is important for the incidence and spread of bacterial disease.

• Animal cells and systems
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• v.3 no.2
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• pp.153-159
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• 1999

In an artificial pH-gradient batch culture system, the effects of acidification on the species composition of a heterotrophic bacterial community were analyzed. As a result of this study, it was found that total bacteria numbers were not affected by acidification and that the population of hetero-trophic bacteria decreased as pH became lower. The heterotrophic bacteria isolated from the entire pH gradient were 12 genera and 22 species. Among them, 64% were gram negative and 36% were gram positive bacteria. As pH decreased, the distribution rate of gram negative bacteria increased while that of gram positive bacteria decreased. The diversity of genera decreased from 13 to 5 as pH decreased from 7 to 3. The G+C content of all of the 202 isolated strains varied from 22.8 to 77.0%, and increased in interspecies of same genus as pH decreased. As a result of clustering analysis, the diversity index of species ranged from 1.13 to 2.37, and it had lower indices as pH decreased. In order to evaluate the diversity of numbers of sample of different size, a rarefaction method was used to analyze the expected number of species appearance according to pH. The statistical significance of species diversity was verified by the fact that the number decreased at lower pH.

• Microbiology and Biotechnology Letters
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• v.37 no.3
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• pp.189-196
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• 2009

Bacteria were isolated from roots of plants belonging to family Solanaceae and Gramineae, inhabited in Dokdo island. Fifty six endospore-forming bacteria grown on tryptic soy broth (TSB) agar medium and 23 nitrogen-fixing bacteria (NFB) grown on nitrogen free agar medium were isolated, respectively. The isolates were partially identified by analyzing the 16S rDNA and categorized into phylogenetic groups. The 16S rDNA sequences of each identified isolates were compared with sequences of each type strains to analyze phylogenetic relationship by phylogenetic tree. As a result, endospore-forming bacteria and nitrogen-fixing bacteria were classified into 4 and 6 lineage groups, respectively. Among these isolated, 18 were presumed to be novel species candidates based on the similarity (lower than 98%) analysis of the l6S rDNA sequences.

• Asian-Australasian Journal of Animal Sciences
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• v.12 no.1
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• pp.129-138
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• 1999

If rumen bacteria can be manipulated to utilize nutrients (i.e., ammonia and plant cell wall carbohydrates) more completely and efficiently, the need for protein supplementation can be reduced or eliminated and the digestion of fiber in forage or agricultural residue-based diets could be enhanced. However, these approaches require a complete and accurate description of the rumen community, as well as methods for the rapid and accurate detection of microbial density, diversity, phylogeny, and gene expression. Molecular ecology techniques based on small subunit (SSU) rRNA sequences, nucleic acid probes and the polymerase chain reaction (PCR) can potentially provide a complete description of the microbial ecology of the rumen of ruminant animals. The development of these molecular tools will result in greater insights into community structure and activity of gut microbial ecosystems in relation to functional interactions between different bacteria, spatial and temporal relationships between different microorganisms and between microorganisms and reed panicles. Molecular approaches based on SSU rRNA serve to evaluate the presence of specific sequences in the community and provide a link between knowledge obtained from pure cultures and the microbial populations they represent in the rumen. The successful development and application of these methods promises to provide opportunities to link distribution and identity of gastrointestinal microbes in their natural environment with their genetic potential and in situ activities. The use of approaches for assessing pupulation dynamics as well as for assessing community functionality will result in an increased understanding and a complete description of the gastrointestinal communities of production animals fed under different dietary regimes, and lead to new strategies for improving animal growth.