• 제목/요약/키워드: archaeal diversity

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Diversity of Halophilic Archaea From Six Hypersaline Environments in Turkey

  • Ozcan, Birgul;Ozcengiz, Gulay;Coleri, Arzu;Cokmus, Cumhur
    • Journal of Microbiology and Biotechnology
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    • 제17권6호
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    • pp.985-992
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    • 2007
  • The diversity of archaeal strains from six hypersaline environments in Turkey was analyzed by comparing their phenotypic characteristics and 16S rDNA sequences. Thirty-three isolates were characterized in terms of their phenotypic properties including morphological and biochemical characteristics, susceptibility to different antibiotics, and total lipid and plasmid contents, and finally compared by 16S rDNA gene sequences. The results showed that all isolates belong to the family Halobacteriaceae. Phylogenetic analyses using approximately 1,388 bp comparisions of 16S rDNA sequences demonstrated that all isolates clustered closely to species belonging to 9 genera, namely Halorubrum (8 isolates), Natrinema (5 isolates), Haloarcula (4 isolates), Natronococcus (4 isolates), Natrialba (4 isolates), Haloferax (3 isolates), Haloterrigena (3 isolates), Halalkalicoccus (1 isolate), and Halomicrobium (1 isolate). The results revealed a high diversity among the isolated halophilic strains and indicated that some of these strains constitute new taxa of extremely halophilic archaea.

Tofua Arc의 열수구환경으로부터 호열성 혐기성 고세균(Thermococcus)의 농화배양 및 동정 (Identification of Anaerobic Thermophilic Thermococcus Dominant in Enrichment Cultures from a Hydrothermal Vent Sediment of Tofua Arc)

  • 차인태;김소정;김종걸;박수제;정만영;주세종;권개경;이성근
    • 미생물학회지
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    • 제48권1호
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    • pp.42-47
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    • 2012
  • 열수구(Hydrothermal vent)는 빛이 없는 환경에서 생명체의 진화가 일어나는 독특한 환경을 유지하고 있다. 남태평양 Tonga의 Tofua arc의 열수구로부터 퇴적물을 채취하여 산화철[iron(III)], 황(elemental sulfur, $S^0$) 그리고 질산염을 전자수용체로 사용하고, 수소($H_2$), yeast extract를 전자공여체로 사용하여 배양에 의한 미생물의 다양성을 연구하였다. 배양 온도는 각각 $65^{\circ}C$$80^{\circ}C$였으며, 연속희석배양법과 16S rRNA 유전자의 PCR-Denaturing Gradient Gel Electrophoresis를 분석하고, 검출된 염기서열의 정보분석을 통하여 고세균을 동정하였다. 16S rRNA 유전자의 계통분류학적 분석 결과 배양된 대부분의 고세균은 Thermococcus 속(T. alcaliphilius, T. litoralis, T. celer, T. barossii, T. thoreducens, T. coalescens)에 속하며 그들과 98-99%의 상동성을 가지고 있었다. Thermococcus 속의 미생물들이 일반적으로 이용할 수 없는 질산염과 산화철을 전자수용체로 첨가한 배양에서 관찰되었으나, 이는 환원제로 첨가한 $Na_2S$의 산화물을 이용하여 성장한 것으로 추정된다. Thermococcus 속에 속하는 고세균 외의 다양한 고세균의 배양을 위해서는 $Na_2S$ 대신 다른 환원제를 사용하는 배양조건의 이용이 요구된다.

Phylogenetic Diversity of Dominant Bacterial and Archaeal Communities in Plant-Microbial Fuel Cells Using Rice Plants

  • Ahn, Jae-Hyung;Jeong, Woo-Suk;Choi, Min-Young;Kim, Byung-Yong;Song, Jaekyeong;Weon, Hang-Yeon
    • Journal of Microbiology and Biotechnology
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    • 제24권12호
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    • pp.1707-1718
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    • 2014
  • In this study, the phylogenetic diversities of bacterial and archaeal communities in a plant-microbial fuel cell (P-MFC) were investigated together with the environmental parameters, affecting its performance by using rice as a model plant. The beneficial effect of the plant appeared only during a certain period of the rice-growing season, at which point the maximum power density was approximately 3-fold higher with rice plants. The temperature, electrical conductivity (EC), and pH in the cathodic and anodic compartments changed considerably during the rice-growing season, and a higher temperature, reduced difference in pH between the cathodic and anodic compartments, and higher EC were advantageous to the performance of the P-MFC. A 16S rRNA pyrosequencing analysis showed that the 16S rRNAs of Deltaproteobacteria and those of Gammaproteobacteria were enriched on the anodes and the cathodes, respectively, when the electrical circuit was connected. At the species level, the operational taxonomic units (OTUs) related to Rhizobiales, Geobacter, Myxococcus, Deferrisoma, and Desulfobulbus were enriched on the anodes, while an OTU related to Acidiferrobacter thiooxydans occupied the highest proportion on the cathodes and occurred only when the circuit was connected. Furthermore, the connection of the electrical circuit decreased the abundance of 16S rRNAs of acetotrophic methanogens and increased that of hydrogenotrophic methanogens. The control of these physicochemical and microbiological factors is expected to be able to improve the performance of P-MFCs.

