• Animal Bioscience
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• v.36 no.9
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• pp.1453-1464
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• 2023

Objective: This study investigated the changes in bacterial communities within decomposing swine microcosms, comparing soil with or without intact microbial communities, and under aerobic and anaerobic conditions. Methods: The experimental microcosms consisted of four conditions: UA, unsterilized soil-aerobic condition; SA, sterilized soil-aerobic condition; UAn, unsterilized soil-anaerobic condition; and San, sterilized soil-anaerobic condition. The microcosms were prepared by mixing 112.5 g of soil and 37.5 g of ground carcass, which were then placed in sterile containers. The carcass-soil mixture was sampled at day 0, 5, 10, 30, and 60 of decomposition, and the bacterial communities that formed during carcass decomposition were assessed using Illumina MiSeq sequencing of the 16S rRNA gene. Results: A total of 1,687 amplicon sequence variants representing 22 phyla and 805 genera were identified in the microcosms. The Chao1 and Shannon diversity indices varied in between microcosms at each period (p<0.05). Metagenomic analysis showed variation in the taxa composition across the burial microcosms during decomposition, with Firmicutes being the dominant phylum, followed by Proteobacteria. At the genus level, Bacillus and Clostridium were the main genera within Firmicutes. Functional prediction revealed that the most abundant Kyoto encyclopedia of genes and genomes metabolic functions were carbohydrate and amino acid metabolisms. Conclusion: This study demonstrated a higher bacteria diversity in UA and UAn microcosms than in SA and SAn microcosms. In addition, the taxonomic composition of the microbial community also exhibited changes, highlighting the impact of soil sterilization and oxygen on carcass decomposition. Furthermore, this study provided insights into the microbial communities associated with decomposing swine carcasses in microcosm.

• Journal of Microbiology and Biotechnology
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• v.17 no.1
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• pp.52-57
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• 2007

Growth promotion of wild plants by some plant growth-promoting rhizobacteria (PGPR) was examined in the microcosms composed of soils collected separately from a grass-covered site and a nongrass-covered site in a lakeside barren area at Lake Paro, Korea. After sowing the seeds of eight kinds of wild plants and inoculation of several strains of PGPR, the total bacterial number and microbial activity were measured during 5 months of study period, and the plant biomasses grown were compared at the end of the study. Acridine orange direct counts in the inoculated microcosms, $1.3-9.8{\times}10^9\;cells{\cdot}g\;soil^{-1}$ in the soil from the grass-covered area and $0.9-7.2{\times}10^9\;cells{\cdot}g\;soil^{-1}$ in the soil from the nongrass-covered site, were almost twice higher than those in the uninoculated microcosms. The number of Pseudomonas sp., well-known bacteria as PGPR, and the soil dehydrogenase activity were also higher in the inoculated soils than the uninoculated soils. The first germination of sowed seeds in the inoculated microcosm was 5 days earlier than the uninoculated microcosm. Average lengths of all plants grown during the study period were 26% and 29% longer in the inoculated microcosms starting with the grass-covered soil and the nongrass-covered soil, respectively, compared with those in the uninoculated microcosms. Dry weights of whole plants grown were 67-82% higher in the inoculated microcosms than the uninoculated microcosms. Microbial population and activity and growth promoting effect by PGPR were all higher in the soils collected from the grass-covered area than in the nongrass-covered area. The growth enhancement of wild plants seemed to occur by the activities of inoculated microorganisms, and this capability of PGPR may be utilized for rapid revegetation of some barren lands.

• Journal of Environmental Health Sciences
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• v.34 no.5
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• pp.387-394
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• 2008

The toxicity of methyl tert-butyl ether (MTBE), tert-butyl alcohol (TBA) and formaldehyde (FA) on the indigenous microbial community in forest soil was studied. MTBE, TBA and FA with different concentrations were added into microcosms containing forest soil samples. After 10 and 30 days, total viable cell number and dehydrogenase activity in the microcosms were evaluated. Bacterial communities in the microcosms were also analyzed using a denaturing gradient gel electrophoresis (DGGE). Dehydrogenase activity and total viable cell number were decreased according to the increase of MTBE, TBA and FA concentrations (P<0.05). FA toxicity was the highest, but TBA toxicity was the lowest. The results of principal component analysis using DGGE fingerprints showed that the microbial communities contaminated MTBE, TBA and FA were grouped by exposure time not exposure concentration. Dominant species in the microcosms were as follows: Photobacterium damselae sub sp. and Bacillus sp. KAR28 for MTBE; Mycobacterium sp. and Uncultured Clostridium sp. for TBA; and Uncultured Paenibacillaceae bacterium and Anxynobacillus, Flavithermus for FA.

