• 미생물학회지
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• 제51권2호
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• pp.133-140
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• 2015

상수리림 산림토양 각 층위 내 물리 화학적, 미생물학적 환경변수간 상관관계를 확인한 결과, 낙엽 분해 층(F)과 부식층(H)은 각 환경변수와 높은 상관관계를 갖는 특징을 나타내었다. 특히, F층에서는 pH가 C 그리고 N과 높은 상관관계를 나타내었고, 부식층(H)에서는 각종 유기산이 토양 세균 밀도와 높은 상관관계를 나타내었다. 상수리림 산림토양의 층위별 세균군집 구조의 계통해석을 위해 각 층위의 계절별 시료로부터 DNA를 직접 추출하고 DGGE 분석한 결과 낙엽층(L)의 경우 43 bands, F층은 42 bands, H층은 43 bands 그리고 근권 토양층(A)은 47 bands로 총 175 bands가 상수리림 산림토양의 DGGE 주요 bands로 선발되었다. 확보된 총 175 DGGE 주요 bands의 16S rRNA 유전자 염기서열 정보를 바탕으로 세균군집의 계통 해석한 결과, 7개 phylum에 32개 order로 세 분류되었다. 각 order에 속하는 염기서열을 heat map 분석하고 상수리림 산림토양의 각 층위을 clustering 한 결과 F층과 H층이 L층 그리고 A층과 서로 다른 cluster를 형성하는 것이 확인되었다. 또한, 산림토양의 각 층위에 존재하는 세균군집 중 약 50%가 ${\alpha}$-proteobacteria로 우점계통군으로 나타났다. 특히, Rhizobiales, Burkholderiales, 그리고 Actinobacteriales 목은 모든 계절과 모든 층위에서 보여지는 세균군집으로 확인되어 상수리림 산림토양에서 대표적인 토착세균 군집임이 확인되었다.

• 한국어병학회지
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• 제20권1호
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• pp.49-60
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• 2007

우리 나라 남해안의 병든 넙치로부터 분리한 non-hemolytic Streptococcus parauberis의 지역적 특성을 구명하고자 균의 생리적, 생화학적 및 분자생물학적 분석을 실시하였다. 먼저, catalase-negative Gram-positive cocci를 대상으로 multiplex PCR을 실시하여 S. parauberis 12 균주를 선정하였으며, 표현형적 동정을 위해 시판되고 있는 API 20 Strep 및 API ZYM kit를 사용하였다. 분리 균주의 API porfile을 분석한 결과, Lactococcus lactis, S. constellatus 및 S. uberis 등으로 동정되었다. 또한, 터봇에서 분리된 S. parauberis와 비교해 볼 때 Voges-Proskauer, arginine, hippurate, alkiline phosphatase 및 pyrroidonyl arylamidase의 반응 결과는 동일하였으나, β-glucuronidase 활성은 다양한 것으로 나타났다. 약제 감수성 시험 결과에서는 florfenicol, ampicillin, ofloxacin 및 vancomycin에 대해 감수성이 있는 것으로 나타났으며, oxolinic acid, flumequine, nalidixic acid 및 sulfisoxazol에 대해 내성이 있는 것으로 나타났다. 그러나, 분리 균주의 16S rDNA 염기서열을 분석한 결과, 참조균주인 S. parauberis KCTC 3651 (AY584477)과 99%의 상동성을 나타내었으며, 넙치 분리 균주들이 유전적으로 동일한 그룹에 속하는 것으로 나타났다.

• Asian-Australasian Journal of Animal Sciences
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• 제29권4호
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• pp.586-593
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• 2016

A new methanogen was isolated from an anaerobic digester using pig slurry in South Korea. Only one strain, designated KOR-1, was characterized in detail. Cells of KOR-1 were straight or crooked rods, non-motile, 5 to $15{\mu}m$ long and $0.7{\mu}m$ wide. They stained Gram-positive and produced methane from $H_2+CO_2$ and formate. Strain KOR-1 grew optimally at $38^{\circ}C$. The optimum pH for growth was 7.0. The strain grew at 0.5% to 3.0% NaCl, with optimum growth at 2.5% NaCl. The G+C content of genomic DNA of strain KOR-1 was 41 mol%. The strain tolerated ampicillin, penicillin G, kanamycin and streptomycin but tetracycline inhibited cell growth. A large fragment of the 16S rRNA gene (~1,350 bp) was obtained from the isolate and sequenced. Comparison of 16S rRNA genes revealed that strain KOR-1 is related to Methanobacterium formicicum (98%, sequence similarity), Methanobacterium bryantii (95%) and Methanobacterium ivanovii (93%). Phylogenetic analysis of the deduced mcrA gene sequences confirmed the closest relative as based on mcrA gene sequence analysis was Methanobacterium formicicum strain (97% nucleic acid sequence identity). On the basis of physiological and phylogenetic characteristics, strain KOR-1 is proposed as a new strain within the genus Methanobacterium, Methanobacterium formicicum KOR-1.

