최소 단어 이상 선택하여야 합니다.
최대 10 단어까지만 선택 가능합니다.
다음과 같은 기능을 한번의 로그인으로 사용 할 수 있습니다.
NTIS 바로가기Frontiers in microbiology, v.6, 2015년, pp.639 -
Lee, Hyo Jung (Department of Life Science, Chung-Ang University Seoul, South Korea) , Jeong, Sang Eun (Department of Life Science, Chung-Ang University Seoul, South Korea) , Kim, Pil Joo (Division of Applied Life Science, Gyeongsang National University Jinju, South Korea) , Madsen, Eugene L. (Department of Microbiology, Cornell University Ithaca, NY, USA) , Jeon, Che Ok (Department of Life Science, Chung-Ang University Seoul, South Korea)
The communities and abundances of methanotrophs and methanogens, along with the oxygen, methane, and total organic carbon (TOC) concentrations, were investigated along a depth gradient in a flooded rice paddy. Broad patterns in vertical profiles of oxygen, methane, TOC, and microbial abundances were...
Biddle J. F. Cardman Z. Mendlovitz H. Albert D. B. Lloyd K. G. Boetius A. . ( 2012 ). Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments . ISME J . 6 , 1018 – 1031 . 10.1038/ismej.2011.164 22094346
Blossfeld S. Gansert D. Thiele B. Kuhn A. J. Lösch R. ( 2011 ). The dynamics of oxygen concentration, pH value, and organic acids in the rhizosphere of Juncus spp . Soil Biol. Biochem . 43 , 1186 – 1197 . 10.1016/j.soilbio.2011.02.007
Bräuer S. Cadillo-Quiroz H. Yashiro E. Yavitt J. B. Zinder S. H. ( 2006 ). Isolation of a novel acidiphilic methanogen from an acidic peat bog . Nature 442 , 192 – 194 . 10.1038/nature04810 16699521
Breidenbach B. Conrad R. ( 2015 ). Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage . Front. Microbiol . 5 : 752 . 10.3389/fmicb.2014.00752 25620960
Bridgham S. D. Cadillo-Quiroz H. Keller J. K. Zhuang Q. ( 2013 ). Methane emissions from wetlands: biogeochemical, microbial, and modeling perspectives from local to global scales . Glob. Change Biol . 19 , 1325 – 1346 . 10.1111/gcb.12131 23505021
Chao A. ( 1987 ). Estimating the population size for capture-recapture data with unequal catchability . Biometrics 43 , 783 – 791 . 10.2307/2531532 3427163
Cole J. R. Wang Q. Cardenas E. Fish J. Chai B. Farris R. J. . ( 2009 ). The Ribosomal Database Project: improved alignments and new tools for rRNA analysis . Nucleic Acids Res . 37 , D141 – D145 . 10.1093/nar/gkn879 19004872
Conrad R. ( 2002 ). Control of microbial methane production in wetland rice fields . Nutr. Cycl. Agroecosyst . 64 , 59 – 69 . 10.1023/A:1021178713988
Conrad R. ( 2007 ). Microbial ecology of methanogens and methanotrophs . Adv. Agron . 96 , 1 – 63 . 10.1016/s0065-2113(07)96005-8
Costa K. C. Leigh J. A. ( 2014 ). Metabolic versatility in methanogens . Curr. Opin. Biotechnol . 29 , 70 – 75 . 10.1016/j.copbio.2014.02.012 24662145
Denman S. E. McSweeney C. S. ( 2006 ). Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen . FEMS Microbiol. Ecol . 58 , 572 – 582 . 10.1111/j.1574-6941.2006.00190.x 17117998
Edgar R. C. Haas B. J. Clemente J. C. Quince C. Knight R. ( 2011 ). UCHIME improves sensitivity and speed of chimera detection . Bioinformatics 21 , 494 – 504 . 10.1093/bioinformatics/btr381 21700674
Eller G. Krüger M. Frenzel P. ( 2005 ). Comparing field and microcosm experiments: a case study on methano- and methylo-trophic bacteria in paddy soil . FEMS Microbiol. Ecol . 51 , 279 – 291 . 10.1016/j.femsec.2004.09.007 16329876
Ettwig K. F. Butler M. K. Le Paslier D. Pelletier E. Mangenot S. Kuypers M. M. . ( 2010 ). Nitrite-driven anaerobic methane oxidation by oxygenic bacteria . Nature 464 , 543 – 548 . 10.1038/nature08883 20336137
Felsenstein J. ( 2002 ). PHYLIP (Phylogeny Inference Package), Version 3.6a . Seattle, WA : Department of Genetics, University of Washington .