• Journal of Microbiology
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• v.40 no.4
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• pp.274-281
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• 2002

The competitive quantitative PCR method targeting pcbC gene was developed for monitoring 4-chlorobiphenyl(4CB)-degrading bacteria, Pseudomonas sp. strain DJ-12, in soil microcosms. The method involves extraction of DNA from soil contaminated with 4CB, PCR amplification of a pcbC gene fragment from the introduced strain with a set of strain-specific primers, and quantification of the elec-trophoresed PCR product by densitometry. To test the adequacy of the method, Pseudomonas sp. strain DJ-12 was introduced into both contaminated and non-contaminated soil microcosms amended with 4CB. Pseudomonas sp. strain DJ-12 was monitored and quantified by a competitive quantitative PCR in comparison with 4CB degradation and the result was compared to those obtained by using the conventional cultivation method. We successfully detected and monitored 4CB-degrading bacteria in each microcosm and found a significant linear relationship between the number of 4CB-degrading bacteria and the capacity for 4CB biodegradation. The results of DNA spiking and cell-spreading experiments suggest that this competitive quantitative PCR method targeting the pcbC gene for monitoring 4CB- degrading bacteria appears to be rapid, sensitive and more suitable than the microbiological approach in estimating the capacity of 4CB biodegradation in environmental samples.

• The Korean Journal of Ecology
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• v.19 no.2
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• pp.179-189
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• 1996

Growth and nitrogen retention of Persicaria thunbergii were investigated in the wetland microcosms which contained the plants growing on soil bed. Nitrogen solution was supplied to the microcosms with the same amount of $NH_4^{+}-N\; and\; NO_3^{-}-N$ at the rates of 0.00, 0.78, 1.57, 3.14g $N{\cdot}m^{-2}{\cdor}wk^{-1}$ from May 1 to August 31, 1995. The solution was detained for 5 days to react with soil and plant and then allowed to leach. The contents of NH_4^{+}-N\;and\; NO_3^{-}-N$ in the leachate, total Kjeldahl nitrogen, plant biomass, and soil characteristics were determined. Nitrogen retained by plant was estimated as the increment of TKN in plant biomass. The addition of 0.78 and 1.57g $N{\cdot}m^{-2}{\cdot}wk^{-1}$ resulted in significant increase of plant biomass. However, plant growth was inhibited when nitrogen was added at the rate of 3.14g $N{\cdot}m^{-2}{\cdot}wk^{-1}$. Overall, the plant biomass was positively correlated with the amount of nitrogen retained by plant and soil system. The amounts of $NO_3^{-}-N$ leached from the microcosms were 5~10 times higher than those of $NH_4^{+}-N$. While total nitrogen added ranged from 143.2 to 576.5g $N/m^2$, total leaching loss of inorganic nitrogen and nitrogen retained by plant was as little as 1.04~22.71g $N/m^2$, and 5.46~12.91g $N/m^2$, respectively. Then, the plant seemed to contribute to KDICical and microbial immobilization of nitrogen in the soil. Finally, it is suggested that a large portion of nitrogen added was lost into the air by denitrification and volatilizaton, and / or leached in organic forms.

• Journal of Microbiology
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• v.42 no.3
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• pp.243-247
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• 2004

Sphingomonas chlorophenolica ATCC39723 was successfully labeled with the gfp (green fluorescent protein) gene inserted into the pcpB gene by homologous recombination. As the gfp recombinant was easily distinguished from other indigenous organisms, the population of gfp recombinant was monitored after being released into the soil microcosms. Their population density dropped from 10$\^$8/ to 10$\^$6/ (cfu/$m\ell$) in the non-sterilized soil microcosms during the first 6 days. Moreover, the gfp recombinant was not detected even at lower dilution rates after a certain time period. The recombinant, however, survived for at least 28 days in the sterilized soil microcosms. Although the gfp recombinant did not degrade pentachlorophenol (PCP), this experiment showed the possibility of using gfp as a monitoring reporter system for S. chlorophenolica ATCC39723 and potentially other species of Sphingomonas.

• Journal of Environmental Health Sciences
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• v.34 no.6
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• pp.403-413
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• 2008

Toxic effect of methyl tert-butyl ether (MTBE), tert-butyl alcohol (TBA) and formaldehyde (FA) on microbial activity and diversity was compared in rice field, leek patch, and tidal mud flat soil samples. MTBE, TBA and FA with different concentrations were added into microcosms containing these soil samples, and placed at room temperature for 30 days. Then the microbial activities such as dehydrogenase and viable cell numbers and microbial community using a DGGE (Denaturing gradient gel electrophoresis) fingerprinting method were measured. Among the samples, dehydrogenase activity in rice field was inhibited the most by MTBE, TBA and FA. The toxic effect was higher according to the following orders: FA > MTBE > TBA. Dominant species in the microcosms contaminated with MTBE, TBA and FA were Chloroflex, Bacilli, gamma-proteobacteria in the rice field sample, Sphingobacteria, Flavobacteria, Actinobacteria, Bacilli, gamma-proteobacteria in the leek patch sample, and Sphingobacteria, Flavobacteria, delta-proteobacteria, gamma-proteobacteria in the tidal mud flat sample.

