• Journal of Microbiology and Biotechnology
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• v.23 no.2
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• pp.137-143
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• 2013

The diversity and distribution of methanogenic archaea in a four-compartment anaerobic baffled reactor (ABR) treating sugar refinery wastewater were investigated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). At an organic loading rate of 5.33 kg $COD/m^3{\cdot}day$, the ABR could perform steadily with the mean chemical oxygen demand (COD) removal of 94.8% and the specific $CH_4$ yield of 0.21 l/g $COD_{removed}$. The $CH_4$ content in the biogas was increased along the compartments, whereas the percentage of $H_2$ was decreased, indicating the distribution characteristics of the methanogens occurred longitudinally down the ABR. A high phylogenetic and ecological diversity of methanogens was found in the ABR, and all the detected methanogens were classified into six groups, including Methanomicrobiales, Methanosarcinales, Methanobacteriales, Crenarchaeota, Arc I, and Unidentified. Among the methanogenic population, the acid-tolerant hydrogenotrophic methanogens including Methanoregula and Methanosphaerula dominated the first two compartments. In the last two compartments, the dominant methanogenic population was Methanosaeta, which was the major acetate oxidizer under methanogenic conditions and could promote the formation of granular sludge. The distribution of the hydrogenotrophic (acid-tolerant) and acetotrophic methanogens in sequence along the compartments allowed the ABR to perform more efficiently and steadily.

• Journal of Korean Society of Environmental Engineers
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• v.35 no.8
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• pp.571-578
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• 2013

In this study, the performance and microbial community of anaerobic digestion fed by food waste leachate at low organic loading rate were investigated with and without internal pH control. Experimental results show that similar biogas yield was achieved in both reactors regardless of increase in pH, the concentrations of free ammonia and volatile fatty acids in case of without internal pH controlled one. The results of a methanogenic community analysis by Polymerase Chain Reaction and Denaturing Gradient Gel Electrophoresis revealed that the apparent preponderance of Methanosarcina sp. could be one of reasons for the maintenance of reactor stability.

• Journal of Ecology and Environment
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• v.41 no.9
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• pp.235-245
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• 2017

Background: Loading of excess nutrient via bioremediation of polluted sediment to overlying water could trigger anoxia and eutrophication in coastal area. The aim of this research was to understand the changes of overlying water features such as dissolved oxygen (DO); pH; oxidation reduction potential (ORP); $chlorophyll-{\alpha}$ ($Chl-{\alpha}$); and nitrogen nutrients ammonia ($N-NH_4{^+}$), nitrate ($N-NO_3{^-}$), and nitrite ($N-NO_2^-$) when the sediment was not treated (control) and treated by calcium peroxide for 5 weeks. Methods: The water samples were analyzed for measuring physical and chemical properties along with the sediment analyzed by polymerase chain reaction (PCR) including denaturing gradient gel electrophoresis (DGGE) for identifying the phylogenetic affiliation of microbial communities. Results: Results showed that due to the addition of calcium peroxide in sediment, the overlying water exposed the rise of dissolve oxygen, pH, and ORP than control. Among the nitrogen nutrients, ammonia inhibition was higher in calcium peroxide treatment than control but in case of nitrate inhibition, it was reversed than control. $Chlorophyll-{\alpha}$ was declined in treatment column water by 30% where it was 20% in control column water. Actibacter and Salegentibacter group were detectable in the calcium-peroxide-treated sediment; in contrary, no detectable community ware found in control sediment. Both phylogenetic groups are closely related to marine microflora. Conclusions: This study emphasizes the importance of calcium peroxide as an oxygen release material. Interaction with peroxide proved to be enhancing the formation of microbial community that are beneficial for biodegradation and spontaneity of nutrient attenuation into overlying water.

• International Journal of Industrial Entomology and Biomaterials
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• v.47 no.1
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• pp.1-11
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• 2023