Gilbert B. Frenzel P. ( 1998 ). Rice roots and CH 4 oxidation: the activity of bacteria, their distribution and the microenvironment . Soil Biol. Biochem . 14 , 1903 – 1916 . 10.1016/S0038-0717(98)00061-3
Groot T. T. van Bodegom P. M. Harren F. J. M. Meijer H. A. J. ( 2003 ). Quantification of methane oxidation in the rice rhizosphere using 13 C-labelled methane . Biogeochemistry 64 , 355 – 372 . 10.1023/A:1024921714852
Gutierrez J. Atulba S. L. Kim G. Kim P. J. ( 2014 ). Importance of rice root oxidation potential as a regulator of CH 4 production under waterlogged conditions . Biol. Fertil. Soils 50 , 861 – 868 . 10.1007/s00374-014-0904-0
Haroon M. F. Hu S. Shi Y. Imelfort M. Keller J. Hugenholtz P. . ( 2013 ). Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage . Nature 500 , 567 – 570 . 10.1038/nature12375 23892779
Henckel T. Roslev P. Conrad R. ( 2000 ). Effects of O 2 and CH 4 on presence and activity of the indigenous methanotrophic community in rice field soil . Environ. Microbiol . 2 , 666 – 679 . 10.1046/j.1462-2920.2000.00149.x 11214799
Herman D. Roberts D. ( 2006 ). The influence of structural components of alkyl esters on their anaerobic biodegradation in marine sediment . Biodegradation 17 , 457 – 463 . 10.1007/s10532-005-9016-8 16477357
IPCC. ( 2007 ). Climate change 2007: the physical science basis, in Working Group I Contribution to the IPCC Fourth Assessment Report . Cambridge; New York : Cambridge University Press .
Jung J. Y. Lee S. H. Kim J. M. Park M. S. Bae J. W. Hahn Y. . ( 2011 ). Metagenomic analysis of kimchi, a traditional Korean fermented food . Appl. Environ. Microbiol . 77 , 2264 – 2274 . 10.1128/AEM.02157-10 21317261
Kerdchoechuen O. ( 2005 ). Methane emission in four rice varieties as related to sugars and organic acids of roots and root exudates and biomass yield . Agric. Ecosyst. Environ . 108 , 155 – 163 . 10.1016/j.agee.2005.01.004
Kimura M. Murase J. Lu Y. ( 2004 ). Carbon cycling in rice field ecosystems in the context of input, decomposition and translocation of organic materials and the fates of their end products (CO 2 and CH 4 ) . Soil Biol. Biochem . 36 , 1399 – 1416 . 10.1016/j.soilbio.2004.03.006
Knief C. Dunfield P. F. ( 2005 ). Response and adaptation of different methanotrophic bacteria to low methane mixing ratios . Environ. Microbiol . 7 , 1307 – 1317 . 10.1111/j.1462-2920.2005.00814.x 16104854
Krause S. Lüke C. Frenzel P. ( 2010 ). Succession of methanotrophs in oxygen-methane counter-gradients of flooded rice paddies . ISME J . 4 , 1603 – 1607 . 10.1038/ismej.2010.82 20574459
Kumaraswamy S. Ramakrishnan B. Satpathy S. N. Rath A. K. Misra S. Rao V. R. ( 1997 ). Spatial distribution of methane-oxidizing activity in a flooded rice soil . Plant Soil 191 , 241 – 248 . 10.1023/A:1004274302326
Lee H. J. Jung J. Y. Oh Y. K. Lee S. S. Madsen E. L. Jeon C. O. ( 2012 ). Comparative survey of rumen microbial communities and metabolites across one caprine and three bovine groups, using bar-coded pyrosequencing and 1 H nuclear magnetic resonance spectroscopy . Appl. Environ. Microbiol . 78 , 5983 – 5993 . 10.1128/AEM.00104-12 22706048
