• 한국토양비료학회지
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• 제45권6호
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• pp.1073-1085
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• 2012

Soil microbial communities are immensely diverse and complex with respect to species richness and community size. These communities play essential roles in agricultural soil because they are responsible for most of the nutrient cycles in the soil and influence the plant diversity and productivity. However, the majority of these microbes remain uncharacterized because of poor culturability. Next-generation sequencing techniques have revolutionized many areas of biology by providing cheaper and faster alternatives to Sanger sequencing. Among them, amplicon pyrosequencing is a powerful tool developed by 454 Life Sciences for assessing the diversity of complex microbial communities by sequencing PCR products or amplicons. This review summarizes the current opinions in amplicon sequencing of soil microbial communities, and provides practical guidance and advice on sequence quality control, aligning, clustering, OTU- and taxon-based analysis. The last section of this article includes a few representative studies conducted using amplicon pyrosequencing.

• 식물조직배양학회지
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• 제28권6호
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• pp.323-328
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• 2001

이탈리안 라이그래스의 종자배양에서 캘러스 형성 및 식물체 재분화 체계를 확립하기 위하여 기본배지와 탄소원의 종류별 식물체 재분화 정도 및 배양효율의 품종 간 차이 등에 대한 실험을 수행하여 얻어진 결과를 요약하면 다음과 같다. 기본배지의 종류에 따른 캘러스 형성 및 식물체 재분화율은 MS 배지가 N6 배지나 B5 배지보다 높게 나타났다. 배지 내에 첨가되는 탄소원의 종류에 따른 식물체 재분화율은 sucrose가 maltose보다 효과적이었다. 이탈리안 라이그래스의 종자배양에 있어서 모식물의 genotype에 따라 식물체 재분화 능력은 큰 차이를 보였으며, 공시품종 중 'Rio' 와 'Jeanne' 의 재분화 능력이 각각 38%와 56%로 가장 높았다.

• Journal of Microbiology
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• 제42권2호
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• pp.69-73
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• 2004

Vibrio vulnificus, a Gram-negative bacterium found in estuarine waters, is responsible for over 95％ of all seafood-related deaths in the United States. As a result of a temperature downshift to 5$^{\circ}C$, this organism enters the viable but nonculturable (VBNC) state. Changes in the membrane fatty acid (FA) composition of V. vulnificus may be a contributing factor to the ability of this organism to enter into and survive in the VBNC state. This hypothesis was tested by incubating the organism at 5$^{\circ}C$ in arti-ficial sea water and analyzing the cells' FAs during the initial hours of temperature and nutrient down-shift. Prior to downshift, the predominant FAs were 16:0, 16:1 and 18:0. During the first four hours of downshift, statistically significant changes occurred in 15:0, 16:1, 16:0, 17:0, and 18:0. These results indicate that changes in FA composition occur prior to entry of V. vulnificus into the VBNC state, suggesting that the ability to maintain membrane fluidity may be a factor in this physiological response. Cells in which fatty acid synthesis was inhibited did not survive, indicating that active fatty acid metab-olism is essential for entry of cells into the VBNC state.

• Journal of Microbiology and Biotechnology
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• 제27권3호
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• pp.417-428
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• 2017

Diseases caused by foodborne or waterborne pathogens are emerging. Many pathogens can enter into the viable but nonculturable (VBNC) state, which is a survival strategy when exposed to harsh environmental stresses. Pathogens in the VBNC state have the ability to evade conventional microbiological detection methods, posing a significant and potential health risk. Therefore, controlling VBNC bacteria in food processing and the environment is of great importance. As the typical one of the gram-negatives, Escherichia coli (E. coli) is a widespread foodborne and waterborne pathogenic bacterium and is able to enter into a VBNC state in extreme conditions (similar to the other gram-negative bacteria), including inducing factors and resuscitation stimulus. VBNC E. coli has the ability to recover both culturability and pathogenicity, which may bring potential health risk. This review describes the concrete factors (nonthermal treatment, chemical agents, and environmental factors) that induce E. coli into the VBNC state, the condition or stimulus required for resuscitation of VBNC E. coli, and the methods for detecting VBNC E. coli. Furthermore, the mechanism of genes and proteins involved in the VBNC E. coli is also discussed in this review.

