• 미생물학회지
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• 제38권3호
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• pp.192-197
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• 2002

러시아 바이칼호에서 해빙기에 부유세균과 aggregates에 부착한 세균의 군집구조를 FISH (fluorescent in situ hybridization)방법으로 0 m부터 250 m수심에서 비교 분석하였다. 조사대상은 Eubacteria에 속하는 세균과 class Proteobacteria에 속하는 세균 중 $\alpha$-, $\beta$-, $\gamma$ -group과 Cytophaga-Flavobacterium group,그리고 Planctomycetales였다. 부유세균의 수는 $0.2{\times}10^6\cells{\cdot}ml^-1 to 3.2{\times}10^6 \cells{\cdot}ml^-1$범위였으며, 수심이 깊어질수록 감소하였다. Aggregate에 부착한 세균은 부유세균과 반대로 수심이 깊어질수록 증가하였고, 개체수의 범위는 0.4~$3.3{\times}10^4$ $cells{\cdot}ml^-1$ 이였다. 총세균수에 대한 Eubacteria 수의 비율은 부유세균의 경우 52.3~74.1%, aggregates에 부착한 세균은 39.6~66.7%로 부유세균보다 부착세균에서 그 비율이 낮았으며, 세균의 군집구조 분석 결과에서도 부유세균과 aggregates애 부착한 세균의 군집구조가 다른 양상으로 나타났다. 특히 두 세균의 군집구조는 식물플랑크톤이 밀집해 있는 25 m 수심에서 급격히 변화하여 식물플랑크톤이 부유세균과 부착세균의 군집의 변화에 밀접한 관련이 있는 것으로 확인되었다, Aggregates에 부착한 세균 군집은 수심에 따라 매우 특이한 변화 양상을 나타내었다. $\beta$-proteobacteria group은 수심이 깊어지면서 그 비율이 높아져, 100m에서는 $\beta$-group이 총세균수는 51.8%를 차지하였으나, 250m에서는 $\gamma$-group이 43.8%를 차지하여, 급격하게 우점 group이 변화하였다. 그러나, 부유세균에서는 전혀 다른 군집 구조를 이루고 있었다. 이러한 결과에서 aggregates에 부착한 세균은 부유세균과는 다른 다양성을 이루고, 다른 천이과정을 거치는 것으로 확인되었다.

• 환경생물
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• 제24권2호
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• pp.172-178
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• 2006

골재채취가 수층의 세균군집구조에 미치는 영향을 알아보기 위해 낙동강 중류, 골재채취가 이루어 지지 않은 수역인 구미대교와 장기간에 걸쳐 연속적으로 골재채취가 행해지는 지역인 성주군 소학리 (성주대교 인근)에서 $\alpha\;\beta\;\gamma-subclass$ proteobacteria, Cytophaga-Flavobacterium (CF) group 세균군과 황산염화원세균을 FISH법으로 정량분석하였다. 아울러 수온, pH, EC, 엽록소-$\alpha$ 양 등의 이화학적인 환경요인도 측정하였다. DAPI로 염색된 세균수로 측정한 총세균수의 경우, 두 정점간의 괄목할 만한 양적인 차이는 없었으나 그 시간차에 따른 변동이 골재채취 수역에서 더욱 심했다. 또한 높은 엽록소-$\alpha$ 양을 나타낸 골재채취 수역에서 검출한 CF group 세균군과 황산염환원세균이 총세균수에서 차지하는 비율이 비골재채취 수역에 비해 높았다. 이같은 결과는 저니질이 수층으로 재유입되었기 때문으로 판단된다. 그러나 본 연구에서 검출한 세균군이 총세균수에서 차지하는 비율을 합하면 그 비율은 골재채취 수역보다 비골재채취 수역에서 더 높았다. FISH법에 의한 세균의 검출가능성이 해당세균의 물질대사능과 연관이 있으므로 골재채취 수역에서의 낮은 세균 검출율은 골재채취가 세균의 물질순환에서의 역기능을 초래하고 이는 또한 연차적으로 그들의 먹이연쇄에 부정적인 영향을 미칠 가능성을 시사하는 것이다.

