• Journal of Microbiology and Biotechnology
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• v.17 no.10
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• pp.1645-1654
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• 2007

The total methylotrophic population associated with rice plants from different cultivars was enumerated at three different stages: vegetative, flowering, and harvesting. The bacterial population in the leaf, rhizosphere soil, endophytic in the stem and roots, and epiphytic in the florets and grains were determined from four rice cultivars, Il-mi, Nam-pyeoung, O-dae, and Dong-jin, sampled from three different field sites. The methylotrophic bacteria isolated on AMS media containing 0.5% methanol as the sole carbon source uniformly showed three distinct morphologies, which were recorded as separate groups and their distribution among the various samples was determined using the ecophysiological index. The growth stage at the time of sampling had a more significant effect on the methylotrophic population and their distribution than the field site or cultivar. A similar effect was also observed for the PPFMs, where their population in different plant parts increased from V10 to R4 and then decreased towards stage R9. A canonical discriminant analysis of the PPFM population from different parts of rice showed clear variations among the cultivars, sampled sites, and growth stages, although the variations were more prominent among the growth stages.

• Korean Journal of Soil Science and Fertilizer
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• v.47 no.6
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• pp.451-456
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• 2014

Organic amendment practices can influence diversity and activities of soil microorganisms. There is a need to investigate this impact compared with other types of materials. This study was carried out to evaluate the long term effects of chemical and organic fertilizer on soil microbial community in upland field. During the last 11 years green manure, rice straw compost, rapeseed cake, pig mature compost, NPK, and NPK + pig mature compost were treated in upland soil. Organic fertilizer treatment found with high bacterial colony forming units (CFUs) as compared to chemical and without fertilizer treatment. There was no significant difference in the actinomycetes and fungal population. The average well color development (AWCD) value was the highest in green manure and, the lowest in without fertilizer treatment. Analyses based on the denaturing gradient gel electrophoresis (DGGE) profile showed that rice straw compost and pig mature compost had a similar banding pattern while rapeseed cake, NPK, NPK + pig mature compost and without fertilizer treatment were clustered in another cluster and clearly distinguished from green manure treatment. Bacterial diversity can be highly increased by the application of organic fertilizer while chemical fertilizer had less impact. It can be concluded that green manure had a beneficial impact on soil microbial flora, while, the use of chemical fertilizer could affect the soil bacterial communities adversely.

• Korean Journal of Environmental Agriculture
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• v.31 no.1
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• pp.52-59
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• 2012

BACKGROUND: Cultivation of genetically modified(GM) crops rapidly has increased in the global agricultural area. Among those, herbicide resistant GM crops are reported to have occupied 89.3 million hectares in 2010. However, cultivation of GM crops in the field evoked the concern of the possibility of gene transfer from transgenic plant into soil microorganisms. In our present study, we have assessed the effects of herbicide-resistant GM Chinese cabbage on the surrounding soil microbial community. METHODS AND RESULTS: The effects of a herbicide-resistant genetically modified (GM) Chinese cabbage on the soil microbial community in its field of growth were assessed using a conventional culture technique and also culture-independent molecular methods. Three replicate field plots were planted with a single GM and four non-GM Chinese cabbages (these included a non-GM counterpart). The soils around these plants were compared using colony counting, denaturing gradient gel electrophoresis and a species diversity index assessment during the growing periods. The bacterial, fungal and actinomycetes population densities of the GM Chinese cabbage soils were found to be within the range of those of the non-GM Chinese cabbage soils. The DGGE banding patterns of the GM and non-GM soils were also similar, suggesting that the bacterial community structures were stable within a given month and were unaffected by the presence of a GM plant. The similarities of the bacterial species diversity indices were consistent with this finding. CONCLUSION: These results indicate that soil microbial communities are unaffected by the cultivation of herbicide-resistant GM Chinese cabbage within the experimental time frame.