Evaluation of Biogas Production Performance and Dynamics of the Microbial Community in Different Straws

  • Li, Xue;Liu, Yan-Hua;Zhang, Xin;Ge, Chang-Ming;Piao, Ren-Zhe;Wang, Wei-Dong;Cui, Zong-Jun;Zhao, Hong-Yan
    • Journal of Microbiology and Biotechnology
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    • 제27권3호
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    • pp.524-534
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    • 2017
  • The development and utilization of crop straw biogas resources can effectively alleviate the shortage of energy, environmental pollution, and other issues. This study performed a continuous batch test at $35^{\circ}C$ to assess the methane production potential and volatile organic acid contents using the modified Gompertz equation. Illumina MiSeq platform sequencing, which is a sequencing method based on sequencing-by-synthesis, was used to compare the archaeal community diversity, and denaturing gradient gel electrophoresis (DGGE) was used to analyze the bacterial community diversity in rice straw, dry maize straw, silage maize straw, and tobacco straw. The results showed that cumulative gas production values for silage maize straw, rice straw, dry maize straw, and tobacco straw were 4,870, 4,032.5, 3,907.5, and $3,628.3ml/g{\cdot}VS$, respectively, after 24 days. Maximum daily gas production values of silage maize straw and rice straw were 1,025 and $904.17ml/g{\cdot}VS$, respectively, followed by tobacco straw and dry maize straw. The methane content of all four kinds of straws was > 60%, particularly that of silage maize straw, which peaked at 67.3%. Biogas production from the four kinds of straw was in the order silage maize straw > rice straw > dry maize straw > tobacco straw, and the values were 1,166.7, 1,048.4, 890, and $637.4ml/g{\cdot}VS$, respectively. The microbial community analysis showed that metabolism was mainly carried out by acetate-utilizing methanogens, and that Methanosarcina was the dominant archaeal genus in the four kinds of straw, and the DGGE bands belonged to the phyla Firmicutes, Bacteroidetes, and Chloroflexi. Silage maize is useful for biogas production because it contains four kinds of straw.

Characterization of the Microbial Diversity in a Korean Solar Saltern by 16S rRNA Gene Analysis

  • Park, Soo-Je;Kang, Cheol-Hee;Rhee, Sung-Keun
    • Journal of Microbiology and Biotechnology
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    • 제16권10호
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    • pp.1640-1645
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    • 2006
  • We studied the diversity of the halophilic archaea and bacteria in crystallizer ponds of a Korean solar saltern by analyzing 16S rRNA gene libraries. Although diverse halophilic archaeal lineages were detected, the majority (56%) were affiliated with the uncultured and cultured Halorubrum group. Halophilic archaea that have been frequently observed in solar saltern environments previously, such as Halogeometricum, Halococcus, Haloarcula, and Haloferax, were not detected in our samples. The majority of clones (53%) belonged to the Cytophaga-Flavobacterium-Bacteroides and ${\alpha}-,\;{\gamma}-,\;and\;{\delta}-Proteobacteria$ groups, with 47% of the clones being affiliated with ${\gamma}-Proteobacteria$. We also identified new ${\delta}-Proteobacteria$-related bacteria that have not been observed in hypersaline environments previously. Our data show that the diversity of the halophilic archaea and bacteria in our Korean saltern differs from that of solar salterns found in other geographic locations. We also showed by quantitative real-time PCR analysis that bacteria can form a significant component of the microbial community in solar salterns.

