• Asian-Australasian Journal of Animal Sciences
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• v.22 no.1
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• pp.113-118
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• 2009

We investigated the structure of bacterial communities present in livestock manure-based composting processes and evaluated the bacterial succession during the composting processes. Compost samples were derived separately from swine manure, dairy manure and sewage sludge. The structure of the bacterial community was analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) using universal eubacterial primers. The genus Bacillus and related genera were mainly detected following the thermophilic composting phase of swine and dairy manure composts, and the members of the phylum Bacteroidetes were mainly detected in the cattle manure waste-based and sewage sludge compost. We recovered and sequenced limited number of the bands; however, the PCR-DGGE analysis showed that predominant diversities during the composting processes were markedly changed. Although PCR-DGGE analysis revealed the presence of different phyla in the early stages of composting, the members of the phylum Firmicutes and Bacteroidetes were observed to be one of the predominant phyla after the thermophilic phase.

• Journal of Soil and Groundwater Environment
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• v.19 no.5
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• pp.9-17
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• 2014

This paper reported the use of real-time polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), and the culture-based method in the intrinsic bioremediation study at a petroleum contaminated site. The study showed that phenol hydroxylase gene was detected in groundwater contaminated with benzene, toluene, ethylbenzene, xylene isomers (BTEX) and methyl tert-butyl ether (MTBE). This indicated that intrinsic bioremediation occurred at the site. DGGE analyses revealed that the petroleum-hydrocarbon plume caused the variation in microbial communities. MTBE degraders including Pseudomonas sp. NKNU01, Bacillus sp. NKNU01, Klebsiella sp. NKNU01, Enterobacter sp. NKNU01, and Enterobacter sp. NKNU02 were isolated from the contaminated groundwater using the cultured-based method. Among these five strains, Enterobacter sp. NKNU02 is the most effective stain at degrading MTBE without the addition of pentane. The MTBE biodegradation experiment indicated that the isolated bacteria were affected by propane. Biodegradation of MTBE was decreased but not totally inhibited in the mixtures of BTEX. Enterobacter sp. NKNU02 degraded about 60% of MTBE in the bioreactor study. Tert-butyl alcohol (TBA), acetic acid, 2-propanol, and propenoic acid were detected using gas chromatography/mass spectrometry during MTBE degraded by the rest cells of Enterobacter sp. NKNU02. The effectiveness of bioremediation of MTBE was assessed for potential field-scale application.

• Journal of Microbiology and Biotechnology
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• v.13 no.6
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• pp.1008-1012
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• 2003

Symbiobacterium toebii has been reported as a thermophile exhibiting a commensal interaction with Geobacillus toebii. The distribution of the commensal thermophiles in various soils was investigated using a denaturing gradient gel electrophoresis (DGGE). Based on the DGGE analysis, the enrichment condition for the growth of Symbiobacterium sp. was found to also enrich populations of several other microbial spp. as well as Symbiobacterium sp. In the enrichment experiment, several different 16S rDNA sequences of commensal thermophiles were detected in all of the soil samples tested, indicating that commensal thermophiles are widely distributed in various soils.

• Journal of Microbiology and Biotechnology
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• v.20 no.9
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• pp.1339-1347
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• 2010

In this study, the identity and distribution of plants and the structure of their associated rhizobacterial communities were examined in an oil-contaminated site. The number of plant species that formed a community or were scattered was 24. The species living in soil highly contaminated with total petroleum hydrocarbon (TPH) (9,000-4,5000 mg/g-soil) were Cynodon dactylon, Persicaria lapathifolia, and Calystegia soldanella (a halophytic species). Among the 24 plant species, the following have been known to be effective for oil removal: C. dactylon, Digitaria sanguinalis, and Cyperus orthostachyus. Denaturing gradient gel electrophoresis (DGGE) profile analysis showed that the following pairs of plant species had highly similar (above 70%) rhizobacterial community structures: Artemisia princeps and Hemistepta lyrata; C. dactylon and P. lapathifolia; Carex kobomugi and Cardamine flexuosa; and Equisetum arvense and D. sanguinalis. The major groups of rhizobacteria were Beta-proteobacteria, Gamma-proteobacteria, Chloroflexi, Actinobacteria, and unknown. Based on DGGE analysis, P. lapathifolia, found for the first time in this study growing in the presence of high TPH, may be a good species for phytoremediation of oil-contaminated soils and in particular, C. soldanella may be useful for soils with high TPH and salt concentrations. Overall, this study suggests that the plant roots, regardless of plant species, may have a similar influence on the bacterial community structure in oil-contaminated soil.

• Korean Journal of Microbiology
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• v.49 no.4
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• pp.377-382
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• 2013

The bacterial community structures of the marine sponge, Dactylospongia metachromia, collected from Chuuk of Micronesia on February 2012, were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints of two individuals of D. metachromia, CH607 and CH840 showed the same band patterns. The sequences derived from DGGE bands revealed 93~100% similarities with known bacterial species in the public database and high similarity with uncultured bacterial clones. The bacterial community structures of both D. metachromia sponges (CH607, CH840) were composed of 6 phyla, 8 classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, Spirochaetes. DGGE fingerprint - based phylogenetic analysis revealed that the bacterial community profiles were identical in two individuals of the same sponge species collected from the same geographical location.