Lee H. J. Kim S. Y. Kim P. S. Madsen E. L. Jeon C. O. ( 2014 ). Methane emission and dynamics of methanotrophic and methanogenic communities in a flooded rice field ecosystem . FEMS Microbiol. Ecol . 88 , 195 – 212 . 10.1111/1574-6941.12282 24410836
Liesack W. Schnell S. Revsbech N. P. ( 2000 ). Microbiology of flooded rice paddies . FEMS Microbiol. Rev . 24 , 624 – 645 . 10.1111/j.1574-6976.2000.tb00563.x 11077155
Liu D. Ishikawa H. Nishida M. Tsuchiya K. Takahashi T. Kimura M. . ( 2015 ). Effect of paddy-upland rotation on methanogenic archaeal community structure in paddy field soil . Microb. Ecol . 69 , 160 – 168 . 10.1007/s00248-014-0477-3 25113614
Lozupone C. Knight R. ( 2005 ). UniFrac: a new phylogenetic method for comparing microbial communities . Appl. Environ. Microbiol . 71 , 8228 – 8235 . 10.1128/AEM.71.12.8228-8235.2005 16332807
Lüdemann H. Arth I. Liesack W. ( 2000 ). Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores . Appl. Environ. Microbiol . 66 , 754 – 762 . 10.1128/AEM.66.2.754-762.2000 10653747
Lüke C. Frenzel P. ( 2011 ). Potential of pmoA amplicon pyrosequencing for methanotroph diversity studies . Appl. Environ. Microbiol . 77 , 6305 – 6309 . 10.1128/AEM.05355-11 21764977
Lüke C. Frenzel P. Ho A. Fiantis D. Schad P. Schneider B. . ( 2014 ). Macroecology of methane-oxidizing bacteria: the β-diversity of pmoA genotypes in tropical and subtropical rice paddies . Environ. Microbiol . 16 , 72 – 83 . 10.1111/1462-2920.12190 24914433
Lu Y. Conrad R. ( 2005 ). In situ stable isotope probing of methanogenic archaea in the rice rhizosphere . Science 309 , 1088 – 1090 . 10.1126/science.1113435 16099988
Lu Y. Wassmann R. Neue H. U. Huang C. Y. ( 2000 ). Dynamics of dissolved organic carbon and methane emissions in a flooded rice soil . Soil Sci. Soc. Am. J . 6 , 2011 – 2017 . 10.2136/sssaj2000.6462011x
Ma K. Conrad R. Lu Y. ( 2012 ). Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil . Appl. Environ. Microbiol . 78 , 445 – 454 . 10.1128/AEM.06934-11 22101043
Ma K. Conrad R. Lu Y. ( 2013 ). Dry/wet cycles change the activity and population dynamics of methanotrophs in rice field soil . Appl. Environ. Microbiol . 79 , 4932 – 4939 . 10.1128/AEM.00850-13 23770899
Ma K. Lu Y. ( 2011 ). Regulation of microbial methane production and oxidation by intermittent drainage in rice field soil . FEMS Microbiol. Ecol . 75 , 446 – 456 . 10.1111/j.1574-6941.2010.01018.x 21198683
Ma K. Qiu Q. Lu Y. ( 2010 ). Microbial mechanism for rice variety control on methane emission from rice field soil . Glob. Change Biol . 16 , 3085 – 3095 . 10.1111/j.1365-2486.2009.02145.x
MaCalady J. L. McMillan A. M. S. Dickens A. F. Tyler S. C. Scow K. M. ( 2002 ). Population dynamics of type I and II methanotrophic bacteria in rice soil . Environ. Microbiol . 4 , 148 – 157 . 10.1046/j.1462-2920.2002.00278.x 12000315
