• 미생물학회지
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• 제35권1호
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• pp.72-77
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• 1999

BIOLOG GN microplate를 이용한 유일탄소원의 이용능 비교를 통한 대사적 유사성과 16S rDNA 의 PCR 증폭산물의 제한효소 지문 분석에 따른 유전적 유사성을 5종의 식생토양에 따른 토양미생물 군집을 대상으로 비교하였다. 16S rDNA를 증폭하여 제한효소 지문을 분석한 결과, 토양으로부터 직접 추출하여 증폭한 토양세균 군집의 16S rDNA의 유전적 유사도는 BIOLOG GN microplate를 이용한 대사적 구조와 일치하는 경향을 보았다. 그러나 배양된 종속영양세균 군집의 다양성과는 유전적 유사도가 매우 낮게 나타났다.

• 미생물학회지
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• 제44권3호
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• pp.237-243
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• 2008

충남 계룡산 북사면 지역의 대표군락인 상수리림과 소나무림 부식토의 화학적 및 미생물학적 특성을 비교검토한 결과, 상수리림 부식토의 pH는 $5.3\pm0.4$, 소나무림의 pH는 $4.1\pm0.9$이었으며, 소나무림 부식토 내 탄질율은 $21.76\pm8%$로 상수리림보다 높게 나타났다. 상수리림과 소나무림 부식토 내 총 유기산은 각각 69.57 mM/g dry soil, 153.72 mM/g dry soil로 나타났으며 소나무림 부식토 내 glutamine, pyruvate, succinate, lactic acid 및 acetic acid의 함량이 상수리림 부식토에 비해 약 $1.5\sim4.5$배 높게 나타났다. 상수리림 부식토 내 전세균수는 소나무림 보다 약 16배, 생균수는 약 2배 높게 검출되었다. 각 부식토로부터 직접 DNA를 추출하여 16S rRNA-ARDRA법에 의한 세균군집의 계통학적 특성을 평가한 결과, 상수리림 부식토로부터 분리된 대표 clone은 ${\alpha}-$, ${\beta}-$, ${\gamma}-$, ${\delta}$-Proteobacteria, Firmicutes, Acidobacteria 및 Actinobacteria의 7개 계통군이 확인되었고, 소나무림 부식토외 대표 clone은 ${\alpha}-$, ${\beta}-$, ${\gamma}$-Proteobacteria, Actinobacteria, Acidobacteria, Planctomycetes, Verrucomicrobia 그리고 Bacteroidetes의 8개의 계통군이 확인되었다. Shannon-Wiener법에 의해 다양성 지수를 산출한 결과, 소나무림 부식토 내 세균군집의 다양도는 3.63으로 상수리림보다 높게 나타났으며 PCA 분석을 실시한 결과, Clusters I에 속하는 모든 clone은 상수리림 부식토에서 유래된 clone이었으며, Clusters II에 속하는 clone의 67%, Clusters III에 속하는 clone의 63%가 소나무림 부식층 토양으로부터 유래된 clone으로 확인되어 상수리림과 소나무림 부식토내 세균 군집구조는 매우 특징적인 계통학적 특성을 나타내었다.

• 생명과학회지
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• 제23권6호
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• pp.770-778
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• 2013

본 연구에서는 광양만 해수의 세균군집 다양성의 계절적인 변화를 분석하기 위해 2011년 2월, 5월, 7월, 10월의 4계절에 총 336 균주를 분리하였다. 분리된 미생물의 16S rRNA를 제한효소 Hae III를 이용하여 Amplified Ribosomal DNA Restriction Analysis 를 실시하여 절편 양상을 군집화 시키고, 다양성 지수를 계산하였다. 80%의 유사도 수준에서 40개의 단일 계통형을 포함한 총 101개의 계통형을 얻을 수 있었다. 각 계통형을 대표할 수 있는 139개 균주를 선택하여 16S rRNA 염기서열을 결정한 후 유전자서열을 비교한 결과, 이들 균주는 Proteobacteria, Actinobacteria, Bacteroidetes 및 Firmicutes를 포함한 4개의 문에 속하였다. 모든 계절에 Proteobacteria 문이 최 우점하였고, 겨울과 봄, 가을에는 Bacteroidetes 문, 여름에는 Actinobacteria 문이 차 우점하였다. 과(family) 수준에서는 겨울과 봄에는 Flavobacteriaceae가 우점하였고, 여름과 가을에는 Pseudoalteromonadaceae가 우점하였다. 모든 계절에 Altererythrobacter, Loktanella, Pseudoalteromonas, Vibrio 속(genus)이 관찰되었다. 미생물 군집의 다양성은 가을에 가장 높았으며, 다음으로 봄, 겨울, 여름 순서였다.

