• Korean Journal of Microbiology
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• v.52 no.3
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• pp.365-374
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• 2016

In high-latitude regions, temperature has risen ($0.6^{\circ}C$ per decade) and this leads to the increase in microbial degradability against soil organic carbon (SOC). Furthermore, the decomposed SOC is converted into green-house gases ($CO_2$ and $CH_4$) and their release could further increase the rate of climate change. Thus, understanding the microbial diversity and their functions linked with SOC degradation in soil-thawing model is necessary. In this study, we divided tundra soil from Council, Alaska into two depth regions (30-40 cm and 50-60 cm of depth, designated as SPF and PF, respectively) and incubated that for 108 days at $0^{\circ}C$. A total of 111,804 reads were obtained through a pyrosequencing-based metagenomic study during the microcosm experiments, and 574-1,128 of bacterial operational taxonomic units (OTUs) and 30-57 of archaeal OTUs were observed. Taxonomic analysis showed that the distribution of bacterial taxa was significantly different between two samples. In detail, the relative abundance of phyla Actinobacteria and Firmicutes largely increased in SPF and PF soil, respectively, while phyla Crenarchaeota was increased in both soil samples. Weight measurement and gel permeation chromatography of the SOC extracts demonstrated that polymerization of humic acids, main component of SOC, occurred during the microcosm experiments. Taken together our results indicate that these bacterial and archaeal phyla could play a key function in SOC degradation and utilization in cold tundra soil.

• Journal of Microbiology and Biotechnology
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• v.28 no.6
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• pp.976-986
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• 2018

Knowledge about the gut bacterial communities associated with insects is essential to understand their roles in the physiology of the host. In the present study, the gut bacterial communities of a laboratory-reared insecticide-susceptible (IS), and a field-collected insecticide-resistant (IR) population of a major rice pest, the brown planthopper Nilaparvata lugens, were evaluated. The deep-sequencing analysis of the V3 hypervariable region of the 16S rRNA gene was performed using Illumina and the sequence data were processed using QIIME. The toxicological bioassays showed that compared with the IS population, IR population exhibited 7.9-, 6.7-, 14.8-, and 18.7-fold resistance to acephate, imidacloprid, thiamethoxam, and buprofezin, respectively. The analysis of the alpha diversity indicated a higher bacterial diversity and richness associated with the IR population. The dominant phylum in the IS population was Proteobacteria (99.86%), whereas the IR population consisted of Firmicutes (46.06%), followed by Bacteroidetes (30.8%) and Proteobacteria (15.49%). Morganella, Weissella, and Enterococcus were among the genera shared between the two populations and might form the core bacteria associated with N. lugens. The taxonomic-to-phenotypic mapping revealed the presence of ammonia oxidizers, nitrogen fixers, sulfur oxidizers and reducers, xylan degraders, and aromatic hydrocarbon degraders in the metagenome of N. lugens. Interestingly, the IR population was found to be enriched with bacteria involved in detoxification functions. The results obtained in this study provide a basis for future studies elucidating the roles of the gut bacteria in the insecticide resistance-associated symbiotic relationship and on the design of novel strategies for the management of N. lugens.

• Weed & Turfgrass Science
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• v.5 no.1
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• pp.29-34
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• 2016

Large patch disease in Zoysia japonica Steud. is the most destructive disease in turfgrass. For large patch management, it has been dependent on chemical controls but pesticides are harmful to soil, water and biodiversity. In this study, we evaluated 4 Streptomyces spp. strains (S2, S5, S8 and S12) which were selected in previous studies using metagenome approaches. Root colonization of the strains, large patch suppressing effect and the pathogen density change in actual golf course were investigated to evaluate biological control potential of the strains. All strains exhibited reliable root colonization ability that strains populations were higher than $6log\;cfu\;g^{-1}$ in turfgrass rhizosphere. The pathogen density, with S8 treatment, was detected average of 0.7 after a week and average of 1.2 after 4 weeks. Disease control and suppressive the pathogen population by S8 strain showed higher efficiency than other strains. S8 was applied in an actual golf course for the large patch control and pathogen density. The pathogen density in S8 treatment plot was detected below 1.6 per toothpick and lower compared with untreated plot. The results indicated that pathogen density was suppressed by S8 and the stain has great potential as a biological control agent for the large patch.