Mills H. J. Hodges C. Wilson K. MacDonald I. R. Sobecky P. A. ( 2003 ). Microbial diversity in sediments associated with surface-breaching gas hydrate mounds in the Gulf of Mexico . FEMS Microbiol. Ecol . 46 , 39 – 52 . 10.1016/S0168-6496(03)00191-0 19719581
Mills H. J. Martinez R. J. Story S. Sobecky P. A. ( 2005 ). Characterization of microbial community structure in Gulf of Mexico gas hydrates: comparative analysis of DNA- and RNA-derived clone libraries . Appl. Environ. Microbiol . 71 , 3235 – 3247 . 10.1128/AEM.71.6.3235-3247.2005 15933026
Noll M. Matthies D. Frenzel P. Derakshani M. Liesack W. ( 2005 ). Succession of bacterial community structure and diversity in a paddy soil oxygen gradient . Environ. Microbiol . 7 , 382 – 395 . 10.1111/j.1462-2920.2005.00700.x 15683399
Op den Camp H. J. Islam T. Stott M. B. Harhangi H. R. Hynes A. Schouten S. . ( 2009 ). Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia . Environ. Microbiol. Rep . 1 , 293 – 306 . 10.1111/j.1758-2229.2009.00022.x 23765882
Pruesse E. Quast C. Knittel K. Fuchs B. M. Ludwig W. Peplies J. . ( 2007 ). SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB . Nucleic Acids Res . 35 , 7188 – 7196 . 10.1093/nar/gkm864 17947321
Pump J. Pratscher J. Conrad R. ( 2015 ). Colonization of rice roots with methanogenic archaea controls photosynthesis-derived CH 4 emission . Environ. Microbiol . [Epub ahead of print]. 10.1111/1462-2920.12675 25367104
Reim A. Lüke C. Krause S. Pratscher J. Frenzel P. ( 2012 ). One millimeter makes the difference: high-resolution analysis of methane-oxidizing bacteria and their specific activity at the oxic-anoxic interface in a flooded paddy soil . ISME J . 6 , 2128 – 2139 . 10.1038/ismej.2012.57 22695859
Revsbech N. P. Pedersen O. Reichardt W. Briones A. ( 1999 ). Microsensor analysis of oxygen and pH in the rice rhizosphere under field and laboratory conditions . Biol. Fertil. Soils 29 , 379 – 385 . 10.1007/s003740050568
Roesch L. F. W. Fulthorpe R. R. Riva A. Casella G. Hadwin A. K. M. Kent A. D. . ( 2007 ). Pyrosequencing enumerates and contrasts soil microbial diversity . ISME J . 1 , 283 – 290 . 10.1038/ismej.2007.53 18043639
Sakai S. Imachi H. Sekiguchi Y. Tseng I. C. Ohashi A. Harada H. . ( 2009 ). Cultivation of methanogens under low-hydrogen conditions by using the coculture method . Appl. Environ. Microbiol . 75 , 4892 – 4896 . 10.1128/AEM.02835-08 19465530
Schloss P. D. Westcott S. L. Ryabin T. Hall J. R. Hartmann M. Hollister E. B. . ( 2009 ). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities . Appl. Environ. Microbiol . 75 , 7537 – 7541 . 10.1128/AEM.01541-09 19801464
Semrau J. D. DiSpirito A. A. Yoon S. ( 2010 ). Methanotrophs and copper . FEMS Microbiol. Rev . 34 , 496 – 531 . 10.1111/j.1574-6976.2010.00212.x 20236329
Shannon C. E. Weaver W. ( 1963 ). The Mathematical Theory of Communication . Urbana, IL : University of Illinois Press .