• 생명과학회지
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• 제26권6호
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• pp.711-720
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• 2016

게놈분석이 완료된 680개의 세균의 공통 유전자 보유 정도와 유연관계를 파악하기 위해 4,631개의 COG (Clusters of Orthologous Groups of protein) 보유 유사도와 COG 보유 계통수를 작성하여 다음과 같은 결과를 얻었다. 균주별 COG 보유개수는 103~2,199개 사이였고 평균 1377.1개 였다. 곤충과 절대공생성인 Candidatus Nasuia deltocephalinicola str. NAS-ALF가 최저였고 기회성병원균인 Pseudomonas aeruginosa PAO1가 최대였다. 2개의 세균들 사이에 나타내는 COG 보유 유무의 유사도는 49.30~99.78% 사이였고 평균 72.65%였다. 초고온성이며 자가영양생활을 하는 Methanocaldococcus jannaschii DSM 2661과 중온성이며 공생생활을 하는 Mesorhizobium loti MAFF303099 사이가 최소였다. 유전자 보유 정도가 생물이 각 서식지에 적응하는 정도를 나타내므로 이 결과는 원핵생물 진화의 역사 혹은 현재 지구의 원핵생물 서식지 범위를 나타내는 것일 수도 있다. COG 보유계통수를 통하여 첫째 진정세균인 Chloroflexi문의 일부는 진정세균보다 고세균과 유연관계가 높았고, 둘째 16S rRNA유전자에서 동일한 문(phylum)이나 강(class)으로 분류되지만 COG 보유 계통수에서는 일치하지 않는 경우가 많았으며, 셋째 delta-와 epsilon-Proteobacteria는 다른 Proteobacteria와 다른 분계(lineage)를 이루었다. 본 연구결과는 생물의 기원 파악과 기능적 연관성 파악 그리고 유용유전자 탐색 등에 이용할 수 있을 것이다.

• Journal of Ecology and Environment
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• 제31권2호
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• pp.131-137
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• 2008

This study investigated the population densities and diversity of heterotrophic bacteria, and the rhizosphere-to-soil ratios (R/S) in the rhizosphere soil of halophyte Phragmites communis at the western coastal mudflats of Korea. The population densities of aerobic heterotrophic bacteria on the rhizosphere soil of P. communis were in the range of $3.3\;{\pm}\;0.9\;{\times}\;10^7\;{\sim}\;1.2\;{\pm}\;0.5\;{\times}\;10^8\;cfu\;g^{-1}$ dry weight (d. wt.). Population densities of amylolytic bacteria ranged from $1.1\;{\pm}\;0.2\;{\times}\;10^6$ to $3.0\;{\pm}\;1.2\;{\times}\;10^6\;cfu\;g^{-1}\;d.\;wt.$, while those of cellulolytic bacteria and proteolytic bacteria ranged from $5.6\;{\pm}\;2.3\;{\times}\;10^6$ to $1.5\;{\pm}\;0.3\;{\times}\;10^7\;cfu\;g^{-1}\;d.\;wt.$ and from $1.4\;{\pm}\;0.3\;{\times}\;10^6$ to $3.5\;{\pm}\;2.3\;{\times}\;10^7 \;cfu\;g^{-1}\;d.\;wt.$, respectively. The R/S ratios ranged from 2.26 to 6.89. Genetic (16S DNA) analysis of fifty-one isolates from the roots of P. communis suggested that the dominant species were closely related to the ${\gamma}$-proteobacteria group (18 clones) and the ${\alpha}$-proteobacteria group (14 clones). We found that halophyte species and mudflat environment both affected the rhizosphere bacterial communities.