• Journal of Life Science
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• v.15 no.6 s.73
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• pp.851-856
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• 2005

Although valuable microbes have been isolated from the soil for the various productions of useful components, the microbes which can be cultivated in the laboratory are only $0.1-1\%$ of all microbes. To solve this problem, the study has recently been tried for making the valuable components from the environment by directly separating unculturable micrbial DNA in the soil. But it is known that humic acid originated from the soil interrupts various restriction enzymes and molecular biological process. Thus, in order to prevent these problems, this study modified the method separated soil DNA with phenol, CTAB and PEG. In order to compare the degree of purity for each DNA and the molecular biological application process, $A_{260}/A_{280}$ ratio, restriction enzymes, and PCR were performed. In case of DNA by the modified method, total yield of DNA was lower but $A_{260}/A_{280}$ ratio was higher than the previously reported methods. It was confirmed that the degree of purity is improved by the modified method. But it was not cut off by all kinds of tested restriction enzymes because of the operation of a very small amount of interrupting substances. When PCR was operated with each diluted DNA in different concentrations and GAPDH primer, the DNA by the modified method could be processed for PCR in the concentration of 100 times higher than by the previously reported separation method. Therefore, this experiment can find out the possibility of utilization for the unknown substances by effectively removing the harmful materials including humic acid and help establishing metagenomic DNA library from the soil DNA having the high degree of purity.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2019.10a
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• pp.46-46
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• 2019

The experiments were performed in the Jinan (elevation: 300 meters above sea level), Jeollabuk-do. Seedlings (n = 63 per $3.3m^2$) of ginseng cultivar (Cheonpung, Yeonpung) were planted on April 10, 2015. Shading material of plastic film house was blue-white film. Before the Planting seedling, silicate (3 kg/10 a) or chitosan (40 kg/10 a) was fertilized and foliar sprayed on the leaves 1000 times dilution solution once a month from May to September every year. The growth results of 5-year old ginseng surveyed in 2018 are as follows. The average air temperature in the plastic film house was the highest at $26.6^{\circ}C$ and $26.5^{\circ}C$ in July and August, respectively, and the highest temperature was $40.5^{\circ}C$ in July. The maximum daily temperature of $35^{\circ}C$ or more was 30 days, with the average soil temperature being $24.9^{\circ}C$ in August. The chemical properties of the test soil are as follows. pH was 6.4~6.9 level and EC was 0.35~0.46 dS/m. The organic matter content was 33.5~41.4 g/kg, and available-P content was 251.9~306.8 mg/kg. Exchangeable cations contents, such as K, Ca and Mg were all the appropriate ranges. The soil microbial density surveyed by the dilution plate method was 10~50 times higher than that of control (Non-treatment) and actinomycete density was 3~6 times higher. Pathogens of the genus Fusarium by Metagenome analysis decreased 91.3% and 68.2% respectively in the foliar sprayed of chitosan and soluble-silicate. The light intensity (PAR) in the blue-white film plastic film house gradually increased until July and then decereased, with the average of light intensity in March-October was $120.3umol/m^2/s$. The growth of aerial parts such as plant height and stem length was better than non-sprayed group in silicate or chitosan treatments and Yeonpung cultivar was superior to the Cheonpung cultivar. The SPAD value was higher in Yeonpung cultivar foliar sprayed with soluble-silicate. The growth of underground parts such as root length and taproot length were better in chitosan and soluble-silicate treatment than control, especially in Yeonpung cultivar foliar sprayed with chitosan was good in taproot length and taproot diameter, and fresh weight of root was 60.1 g. Ginsenoside contents were 24.9 mg/g and 22.4 mg/g, in the Cheonpung cultivar foliar sprayed with soluble-silicate or chitosan respectively, 28% and 15% higher than control (19.5 mg/g). The incidence of disease by Alteraria panax and Botrytis cinerea was 3~9% and 4~9%, respectively. High temperature damage rate was 3~5%.