• Journal of Microbiology and Biotechnology
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• 제26권3호
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• pp.540-548
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• 2016

Microbially induced calcium carbonate precipitation (CCP) is a long-standing but re-emerging environmental engineering process for production of self-healing concrete, bioremediation, and long-term storage of CO₂. CCP-capable bacteria, two Bacillus strains (JH3 and JH7) and one Sporosarcina strain (HYO08), were isolated from two samples of concrete and characterized phylogenetically. Calcium carbonate crystals precipitated by the three strains were morphologically distinct according to field emission scanning electron microscopy. Energy dispersive X-ray spectrometry mapping confirmed biomineralization via extracellular calcium carbonate production. The three strains differed in their physiological characteristics: growth at alkali pH and high NaCl concentrations, and urease activity. Sporosarcina sp. HYO08 and Bacillus sp. JH7 were more alkali- and halotolerant, respectively. Analysis of the community from the same concrete samples using barcoded pyrosequencing revealed that the relative abundance of Bacillus and Sporosarcina species was low, which indicated low culturability of other dominant bacteria. This study suggests that calcium carbonate crystals with different properties can be produced by various CCP-capable strains, and other novel isolates await discovery.

• 식물조직배양학회지
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• 제21권1호
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• pp.35-39
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• 1994

내냉성의 지표로 이용되는 적고의 발현정도가 상이한 벼품종 및 유성계통과 그들이 상호교잡된 F$_1$씨 청배양에서 최초 형성된 캘러스(primary callus)를 저온 스트레스 (stress) 처리하여 내냉성 세포의 기내선발 가능성을 검토하였다. 캘러스 형성율이나 저온 스트레스를 통한 식물체 분화율은 자포니카형이나 자포니카형/통일형 조합이 통일형이나 통일형간 조합보다 높았으며 저온 스트레스 처리일수의 증가에 따라 백색체 분화율이 증가하는 경향을 보였다. 약배양 효율에 있어서 상호교잡에 따른 세질효과는 나타나지 많았다. 고정도가 높은 품종이나 교잡 F$_1$의 약배양 후대 계통에서 캘러스의 저온 stress처리일수에 따른 적고 발현정도의 변이가 인정되지 많았다. 적고발현 정도가 상이한 품종간 교잡 F$_1$에서 유래된 연배양 후대 계통의 적고 발현은 양친 범위 내에 대부분이 분포하였으나 적고 발현이 낮은 방향의 초월분리계통도 나타났다. 최초 형성된 캘러스의 저온 stress 처리($0^{\circ}C$ 10일)에서 분화된 약배양 계통, 무처리에서 분화된 약배양 계통과 F$_2$ 집단간에는 적고 배양의 빈도 분포에서 차이가 인정되지 않았다. 따라서 벼 약배양에서 최초 형성된 캘러스 수준에서 저온 스트레스를 통해 내냉성 세포를 직접적인 기내선발방법은 효과적이지 못함이 밝혀졌다.

• Journal of Microbiology
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• 제44권2호
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• pp.155-161
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• 2006

Comparative analysis of microbial communities in a sequencing batch reactor which performed enhanced biological phosphorus removal (EBPR) was carried out using a cultivation-based technique and 16S rRNA gene clone libraries. A standard PCR protocol and a modified PCR protocol with low PCR cycle was applied to the two clone libraries of the 16S rRNA gene sequences obtained from EBPR sludge, respectively, and the resulting 424 clones were analyzed using restriction fragment length polymorphisms (RFLPs) on 16S rRNA gene inserts. Comparison of two clone libraries showed that the modified PCR protocol decreased the incidence of distinct fragment patterns from about 63 % (137 of 217) in the standard PCR method to about 34 % (70 of 207) under the modified protocol, suggesting that just a low level of PCR cycling (5 cycles after 15 cycles) can significantly reduce the formation of chimeric DNA in the final PCR products. Phylogenetic analysis of 81 groups with distinct RFLP patterns that were obtained using the modified PCR method revealed that the clones were affiliated with at least 11 phyla or classes of the domain Bacteria. However, the analyses of 327 colonies, which were grouped into just 41 distinct types by RFLP analysis, showed that they could be classified into five major bacterial lineages: ${\alpha},\;{\beta},\;{\gamma}-$ Proteobacteria, Actinobacteria, and the phylum Bacteroidetes, which indicated that the microbial community yielded from the cultivation-based method was still much simpler than that yielded from the PCR-based molecular method. In this study, the discrepancy observed between the communities obtained from PCR-based and cultivation-based methods seems to result from low culturabilities of bacteria or PCR bias even though modified culture and PCR methods were used. Therefore, continuous development of PCR protocol and cultivation techniques is needed to reduce this discrepancy.

• 식물조직배양학회지
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• 제27권3호
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• pp.163-167
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• 2000

벼 약배양에서 식물체 재분화 능력의 품종간 차이와 유전 양식에 대해 연구한 결과는 다음과 같다. ‘일미벼’ 외 46품종의 녹색체 재분화율은 자포니카형이 통일형이나 인디카형보다 높게 나타났고, 동일 품종 생태형간에도 배양 효율은 다양한 변이폭을 나타내었다. 자포니카 품종중에서 ‘일미벼’와 ‘향남벼’는 각각 19.4%와 18.1%의 높은 재분화 능력을 나타내었다. ‘밀양 23호’와 ‘추청벼’가 교배된 F$_2$집단의 녹색체 재분화율은 평균 6.6%로 나타났고 0~33.3%까지 넓은 변이폭을 가지는 연속적인 빈도 분포양상을 나타내었다. 캘러스 형성률과 식물체 재분화 능력에 대해 추정된 광의의 유전력은 각각 72.8%와 82.7%로 추정되었다.