지하수 히트펌프 시스템의 지중 환경관리를 위한 시추 슬라임의 원핵생물 유전자 다양성 (Genetic Prokaryotic Diversity in Boring Slime from the Development of a Groundwater Heat Pump System)

  • 김희정;이시원;박정희;전원탁;김재연;김홍현;이강근
    • 한국미생물·생명공학회지
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    • 제44권4호
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    • pp.550-556
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    • 2016
  • 지하수의 열을 이용한 히트펌프 시스템에서는 열 효율 유지를 위한 클로깅 현상이 고려되어야 한다. 클로깅 현상은 토양 지하수 환경에서 이화학적 요인 외에도 미생물학적 요인으로 발생한다. 이번 연구에서는 안정적인 지하수 열원 냉난방 시스템 운영을 위하여, 대수층 수위강하의 영향을 받지 않는 지하 10 미터 지점에서 불교란 시추 슬라임의 초기상태 원핵생물 다양성을 조사하였다. 세균은 문 수준에서 Proteobacteria (20.8%), Acidobacteria (18.8%), Chloroflexi (16.9%) 및 Firmicutes (10.2%) 등으로 나타났고, 속 수준에서는 Koribacter속 등 144개속이 분석되었다. 고세균은 문 수준에서 Thaumarchaeota (42.8%), Crenarchaeota (36.9%) 및 Euryarchaeota (17.4%)이 나타났으며, 강 수준에서 약 69.4% 비율로 Miscellaneous Crenarchaeota Group (MCG), Finnish Forest Soil Type B (FFSB) 및 Thermoplasmata가 분석되었다. Operational taxonomic units (OTUs)는 세균 3,565 및 고세균 836 OTUs로 나타났고, 세균이 고세균에 비해 풍부하며 우점도가 낮게 나타났다. 또한, 관정 막힘 현상을 유발할 가능성 있는 세균 후보군 135개(1.9%) reads가 분석되었으며, 향후 클로깅 현상에 대한 연구에 자료로 활용할 수 있을 것으로 기대된다.

한국 시화호와 중국 Aha호 저질토에 분포하는 이화성 아황산염 환원효소 유전자의 비교 분석 (Comparative Analysis of Dissimilatory Sulfite Reductase (dsr) Gene from Sediment of Lake Sihwa, Korea and Lake Aha, China)

  • 김인선;김옥선;전선옥;;안태석
    • 미생물학회지
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    • 제44권2호
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    • pp.147-155
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    • 2008
  • 한국의 시화호와 중국의 Aha호 저질토에서 서식하는 황산염 환원세균(sulfate reducing bacteria, SRB)의 깊이에 따른 군집구조를 비교하기 위하여, 이화성 아황산염 환원효소(EC 1.8.99.1; dissimilatory sulfite reductase, dsr) 유전자를 대상으로, polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE) 및 클론 라이브러리를 이용하여 미생물의 군집구조를 분석하였다. DGGE band 양상을 분석한 결과, Aha호 보다는 시화호에서 더 맡은 밴드를 보여 다양성이 높았고, 깊이별 차이는 나타나지 않았다. 두 서식지에서 얻은총68개 클론의 염기서열을 가지고 계통학적 분석을 한 결과 시화호에서는 Deltaproteobacteria 그룹, Firmicutes 그룹에 속해있는 Desulfotomaculum 종과 archaeal thermophilic SRB 그룹에 속해있는 Archaeoglobus 종이, Aha호에서는 Desulfotomaculum 그룹과 유사성이 높았다. 분리된 대부분의 클론들(59%)은 배양된 황산염 환원세균과는 매우 낮은 유사도를 보였고, 환경에서 분리된 클론들과도90% 이하의 유사도를 나타냈다. 총 클론을 88% 유사도를 기준으로 9그룹으로 나뉘었을 때 시하호와 Aha호의 각 클론은 서로 다른 그룹으로 존재하였다. 이러한 결과는 두 서식지의 이화성 아황산염 환원효소를 가지고 있는 미생물의 군집구조는 확연히 다르고 각 서식지에 특이적인 황산염 환원 미생물이 존재함을 시사한다.

