• Journal of Microbiology and Biotechnology
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• v.23 no.7
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• pp.993-1003
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• 2013

Methanotrophs are the most important sink of $CH_4$, which is a more highly potent greenhouse gas than $CO_2$. Methanotrophic abundance and community diversity in cover soils from two typical semi-aerobic landfills (SALs) in China were detected using real-time polymerase chain reaction (real-time-PCR) and denaturing gradient gel electrophoresis (DGGE) based on 16S rRNA genes, respectively. Real time-PCR showed that Type I methanotrophs ranged from $1.07{\times}10^6$ to $2.34{\times}10^7$ copies/g soil and that of Type II methanotrophs from $1.51{\times}10^7$ to $1.83{\times}10^8$ copies/g soil. The ratio of Type II to Type I methanotrophic copy numbers ranged from 5.61 to 21.89, indicating that Type II methanotrophs dominated in SAL. DGGE revealed that Type I methanotrophs responded more sensitively to the environment, changing as the community structure varied with different soil types and locations. Methylobacter, Methylosarcina, and Methylomicrobium for Type I, and Methylocystis for Type II were most prevalent in the SAL cover layer. Abundant interflow $O_2$ with high $CH_4$ concentration in SALs is the reason for the higher population density of methanotrophs and the higher enrichment of Type II methanotrophs compared with anaerobic landfills and other ecosystems, which proved a conclusion that increasing the oxygen supply in a landfill cover layer would greatly improve $CH_4$ mitigation.

• Journal of Korean Society of Environmental Engineers
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• v.31 no.2
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• pp.139-146
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• 2009

In this study, characteristics of biological hydrogen production and microbial distribution were investigated with the wastewater of Tofu manufacturing process. Comparison of hydrogen production was conducted with acid or base pre-treatment of the wastewater. Maximum hydrogen production was acquired with combination of heat and acid treatment. Hydrogen production ($P_h$) and maximum hydrogen production rate ($R_h$) was calculated 661.01 mL and 12.21 mL/g dry wt biomass/hr from the modified Gompartz equation. Most of microbial community was analyzed as Streptococcus sp. from PCR-DGGE experiment of 16S rDNA. It was concluded that most significant microorganism for hydrogen production was Streptococcus gallolyticus sub sp. in this experiment.

• Journal of Korean Society of Environmental Engineers
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• v.36 no.10
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• pp.672-678
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• 2014

In this study, variations of fermentative hydrogen production and microbial community were investigated with different nitrogen concentration of food waste. Optimum hydrogen production rate was acquired at 200 mg/L nitrogen concentration of the food waste. Which was eqivalent to 83.43 mL/g dry biomass/hr. However, bio-hydrogen production was inhibitedly reduced at over 600 mg/L of nitrogen concentration whereas proportional relation between hydrogen production and B/A ratio were not observed. Most dominant specie of the microbial community analyzed was Clostridium sp. throughout PCR-DGGE analysis of 16S rDNA. It revealed that most contributing microorganism producing hydrogen were Enterococcus faecium partial, Klebsiella pneumoniae strain ND6, Enterobacter sp. NCCP-231, and Clostridium algidicarnis strain E107 in this experiment.

• Journal of Microbiology and Biotechnology
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• v.17 no.5
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• pp.753-760
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• 2007

The diversity of Paenibacillus species was assessed in the rhizospheres of four cultivars of sorghum sown in Cerrado soil amended with two levels of nitrogen fertilizer(12 and 120 kg/ha). Two cultivars(IS 5322-C and IS 6320) demanded the higher amount of nitrogen to grow, whereas the other two(FBS 8701-9 and IPA 1011) did not. Using the DNA extracted from the rhizospheres, a Paenibacillus-specific PCR system based on the RNA polymerase gene(rpoB) was chosen for the molecular analyses. The resulting PCR products were separated into community fingerprints by DGGE and the results showed a clear distinction between cultivars. In addition, clone libraries were generated from the rpoB fragments of two cultivars(IPA 1011 and IS 5322-C) using both fertilization conditions, and 318 selected clones were sequenced. Analyzed sequences were grouped into 14 Paenibacillus species. A greater diversity of Paenibacillus species was observed in cultivar IPA 1011 compared with cultivar IS 5322-C. Moreover, statistical analyses of the sequences showed that the bacterial diversity was more influenced by cultivar type than nitrogen fertilization, corroborating the DGGE results. Thus, the sorghum cultivar type was the overriding determinative factor that influenced the community structures of the Paenibacillus communities in the habitats investigated.