• 한국토양비료학회지
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• 제49권2호
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• pp.144-156
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• 2016

Soil is a dynamic biological system, in which it is difficult to determine the composition of microbial communities. Knowledge of microbial diversity and function in soils are limited because of the taxonomic and methodological limitations associated with studying the organisms. In this review, approaches to measure microbial diversity in soil were discussed. Research on soil microbes can be categorized as structural diversity, functional diversity and genetic diversity studies, and these include cultivation based and cultivation independent methods. Cultivation independent technique to evaluate soil structural diversity include different techniques such as Phospholipid Fatty Acids (PLFA) and Fatty Acid Methyl Ester (FAME) analysis. Carbon source utilization pattern of soil microorganisms by Community Level Physiological Profiling (CLPP), catabolic responses by Substrate Induced Respiration technique (SIR) and soil microbial enzyme activities are discussed. Genetic diversity of soil microorganisms using molecular techniques such as 16S rDNA analysis Denaturing Gradient Gel Electrophoresis (DGGE) / Temperature Gradient Gel Electrophoresis (TGGE), Terminal Restriction Fragment Length Polymorphism (T-RFLP), Single Strand Conformation Polymorphism (SSCP), Restriction Fragment Length Polymorphism (RFLP) / Amplified Ribosomal DNA Restriction Analysis (ARDRA) and Ribosomal Intergenic Spacer Analysis (RISA) are also discussed. The chapter ends with a final conclusion on the advantages and disadvantages of different techniques and advances in molecular techniques to study the soil microbial diversity.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2002년도 추계학술대회
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• pp.90-93
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• 2002

The revolution in molecular biology has given us greatly increased ability to obtain and to modify biological resources and to use them for the benefit of all humankind. The sequencing and the associated analysis of gene functions for a growing number of genomes will have an unprecedented effect on the uses of biological resources and the need for access to them. To investigate the diversity of microbial community in swamp, molecular systematic methods were applied. By amplified rDNA restriction analysis (ARDRA) and rDNA partial sequence analysis, $75\%$ of the isolates were known species. In case of uncultured analysis, almost all the selected clones were new species candidate. Especially archea and uncultured bacterial analyses, all clones were new taxon candidates. As for the eukaryotic diversity, several yeast form cultures were isolated from various samples of swamp. Among them, about $60\%$ of the isolates were easily identified. In case of a new species candidate, most strain were included in hymenomycetal yeasts.

• 한국치위생학회지
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• 제13권5호
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• pp.889-900
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• 2013

Objectives : Molecular biology techniques were employed to assess diversity of bacterial in children's dental caries. Methods : DNA of germs was extracted and the diversity of the 16S rRNA clones was analyzed by amplified rDNA restriction analysis and sequencing. The experimental samples were pit and fissure caries (PC), deep dentinal caries (DC), smooth surface caries (SC), and supragingival plaque (PQ) from 50 children of age less than 12 years old. The control group was healthy teeth supragingival plaque (HT). Thirty clones from each 16S rRNA clone library of 5 samples were randomly selected, thus a total of 150 clones were analyzed. Results : Amplified rDNA restriction analysis uncovered 18, 20, 11, 17, and 22 phylotypes from healthy teeth, pit and fissure caries, deep dentinal caries, smooth surface caries, and supragingival plaque, respectively. Sequencing analysis found the dominance of Actinomycs naeslundii and Fusobacterium nucleatum in the healthy teeth; Leptotrichia sp. in the pit and fissure caries; Actinomyces sp., Streptococcus mutans, and Rahnella aquatilis in the deep dentinal caries; Streptococcus mutans and Actinomyces sp. in the smooth surface caries; Enterobacter hormaechei and Streptococcus sanguinis in the supragingival plaque. Conclusions : Clonal analysis identified 6 phyla, 20 genera, and 51 species.