Shen L. D. Liu S. Huang Q. Lian X. He Z. F. Geng S. ( 2014 ). Evidence for the cooccurrence of nitrite-dependent anaerobic ammonium and methane oxidation processes in a flooded paddy field . Appl. Environ. Microbiol . 80 , 7611 – 7619 . 10.1128/AEM.02379-14 25261523
Shimane Y. Hatada Y. Minegishi H. Echigo A. Nagaoka S. Miyazaki M. . ( 2011 ). Salarchaeum japonicum gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea isolated from commercial salt . Int. J. Syst. Evol. Microbiol . 61 , 2266 – 2270 . 10.1099/ijs.0.025064-0 20952548
Shrestha M. Abraham W. R. Shrestha P. M. Noll M. Conrad R. ( 2008 ). Activity and composition of methanotrophic bacterial communities in planted rice soil studied by flux measurements, analyses of pmoA gene and stable isotope probing of phospholipid fatty acids . Environ. Microbiol . 10 , 400 – 412 . 10.1111/j.1462-2920.2007.01462.x 18177369
Shrestha M. Shrestha P. M. Frenzel P. Conrad R. ( 2010 ). Effect of nitrogen fertilization on methane oxidation, abundance, community structure, and gene expression of methanotrophs in the rice rhizosphere . ISME J . 4 , 1545 – 1556 . 10.1038/ismej.2010.89 20596069
Takai K. Horikoshi K. ( 2000 ). Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes . Appl. Environ. Microbiol . 66 , 5066 – 5072 . 10.1128/AEM.66.11.5066-5072.2000 11055964
Wainø M. Tindall B. J. Ingvorsen K. ( 2000 ). Halorhabdus utahensis gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea from Great Salt Lake, Utah . Int. J. Syst. Evol. Microbiol . 50 , 183 – 190 . 10.1099/00207713-50-1-183 10826803
Watanabe T. Wang G. Taki K. Ohashi Y. Kimura M. Asakawa S. ( 2010 ). Vertical changes in bacterial and archaeal communities with soil depth in Japanese paddy fields . Soil Sci. Plant Nutr . 56 , 705 – 715 . 10.1111/j.1747-0765.2010.00511.x
Wu L. Ma K. Lu Y. ( 2009 ). Rice roots select for type I methanotrophs in rice field soil . Syst. Appl. Microbiol . 32 , 421 – 428 . 10.1016/j.syapm.2009.05.001 19481894
Yuan Q. Pump J. Conrad R. ( 2012 ). Partitioning of CH 4 and CO 2 production originating from rice straw, soil and root organic carbon in rice microcosms . PLoS ONE 7 : e49073 . 10.1371/journal.pone.0049073 23162678
Yuan Y. Conrad R. Lu Y. ( 2009 ). Responses of methanogenic archaeal community to oxygen exposure in rice field soil . Environ. Microbiol. Rep . 1 , 347 – 354 . 10.1111/j.1758-2229.2009.00036.x 23765886
Yuan Y. Conrad R. Lu Y. ( 2011 ). Transcriptional response of methanogen mcrA genes to oxygen exposure of rice field soil . Environ. Microbiol. Rep . 3 , 320 – 328 . 10.1111/j.1758-2229.2010.00228.x 23761278
Zhou J. Wu L. Deng Y. Zhi X. Jian Y. H. Tu Q. . ( 2011 ). Reproducibility and quantitation of amplicon sequencing-based detection . ISME J . 5 , 1303 – 1313 . 10.1038/ismej.2011.11 21346791
*원문 PDF 파일 및 링크정보가 존재하지 않을 경우 KISTI DDS 시스템에서 제공하는 원문복사서비스를 사용할 수 있습니다.
오픈액세스 학술지에 출판된 논문
※ AI-Helper는 부적절한 답변을 할 수 있습니다.