• Journal of Microbiology and Biotechnology
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• v.26 no.6
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• pp.1057-1062
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• 2016

Kimchi is a traditional Korean fermented vegetable food, the production of which involves brining of Korean cabbage, blending with various other ingredients (red pepper powder, garlic, ginger, salt-pickled seafood, etc.), and fermentation. Recently, kimchi has also become popular in the Western world because of its unique taste and beneficial properties such as antioxidant and antimutagenic activities, which are derived from the various raw materials and secondary metabolites of the fermentative microorganisms used during production. Despite these useful activities, analysis of the microbial community present in kimchi has received relatively little attention. The objective of this study was to evaluate the bacterial community structure from the raw materials, additives, and final kimchi product using the culture-independent method. Specifically, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze the 16S rRNA partial sequences of the microflora. One primer set for bacteria, 341F^GC-518R, reliably produced amplicons from kimchi and its raw materials, and these bands were clearly separated on a 35-65% denaturing gradient gel. Overall, 117 16S rRNA fragments were identified by PCR-DGGE analysis. Pediococcus pentosaceus, Leuconostoc citreum, Leuconostoc gelidum, and Leuconostoc mesenteroides were the dominant bacteria in kimchi. The other strains identified were Tetragenococcus, Pseudomonas, Weissella, and uncultured bacterium. Comprehensive analysis of these microorganisms could provide a more detailed understanding of the biologically active components of kimchi and help improve its quality. PCR-DGGE analysis can be successfully applied to a fermented food to detect unculturable or other species.

• Korean Journal of Organic Agriculture
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• v.19 no.3
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• pp.417-425
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• 2011

This study was conducted to investigate the changes in physicochemical and microbiological properties during fermenting process of farm-made organic liquid fertilizer made of the mixture of organic materials such as blood meal and molasse during fermenting process. The pH level of organic liquid fertilizer during the ermentation decreased from 7.2 to 4.3. The EC of organic liquid fertilizer was increased from 13.9 dS/m to 99.3 dS/m during the fermentation. The total population of aerobic bacteria decreased from $8.2{\times}10^5$ cfu/ml to $3{\times}10^4$ cfu/ml, but Bacillus spp. increased from $2.1{\times}10^2$ cfu/ml to $4.2{\times}10^3$ cfu/ml during the fermentation. Bacterial isolates were obtained from organic liquid fertilizers and identified by fatty acid-base typing. The Genus Bacillus was dominant as fermenting proceeded. The denaturing gradient gel electrophoresis (DGGE) profile showed changes of bacterial communities in organic liquid fertilizers.

• Korean Journal of Organic Agriculture
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• v.19 no.spc
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• pp.190-193
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• 2011

Organic and chemical fertilizer amendments are an important agricultural practice for increasing crop yields. In order to maintain the soil sustainability, it is important to monitor the effects of fertilizer applications on the shift of soil microorganism, which control the cycling of many nutrients in the soils. Here, culture-dependent and culture-independent approaches were used to analyze the soil microorganism and community structure under six fertilization treatments, including green manure, rice straw compost, rapeseed cake, pig mature compost, NPK +pig mature compost, NPK and control. Both organic and chemical fertilizers caused a shift of the cultural microorganism CFUs after treatments. Bacterial CFUs of the organic fertilization treatments were significantly higher than that of chemical fertilization treatments. The DGGE profiles of the bacterial communities of the samples showed that the green manure treatment was a distinct difference in bacterial community, with a greater complexity of the band pattern than other treatments. Cluster analyses based on the DGGE profile showed that rice straw compost and pig mature compost had a similar banding pattern and clustered together firstly. Rapeseed cake, NPK, NPK +pig manure compost and control clustered together in other sub-cluster and clearly distinguished from green manure.

