메뉴 건너뛰기




Volumn 12, Issue 4, 2008, Pages 605-615

Comparative analysis of archaeal 16S rRNA and amoA genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments

Author keywords

16S rRNA; Ammonia oxidizing archaea; amoA; Marine sediment

Indexed keywords

AMMONIA; AMMONIA MONOOXYGENASE; OXIDOREDUCTASE; OXYGEN; RNA 16S; SEA WATER;

EID: 46149095739     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-008-0165-7     Document Type: Article
Times cited : (160)

References (54)
  • 2
    • 33845520639 scopus 로고    scopus 로고
    • Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico
    • Beman JM, Francis CA (2006) Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico. Appl Environ Microbiol 72:7767-7777
    • (2006) Appl Environ Microbiol , vol.72 , pp. 7767-7777
    • Beman, J.M.1    Francis, C.A.2
  • 4
    • 0031733317 scopus 로고    scopus 로고
    • Phylogenetic analysis of nonthermophilic members of the kingdom crenarchaeota and their diversity and abundance in soils
    • Buckley DH, Graber JR, Schmidt TM (1998) Phylogenetic analysis of nonthermophilic members of the kingdom crenarchaeota and their diversity and abundance in soils. Appl Environ Microbiol 64:4333-4339
    • (1998) Appl Environ Microbiol , vol.64 , pp. 4333-4339
    • Buckley, D.H.1    Graber, J.R.2    Schmidt, T.M.3
  • 5
    • 0026755238 scopus 로고
    • Archaea in coastal marine environments
    • DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685-5689
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 5685-5689
    • Delong, E.F.1
  • 6
    • 0000461280 scopus 로고
    • Confidence limit on phylogenies: An approach using the bootstrap
    • Felsenstein J (1985) Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39:783-791
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 7
    • 26844541457 scopus 로고    scopus 로고
    • Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean
    • Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci USA 102:14683-14688
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 14683-14688
    • Francis, C.A.1    Roberts, K.J.2    Beman, J.M.3    Santoro, A.E.4    Oakley, B.B.5
  • 8
    • 0026525546 scopus 로고
    • Novel major archaebacterial group from marine plankton
    • Fuhrman JA, McCallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356:148-149
    • (1992) Nature , vol.356 , pp. 148-149
    • Fuhrman, J.A.1    McCallum, K.2    Davis, A.A.3
  • 9
    • 0000803388 scopus 로고
    • The population frequencies of species and the estimation of population parameters
    • Good IJ (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40:237-264
    • (1953) Biometrika , vol.40 , pp. 237-264
    • Good, I.J.1
  • 10
    • 33646260901 scopus 로고    scopus 로고
    • Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota
    • Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K, Richardson PM, DeLong EF (2006) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 4:e95
    • (2006) PLoS Biol , vol.4 , pp. 95
    • Hallam, S.J.1    Mincer, T.J.2    Schleper, C.3    Preston, C.M.4    Roberts, K.5    Richardson, P.M.6    Delong, E.F.7
  • 12
  • 14
    • 10444248885 scopus 로고    scopus 로고
    • Characterization of C1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, southern Ryukyu Arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes
    • Inagaki F, Tsunogai U, Suzuki M, Kosaka A, Machiyama H, Takai K, Nunoura T, Nealson KH, Horikoshi K (2004) Characterization of C1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, southern Ryukyu Arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes. Appl Environ Microbiol 70:7445-7455
    • (2004) Appl Environ Microbiol , vol.70 , pp. 7445-7455
    • Inagaki, F.1    Tsunogai, U.2    Suzuki, M.3    Kosaka, A.4    MacHiyama, H.5    Takai, K.6    Nunoura, T.7    Nealson, K.H.8    Horikoshi, K.9
  • 16
    • 0030894624 scopus 로고    scopus 로고
    • Novel group within the kingdom Crenarchaeota from boreal forest soil
    • Jurgens G, Lindstrom K, Saano A (1997) Novel group within the kingdom Crenarchaeota from boreal forest soil. Appl Environ Microbiol 63:803-805
    • (1997) Appl Environ Microbiol , vol.63 , pp. 803-805
    • Jurgens, G.1    Lindstrom, K.2    Saano, A.3
  • 17
    • 0032784378 scopus 로고    scopus 로고
    • Diversity of soil Archaea in boreal forest before, and after clear-cutting and prescribed burning
    • Jurgens G, Sanno A (1999) Diversity of soil Archaea in boreal forest before, and after clear-cutting and prescribed burning. FEMS Microbiol Ecol 29:205-213
    • (1999) FEMS Microbiol Ecol , vol.29 , pp. 205-213