• Journal of Microbiology and Biotechnology
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• 제21권6호
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• pp.545-555
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• 2011

The diversity elucidation by amplified ribosomal DNA restriction analysis and 16S rDNA sequencing of 96 associative diazotrophs, isolated from the feeder roots of tea on enriched nitrogen-free semisolid media, revealed the predominance of Gram-positive over Gram-negative bacteria within the Kangra valley in Himachal Pradesh, India. The Gram-positive bacteria observed belong to two taxonomic groupings; Firmicutes, including the genera Bacillus and Paenibacillus; and Actinobacteria, represented by the genus Microbacterium. The Gram-negative bacteria included ${\alpha}$-Proteobacteria genera Brevundimonas, Rhizobium, and Mesorhizobium; ${\gamma}$-Proteobacteria genera Pseudomonas and Stenotrophomonas; and ${\beta}$-Proteobacteria genera Azospira, Burkholderia, Delftia, Herbaspirillum and Ralstonia. The low level of similarity of two isolates, with the type strains Paenibacillus xinjiangensis and Mesorhizobium albiziae, suggests the possibility of raising species novum. The bacterial strains of different phylogenetic groups exhibited distinct carbon-source utilization patterns and fatty acid methyl ester profiles. The strains differed in their nitrogenase activities with relatively high activity seen in the Gramnegative strains exhibiting the highest similarity to Azospira oryzae, Delftia lacustris and Herbaspirillum huttiense.

• Journal of Microbiology and Biotechnology
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• 제21권8호
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• pp.777-790
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• 2011

To elucidate the biodiversity of plant growth-promoting rhizobacteria (PGPR) in Korea, 7,638 bacteria isolated from the rhizosphere of plant species growing in many different regions were screened. A large number of PGPR were identified by testing the ability of each isolate to promote the growth of cucumber seedlings. After redundant rhizobacteria were removed via amplified rDNA restriction analysis, 90 strains were finally selected as PGPR. On the basis of 16S ribosomal RNA sequences, 68 Gram-positive (76%) and 22 Gram-negative (24%) isolates were assigned to 21 genera and 47 species. Of these genera, Bacillus (32 species) made up the largest complement, followed by Paenibacillus (19) and Pseudomonas (11). Phylogenetic analysis showed that most of the Grampositive PGPR fell into two categories: low- and high- G+C (Actinobacteria) strains. The Gram-negative PGPR were distributed in three categories: ${\alpha}$-proteobacteria, ${\beta}$- proteobacteria, and ${\gamma}$-proteobacteria. To our knowledge, this is the largest screening study designed to isolate diverse PGPR. The enlarged understanding of PGPR genetic diversity provided herein will expand the knowledge base regarding beneficial plant-microbe interactions. The outcome of this research may have a practical effect on crop production methodologies.

• Journal of Ecology and Environment
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• 제29권4호
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• pp.399-404
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• 2006

This study was carried out to investigate the population densities, R/S ratios, and identification of heterotrophic bacteria on the rhizosphere soil of halophyte Suaeda japonica found on the western and southern mudflats of Korea. The population densities of aerobic and anaerobic heterotrophic bacteria on the rhizosphere soil of Suaeda japonica were in the range of $1.3\;{\pm}\;0.3\;{\times}\;10^6\;{\sim}\;6.3\;{\pm}\;3.3\;{\times}\;10^7\;and\;2.8\;{\pm}\;1.3\;{\times}\;10^4\;{\sim}\;1.8\;{\pm}\;0.7\;{\times}\;10^7\;cfu\;g^{-1}\;d.\;wt.$, respectively. In case of physiologically specific bacteria, population densities of amylolytic bacteria on the rhizosphere soil of Suaeda japonica were in the range of $4.4\;{\pm}\;0.6\;{\times}\;10^6\;{\sim}\;2.5\;{\pm}\;1.2\;{\times}\;10^7\;cfu\;g^{-1}\;d.\;wt.$, those of cellulolytic bacteria were from $8.5\;{\pm}\;6.0\;{\times}\;10^4\;{\sim}\;2.3\;{\pm}\;1.6\;{\times}\;10^6\;cfu\;g^{-1}\;d.\;wt.$, and those of proteolytic bacteria were from $3.8\;{\pm}\;1.8\;{\times}\;10^5\;{\sim}\;4.2\;{\pm}\;2.9\;{\times}\;10^6\;cfu\;g^{-1}\;d.\;wt.$, respectively. The R/S ratios were ranged from 2.33 to 2.39. Among eleven isolates from the roots of halophyte Suaeda japonica of Goheung bay by using 16S rDNA analysis, five clones were closely related to ${\gamma}-Proteobacteria$ group and six clones were closely related to ${\alpha}-Proteobacteria$ group. Among four isolates from Suncheon bay, two strains were related to ${\gamma}-Proteobacteria$ group and another two were related to Actinobacteria and Bacilli group, respectively.

