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Volumn 44, Issue 1, 2007, Pages 121-130

Molecular identification of methane oxidizing bacteria in a Japanese rice field soil

Author keywords

Methane oxidizing bacteria; Microbial community change; Rice field soil

Indexed keywords

AGRICULTURAL SOIL; COMMUNITY RESPONSE; COMMUNITY STRUCTURE; CULTIVATION; IDENTIFICATION METHOD; METHANOGENIC BACTERIUM; OXIDATION; PADDY FIELD; SOIL PROPERTY;

EID: 34648830657     PISSN: 01782762     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00374-007-0186-x     Document Type: Article
Times cited : (13)

References (56)
  • 1
    • 34648855533 scopus 로고    scopus 로고
    • Aoki S (1996) http://aoki2.si.gunma-u.ac.jp/bb0/BlackBox0.html
    • (1996)
    • Aoki, S.1
  • 2
    • 0024633896 scopus 로고
    • +, and CO oxidation by methanotrophs and nitrifiers
    • +, and CO oxidation by methanotrophs and nitrifiers. Microbiol Rev 53:68-84
    • (1989) Microbiol Rev , vol.53 , pp. 68-84
    • Bedard, C.1    Knowles, R.2
  • 3
    • 0035458352 scopus 로고    scopus 로고
    • Comparison of pmoA PCR primer sets as tools for investigating methanotroph diversity in three Danish soils
    • Bourne DG, McDonald IR, Murrell JC (2001) Comparison of pmoA PCR primer sets as tools for investigating methanotroph diversity in three Danish soils. Appl Environ Microbiol 67:3802-3809
    • (2001) Appl Environ Microbiol , vol.67 , pp. 3802-3809
    • Bourne, D.G.1    McDonald, I.R.2    Murrell, J.C.3
  • 4
    • 0042239255 scopus 로고    scopus 로고
    • Succession and phylogenetic composition of microbial communities responsible for the composting process of rice straw estimated by PCR-DGGE analysis
    • Cahyani VR, Watanabe A, Matsuya K, Asakawa S, Kimura M (2003) Succession and phylogenetic composition of microbial communities responsible for the composting process of rice straw estimated by PCR-DGGE analysis. Soil Sci Plant Nutr 49:619-630
    • (2003) Soil Sci Plant Nutr , vol.49 , pp. 619-630
    • Cahyani, V.R.1    Watanabe, A.2    Matsuya, K.3    Asakawa, S.4    Kimura, M.5
  • 5
    • 0032746991 scopus 로고    scopus 로고
    • Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments
    • Costello AM, Lidstrom ME (1999) Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Appl Environ Microbiol 65:5066-5074
    • (1999) Appl Environ Microbiol , vol.65 , pp. 5066-5074
    • Costello, A.M.1    Lidstrom, M.E.2
  • 6
    • 0347760409 scopus 로고    scopus 로고
    • Bacterial diversity in agricultural soils during litter decomposition
    • Dilly O, Bloem J, Vos A, Munch JC (2004) Bacterial diversity in agricultural soils during litter decomposition. Appl Environ Microbiol 70:468-474
    • (2004) Appl Environ Microbiol , vol.70 , pp. 468-474
    • Dilly, O.1    Bloem, J.2    Vos, A.3    Munch, J.C.4
  • 7
    • 11144303552 scopus 로고    scopus 로고
    • Comparing field and microcosm experiments: A case study on methano- and methylo-trophic bacteria in paddy soil
    • 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
    • (2005) FEMS Microbiol Ecol , vol.51 , pp. 279-291
    • Eller, G.1    Krüger, M.2    Frenzel, P.3
  • 8
    • 2342589763 scopus 로고    scopus 로고
    • Available at:
    • FAO (2003) FAOSTAT agriculture data. Available at: http://apps.fao.org/ page/collections?subset=agriculture
    • (2003) FAOSTAT Agriculture Data
  • 9
    • 0034879576 scopus 로고    scopus 로고
    • Methanotrophic diversity in an agricultural soil as evaluated by denaturing gradient gel electrophoresis profiles of pmoA, mxaF and 16S rDNA sequences
    • Fjellbirkeland A, Torsvik V, Øvreås L (2001) Methanotrophic diversity in an agricultural soil as evaluated by denaturing gradient gel electrophoresis profiles of pmoA, mxaF and 16S rDNA sequences. Antonie van Leeuwenhoek 79:209-217
    • (2001) Antonie Van Leeuwenhoek , vol.79 , pp. 209-217
    • Fjellbirkeland, A.1    Torsvik, V.2    Øvreås, L.3
  • 10
    • 0030003012 scopus 로고    scopus 로고
    • Methanotrophic bacteria
