• Microbiology and Biotechnology Letters
• /
• v.36 no.4
• /
• pp.336-342
• /
• 2008

The effect of methyl tert-butyl ether (MTBE) and its metabolites like tert-butyl alcohol (TBA), and formaldehyde (FA) on microbial activity and diversity in tidal mud flat was studied. MTBE, TBA, and FA with different concentrations were added into microcosms containing tidal mud samples, and placed at room temperature for 30 days. Then the physico-chemical properties such as pH, moisture contents and organic matter contents in the microcosms were measured. In addition, the total viable cell number and dehydrogenase activity were measured. Bacterial communities in the microcosms were monitored using a 16S rRNA-PCR-DGGE (Denaturing gradient gel electrophoresis) fingerprinting method. As a result, the exposure concentrations of MTBE and its metabolites showed no correlation with the physico-chemical factors (P>0.05). Dehydrogenase activity and total viable cell number were decreased with increasing MTBE, TBA and FA concentrations (P<0.05). The toxic effect was higher the following order: FA > MTBE > TBA. Dominant species in the microcosms contaminated with MTBE and its metabolites were Sphingobacteria, Flavobacteria, delta-proteobacteria, gamma-proteobacteria. The diversity of bacterial community was not significantly influenced by MTBE and its metabolites.

• Microbiology and Biotechnology Letters
• /
• v.44 no.4
• /
• pp.550-556
• /
• 2016

Groundwater heat pump (GWHP) systems must consider phenomena such as clogging to improve system efficiency and maintenance. In this study, we evaluated the prokaryotic diversity in a boring slime sample obtained at a depth of 10 m, which represented an undisturbed sample not affected by aquifer drawdown. Bacteria belonging to the phyla Proteobacteria (20.8%), Acidobacteria (18.8%), Chloroflexi (16.9%), and Firmicutes (10.2%) were found. Additionally, 144 species were identified as belonging to the genus Koribacter. Archaeal phyla were detected including Thaumarchaeota (42.8%), Crenarchaeota (36.9%), and Euryarchaeota (17.4%) and the class level comprised the miscellaneous Crenarchaeota group (MCG), Finnish forest soil type B (FFSB), and Thermoplasmata, which collectively accounted for approximately 69.4% of the detected Archaea. Operational taxonomic units (OTUs) were analyzed to reveal 3,565 bacterial and 836 archaeal OTUs, with abundances of 7.81 and 6.68, and richnesses of 5.96E-4 and 2.86E-3, respectively. The distribution of the groundwater microbial community in the study area showed a higher proportion of non-classified or unidentified groups compared to typical communities in surface water and air. In addition, 135 (approx. 1.9%) reads were assigned to a bacterial candidate associated with clogging.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.364-364
• /
• 2017

Saemangeum reclaimed land is a part of Saemangeum Development Project. Most of the persistent problems of Saemangeum reclaimed land remain to be related to soil salinity. Soil salinity is a major abiotic factor related to microbial community structure and also fungi have been reported to be more sensitive to salinity stress than bacteria. The aim of this study was conducted to investigate the effect of soil salinity levels on the microbial communities in Saemangeum reclaimed land using 454 pyrosequencing analysis. Soil samples was collected from 12 sites of in Saemangeum reclaimed land. For pyrosequencing, 27F/518R (bacteria) and ITS3/ITS4 (fungi) primers were used containing the Roche 454 pyrosequencing adaptor-key-linker (underlined) and unique barcodes (X). Pyrosequencing was performed by Chun's Lab (Seoul, Korea) using the standard shotgun sequencing reagents and a 454 GS FLX Titanium sequencing System (Roche, Inc.). In the soil samples, Proteobacteria (bacteria) and Ascomycota (fungi) shows the highest relative abundance in all the soil sample sites. Proteobacteria, Bacteroidetes, Plantomycetes, Gemmatimonadetes and Parcubacteria were shown to have significantly higher abundance in high salinity level soils than low salinity level soils, while Acidobacteria and Nitrospirae has significantly higher relative abundance in low salinity level soils. The abundance of fungal, Ascomycota has the highest relative abundance in soil samples, followed by Basidiomycota, Chlorophyta, Zygomycota and Chytridiomycota. Basidiomycota, Zygomycota, Glomeromycota and Cerozoa were show significantly higher relative abundance in low salinity level soils. The principal coordinate analysis (PCoA) and correlation analysis shown to salinity-related soil parameters such as ECe, Na+, SAR and EPS were affected to bacterial and fungal community structure. Proteobacteria, Bacteroidetes, Plantomycetes exhibited significantly positive correlation with soil salinity, while Acidobacteria exhibited significantly negative correlation. In the case of fungal community, Basidiomycota and Zygomycota were seen show significantly negative correlation with salinity related soil parameters. These results suggest that provide understanding effect of soil salinity on microbial community structure and correlation of microbial community with soil parameters in Saemangeum reclaimed land.