• 보존과학연구
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• 통권31호
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• pp.69-77
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• 2010

Preservation of artifacts that are excavated from archeological sites is closely related to soil environment. Biological remains are especially influenced by degradation activity of microorganism from soil environment. In this study a preserved human bone in archaeological tomb, Tou-kwang-myo from Joseon Period was analyzed to characterize bacteria groups by molecular genetic tools using 16S rDNA sequences. 117 clones were identified and classified 9 phylogenetic groups : ${\alpha}$-, ${\beta}$-, ${\gamma}$-, ${\delta}$-Proteobacteria, Sphingobacteria, Clostridia, Actinobacteridae, Nitrospiraceae, and Gemmatimonadetes according to homologous 16S rDNA sequences submitted in NCBI. ${\gamma}$-Proteobacteria group appears the highest ratio in bones (about 35%) while about 19.6% belong to the Actinobacteria group. The results may contribute to study on the effect of microorganisms on the human remains with burial method.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2002년도 추계학술대회
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• pp.15-21
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• 2002

Terminal-restriction fragment length polymorphism (T-RFLP) analysis has been optimized by using in vitro model community composed of genomic DNAs of known bacterial strains and has been applied to assess the bacterial community structure in marine sediments. The specific fluorescence-labeled terminal restriction fragments (T-RFs) between 39 and 839 base long specifying each strain were precisely measured for known bacterial strains. The addition of a co-solvent (dimethylsulfoxide or glycerol) into PCR reactions has reduced differential PCR amplification. Comparative bacterial community structure was investigated for pristine and polluted sediments. A complex T-RFLP pattern showing complex bacterial community structure was obtained in the pristine sediment, whereas simple T-RFLP pattern (low bacterial diversity) was shown in polluted sediments where caged aquaculture has been conducted for several years. The results of T-RFLP analysis were compared with that of cloning and sequencing 16S rDNA clones from the same sediments. Sequence analysis of 16S rDNA clones (72) of the pristine sediment revealed a diverse collection of lineages, largely of the class Proteobacteria ($6\%$ alpha subdivision, $46\%$ gamma subdivision, $13\%$ delta subdivision, and $3\%$ epsilon subdivision), Nitrospina $(8\%)$, high G+C gram positive $(8\%)$, Verrucomicrobia $(7\%)$, and Planctomycetes $(6\%)$. In the contaminated sediments, 17 $(59\%)$ of the 16S rDNA clones (29) were related to Campylobacter and symbiont of Rimicaris exoculata belonging to epsilon subdivision of Proteobacteria. The results obtained indicated that T-RFLP analysis is a rapid and precise technique for comparative bacterial community analysis.

• Journal of Microbiology and Biotechnology
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• 제14권1호
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• pp.205-211
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• 2004

A 16S rDNA clone library was generated to investigate the bacterial diversity in tidal flat sediment in Ganghwa Island, Republic of Korea. A total of 103 clones were sequenced and analyzed by comprehensive phylogenetic analyses. No clones were identical to any of known 16S rRNA sequences in public databases. Sequenced clones fell into thirteen lineages of the domain Bacteria: the alpha, beta, gamma, delta, and epsilon Proteobacteria, Actinobacteria, CFB group, Chloroflexi, Acidobacteria, Planctomycetes, Verrucomicrobia, and known uncultured candidate divisions (OP11, BRC1, KSB1, and WS1). Two clones were not associated with any known bacterial divisions. The majority of clones belonged to the gamma and delta Proteobacteria (46.7%). Clones of Actinobacteria were distantly related to known taxa. It is evident from 16S rDNA-based community analysis that the bacterial community in tidal flat sediment is remarkably diverse and unique among other marine environments examined so far.