    • Jurgens, G.1    Sanno, A.2
  • 18
    • 0033771975 scopus 로고    scopus 로고
    • Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization
    • Jurgens G, Glockner F, Amann R, Saano A, Montonen L, Likolammi M, Munster U (2000) Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization. FEMS Microbiol Ecol 34:45-56
    • (2000) FEMS Microbiol Ecol , vol.34 , pp. 45-56
    • Jurgens, G.1    Glockner, F.2    Amann, R.3    Saano, A.4    Montonen, L.5    Likolammi, M.6    Munster, U.7
  • 19
    • 0035945618 scopus 로고    scopus 로고
    • Archaeal dominance in the mesopelagic zone of the Pacific Ocean
    • Karner MB, DeLong EF, Karl DM (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507-510
    • (2001) Nature , vol.409 , pp. 507-510
    • Karner, M.B.1    Delong, E.F.2    Karl, D.M.3
  • 22
    • 33745053633 scopus 로고    scopus 로고
    • A cold-loving crenarchaeon is a substantial part of a novel microbial community in cold sulphidic marsh water
    • Koch M, Rudolph C, Moissl C, Huber R (2006) A cold-loving crenarchaeon is a substantial part of a novel microbial community in cold sulphidic marsh water. FEMS Microbiol Ecol 57:55-66
    • (2006) FEMS Microbiol Ecol , vol.57 , pp. 55-66
    • Koch, M.1    Rudolph, C.2    Moissl, C.3    Huber, R.4
  • 25
    • 3242810318 scopus 로고    scopus 로고
    • MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
    • Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5:150-163
    • (2004) Brief Bioinform , vol.5 , pp. 150-163
    • Kumar, S.1    Tamura, K.2    Nei, M.3
  • 27
    • 0032882298 scopus 로고    scopus 로고
    • Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench
    • Li L, Kato C, Horikoshi K (1999) Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench. Mar Biotechnol (NY) 1:391-400
    • (1999) Mar Biotechnol (NY) , vol.1 , pp. 391-400
    • Li, L.1    Kato, C.2    Horikoshi, K.3
  • 29
    • 0030620440 scopus 로고    scopus 로고
    • Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel
    • Massana R, Murray AE, Preston CM, DeLong EF (1997) Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl Environ Microbiol 63:50-56
    • (1997) Appl Environ Microbiol , vol.63 , pp. 50-56
    • Massana, R.1    Murray, A.E.2    Preston, C.M.3    Delong, E.F.4
  • 30
    • 0037345250 scopus 로고    scopus 로고
    • The impact of grassland management on archaeal community structure in upland pasture rhizosphere soil
    • Nicol GW, Glover LA, Prosser JI (2003) The impact of grassland management on archaeal community structure in upland pasture rhizosphere soil. Environ Microbiol 5:152-162
    • (2003) Environ Microbiol , vol.5 , pp. 152-162
    • Nicol, G.W.1    Glover, L.A.2    Prosser, J.I.3
  • 31
    • 14344252220 scopus 로고    scopus 로고
    • Primary succession of soil Crenarchaeota across a receding glacier foreland
    • Nicol GW, Tscherko D, Embley TM, Prosser JI (2005) Primary succession of soil Crenarchaeota across a receding glacier foreland. Environ Microbiol 7:337-347
    • (2005) Environ Microbiol , vol.7 , pp. 337-347
    • Nicol, G.W.1    Tscherko, D.2    Embley, T.M.3    Prosser, J.I.4
  • 32
    • 0042853314 scopus 로고    scopus 로고
    • Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR
    • Ochsenreiter T, Selezi D, Quaiser A, Bonch-Osmolovskaya L, Schleper C (2003) Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ Microbiol 5:787-797
    • (2003) Environ Microbiol , vol.5 , pp. 787-797
    • Ochsenreiter, T.1    Selezi, D.2    Quaiser, A.3    Bonch-Osmolovskaya, L.4    Schleper, C.5
  • 33
    • 33845342557 scopus 로고    scopus 로고
    • Microfluidic digital PCR enables multigene analysis of individual environmental bacteria
    • Ottesen EA, Hong JW, Quake SR, Leadbetter JR (2006) Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science 314:1464-1467
    • (2006) Science , vol.314 , pp. 1464-1467
    • Ottesen, E.A.1    Hong, J.W.2    Quake, S.R.3    Leadbetter, J.R.4
  • 34
    • 0030805150 scopus 로고    scopus 로고
    • Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA
    • Ovreas L, Forney L, Daae FL, Torsvik V (1997) Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63:3367-3373
    • (1997) Appl Environ Microbiol , vol.63 , pp. 3367-3373
    • Ovreas, L.1    Forney, L.2    Daae, F.L.3    Torsvik, V.4
  • 35
    • 33747341311 scopus 로고    scopus 로고
    • Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors
    • Park HD, Wells GF, Bae H, Criddle CS, Francis CA (2006) Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors. Appl Environ Microbiol 72:5643-5647