• Journal of Microbiology and Biotechnology
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• v.16 no.10
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• pp.1561-1569
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• 2006

Denaturing gradient gel electrophoresis (DGGE) is one of the most frequently used methods for analysis of soil microbial community structure. Unbiased PCR amplification of target DNA templates is crucial for efficient detection of multiple microbial populations mixed in soil. In this study, DGGE profiles were compared using different pairs of primers targeting different hypervariable regions of thirteen representative soil bacteria and clones. The primer set (1070f-1392r) for the E. coli numbering 1,071-1,391 region could not resolve all the 16S rDNA fragments of the representative bacteria and clones, and moreover, yielded spurious bands in DGGE profiles. For the E. coli numbering 353-514 region, various forward primers were designed to investigate the efficiency of PCR amplification. A degenerate forward primer (F357IW) often yielded multiple bands for a certain single 16S rDNA fragment in DGGE analysis, whereas nondegenerate primers (338f, F338T2, F338I2) differentially amplified each of the fragments in the mixture according to the position and the number of primer-template mismatches. A forward primer (F352T) designed to have one internal mismatch commonly with all the thirteen 16S rDNA fragments efficiently produced and separated all the target DNA bands with similar intensities in the DGGE profiles. This primer set F352T-519r consistently yielded the best DGGE banding profiles when tested with various soil samples. Touchdown PCR intensified the uneven amplification, and lowering the annealing temperature had no significant effect on the DGGE profiles. These results showed that PCR amplification bias could be much improved by properly designing primers for use in fingerprinting soil bacterial communities with the DGGE technique.

• Korean Journal of Microbiology
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• v.40 no.3
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• pp.205-210
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• 2004

The change of bacterial communities during cyanobacterial bloom was analyzed by DGGE in Daechung Reservoir from July to October in 2003. The traditional morphological analysis showed that the genera of Microcystis, Chroococcus, Oscillatoria, and Phormidium were dominated. The most frequent band in the DGGE profile by 16S rDNA sequence analysis was identified as Microcystis flos-aquae and the cyanobacterial bloom was peaked on September 2. Oscillatoria spp. were also identified and Aphanizomenon flos-aquae dominated in the middle of August. Judging from the analysis of the digitalized DGGE profiles using the cluster analysis technique, the microbial community on September 2 was considerably different from others. Consequently, it seems that the gene fingerprinting method can give not only the similar results to the traditional morphological method but also additional information on the bacterial species and similarity among the examined microbial communities.

• Korean Journal of Environmental Biology
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• v.24 no.3
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• pp.221-229
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• 2006

The effects of ultrasonication on phytoplankton were investigated in two ponds in which physicochemical and biological water quality was similar, one as a treatment and the other as a control. The samples were collected from August 18 to September 30 in 2003. Traditional morphological analysis showed that Bacillariophyceae dominated phytoplankton community in both ponds. The abundance of Cyanophyceae was lower in the phytoplankton community of the sonicated pond than that of control pond. We used DGGE (denaturing gradient gel electrophoresis) to analyze the diversity and change of phytoplankton community in two ponds. The DGGE banding patterns of 16S rRNA gene and sequence analysis demonstrated that Oscillatoria acuminata and CFB (Cytophaga-Flavobacterium-Bacteroides) group bacterium appeared in the treated pond, and the control pond was dominated by Synechococcus sp. and Aphanizomenon flos-aquae. Especially, Pseudanabaena sp. dominated during the ultrasonic cessation in the treated pond. The DGGE profiles of 18S rRNA gene and sequence analysis showed that the treated pond was dominated by Chlamydomonas reinhardtii and the control pond by C. reinhardtii and Pteromonas protracta. In conclusion, the ultrasonication affected the reduced growth of cyanobacteria, particularly Pseudanabaena.

• Proceedings of the Zoological Society Korea Conference
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• 2000.10a
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• pp.133.3-134
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• 2000

No Abstract, See Full Text

• Journal of Life Science
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• v.22 no.2
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• pp.232-238
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• 2012

Kumjungsansung-Makgeolli$^{(R)}$ is a traditional Korean rice wine that is fermented from traditional nuruk and rice. In this study, we performed the PCR-denaturing gradient gel electrophoresis (DGGE) analysis targeting the 16S and 28S rRNA genes to characterize bacterial and fungal diversity during Makgeolli fermentation. The predominant bacteria in the PCR-DGGE profile during Makgeolli fermentation were Lactobacillus spp. (Lactobacillus curvatus, L. kisonensis, L. plantarum, L. sakei, and L. gasseri), Pediococcus spp. (P. acidilactici, P. parvulus, P. agglomerans, and P. pentosaceus), Pantoea spp. (P. agglomerans and P. ananatis), and Citrobacter freundii; these were identified on the base of analysis of 16S rRNA gene sequences. The dominant bacterium during Makgeolli fermentation was L. curvatus. The predominant fungi in PCR-DGGE profile during Makgeolli fermentation were Pichia kudriavzevii, Saccharomyces cerevisiae, Asidia idahoensis, Kluyveromyces marxianus, Saccharomycopsis fibuligera, and Torulaspora delbrueckii, and these were identified on the basis of analysis of 28S rRNA gene sequences. The dominant fungal species during Makgeolli fermentation changed from P. kudriavzevii at 0-2 days incubation to S. cerevisiae at 3-6 days incubation. This study suggests that PCR-DGGE analysis could be a suitable tool for the understanding of microbial diversity and structure during Makgeolli fermentation.