Biomethanation of Sewage Sludge with Food Waste Leachate Via Co-Digestion

  • Shin, Jingyeong;Kim, Young Beom;Jeon, Jong Hun;Choi, Sangki;Park, In Kyu;Kim, Young Mo
    • Journal of Microbiology and Biotechnology
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    • 제27권8호
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    • pp.1513-1518
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    • 2017
  • Anaerobic mono- and co-digestion of sewage sludge and food waste leachate (FWL) were performed by assessing methane production and characterizing microbial communities. Anaerobic digestion (AD) of waste activated sludge (WAS) alone produced the lowest methane ($281ml\;CH_4$), but an approximately 80% increase in methane production was achieved via co-digestion of WAS and FWL ($506ml\;CH_4$). There were less differences in the diversity of bacterial communities in anaerobic digesters, while archaeal (ARC) and bacterial (BAC) amounts reflected AD performance. Compared with the total ARC and BAC amounts in the mono-digestion of WAS, the ARC and BAC amounts increased two and three times, respectively, during co-digestion of FWL and WAS. In characterized archaeal communities, the dominant ratio of hydrogenotrophic methanogens in the mono-digestion of WAS approached nearly a 1:1 ratio of the two acetoclastic and hydrogenotrophic methanogens in the co-digestion of FWL and WAS. The ARC/BAC ratio in the digesters varied in the range of 5.9% to 9.1%, indicating a positive correlation with the methane production of AD.

반추위 마이크로바이옴 내 메탄생성고세균 조사 (Methanogenic Archaeal Census of Ruminal Microbiomes)

  • 이슬;백열창;이진욱;김민석
    • 한국산학기술학회논문지
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    • 제21권7호
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    • pp.312-320
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    • 2020
  • 본 연구의 목적은 Ribosomal Database Project에서 공적으로 활용 가능한 16S rRNA 유전자 시퀀스들의 메타분석을 통해 반추위 고세균의 계통발생 다양성을 조사하는 것이다. 총 8,416개의 시퀀스가 Ribosomal Database Project(출시버전 11, 업데이트 5)로부터 회수되었고, taxonomy tree를 구축하는데 사용되었다. Species 수준의 OTUs가 97% sequence 유사성 기준으로 QIIME 프로그램을 사용하여 분석되었다. 총 8,416개의 시퀀스 중에서 8,412개의 시퀀스는 총 3개의 문으로 분류되었고, 나머지 4개의 시퀀스는 어떤 알려진 문으로 분류되지 못했다. Euryarchaeota는 가장 우점하는 문으로, 전체 고세균 시퀀스의 99.8%를 차지하였다. 이 중에서 차례로 Methanobrevibacter가 65.4%, Methanosphaera가 10.4%, Methanomassillicoccus가 10.4%, Methanomicrobium가 7.9%, Methanobacterium가 1.9%, Methanimicrococcus가 0.5%, Methanosarcina가 0.1%, Methanoculleus가 0.1%를 차지하였다. V2와 V3 영역으로 자른 7,544개의 시퀀스는 493개의 OTUs로 분류되었다. 총 493 OTUs 중에서 단지 17개만 우점하였고, 총 7,544 시퀀스 중 1% 이상을 차지하였다. 본 연구는 반추동물로 부터 메탄발생에 크게 기여하는 반추위 우점 메탄생성균 분석에 대한 향후 연구를 인도하는데 도움을 주고, 사료나 가축품종이 달라져도 이러한 메탄생성균을 억제하는 메탄저감제를 개발하는데 도움을 줄 것이다.

Sulphate Reducing Bacteria and Methanogenic Archaea Driving Corrosion of Steel in Deep Anoxic Ground Water

  • Rajala, P.;Raulio, M.;Carpen, L.
    • Corrosion Science and Technology
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    • 제18권6호
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    • pp.221-227
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    • 2019
  • During the operation, maintenance and decommissioning of nuclear power plant radioactive contaminated waste is produced. This waste is stored in an underground repository 60-100 meters below the surface. The metallic portion of this waste comprises mostly carbon and stainless steel. A long-term field exposure showed high corrosion rates, general corrosion up to 29 ㎛ a-1 and localized corrosion even higher. High corrosion rate is possible if microbes produce corrosive products, or alter the local microenvironment to favor corrosion. The bacterial and archaeal composition of biofilm formed on the surface of carbon steel was studied using 16S rRNA gene targeting sequencing, followed by phylogenetic analyses of the microbial community. The functional potential of the microbial communities in biofilm was studied by functional gene targeting quantitative PCR. The corrosion rate was calculated from weight loss measurements and the deposits on the surfaces were analyzed with SEM/EDS and XRD. Our results demonstrate that microbial diversity on the surface of carbon steel and their functionality is vast. Our results suggest that in these nutrient poor conditions the role of methanogenic archaea in corrosive biofilm, in addition to sulphate reducing bacteria, could be greater than previously suspected.