The Indian golden muga silkworm, Antheraea assamensis Helfer is an economically important wild silkworm endemic to Northeastern part of India. In recent years, climate change has posed a threat to muga silk production due to the requirement that larvae be reared outdoors. Since the muga silkworm larvae are exposed to the vagaries of nature, the changing climate has increased the incidence of microbial diseases in the rearing fields. Accurate diagnosis of the disease causing pathogens and its associated epidemiology are prerequisites to manage the diseases in the rearing field. Although conventional microbial culturing methods are widely used to identify pathogenic bacteria, they would not provide meaningful information on a wide variety of silkworm pathogens. The information on use of molecular diagnostic tools in detection of microbial pathogens of wild silk moths is very limited. A wide range of molecular and immunodiagnostic techniques including denaturing gradient gel electrophoresis (DGGE), random amplified polymorphism (RAPD), 16S rRNA/ITSA gene sequencing, multiplex polymerase chain reaction (M-PCR), fluorescence in situ hybridization (FISH), immunofluorescence, and repetitive-element PCR (Rep-PCR), have been used for detecting and characterizing the pathogens of insects with economic significance. Nevertheless, the application of these molecular tools for detecting and typing entomopathogens in surveillance studies of muga silkworm rearing is very limited. Here, we discuss the possible application of these molecular techniques, their advantages and major limitations. These methods show promise in better management of diseases in muga ecosystem.

• Korean Journal of Environmental Agriculture
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• v.32 no.2
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• pp.95-101
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• 2013

BACKGROUND: Rice (Oryza sativa) is the most important staple food of over half the world's population. This study was conducted to evaluate the possible impact of transgenic rice cultivation on the soil microbial community. METHODS AND RESULTS: Microorganisms were isolated from the rhizosphere of GM and non-GM rice cultivation soils. Microbial community was identified based on the culture-dependent and molecular biology methods. The total numbers of bacteria, fungi, and actinomycete in the rhizosphere soils cultivated with GM and non-GM rice were similar to each other, and there was no significant difference between GM and non-GM rice. Dominant bacterial phyla in the rhizosphere soils cultivated with GM and non-GM rice were Actinobacteria, Firmicutes, and Proteobacteria. The microbial communities in GM and non-GM rice cultivated soils were characterized using the denaturing gradient gel electrophoresis (DGGE). The DGGE profiles showed similar patterns, but didn't show significant difference to each other. DNAs were isolated from soils cultivating GM and non-GM rice and analyzed for persistence of inserted gene in the soil by using PCR. The PCR analysis revealed that there were no amplified protox gene in soil DNA. CONCLUSION(S): These data suggest that transgenic rice does not have a significant impact on soil microbial communities, although continued research may be necessary.

• Journal of Microbiology and Biotechnology
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• v.18 no.2
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• pp.207-218
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• 2008

The impacts of planted transgenic rice varieties on bacterial communities in paddy soils were monitored using both cultivation and molecular methods. The rice field plot consisted of eighteen subplots planted with two genetically modified (GM) rice and four non-GM rice plants in three replicates. Analysis with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes revealed that the bacterial community structures were quite similar to each other in a given month, suggesting that there were no significant differences in bacterial communities between GM and non-GM rice soils. The bacterial community structures appeared to be generally stable with the seasons, as shown by a slight variation of microbial population levels and DGGE banding patterns over the year. Comparison analysis of 16S rDNA clone libraries constructed from soil bacterial DNA showed that there were no significant differences between GM and non-GM soil libraries but revealed seasonal differences of phyla distribution between August and December. The composition profile of phospholipid fatty acids (PLFA) between GM and non-GM soils also was not significantly different to each other. When soil DNAs were analyzed with PCR by using primers for the bar gene, which was introduced into GM rice, positive DNA bands were found in October and December soils. However, no bar gene sequence was detected in PCR analysis with DNAs extracted from both cultured and uncultured soil bacterial fractions. The result of this study suggested that, in spite of seasonal variations of bacterial communities and persistence of the bar gene, the bacterial communities of the experimental rice field were not significantly affected by cultivation of GM rice varieties.

• KSBB Journal
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• v.20 no.6
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• pp.431-437
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• 2005

Molecular methods were employed to investigate microorganisms in a thermophilic continuous stirred tank reactor(CSTR) used for continuous $H_2$ production. The reactor was inoculated with heat-treated anaerobic sludge and fed with a glucose-based medium. Denaturing gradient gel electrophoresis showed dynamic changes of bacterial populations in the reactor during 43 days of operation. Gas composition was constant from approximately 14 days but population shift still occurred. Populations affiliated with Fervidobactrium gondwanens and Thermoanaerobacterium thermosaccharolyticum were dominant on 21 and 41 days, respectively. Keeping pH of the medium at 5.0 could suppress methanogenic activity that was detected during initial operation period. $CH_4$ and mcrA detected in the samples obtained from the reactor or inoculum suggested the heat treatment condition employed in this study is not enough to remove methanogens in the inoculum. PCR using primer sets specific to 4 main orders of methanogens suggested that major $H_2$-consuming methanogens in the CSTR belong to the order Methanobacteriales.