• Journal of Microbiology and Biotechnology
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• v.22 no.12
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• pp.1613-1620
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• 2012

Bacterial wilt caused by Ralstonia solanacearum is a devastating disease of many economically important crops. Since there is no promising control strategy for bacterial wilt, phage therapy could be adopted using virulent phages. We used phage PE204 as a model lytic bacteriophage to investigate its biocontrol potential for bacterial wilt on tomato plants. The phage PE204 has a short-tailed icosahedral structure and double-stranded DNA genome similar to that of the members of Podoviridae. PE204 is stable under a wide range of temperature and pH, and is also stable in the presence of the surfactant Silwet L-77. An artificial soil microcosm (ASM) to study phage stability in soil was adopted to investigate phage viability under a controlled system. Whereas phage showed less stability under elevated temperature in the ASM, the presence of host bacteria helped to maintain a stable phage population. Simultaneous treatment of phage PE204 at $10^8$ PFU/ml with R. solanacearum on tomato rhizosphere completely inhibited bacterial wilt occurrence, and amendment of Silwet L-77 at 0.1% to the phage suspension did not impair the disease control activity of PE204. The biocontrol activities of phage PE204 application onto tomato rhizosphere before or after R. solanacearum inoculation were also investigated. Whereas pretreatment with the phage was not effective in the control of bacterial wilt, post-treatment of PE204 delayed bacterial wilt development. Our results suggested that appropriate application of lytic phages to the plant root system with a surfactant such as Silwet L-77 could be used to control the bacterial wilt of crops.

• Research in Plant Disease
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• v.18 no.4
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• pp.361-369
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• 2012

A population density model for bacterial wilt, which is caused by Ralstonia solanacearum, in hot pepper was developed to estimate the primary infection date after overwintering in the field. We developed the model mechansitically to predict reproduction of the pathogen and pathogensis on seedlings of the host. The model estimates the pathogen's populations both in the soil and in the host. In order to quantify environmental infection factors, various temperatures and initial population densities were determined for wilt symptoms on the seedlings of hot pepper in a chamber. Once, the pathogens living in soil multiply up to 400 cells/g of soil, they can infect successfully in the host. Primary infection in a host was supposed to be started when the population of the pathogen were over $10^9$ cells/g of root tissue. The estimated primary infection dates of bacterial wilt in 2011 in Korea were mostly mid-July or late-July which were 10-15 days earlier than those in 2010. Two kinds of meterological data, synoptic observation and field measurements from paddy field and orchard in Kyunggi, were operated the model for comparing the result dates. About 1-3 days were earlier from field data than from synoptic observation.

• 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.

• Korean Journal Plant Pathology
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• v.2 no.3
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• pp.165-173
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• 1986

Accumulation of Pseudomonas sp., P. fluorescens and Erwinia carotovora in 60 min treatment was greater in extracts from soil, exudate from ginseng root and solutions than distilled water. In bacterial movement toward rubber tube soil from chamber, accumulation of P. fluorescens in response to soil supplemented with soil extracts, exudate and solutions was generally greater in soil extracts compared to control and other solutions, but Pseudomonas sp. and E. carotovora were not much response to supplemented extracts, exudate and solutions. Accumulation of the bacteria in capillaries containing various exudates from fungal propagules with not attracted to the exudates. For an accumulation of bacteria in rubber tubes containing soil inoculated with fungal propagules, the Pseudomonas sp. was not attracted in soil inoculated by the organisms as attractant but P. fluorescens and E. carotovora to fungi were attracted to F. solani, F. oxysporum and mixed organism Alternaria panax did not affect on bacterial movement except E. carotovora. The organic matter conten in Kangwha and Kimpo soil were low in diseased and healthy soil. The K content was especially high in Kimpo healthy soil. Bacterial population in Goesan and Kangwha were more abundant than other soil. The number actinomycetes was populated abundant in healthy soil of Goesan and diseased soil of Poonggi.