• Animal Bioscience
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• v.35 no.11
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• pp.1808-1816
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• 2022

Objective: The study of Hanwoo (Korean native cattle) has mainly been focused on meat quality and productivity. Recently the field of microbiome research has increased dramatically. However, the information on the microbiome in Hanwoo is still insufficient, especially relationship between vagina and feces. Therefore, the purpose of this study is to examine the microbial community characteristics by analyzing the 16S rRNA sequencing data of Hanwoo vagina and feces, as well as to confirm the difference and correlation between vaginal and fecal microorganisms. As a result, the goal is to investigate if fecal microbiome can be used to predict vaginal microbiome. Methods: A total of 31 clinically healthy Hanwoo that delivered healthy calves more than once in Cheongju, South Korea were enrolled in this study. During the breeding season, we collected vaginal and fecal samples and sequenced the microbial 16S rRNA genes V3-V4 hypervariable regions from microbial DNA of samples. Results: The results revealed that the phylum-level microorganisms with the largest relative distribution were Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria in the vagina, and Firmicutes, Bacteroidetes, and Spirochaetes in the feces, respectively. In the analysis of alpha, beta diversity, and effect size measurements (LefSe), the results showed significant differences between the vaginal and fecal samples. We also identified the function of these differentially abundant microorganisms by functional annotation analyses. But there is no significant correlation between vaginal and fecal microbiome. Conclusion: There is a significant difference between vaginal and fecal microbiome, but no significant correlation. Therefore, it is difficult to interrelate vaginal microbiome as fecal microbiome in Hanwoo. In a further study, it will be necessary to identify the genetic relationship of the entire microorganism between vagina and feces through the whole metagenome sequencing analysis and meta-transcriptome analysis to figure out their relationship.

• Journal of Microbiology and Biotechnology
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• v.33 no.2
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• pp.219-227
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• 2023

Lettuce is one of the most consumed vegetables worldwide. However, it has potential risks associated with pathogenic bacterial contamination because it is usually consumed raw. In this study, we investigated the changes in the bacterial community on lettuce (Lactuca sativa L.) in Chungcheong-do, South Korea, and the prevalence of foodborne pathogens on lettuce in different seasons using 16S rRNA gene-based sequencing. Our data revealed that the Shannon diversity index showed the same tendency in term of the number of OTUs, with the index being greatest for summer samples in comparison to other seasons. Moreover, the microbial communities were significantly different between the four seasons. The relative abundance of Actinobacteriota varied according to the season. Family Micrococcaceae was most dominant in all samples except summer, and Rhizobiaceae was predominant in the microbiome of the summer sample. At the genus level, the relative abundance of Bacillus was greatest in spring samples, whereas Pseudomonas was greatest in winter samples. Potential pathogens, such as Staphylococcus and Clostridium, were detected with low relative abundance in all lettuce samples. We also performed metagenome shotgun sequencing analysis on the selected summer and winter samples, which were expected to be contaminated with foodborne pathogens, to support 16S rRNA gene-based sequencing dataset. Moreover, we could detect seasonal biomarkers and microbial association networks of microbiota on lettuce samples. Our results suggest that seasonal characteristics of lettuce microbial communities, which include diverse potential pathogens, can be used as basic data for food safety management to predict and prevent future outbreaks.

• Journal of Marine Life Science
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• v.8 no.1
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• pp.43-49
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• 2023

This study applied a metagenomic analysis of the penguins' gut microbiome from fecal samples of Adélie Penguin (Pygoscelis adeliae) and Emperor Penguin (Aptenodytes forsteri) living along the Ross Sea, Antarctica. As a result of taxonomic analysis, 7 phyla and 18 families were mainly present in the gut microbiome of Adélie and Emperor penguins. To assess microbial diversity, we performed alpha diversity and OTU abundance analyses. It was confirmed that the Adélie Penguin's gut microbial species had a higher diversity than Emperor Penguin's. Based on the Beta diversity analysis using PCoA, differences were observed in the clustering between Adélie and Emperor penguins, respectively. Through the KEGG pathway analysis using PICRUSt, the nucleoside and nucleotide biosynthesis pathway was the most prevalent in Adélie and Emperor penguins. This study enabled a comparison and analysis of the composition and diversity of the gut microbiome in Adélie and Emperor Penguins. It could be utilized for future research related to penguin feeding habits and could serve as a foundation for analyzing the gut microbiomes of various other Antarctic organisms.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2023.04a
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• pp.37-37
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• 2023