• Journal of Microbiology
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• 제43권5호
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• pp.383-390
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• 2005

The diversity of the denitrifying bacterial populations in Daejeon Sewage Treatment Plant was examined using a culture-dependent approach. Of the three hundred and seventy six bacterial colonies selected randomly from agar plates, thirty-nine strains that showed denitrifying activity were selected and subjected to further analysis. According to the morphological and biochemical properties, the thirty nine isolates were divided into seven groups. This grouping was supported by an unweighted pair group method, using an arithmetic mean (UPGMA) analysis with fatty acid profiles. Restriction pattern analysis of 16S rDNA with four endonucleases (AluI, BstUI, MspI and RsaI) again revealed seven distinct groups, consistent with those defined from the morphological and biochemical properties and fatty acid profiles. Through the phylogenetic analysis using the 16S rDNA partial sequences, the main denitrifying microbial populations were found to be members of the phylum, Proteobacteria; in particular, classes Gammaproteobacteria (Aeromonas, Klebsiella and Enterobacter) and Betaproteobacteria (Acidovorax, Burkholderia and Comamonas), with Firmicutes, represented by Bacillus, also comprised a major group.

• The Plant Pathology Journal
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• 제29권2호
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• pp.144-153
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• 2013

Diverse bacteria are known to colonize plants. However, only a small fraction of that diversity has been evaluated for their biopesticide potential. To date, the criteria for sampling and selection in such bioprospecting endeavors have not been systematically evaluated in terms of the relative amount of diversity they provide for analysis. The present study aimed to enhance the success of bioprospecting efforts by increasing the diversity while removing the genotypic redundancy often present in large collections of bacteria. We developed a multivariate sampling and marker-based selection strategy that significantly increase the diversity of bacteria recovered from plants. In doing so, we quantified the effects of varying sampling intensity, media composition, incubation conditions, plant species, and soil source on the diversity of recovered isolates. Subsequent sequencing and high-throughput phenotypic analyses of a small fraction of the collected isolates revealed that this approach led to the recovery of over a dozen rare and, to date, poorly characterized genera of plant-associated bacteria with significant biopesticide activities. Overall, the sampling and selection approach described led to an approximately 5-fold improvement in efficiency and the recovery of several novel strains of bacteria with significant biopesticide potential.

• 한국미생물·생명공학회지
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• 제47권3호
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• pp.401-411
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• 2019

All Idiomarina species are isolated from saline environments; microorganisms in such extreme habitats develop metabolic adaptations and can produce compounds such as proteases with an industrial potential. ARDRA and 16S rRNA gene sequencing are established methods for performing phylogenetic analysis and taxonomic identification. However, 16S-23S ITS is more variable than the 16S rRNA gene within a genus, and is therefore, used as a marker to achieve a more precise identification. In this study, ten protease producing Idiomarina strains isolated from the Peruvian salterns were characterized using biochemical and molecular methods to determine their bacterial diversity and industrial potential. In addition, comparison between the length and nucleotide sequences of a 16S-23S ITS region allowed us to assess the inter and intraspecies variability. Based on the 16S rRNA gene, two species of Idiomarina were identified (I. zobellii and I. fontislapidosi). However, biochemical tests revealed that there were differences between the strains of the same species. Moreover, it was found that the ITS contains two tRNA genes, $tRNA^{Ile(GAT)}$ and $tRNA^{Ala(TGC)}$, which are separated by an ISR of a variable size between strains of I. zobellii. In one strain of I. zobellii (PM21), we found nonconserved nucleotides that were previously not reported in the $tRNA^{Ala}$ gene sequences of Idiomarina spp. Thus, based on the biochemical and molecular characteristics, we can conclude that protease producing Idiomarina strains have industrial potential; only two I. zobellii strains (PM48 and PM72) exhibited the same properties. The differences between the other strains could be explained by the presence of subspecies.