• Journal of Microbiology and Biotechnology
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• 제19권1호
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• pp.5-10
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• 2009

A freshwater bacterium, designated $IMCC1713^T$, was isolated from a highly eutrophic artificial pond. Cells of the strain were Gram-negative, chemoheterotrophic, poly-$\beta$-hydroxybutyrate granule containing and obligately aerobic short rods that were motile with a single polar flagellum. The 16S rRNA gene sequence similarity analysis showed that the novel strain was most closely related to the species Roseateles depolymerans (96.3%), Mitsuaria chitosanitabida (96.2%), Ideonella dechloratans (96.2%), and Pelomonas saccharophila (96.1%) in the Sphaerotilus-Leptothrix group within the order Burkholderiales. Phylogenetic trees based on 16S rRNA gene sequences indicated that the isolate formed an independent monophyletic clade within the order Burkholderiales. The relatively low DNA G+C content (57.4mol%), together with several phenotypic characteristics, differentiated the novel strain from other members of the Sphaerotilus-Leptothrix group. From the taxonomic data, therefore, the strain should be classified as a novel genus and species, for which the name Inhella inkyongensis gen. nov., sp. nov. is proposed. The type strain of the proposed species is strain $IMCC1713^T$ (=KCTC $12791^T$=NBRC $103252^T$=CCUG $54308^T$).

• 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.

• 생명과학회지
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• 제16권5호
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• pp.723-728
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• 2006

The species of Grateloupia filicina, Grateloupia divaricata in East Sea were investigated taxonmically in order to clarify taxonomic position. The ecological character, external morphology, anatomy of vegetative structure. Blade length are $15{\sim}40\;cm$, erect from discoidal holdfast of $3{\sim}10\;mm$ in diameter. Stipe $1{\sim}2.5\;cm$ long, narrowly cylindrical below, compressed above Grateloupia filicina. Main axis are long and compressed, $3{\sim}7\;mm$ broad in broadest part. Colors are scarlet to light red. Blade length are $10{\sim}25\;cm$, erect from discoidal holdfast of $3{\sim}8\;cm$ in diameter Grateloupia divaricata. Stipe are single and simple $2{\sim}5\;mm$ broad. Thallus composed of cortex and medulla in section ; cortex composed of $9{\sim}10$ layers of anticlinally arranged cortical cell, divided into outer, middle and inner parts. Partial fragments of nuclear 18S rDNAs from the two species of Grateloupia (Rhodophyta) were amplified using the PCR reaction and sequenced to compare their similarity. The partial sequences showed 98.9% similarity each other. Grateloupia filicina has 371 bp sizes and Grateloupia divaricata has 372 bp size. The G+C contents of Grateloupia filicina is 54.3% and Grateloupia divaricata is 53.64%.

• Journal of Microbiology and Biotechnology
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• 제32권12호
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• pp.1553-1560
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• 2022

A Gram-stain-negative, rod-shaped bacterial strain, JC4^T, was isolated from a freshwater sample and determined the taxonomic position. Initial identification based on 16S rRNA gene sequences revealed that strain JC4^T is affiliated to the genus Mucilaginibacter with a sequence similarity of 97.97% to Mucilaginibacter rigui WPCB133^T. The average nucleotide identity and digital DNA-DNA hybridization values between strain JC4^T and Mucilaginibacter species were estimated below 80.92% and 23.9%, respectively. Strain JC4^T contained summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c) and iso-C_15:0 as predominant cellular fatty acids. The dominant polar lipids were identified as phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, and two unidentified lipids. The respiratory quinone was MK-7. The genomic DNA G+C content of strain JC4^T was determined to be 42.44%. The above polyphasic evidences support that strain JC4^T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter aquariorum sp. nov. is proposed. The type strain is JC4^T (= KCTC 92230^T = LMG 32715^T).