    • (2006) Appl Environ Microbiol , vol.72 , pp. 5643-5647
    • Park, H.D.1    Wells, G.F.2    Bae, H.3    Criddle, C.S.4    Francis, C.A.5
  • 36
    • 0034466757 scopus 로고    scopus 로고
    • Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: Implications for molecular diversity surveys
    • Purkhold U, Pommerening-Roser A, Juretschko S, Schmid MC, Koops HP, Wagner M (2000) Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl Environ Microbiol 66:5368-5382
    • (2000) Appl Environ Microbiol , vol.66 , pp. 5368-5382
    • Purkhold, U.1    Pommerening-Roser, A.2    Juretschko, S.3    Schmid, M.C.4    Koops, H.P.5    Wagner, M.6
  • 38
    • 0030814870 scopus 로고    scopus 로고
    • The ammonia monooxygenase structural gene amoA as a functional marker: Molecular fine-scale analysis of natural ammonia-oxidizing populations
    • Rotthauwe JH, Witzel KP, Liesack W (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microbiol 63:4704-4712
    • (1997) Appl Environ Microbiol , vol.63 , pp. 4704-4712
    • Rotthauwe, J.H.1    Witzel, K.P.2    Liesack, W.3
  • 39
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 40
    • 0032792809 scopus 로고    scopus 로고
    • Abundance and diversity of Archaea in heavy-metal-contaminated soils
    • Sandaa RA, Enger O, Torsvik V (1999) Abundance and diversity of Archaea in heavy-metal-contaminated soils. Appl Environ Microbiol 65:3293-3297
    • (1999) Appl Environ Microbiol , vol.65 , pp. 3293-3297
    • Sandaa, R.A.1    Enger, O.2    Torsvik, V.3
  • 41
    • 33745121530 scopus 로고    scopus 로고
    • Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCR
    • Schippers A, Neretin LN (2006) Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCR. Environ Microbiol 8:1251-1260
    • (2006) Environ Microbiol , vol.8 , pp. 1251-1260
    • Schippers, A.1    Neretin, L.N.2
  • 42
    • 0031033384 scopus 로고    scopus 로고
    • Recovery of crenarchaeotal ribosomal DNA sequences from freshwater-lake sediments
    • Schleper C, Holben W, Klenk HP (1997) Recovery of crenarchaeotal ribosomal DNA sequences from freshwater-lake sediments. Appl Environ Microbiol 63:321-323
    • (1997) Appl Environ Microbiol , vol.63 , pp. 321-323
    • Schleper, C.1    Holben, W.2    Klenk, H.P.3
  • 44
    • 1642296563 scopus 로고    scopus 로고
    • Spatial heterogeneity of crenarchaeal assemblages within mesophilic soil ecosystems as revealed by PCR-single-stranded conformation polymorphism profiling
    • Sliwinski MK, Goodman RM (2004) Spatial heterogeneity of crenarchaeal assemblages within mesophilic soil ecosystems as revealed by PCR-single-stranded conformation polymorphism profiling. Appl Environ Microbiol 70:1811-1820
    • (2004) Appl Environ Microbiol , vol.70 , pp. 1811-1820
    • Sliwinski, M.K.1    Goodman, R.M.2
  • 45
    • 34547492897 scopus 로고    scopus 로고
    • Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time
    • Stepanauskas R, Sieracki ME (2007) Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc Natl Acad Sci USA 104:9052-9057
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 9052-9057
    • Stepanauskas, R.1    Sieracki, M.E.2
  • 47
    • 85023884574 scopus 로고    scopus 로고
    • Microbial communities of deep marine subsurface sediments: Molecular and cultivation surveys
    • Teske A (2006) Microbial communities of deep marine subsurface sediments: molecular and cultivation surveys. Geomicrobiol J 23:357-368
    • (2006) Geomicrobiol J , vol.23 , pp. 357-368
    • Teske, A.1
  • 48
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X 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 CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882
    • (1997) Nucleic Acids Res , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 49
    • 28644435323 scopus 로고    scopus 로고
    • Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling
    • Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk HP, Schleper C (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol 7:1985-1995
    • (2005) Environ Microbiol , vol.7 , pp. 1985-1995
    • Treusch, A.H.1    Leininger, S.2    Kletzin, A.3    Schuster, S.C.4    Klenk, H.P.5    Schleper, C.6
  • 50
    • 0028983870 scopus 로고
    • Molecular phylogenetic analysis of a soil microbial community in a soybean field
    • Ueda T, Suga Y, Matsuguchi T (1995) Molecular phylogenetic analysis of a soil microbial community in a soybean field. Eur J Soil Sci 46:415-421
    • (1995) Eur J Soil Sci , vol.46 , pp. 415-421
    • Ueda, T.1    Suga, Y.2    Matsuguchi, T.3
  • 52


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.