    • Hanson R, Hanson T (1996) Methanotrophic bacteria. Microbiol Rev 60:439-471
    • (1996) Microbiol Rev , vol.60 , pp. 439-471
    • Hanson, R.1    Hanson, T.2
  • 11
    • 0032925877 scopus 로고    scopus 로고
    • Molecular analyses of the methane-oxidizing microbial community in rice field soils by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase
    • Henckel T, Friedrich M, Conrad R (1999) Molecular analyses of the methane-oxidizing microbial community in rice field soils by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Appl Environ Microbiol 65:1980-1990
    • (1999) Appl Environ Microbiol , vol.65 , pp. 1980-1990
    • Henckel, T.1    Friedrich, M.2    Conrad, R.3
  • 12
    • 0034353644 scopus 로고    scopus 로고
    • 4 on presence and activity of the indigenous methanotrophic community in rice field soils
    • 4 on presence and activity of the indigenous methanotrophic community in rice field soils. Environ Microbiol 2:666-679
    • (2000) Environ Microbiol , vol.2 , pp. 666-679
    • Henckel, T.1    Roslev, P.2    Conrad, R.3
  • 13
    • 0034537565 scopus 로고    scopus 로고
    • Vertical distribution of the methanotrophic community after drainage of rice field soils
    • Henckel T, Jackel U, Conrad R (2001) Vertical distribution of the methanotrophic community after drainage of rice field soils. FEMS Microbiol Ecol 34:279-291
    • (2001) FEMS Microbiol Ecol , vol.34 , pp. 279-291
    • Henckel, T.1    Jackel, U.2    Conrad, R.3
  • 14
    • 0036671356 scopus 로고    scopus 로고
    • Diversity of the particulate methane monooxygenase gene in methanotrophic samples from different rice fields in China and the Philippines
    • Hoffmann T, Horz HP, Kemnitz D, Conrad R (2002) Diversity of the particulate methane monooxygenase gene in methanotrophic samples from different rice fields in China and the Philippines. Syst Appl Microbiol 25:267-274
    • (2002) Syst Appl Microbiol , vol.25 , pp. 267-274
    • Hoffmann, T.1    Horz, H.P.2    Kemnitz, D.3    Conrad, R.4
  • 15
    • 0028791540 scopus 로고
    • Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related
    • Holmes AJ, Costello A, Lidstrom ME, Murrell JC (1995) Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol Lett 132:1225-1228
    • (1995) FEMS Microbiol Lett , vol.132 , pp. 1225-1228
    • Holmes, A.J.1    Costello, A.2    Lidstrom, M.E.3    Murrell, J.C.4
  • 17
    • 0035458355 scopus 로고    scopus 로고
    • Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA, mmoX, mxaF, and 16S rRNA and ribosomal DNA, including pmoA-based terminal restriction fragment length polymorphism profiling
    • Horz HP, Yimga M, Liesack W (2001) Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA, mmoX, mxaF, and 16S rRNA and ribosomal DNA, including pmoA-based terminal restriction fragment length polymorphism profiling. Appl Environ Microbiol 67:4177-4185
    • (2001) Appl Environ Microbiol , vol.67 , pp. 4177-4185
    • Horz, H.P.1    Yimga, M.2    Liesack, W.3
  • 18
    • 18444409388 scopus 로고    scopus 로고
    • Methane-oxidizing bacteria in a California upland grassland soil: Diversity and response to simulated global change
    • Horz HP, Rich V, Avrahami S, Bohannan BJM (2005) Methane-oxidizing bacteria in a California upland grassland soil: diversity and response to simulated global change. Appl Environ Microbiol 71:2642-2652
    • (2005) Appl Environ Microbiol , vol.71 , pp. 2642-2652
    • Horz, H.P.1    Rich, V.2    Avrahami, S.3    Bohannan, B.J.M.4
  • 20
    • 0042239256 scopus 로고    scopus 로고
    • Bacterial communities associated with nodal roots of rice plants along with the growth stages: Estimation by PCR-DGGE and sequence analyses
    • Ikenaga M, Asakawa S, Muraoka Y, Kimura M (2003) Bacterial communities associated with nodal roots of rice plants along with the growth stages: estimation by PCR-DGGE and sequence analyses. Soil Sci Plant Nutr 49:591-602
    • (2003) Soil Sci Plant Nutr , vol.49 , pp. 591-602