• Journal of Microbiology and Biotechnology
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• 제15권6호
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• pp.1286-1298
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• 2005

The genus Paenibacillus is a new group of bacilli separated from the genus Bacillus, and most of species have been isolated from soil. In the present study, we collected 450 spore-forming bacilli from the roots of winter crops, such as barley, wheat, onion, green onion, and Chinese cabbage, which were cultivated in the southern part of Korea. Among these 450 isolates, 104 Paenibacillus-like isolates were selected, based on their colony shape, odor, color, and endospore morphology, and 41 isolates were then finally identified as Paenibacillus spp. by 16S rDNA sequencing. Among the 41 Paenibacillus isolates, 23 were classified as P. polymyxa, a type species of the genus Paenibacillus, based on comparison of the 16S rDNA sequences with those of 32 type strains of the genus Paenibacillus from the GenBank database. Thirty-five isolates among the 41 Paenibacillus isolates exhibited antagonistic activity towards plant fungal and bacterial pathogens, whereas 24 isolates had a significant growth-enhancing effect on cucumber seedlings, when applied to the seeds. An assessment of the root-colonization capacity under gnotobiotic conditions revealed that all 41 isolates were able to colonize cucumber roots without any significant difference. Twenty-one of the Paenibacillus isolates were shown to contain the nifH gene, which is an indicator of $N_{2}$ fixation. However, the other 20 isolates, including the reference strain E681, did not incorporate the nifH gene. To investigate the diversity of the isolates, a BOX-PCR was performed, and the resulting electrophoresis patterns allowed the 41 Paenibacillus isolates to be divided into three groups (Groups A, B, and C). One group included Paenibacillus strains isolated mainly from barley or wheat, whereas the other two groups contained strains isolated from diverse plant samples. Accordingly, the present results showed that the Paenibacillus isolates collected from the rhizosphere of winter crops were diverse in their biological and genetic characteristics, and they are good candidates for further application studies.

• 농약과학회지
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• 제16권4호
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• pp.383-386
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• 2012

비농경지의 식물 근권토양에서 식물체의 초기생육촉진 효과가 있는 방선균을 분리하였다. 분리된 미생물의 16S rDNA 염기서열을 분석한 결과 Streptomyces spp.로 동정되었다. Streptomyces griseus (MSS181), Streptomyces griseoaurantiacus (MSS269), Streptomyces microflavus (MSS275), Streptomyces herbaricolor (MSS276)의 배양액을 오이, 고추, 담배와 토마토의 생육초기단계에 관주 처리하여 식물체의 초장, 건조중량을 측정하였다. 방선균 처리에 의해 오이의 초장은 대조구에 비해 16-29% 증가하였으나 건조중량에는 통계적으로 유의한 차이가 없었다. 같은 방선균을 고추에 처리하였을 때 고추의 초장은 대조구에 비해 10-19%, 건조중량은 19-25% 증가하였다. 담배의 건조중량은 44-73% 증가하였고 토마토의 건조중량도 65-165% 증가하였다. 공시균주의 식물병원균에 대한 항균활성을 검정한 결과, MSS275의 Phytophthora capsici, Fusarium oxysporum, Rhizoctonia solani와 Sclerotinia sclerotiorum에 대한 강한 항균활성을 확인하였다.

• 한국자원식물학회지
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• 제34권1호
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• pp.1-16
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• 2021

남부 지방의 밀양 근교에 자생하고 있는 야생 동충하초 균주(Cordyceps sp., Paecilomyces sp., Beauveria sp., Aranthomyces sp., Isaria sp., Himenostilbe sp.)를 채집 분리하여 rDNA 및 internal transcribed spacer (ITS) 부위의 염기서열을 비교하였다. ITS 영역에 특정적인 프라이머인 ITS1과 ITS4를 이용하여 PCR을 수행하여 증폭하였다. 다양한 균주에서 같은 크기의 PCR 생산물을 얻을 수 있었고, 이들의 서열분석을 위하여 pGEM-T easy 벡터에 클로닝하였으며, ITS1, 5.8S, ITS2 영역 부위의 염기서열들을 BLAST 수행하여 유연관계를 분석하였다. 밀양 근교에서 분리한 32개의 균주 중에 Cordyceps militaris는 서열이 등록된 유전정보 AY49191, EU825999, AY491992와 100% 일치하였으며, 몇 개의 종은 보고된 서열과 모두 일치하지는 않았다. 예를 들어 strain P17은 울주군 가지산에서 분리한 P. tenuipes로서 밀양시 조천읍 가지산에서 분리한 P. tenuipes와는 서열상에서 다른 부분들이 있었다. 결론적으로 밀양 근교의 균주들을 분리하는데 ITS영역분석이 분류와 검정에 효율적이고, 본 연구를 통하여 동충하초의 생태학적인 유전자원들을 확보할 수 있었다.