• Journal of Environmental Health Sciences
• /
• v.37 no.4
• /
• pp.279-288
• /
• 2011

Objectives: This study investigated the levels and components of floor-settled dust in two elementary schools located at different sites (one near the Shihwa industrial complex and the other in a rural area) in order to evaluate the amounts of trace metal elements (As, Cd, Co, Cr, Cu, Ni, Pb and Zn) and microorganisms. Methods: Over twenty settled-dust samples were collected from the two elementary schools. Trace metal elements were extracted from the dust using hydrochloric acid and nitric acid, and the amounts were measured by ICP-OES. Microbiological analysis was performed by bacterial culturing using R2A medium and denaturing gradient gel electrophoresis (DGGE). Results: The results showed that the amounts of three metal elements (Cr, Pb, and Zn) were significantly different between the schools (${\alpha}$=0.05, p<0.04). In addition, microbial communities in each school were highly correlated with one another. Among the identified microorganisms, a number of potentially opportunistic microorganisms, including antibiotic-resistant bacteria such as Acinetobacter baumannii, were found. Conclusions: This study will provide preliminary data for assessing levels and types of chemical and microbiological agents in elementary schools and for further evaluating human health risks associated with the agents.

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

• Journal of Microbiology and Biotechnology
• /
• v.26 no.1
• /
• pp.130-138
• /
• 2016

The use of antibiotics in aquaculture raises environmental and food safety concerns because chronic exposure of an aquatic ecosystem to antibiotics can result in the spread of antibiotic resistance, bioaccumulation of antibiotics in the organisms, and transfer of antibiotics to humans. In an attempt to overcome these problems, high-concentration red clay was applied as an alternative antibiotic against the following common fish pathogens: Aeromonas salmonicida, Vibrio alginolyticus, and Streptococcus equinus. The growth of A. salmonicida and V. alginolyticus was retarded by red clay, whereas that of S. equinus was promoted. Phase contrast and scanning electron microscopy analyses confirmed the attachment of red clay on cell surfaces, resulting in rapid gravitational removal and cell surface damage in both A. salmonicida and V. alginolyticus, but not in S. equinus. Different cell wall properties of grampositive species may explain the unharmed cell surface of S. equinus. Significant levels of oxidative stress were generated in only the former two species, whereas significant changes in membrane permeability were found only in S. equinus, probably because of its physiological adaptation. The bacterial communities in water samples from Oncorhynchus mykiss aquacultures supplemented with red clay showed similar structure and diversity as those from oxytetracycline-treated water. Taken together, the antibiotic effects of high concentrations of red clay in aquaculture can be attributed to gravitational removal, cell surface damage, and oxidative stress production, and suggest that red clay may be used as an alternative for antibiotics in aquaculture.

• Journal of Microbiology and Biotechnology
• /
• v.25 no.5
• /
• pp.569-578
• /
• 2015

Cold water paddy field soils are relatively unproductive, but can be ameliorated by supplementing with inorganic fertilizer from animal waste-based composts. The yield of two rice cultivars was significantly raised by providing either chicken manure or cow dung-based compost. The application of these composts raised the soil pH as well as both the total nitrogen and ammonium nitrogen content, which improved the soil's fertility and raised its nitrification potential. The composts had a measurable effect on the abundance of nitrogencycling-related soil microbes, as measured by estimating the copy number of various bacterial and archaeal genes using quantitative real-time PCR. The abundance of ammonia oxidizing archaea and bacteria was markedly encouraged by the application of chicken manure-based compost. Supplementation with the composts helped promote the availability of soil nitrogen in the cold water paddy field, thereby improving the soil's productivity and increasing the yield of the rice crop.