    • Ikenaga, M.1    Asakawa, S.2    Muraoka, Y.3    Kimura, M.4
  • 21
    • 0033949683 scopus 로고    scopus 로고
    • Detection of methane oxidizing bacteria in forest soil by monooxygenase PCR amplification
    • Jensen S, Holmes AJ, Olsen RA, Murrell JC (2000) Detection of methane oxidizing bacteria in forest soil by monooxygenase PCR amplification. Microb Ecol 39:282-289
    • (2000) Microb Ecol , vol.39 , pp. 282-289
    • Jensen, S.1    Holmes, A.J.2    Olsen, R.A.3    Murrell, J.C.4
  • 22
    • 0002891608 scopus 로고    scopus 로고
    • Anaerobic microbiology in waterlogged rice fields
    • Marcel Dekker New York
    • Kimura M (2000) Anaerobic microbiology in waterlogged rice fields. In: Bollag JM, Stotzky G (eds) Soil biochemistry. Marcel Dekker, New York, pp 35-138
    • (2000) Soil Biochemistry , pp. 35-138
    • Kimura, M.1    Bollag, J.M.2    Stotzky, G.3
  • 23
    • 0036944004 scopus 로고    scopus 로고
    • Community structure of the microbiota in the floodwater of a Japanese paddy field estimated by restriction fragment length polymorphism and denaturing gradient gel electrophoresis pattern analyses
    • Kimura M, Shibagaki T, Nakajima Y, Matsuya K, Ikenaga M (2002) Community structure of the microbiota in the floodwater of a Japanese paddy field estimated by restriction fragment length polymorphism and denaturing gradient gel electrophoresis pattern analyses. Biol Fertil Soils 36:306-312
    • (2002) Biol Fertil Soils , vol.36 , pp. 306-312
    • Kimura, M.1    Shibagaki, T.2    Nakajima, Y.3    Matsuya, K.4    Ikenaga, M.5
  • 25
    • 0000911457 scopus 로고
    • Ecological aspects of methane oxidation, a key determinant of global methane dynamics
    • King GM (1992) Ecological aspects of methane oxidation, a key determinant of global methane dynamics. Adv Microbiol Ecol 12:431-468
    • (1992) Adv Microbial Ecol , vol.12 , pp. 431-468
    • King, G.M.1
  • 26
    • 84959104794 scopus 로고
    • Aerenchyma formation and methane and oxygen exchange in rice
    • Kludze KL, Delaune RD, Patrick Jr WH (1993) Aerenchyma formation and methane and oxygen exchange in rice. Soil Sci Soc Am J 57:386-391
    • (1993) Soil Sci Soc Am J , vol.57 , pp. 386-391
    • Kludze, K.L.1    Delaune, R.D.2    Patrick Jr., W.H.3
  • 27
    • 0242405670 scopus 로고    scopus 로고
    • Diversity and activity of methanotrophic bacteria in different upland soils
    • Knief C, Lipski A, Dunfield PF (2003) Diversity and activity of methanotrophic bacteria in different upland soils. Appl Environ Microbiol 69:6703-6714
    • (2003) Appl Environ Microbiol , vol.69 , pp. 6703-6714
    • Knief, C.1    Lipski, A.2    Dunfield, P.F.3
  • 28
    • 0037110312 scopus 로고    scopus 로고
    • Reduced methane emissions from large-scale changes in water management of China's rice paddies during 1980-2000
    • Li CS, Qiu JJ, Frolking S, Xiao XM, Salas W, Moore B, Boles S, Huang Y, Sass R (2002) Reduced methane emissions from large-scale changes in water management of China's rice paddies during 1980-2000. J Geophys Res 29:33-38
    • (2002) J Geophys Res , vol.29 , pp. 33-38
    • Li, C.S.1    Qiu, J.J.2    Frolking, S.3    Xiao, X.M.4    Salas, W.5    Moore, B.6    Boles, S.7    Huang, Y.8    Sass, R.9
  • 32
    • 0034233490 scopus 로고    scopus 로고
    • Soil community analysis using DGGE of 16S rDNA polymerase chain reaction products
    • Nakatsu CH, Torsvik V, Øvreås L (2000) Soil community analysis using DGGE of 16S rDNA polymerase chain reaction products. Soil Sci Soc Am J 64:1382-1388
    • (2000) Soil Sci Soc Am J , vol.64 , pp. 1382-1388
    • Nakatsu, C.H.1    Torsvik, V.2    Øvreås, L.3
  • 33
    • 0036242855 scopus 로고    scopus 로고
    • Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria
    • Nicolaisen MH, Ramsing NB (2002) Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria. J Microbiol Methods 50:189-203
    • (2002) J Microbiol Methods , vol.50 , pp. 189-203
    • Nicolaisen, M.H.1    Ramsing, N.B.2
  • 34
    • 3042845914 scopus 로고    scopus 로고