• Journal of Ginseng Research
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• v.40 no.1
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• pp.28-37
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• 2016

Background: Panax ginseng cannot be cultivated on the same land consecutively for an extended period, and the underlying mechanism regarding microorganisms is still being explored. Methods: Polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) and BIO-LOG methods were used to evaluate the microbial genetic and functional diversity associated with the P. ginseng rhizosphere soil in various cultivation ages and modes. Results: The analysis of microbial diversity using PCR-DGGE showed that microbial communities were significantly variable in composition, of which six bacterial phyla and seven fungal classes were detected in P. ginseng soil. Among them, Proteobacteria and Hypocreales dominated. Fusarium oxysporum, a soilborne pathogen, was found in all P. ginseng soil samples except R0. The results from functional diversity suggested that the microbial metabolic diversity of fallow soil abandoned in 2003was the maximum and transplanted soil was higher than direct-seeding soil and the forest soil uncultivated P. ginseng, whereas the increase in cultivation ages in the same mode led to decreases in microbial diversity in P. ginseng soil. Carbohydrates, amino acids, and polymers were the main carbon sources utilized. Furthermore, the microbial diversity index and multivariate comparisons indicated that the augmentation of P. ginseng cultivation ages resulted in decreased bacterial diversity and increased fungal diversity, whereas microbial diversity was improved strikingly in transplanted soil and fallow soil abandoned for at least one decade. Conclusion: The key factors for discontinuous P. ginseng cultivation were the lack of balance in rhizosphere microbial communities and the outbreak of soilborne diseases caused by the accumulation of its root exudates.

• Korean Journal of Environmental Agriculture
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• v.30 no.4
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• pp.466-472
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• 2011

BACKGROUND: Soybean [Glycine max (L.) Merrill] is a legume and an important oil crop worldwide. This study was conducted to evaluate the possible impact of transgenic soybean cultivation on the soil microbial community. METHODS AND RESULTS: Microorganisms were isolated from the rhizosphere soils. Microbial community was identified based on the culture-dependent and molecular biology methods. The total numbers of bacteria, fungi, and actinomycete in the rhizosphere soils cultivated with transgenic and non-transgenic soybeans were similar to each other, and there was no significant difference between transgenic and non-transgenic soybeans. Dominant bacterial phyla in the rhizosphere soils cultivated with transgenic or non-transgenic soybeans were Actinobacteria, Firmicutes, and Proteobacteria. The microbial communities in transgenic and non-transgenic soybean soils were characterized using the denaturing gradient gel electrophoresis (DGGE). The DGGE profiles showed the different patterns, but didn't show significant difference to each other at 0.05 significance level. DNAs were isolated from soils cultivating transgenic or non-transgenic soybeans and analyzed for persistence of transgenes in the soil by using PCR. PCR analysis revealed that there were no amplified ${\gamma}$-tmt and bar gene in soil DNA. CONCLUSION(S): The results of this study suggested that microbial community of soybean field were not significantly affected by cultivation of the transgenic soybeans.

• Journal of Life Science
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• v.31 no.1
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• pp.10-16
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• 2021

The consumption of fresh-cut agricultural materials is increasing due to increased public interest in health and the increase of single-person households. Most fresh-cut agricultural materials can be eaten without heating, thus easily exposing the consumer to food-borne pathogens. As a result, food-borne diseases are increasing worldwide. In the analysis of food-borne pathogens, it is important to detect the strains, but this is time consuming and laborious. Alternative detection methods that have been introduced, include polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), which is performed without prior culturing. Samples of fresh-cut agricultural materials, such as vegetables, were analyzed by the culture-based method. In 129 samples, non-pathogenic Escherichia coli (3.9%), Bacillus cereus (31.8%), Clostridium perfringens (5.4%), Yersinia enterocolitica (0.8%), and enterohemorrhagic E. coli (0.8%) were detected. Eight samples contaminated with bacteria were randomly selected, further analyzed by PCR-DGGE, and compared with the culture-based method. Two cases detected non-pathogenic E. coli by PCR-DGGE only, despite a lack of detection by the culture method. It was supposed there was possibility of sample loss during its 10-fold dilution for appropriate cultivation. In the detection of high-risk food-borne pathogens, it was found that the detection limit was lower in PCR-DGGE than in the culture-based method (10 CFU/g). This suggests that PCR-DGGE can be alternatively used to detect strains. On the other hand, low-risk food-borne pathogens seem to have higher detection limits in PCR-DGGE. Consequentially, this study contributes to the improvement of food-borne pathogen detection and the prevention of its related-diseases in fresh-cut agricultural materials.