• Journal of Life Science
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• v.8 no.3
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• pp.299-304
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• 1998

In order to clarify the effects of acid rain on soil microorganisms, the inpact of acid to soil microorganisms was survyed for 14 weeks using soil microcosms from industrial site A and B, Gaejok mountain, and Daechong lake in Taejeon area. The acid tolerant-microorganisms in natural soil, using culturing method were counted to be 5.8 - $8.0{\times}10^6$CFU/g soil. The number of microorganisms using ATP-biomass analysis for natural soil samples were also analyzed and 2.2 - $2.6{\times}10^9$ cell/g soil in industrial site A and B, Gaejok mountain, and Daechong lake were determined. In soil samples, which were treated with artificial acid rain, the number of acid tolerant microorganisms were counted 2.9 - $5.8{\times}10^5$ and 2.8 - $7.5{\times}10^8$, respectively. Therefore, we conformed that the numver of soil microorganisms were influenced by acid rain. Also, long term acid tolerant microorganisms were identified as Rhodotorula sp. and Pseudomonas sp.

• Asian-Australasian Journal of Animal Sciences
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• v.12 no.4
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• pp.629-632
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• 1999

Constructed wetlands are being used for the removal of nutrients from livestock wastewater. However, natural vegetation typically used in constructed wetlands does not have marketable value. As an alternative, agronomic plants grown under flooded or saturated soil conditions that promote denitrification can be used. Studies on constructed wetlands for swine wastewater were conducted in wetland cells that contained either natural wetland plants or a combination of soybeans and rice for two years with the objective of maximum nitrogen reduction to minimize the amount of land required for terminal treatment. Three systems, of two 3.6 by 33.5 m wetland cells connected in series were used; two systems each contained a different combination of emergent wetland vegetation: rush/bulrush (system 1) and bur-reed/cattail (system 2). The third system contained soybean (Glycine max) in saturated-soil-culture (SSC) in the first cell, and flooded rice (Oryza sativa) in the second cell. Nitrogen (N) loading rates of 3 and $10kg\;ha^{-1}\;day^{-1}$ were used in the first and second years, respectively. These loading rates were obtained by mixing swine lagoon liquid with fresh water before it was applied to the wetland. The nutrient removal efficiency was similar in the rush/bulrush, bur-reed/cattails and agronomic plant systems. Mean mass removal of N was 94 % at the loading rate of $3kg\;N\;ha^{-1}\;day^{-1}$ and decreased to 71% at the higher rate of $10kg\;N\;ha^{-1}\;day^{-1}$. The two years means for above-ground dry matter production for rush/bulrushes and bur-reed/cattails was l2 and $33Mg\;ha^{-1}$, respectively. Flooded rice yield was $4.5Mg\;ha^{-1}$ and soybean grown in saturation culture yielded $2.8Mg\;ha^{-1}$. Additionally, the performance of seven soybean cultivars using SSC in constructed wetlands with swine wastewater as the water source was evaluated for two years, The cultivar Young had the highest yield with 4.0 and $2.8Mg\;ha^{-1}$ in each year, This indicated that production of acceptable soybean yields in constructed wetlands seems feasible with SSC using swine lagoon liquid. Two microcosms studies were established to further investigate the management of constructed wetlands. In the first microcosm experiment, the effects of swine lagoon liquid on the growth of wetland plants at half (about 175 mg/l ammonia) and full strength (about 350 mg/l ammonia) was investigated. It was concluded that wetland plants can grow well in at least half strength lagoon liquid. In the second microcosm experiment, sequencing nitrification-wetland treatments was studied. When nitrified lagoon liquid was added in batch applications ($48kg\;N\;ha^{-1}\;day^{-1}$) to wetland microcosms the nitrogen removal rate was four to five times higher than when non-nitrified lagoon liquid was added. Wetland microcosms with plants were more effective than those with bare soil. These results suggest that vegetated wetlands with nitrification pretreatment are viable treatment systems for removal of large quantities of nitrogen from swine lagoon liquid.

• Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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• 2003.04a
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• pp.192-195
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• 2003

As a part of our research project for in-situ bioremediation of nitrate contaminated. groundwater, screening studies to determine an effective electron donor (EO) and/or carbon source (CS) such as acetate, ethanol, formate, fumarate, lactate, and propionate were conducted. To evaluate the feasibility for the biological degradation of nitrate, soil microcosm studies using nitrate-contaminated soil and groundwater were performed. The nitrate removal percentage in the order from the highest to the lowest was: formate, fumarate, and ethanol > lactate > propionate. Essentially no nitrate consumption was observed In acetate-fed microcosms. The order of nitrate removal rate from the highest to lowest was fumarate, formate, lactate, ethanol, and propionate. These results suggest that fumarate and formate are promising EDs/CSs for in-situ bioremediation of nitrate - contaminated oxygenated groundwater.