• 미생물학회지
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• 제34권3호
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• pp.154-161
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• 1998

자연미생물, KP964에 luxAB 유전자를 주입하여 발광기능을 부여함으로써 그들의 발광정도가 스트레스에 대한 적응, 생존 및 활성도를 나타내는 색인이 될 수 있는가, 그리고 특히 non-culturable but viable(NCBV) 상태로 존재하는 미생물의 활성에 대한 정보를 제공할 수 있는가를 알아보았다. 영양결핍조건 하에서 그들의 총 세균수, 배양가능세균(colony-forming-unit; CFU)수, viable cell 수, 그리고 발광정도(relative light unit; RLU)의 변화를 조사하였다. 형광현미경으로 확인된 총 수는 변화가 없었으며, 첨가된 yeast extract에 의해 성장하는 viable cell 수는 완만하게 감소하였으나 CFU 수는 급격히 줄어들어 37일 째 이후에는 탐지한계 이하로 감소하였다. RLU의 경우, 처음 7일의 영양결핍동안 0.016%까지 감소하였으며, 그 이후에는 탐지한계수준 이하로 검출되었다. 아울러 스트레스를 받는 4시간 동안 CFU수와 RLU의 관계를 알아보기 위하여 발광 KP964 균주에게 독성유해물질, acid shock, osmotic shocks를 접촉시킨 후 시간별로 CFU와 RLU를 측정한 결과, KP964 CFU 당 RLU는 9.1-26% 까지 감소하였다. 이는 스트레스의 종류에 따라 접촉시간이 길수록 CFU 당 나오는 빛의 양이 줄어듬을 보인 것이다. 이러한 결과는 영양결핍조건 시 RLU의 감소율이 CFU의 감소율보다 더 크며 영양결핍 이외의 다른 스트레스 조건 하에서도 RLU의 감소율과 CFU의 감소율의 연관성을 찾을 수 없음을 보이므로, 발하는 빛의 정량만으로는 NCBV 상태는 물론 배양가능한 세균의 양이나 활성을 나타내지 못하는 듯 하였다. 그러나 스트레스를 받은 KP964의 활성 정도와 잠재발광능력과의 관계는 좋은 연관성을 보여주었다. 즉, p-xylene, hypo-osmotic stress, 또는 영양결핍에 노출된 세균으로부터 각 스트레스를 제거하였을 시 나타나는 발광증가 유형을 조사하였는데, 증가가 시작하기까지의 lag period는 각각 32, 26, 22분으로 나타났다. 즉 미생물에 강력한 스트레스로 작용한 경우일수록 lag time이 길고, 또한 발광의 증가율이 느리며 도달하는 최대 RLU값도 낮음이 관찰되었다. 따라서 스트레스 하의 세균으로부터 직접적인 RLU의 측정보다는 이들이 스트레스 조건으로부터 재성장 또는 소생되는 과정에서의 잠재 발광능력의 분석이 자연세균의 적응, 활성 및 생존의 정도를 나타내주었다.

• 한국환경과학회지
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• 제17권5호
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• pp.555-564
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• 2008

The bacterial community structure in biological activated carbon (BAC) process in drinking water treatment plant was investigated by Fluorescent in situ Hybridization (FISH) with rRNA-targeted oligonucleotide probe. Samples were collected at different three points in BAC process every month for one year. They were hybridized with a probe specific for the alpha, beta, gamma subclass of the class Proteobacteria, Cytophaga-Flavobacteria group and Gram-positive high G+C content (HGC) group. Total numbers of bacteria in BAC process counted by 4',6-diamidino-2-phenylindole (DAPI) staining were $5.4{\times}10^{10}$ (top), $4.0{\times}10^{10}$ (middle) and $2.8{\times}10^{10}$ cells/ml (bottom). The number of the culturable bacteria was from $1.0{\times}10^7$ to $3.6{\times}10^7$ cells/ml and the culturability was about 0.05%. The faction of bacteria detectable by FISH with the probe EUB338 was about 83% of DAPI counts. Gamma and alpha subclass of the class Proteobacteria were predominant in BAC process and their ratios were over 20% respectively. In top and middle, alpha, beta and gamma subclass of the class Proteobacteria competed with each other and their percentages was changed according to the season. In bottom, gamma subclass of the class Proteobacteria was predominant all through the year. It could be successfully observed the seasonal distribution of bacterial community in biological activated carbon process using FISH.