    • Analysis of communities of ammonia oxidizers, methanotrophs, and methanogens associated with microcrustaceans in the floodwater of a rice field microcosm
    • Niswati A, Murase J, Asakawa S, Kimura M (2004) Analysis of communities of ammonia oxidizers, methanotrophs, and methanogens associated with microcrustaceans in the floodwater of a rice field microcosm. Soil Sci Plant Nutr 50:447-455
    • (2004) Soil Sci Plant Nutr , vol.50 , pp. 447-455
    • Niswati, A.1    Murase, J.2    Asakawa, S.3    Kimura, M.4
  • 35
    • 0033770988 scopus 로고    scopus 로고
    • Pacific northwest marine sediments contain ammonia-oxidizing bacteria in the beta subdivision of the proteobacteria
    • Nold SC, Zhou J, Devol AH, Tiedje JM (2000) Pacific northwest marine sediments contain ammonia-oxidizing bacteria in the beta subdivision of the proteobacteria. Appl Environ Microbiol 66:4532-4535
    • (2000) Appl Environ Microbiol , vol.66 , pp. 4532-4535
    • Nold, S.C.1    Zhou, J.2    Devol, A.H.3    Tiedje, J.M.4
  • 36
    • 0030014717 scopus 로고    scopus 로고
    • The gene encoding ammonia monooxygenase subunit a exists in three nearly identical copies in Nitrosospira sp. NpAV
    • Norton JM, Low JM, Klotz MG (1996) The gene encoding ammonia monooxygenase subunit A exists in three nearly identical copies in Nitrosospira sp. NpAV. FEMS Microbiol Lett 139:181-188
    • (1996) FEMS Microbiol Lett , vol.139 , pp. 181-188
    • Norton, J.M.1    Low, J.M.2    Klotz, M.G.3
  • 37
    • 0036167265 scopus 로고    scopus 로고
    • Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria
    • Norton JM, Alzerreca JJ, Suwa Y. Klotz MG (2002) Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Arch Microbiol 177:139-149
    • (2002) Arch Microbiol , vol.177 , pp. 139-149
    • Norton, J.M.1    Alzerreca, J.J.2    Suwa, Y.3    Klotz, M.G.4
  • 39
    • 0030203863 scopus 로고    scopus 로고
    • TreeView: An application to display phylogenetic trees on personal computers
    • Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357-358
    • (1996) Comput Appl Biosci , vol.12 , pp. 357-358
    • Page, R.D.1
  • 41
    • 2442719342 scopus 로고    scopus 로고
    • Comparative analysis of the conventional and novel pmo (particulate methane monooxygenase) operons from Methylocystis strain SC2
    • Ricke P, Erkel C, Kube M, Reinhardt R, Liesack W (2004) Comparative analysis of the conventional and novel pmo (particulate methane monooxygenase) operons from Methylocystis strain SC2. Appl Environ Microbiol 70:3055-3063
    • (2004) Appl Environ Microbiol , vol.70 , pp. 3055-3063
    • Ricke, P.1    Erkel, C.2    Kube, M.3    Reinhardt, R.4    Liesack, W.5
  • 44
    • 0031460011 scopus 로고    scopus 로고
    • Effects of field drainage on soil parameters related to methane production and emission from rice paddies
    • Sigren LK, Lewis FT, Fisher FM, Sass RL (1997) Effects of field drainage on soil parameters related to methane production and emission from rice paddies. Global Biogeochem Cycles 11:151-162
    • (1997) Global Biogeochem Cycles , vol.11 , pp. 151-162
    • Sigren, L.K.1    Lewis, F.T.2    Fisher, F.M.3    Sass, R.L.4
  • 45
    • 0032923140 scopus 로고    scopus 로고
    • Role of multiple gene copies in particulate methane monooxygenase activity in the methane oxidizing bacterium Methylococcus capsulatus Bath
    • Stolyar S, Costello AM, Peeples TL, Lidstrom ME (1999) Role of multiple gene copies in particulate methane monooxygenase activity in the methane oxidizing bacterium Methylococcus capsulatus Bath. Microbiology 145:1235-1244
    • (1999) Microbiology , vol.145 , pp. 1235-1244
    • Stolyar, S.1    Costello, A.M.2    Peeples, T.L.3    Lidstrom, M.E.4
  • 46
    • 0029859713 scopus 로고    scopus 로고
    • Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes
    • Sugimoto N, Nakano S, Yoneyama M, Honda K (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 24:4501-4505
    • (1996) Nucleic Acids Res , vol.24 , pp. 4501-4505