• Journal of Microbiology and Biotechnology
• /
• v.15 no.5
• /
• pp.952-964
• /
• 2005

The diesel-degrading activities of biofilms sampled from petroleum-contaminated groundwaters in urban subway drainage systems were examined in liquid cultures, and the microbial populations of the biofilms were characterized by denaturing gel gradient electrophoresis (DGGE) and 16S rDNA sequence analysis. Biofilm samples derived from two sites (19 K and 20 K) at subway Station N and Station I could degrade around $80\%$ of applied diesel within 20 and 40 days, respectively, at $15^{\circ}C$, and these results were strongly correlated with the growth patterns of the biofilms. The closest phylogenetic neighbor of a dominant component in the 19 K biofilm was Thiothrix fructosivorans strain Q ($100\%$ similarity). Four dominant strains in the 20 K biofilm were closely related to Thiothrix fructosivorans strain Q ($100\%$ similarity), Thiothrix sp. CC-5 ($100\%$ similarity), Sphaerotilus sp. IF14 ($99\%$ similarity), and Cytophaga-Flexibacter-Bacterioides (CFB) group bacterium RW262 ($98\%$ similarity). Three dominant members in the Station I biofilms were very similar to uncultured Cytophagales clone CRE-PA82 ($91\%$ similarity), Pseudomonas sp. WDL5 ($97\%$ similarity), and uncultured CFB group bacterium LCK-64 ($94\%$ similarity). The microbial components of the biofilms differed depending on the sampling site. This is the first report on the isolation of clones highly similar to Thiothrix fructosivorans and Thiothrix sp. from biofilms in petroleum-polluted groundwaters, and the first evidence that these organisms may play major roles in petroleum degradation and/or biofilm-development.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.11
• /
• pp.1772-1781
• /
• 2007

Activated sludge was sequentially adapted to benzene, toluene, and o-xylene (BTX) to study the effects on the change of microbial community. Sludge adapted to BTX separately degraded each by various rates in the following order; toluene>o-xylene>benzene. Degradation rates were increased after exposure to repeated spikes of substrates. Eleven different kinds of sludge were prepared by the combination of BTX sequential adaptations. Clustering analyses (Jaccard, Dice, Pearson, and cosine product coefficient and dimensional analysis of MDS and PCA for DGGE patterns) revealed that acclimated sludge had different features from nonacclimated sludge and could be grouped together according to their prior treatment. Benzene- and xylene-adapted sludge communities showed similar profiles. The sludge profile was affected from the point of the final adaptation substrate regardless of the adaptation sequence followed. In the sludge adapted to 50 ppm toluene, Nitrosomonas sp. and bacterium were dominant, but these bands were not dominant in benzene and benzene after toluene adaptations. Instead, Flexibacter sp. was dominant in these cultures. Dechloromonas sp. was dominant in the culture adapted to 50 ppm benzene. Thauera sp. was the main band in the sludge adapted to 50 ppm xylene, but became vaguer as the xylene concentration was increased. Rather, Flexibacter sp. dominated in the sludge adapted to 100 ppm xylene, although not in the culture adapted to 250 ppm xylene. Two bacterial species dominated in the sludge adapted to 250 ppm xylene, and they also existed in the sludge adapted to 250 ppm xylene after toluene and benzene.

• Korean Journal of Veterinary Service
• /
• v.43 no.1
• /
• pp.39-44
• /
• 2020

The aim of this study is to investigate how the gut microbiome shifts when pigs were exposed with low concentrations of mycotoxins, deoxynivalenol (DON) and zearalenone (ZEN) in feed. Fifteen of pigs, 15 kg in weight which were negative for PRRSV and PCV2 were purchased, acclimatized until 20 kg in weight, and randomly divided into 3 groups; the DON group (DON treated), the ZEN group (ZEN treated) and the CTL (untreated negative control). DON and ZEN administered to each group for 30 days at 0.8 mg/kg (800 ppb) and 0.20 mg/kg (200 ppb) in feed, respectively. After extraction of microbial DNA from intestine and fecal samples, sequencing procedures were performed in the Ion PGM using an Ion 316 V2 chip and Ion PGM sequencing 400 kit. The results suggested that the bacterial communities in duodenum, jejunum and ileum of the DON and ZEN groups presented low-abundant OTUs compared with the CTL group. OTUs in cecum, colon and feces were determined more than in small intestine of all three groups. However, the CTL group yielded more OTUs than other two groups in inter-group comparison. It is not fully clarified how the richness and abundance in microbiome functions in the health condition of animals, however, the exposure to DON and ZEN has caused microbial population shifts representing microbial succession and changes following the diversity and abundance of porcine gut microbiome. The metabolomic analysis correlate with microbiome analysis is needed for further study.