• Journal of Life Science
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• v.24 no.5
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• pp.522-531
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• 2014

Seasonal variations in the bacterial community of Gwangyang Bay seawater were analyzed using both isolation and cultivation-independent methods. Amplified rDNA restriction analysis was applied to 200 bacterial isolates. Bacterial isolates were composed of four phyla: Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. Pyrosequencing was conducted, in addition to denaturing gradient gel electrophoresis (DGGE) of genomic DNA extracted directly from the water samples. The bacterial sequences obtained by pyrosequencing of 16S rRNA genes consisted of 24 phyla in the spring and summer, 39 in the fall, and 32 in the winter. The diversity index was high in the fall, whereas the dominancy index was high in the spring. In the spring, phylum Firmicutes was dominant, whereas phylum Proteobacteria dominated in the other three seasons. The second most dominant phyla were Proteobacteria in the spring, Firmicutes in the summer, and Bacteroidetes both in the fall and winter. Bacilliaceae was the most predominant family in the spring. Rhodobacteraceae and Bacilliaceae dominated in the summer, and Rhodobacteraceae dominated in the winter. Neither was dominant in the fall Twenty-seven bands purified from DGGE profiles were cloned and analyzed phylogenetically. In the spring, phylum Firmicutes dominated, followed by Proteobacteria. Proteobacteria dominated in all other seasons. Thus, two cultivation-independent methods for determination of seasonal variation patterns at the phylum level were in accordance with each other.

• Journal of Korean Society of Environmental Engineers
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• v.29 no.1
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• pp.106-112
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• 2007

Ammonia oxidizing bacteria(AOB) oxidize ammonia to nitrite and are important microorganisms which control nitrification. Several environmental factors such as dissolved oxygen(DO), temperature and pH influence the growth of AOB. In this work, to assess the effect of DO concentration on AOB, four aerobic biofilm reactors packed with ceramic media were operated 1, 3, 5 and 7 mgDO/L, respectively. The optimal DO concentration with stable nitrification efficiency in aerobic biofilm reactor was above 5.0 mg/L. To assess the relationship between the DO concentration and the characteristics of AOB in aerobic biofiim reactor, DGGE and cloning based on PCR targeting 16S rRNA and amoA gene were performed. Additionally, INT-DHA activity test was proceeded to estimate the activity of AOB. As the results of DGCE and cloning, the community of AOB and the ratio of Nitrosomonas sp. changed little in spite of different nitrification efficiencies. INT-DHA activity test showed that the activity of AOB decreased as DO concentration decreased. It means that DO concentration does not affect the community of AOB, but the activity of AOB.

• Journal of Korean Society of Environmental Engineers
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• v.28 no.2
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• pp.165-172
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• 2006

In order to analyze the bacterial community structure including P-removal related organisms, PAOs(polyphosphate accumulating organisms) and GAOs(glycogen-accumulating non-poly-P organisms) occurred in biological phosphate removing process, 2 reactors(SBR; sequencing batch reactor) were operated on different carbon sources(sodium acetate, glucose). For the analysis of bacterial community structure, molecular methods(FISH: fluorescent in situ hybridization and DGGE; denaturing gel gradient electrophoresis) were employed. After 100 days reaction, $PO_4-P$ in effluent dropped to 3.92 mg/L in SBR #1(60.8% removal) fed by sodium acetate, and at the same time FISH results showed that ${\beta}$-subclass proteobacteria(39.67%) and PAOs(45.10%) were dominantly present whereas those value in SBR #2 fed by glucose was 8.30 mg/L(17% removal), and ${\gamma}$-subclass proteobacteria were considerably observed(23.89%) and PAOs was 21.42%. Also the result of DGGE indicated that ${\beta}$-subclass proteobacteria was dominantly observed in SBR #1. However as the temperature increased, the proportion of ${\beta}$-subclass proteobacteria and PAOs decreased, but phosphorus removing inhibitors(GAOs) increased. It suggests that the environmental factor like as temperature and types of carbon source had influence on the prevalence of phosphorus removing organism(PAOs) and phosphorus removing inhibitors(GAOs) in biological phosphate removing process.