천마(天麻, Gastrodia elata Blume)는 난초과(蘭草科, Orchidaceae)에 속하는 식물로 잎과 뿌리가 없어 탄소동화능력이 없으며, 뽕나무버섯균과 공생하는 기생식물이다. 천마는 노지재배 시 혹한, 폭우 등 기상환경에 따른 연차간 수량성 차가 673~1,175kg/10a로 크고, 연작에 따른 수량성이 연작 1회 시 29%, 연작 2회 시 68%가 감소하는 경향을 보이고 있다. 최근 기후변화 대응으로 비가림시설재배가 이뤄지고 있으나, 비가림 시설재배 또한 연작장해가 발생하고 있다. 따라서, 본 연구는 비가림시설을 활용한 천마 재배의 연작장해 경감을 위해 태양열(6~10월, 비닐피복) 및 토양훈증(메탐소듐, 30 L/1,000 m²)으로 토양소독 처리를 하였고, 윤작(수단그라스)을 대조구로 설정하여 토양 화학성, 미생물상 및 수량성을 분석하였다. 토양소독 전·후 토양내 화학성을 분석한 결과, 비가림시설재배 시 토양 화학성의 변화는 거의 없었다. 토양소독 후 metagenome 분석 결과, JCR21(윤작), JCS21(태양열), JCF21(토양훈증)의 시료로부터 확보한 총 read는 598,425개였으며, 이 중에서 Eukaryota로 분류되지 않은 read는 2,397개(0.4%), no hit, not assign된 read는 17,094개 (2.9%), Bacteria로 분류된 read는 281,391개(47.0%), Eukaryota로 분류된 read는 총 297,543개(49.7%)였다. JCR21은 전체 read의 35.0%, JCS21은 34.0%, JCF21은 31.0%를 차지했고, Eukaryota는 JCR21 대비 JCS21, JCF21에서 각각 9.9%, 18.9% 낮았다. 그리고, Bacteria는 JCR21 대비 JCF21은 5.4% 감소하였으나, JCS21은 1.4% 증가하였다. 이 중 Eukaryota에서 종(species)명까지 정확하게 밝혀진 것은 27종이었고 속(genus) 으로는 18속이었다. JCF21은 전체 read의 30.2%, JCS21은 33.8%, JCR21은 36.0%를 차지했고, JCF21 포장은 토양훈증으로 JCS21에 비해 3.6%, JCR21에 비해 5.8%까지 균수가 감소함을 알 수 있었다. 대체적으로 발견된 균은 고르게 분포하고 있었으나 초작지, 연작 1회지, 연작 2회지에서는 많이 발견되지 않았던 Mucoromycota (41,490 read, 13.9%), Agaricales (10,586 read, 3.6%)가 높은 비율로 분포를 하고 있었다. 토양소독 처리에 따른 10a 당 수량을 살펴본 결과, 윤작 1,309 kg, 태양열소독 1,609 kg, 토양훈증 1,733 kg으로 나타났고, 수량지수가 윤작 처리구 대비 태양열소독은 23%, 토양훈증은 32% 높았다. 성마율은 윤작 51%, 태양열소독 63%, 토양훈증 68%으로 나타났으며, 자마율은 윤작 49%, 태양열소독 37%, 토양훈증 32%으로 나타났다. 괴경썩음 정도는 윤작 30-49%, 태양열소독 10-19%, 토양훈증 5-9%로 나타났다. 따라서, 비가림시설을 활용한 천마 재배 시 토양훈증 소독 처리를 하면 연작이 가능할 것으로 판단되었다.

• Applied Biological Chemistry
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• v.50 no.4
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• pp.268-275
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• 2007

Diversity of the mud flat microbial population in Suncheon Bay was investigated by studying extracellular enzyme activities and 16S rDNA sequences. Four culturable bacterial strains with CMCase, xylanase and protease activities were isolated from the wetland and the mud flat. All the strains produced more xylanase activity than CMCase or protease activity, and the properties of the isolate enzymes from the wetland were similar to those from the mud flat. About 2,000 clones were obtained with the 16S rDNA amplified from the metagenomic DNA isolated from the mud samples. Based on the restriction pattern(s), seventeen clones were selected for base sequence analysis. Of the 17 clones, only 35% (6 clones) were found to be cultured strains and 65% (11 clones) to be uncultured strains. The similarities in the base sequences of the clones ranged from 91.0% to 99.9% with an average similarity of 97.3%. The clones could be divided into 7 groups, Proteobacteria (9 clones, 52.9%), Firmicutes (3 clones, 17.6%), Bacteroidetes (1 clone), Flavobacteria (1 clone), Verrucomicrobia (1 clone), Acidobacteria (1 clone), and Chloroflexi (1 clone). Most of the Proteobacteria clones were gamma Proteobacteria associated with oxidation-reduction of sulfur.