• Korean Journal of Soil Science and Fertilizer
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• v.47 no.1
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• pp.28-35
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• 2014

Due to recent interest of the consumers on safe farm products and the government's political support for eco-friendly agriculture, organic fruit production has been growing continuously. This research was conducted in order to study the effect of cover plants on soil microbial community on cover plants and establish an organic fruit cultivation method through choosing optimal cover plant. As a result of investigating soil microbial population density, the bacterial density in soil showed an increasing trend in June compared to April, and there was a decreasing trend in bacterial density of the soil in August compared to June. The density of actinomycetes in soil increased around 1.6 times in June compared to April when the soil was covered with hairy vetch. The increase of filamentous fungus in crimson clover group was 6.1 times higher in June compared to April and in hairy vetch group, the increase was 4.9 times higher in June compared to April. As a result of analyzing DNA extracted from the soil categorized by different types of cover plants using DGGE method, soil collected from April had higher number of bands detected from different locations according to different types of cover plants. Diversity of the bands from the soil collected from August showed higher range of reduction. As a result of analyzing soil microbial community by different period and the types of cover plants using Pyrosequencing method, microbes were detected in the order of Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Firmicutes. Distribution rate of Firmicutes increased in the soil collected in August compared to June and this was shown in all types of cover plants by twice the amount.

• The Plant Pathology Journal
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• v.22 no.4
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• pp.364-368
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• 2006

Survival of biocontrol agents and their effective colonization of rhizhosphere are the essential components for successful disease suppression. The effects of hydrogel supplement on bacterial survival and disease control were evaluated in pot and in the field. Addition of 2% hydrogel material to potting soil resulted in significant enhancement of colonization of biocontrol agent Serratia plymuthica A21-4 both in soil and rhizosphere of pepper plants. Rhizosphere colonization of S. plymuthica A21-4 retrieved from 40 days old pepper seedlings indicated 100 times higher bacterial population in hydrogel treated soil than in ordinary pot soil. The pepper plants sown in hydrogelated potting soil showed higher seed germination rate and the better growth of pepper plant than those in ordinary commercial pot soil. Although the suppression of Phytophthora capsid density in the potting soil by treatment of biocontrol agent A21-4 was not significantly different between in hydrogelated soil and ordinary potting soil, the suppression of Phytophthora blight between two treatments was significantly different. A21-4 treatment in hydrogelated potting soil was completely disease-free while same treatment in ordinary potting soil revealed 36% disease incidence. Our field study under natural disease occurrence also showed significantly less disease incidence(12.3%) in the A21-4 treatment in the hydrogelated soil compared to other treatments. Yield promotion of pepper by the A21-4 treatment in the hydrogelated potting soil was also recognized. Our results indicated that hydrogel amendment with biocontrol agent in pot soil would be a good alternative to protect pepper seedlings and increase plant yield.

• Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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• 2005.04a
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• pp.28-30
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• 2005

Because of high population diversity in soil microbial communities, it is difficult to accurately assess the capability of biodegradation of toxicant by microbes in soil and sediment. Identifying biodegradative microorganisms is an important step in designing and analyzing soil bioremediation. To remove non-important noise information, it is necessary to selectively enrich genomes of biodegradative microorganisms fromnon-biodegradative populations. For this purpose, a stable isotope probing (SIP) technique was applied in selectively harvesting the genomes of biphenyl-utilizing bacteria from soil microbial communities. Since many biphenyl-using microorganisms are responsible for aerobic PCB degradation In soil and sediments, biphenyl-utilizing bacteria were chosen as the target organisms. In soil microcosms, 13C-biphenyl was added as a selective carbon source for biphenyl users, According to $13C-CO_2$ analysis by GC-MS, 13C-biphenyl mineralization was detected after a 7-day of incubation. The heavy portion of DNA(13C-DNA) was separated from the light portion of DNA (12C-DNA) using equilibrium density gradient ultracentrifuge. Bacterial community structure in the 13C-DNAsample was analyzed by t-RFLP (terminal restriction fragment length polymorphism) method. The t-RFLP result demonstates that the use of SIP efficiently and selectively enriched the genomes of biphenyl degrading bacteria from non-degradative microbes. Furthermore, the bacterial diversity of biphenyl degrading populations was small enough for environmental genomes tools (metagenomics and DNA microarrays) to be used to detect functional (biphenyl degradation) genes from soil microbial communities, which may provide a significant progress in assessing microbial capability of PCB bioremediation in soil and groundwater.