    • Sugimoto, N.1    Nakano, S.2    Yoneyama, M.3    Honda, K.4
  • 47
    • 0031574072 scopus 로고    scopus 로고
    • The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876-4882
    • (1997) Nucleic Acids Res , vol.24 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 48
    • 0035542324 scopus 로고    scopus 로고
    • Structural and functional model of methane hydroxylase of membrane-bound methane monooxygenase from Methylococcus capsulatus (Bath)
    • Tukhvatullin IA, Gvozdev RI, Anderson KK (2001) Structural and functional model of methane hydroxylase of membrane-bound methane monooxygenase from Methylococcus capsulatus (Bath). Russ Chem Bull 50:1867-1876
    • (2001) Russ Chem Bull , vol.50 , pp. 1867-1876
    • Tukhvatullin, I.A.1    Gvozdev, R.I.2    Anderson, K.K.3
  • 49
    • 8844264574 scopus 로고    scopus 로고
    • Genomic insights into methanotrophy: The complete genome sequence of Methylococcus capsulatus (Bath)
    • Ward N et al (2004) Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol 2:1616-1628
    • (2004) PLoS Biol , vol.2 , pp. 1616-1628
    • Ward, N.1
  • 50
    • 0034008147 scopus 로고    scopus 로고
    • The role of rice plants in regulating mechanisms of methane missions
    • Wassmann R, Aulakh MS (2000) The role of rice plants in regulating mechanisms of methane missions. Biol Fertil Soils 31:20-29
    • (2000) Biol Fertil Soils , vol.31 , pp. 20-29
    • Wassmann, R.1    Aulakh, M.S.2
  • 51
    • 0027951994 scopus 로고
    • Methane production and its fate in paddy fields. V. Fate of methane remaining in paddy soil at harvesting stage
    • Watanabe A, Murase J, Katoh K, Kimura M (1994) Methane production and its fate in paddy fields. V. Fate of methane remaining in paddy soil at harvesting stage. Soil Sci Plant Nutr 40:221-230
    • (1994) Soil Sci Plant Nutr , vol.40 , pp. 221-230
    • Watanabe, A.1    Murase, J.2    Katoh, K.3    Kimura, M.4
  • 52
    • 1842576603 scopus 로고    scopus 로고
    • DGGE method for analyzing 16S rDNA of methanogenic archaeal community in paddy field soil
    • Watanabe T, Asakawa S, Nakamura A, Nagaoka K, Kimura M (2004) DGGE method for analyzing 16S rDNA of methanogenic archaeal community in paddy field soil. FEMS Microbiol Lett 232:153-163
    • (2004) FEMS Microbiol Lett , vol.232 , pp. 153-163
    • Watanabe, T.1    Asakawa, S.2    Nakamura, A.3    Nagaoka, K.4    Kimura, M.5
  • 53
    • 0041629119 scopus 로고    scopus 로고
    • Soil moisture between rice-growing seasons affects methane emission, production, and oxidation
    • Xu H, Cai ZC, Tsuruta H (2003) Soil moisture between rice-growing seasons affects methane emission, production, and oxidation. Soil Sci Soc Am J 67:1147-1157
    • (2003) Soil Sci Soc Am J , vol.67 , pp. 1147-1157
    • Xu, H.1    Cai, Z.C.2    Tsuruta, H.3
  • 54
    • 0037294599 scopus 로고    scopus 로고
    • Development of region-specific emission factors and estimation of methane emission from rice fields in the East, Southeast and South Asian countries
    • Yan X, Ohara T, Akimoto H (2003) Development of region-specific emission factors and estimation of methane emission from rice fields in the East, Southeast and South Asian countries. Global Change Biol 9:237-254
    • (2003) Global Change Biol , vol.9 , pp. 237-254
    • Yan, X.1    Ohara, T.2    Akimoto, H.3
  • 55
    • 9644263929 scopus 로고    scopus 로고
    • Optimized sequence retrieval from single bands of temperature gradient gel electrophoresis profiles of the amplified 16S rDNA fragments from an activated sludge system
    • Zhang XL, Yan X, Gao PP, Wang LH, Zhou ZH, Zhao LP (2005) Optimized sequence retrieval from single bands of temperature gradient gel electrophoresis profiles of the amplified 16S rDNA fragments from an activated sludge system. J Microbiol Methods 60:1-11
    • (2005) J Microbiol Methods , vol.60 , pp. 1-11
    • Zhang, X.L.1    Yan, X.2    Gao, P.P.3    Wang, L.H.4    Zhou, Z.H.5    Zhao, L.P.6


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