메뉴 건너뛰기




Volumn 3, Issue 2, 2011, Pages 245-253

Community profiling and quantification of putative autotrophic thaumarchaeal communities in environmental samples

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA;

EID: 79954572877     PISSN: None     EISSN: 17582229     Source Type: Journal    
DOI: 10.1111/j.1758-2229.2010.00217.x     Document Type: Article
Times cited : (19)

References (51)
  • 1
    • 57649114800 scopus 로고    scopus 로고
    • Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic
    • Agogué, H., Brinke, M., Dinasquet, J., and Herndl, G.J. (2008) Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic. Nature 456: 788-791.
    • (2008) Nature , vol.456 , pp. 788-791
    • Agogué, H.1    Brinke, M.2    Dinasquet, J.3    Herndl, G.J.4
  • 2
    • 0036682224 scopus 로고    scopus 로고
    • PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database
    • Ashelford, K.E., Weightman, A.J., and Fry, J.C. (2002) PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res 30: 3481-3489.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3481-3489
    • Ashelford, K.E.1    Weightman, A.J.2    Fry, J.C.3
  • 3
    • 42049122119 scopus 로고    scopus 로고
    • Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California
    • Beman, J.M., Popp, B.N., and Francis, C.A. (2008) Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. ISME J 2: 429-441.
    • (2008) ISME J , vol.2 , pp. 429-441
    • Beman, J.M.1    Popp, B.N.2    Francis, C.A.3
  • 4
    • 37249052742 scopus 로고    scopus 로고
    • A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in archaea
    • Berg, I.A., Kockelkorn, D., Buckel, W., and Fuchs, G. (2007) A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in archaea. Science 318: 1782-1786.
    • (2007) Science , vol.318 , pp. 1782-1786
    • Berg, I.A.1    Kockelkorn, D.2    Buckel, W.3    Fuchs, G.4
  • 5
    • 47749152557 scopus 로고    scopus 로고
    • Response to comment on 'A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in archaea'
    • Berg, I.A., Kockelkorn, D., Buckel, W., and Fuchs, G. (2008) Response to comment on 'A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in archaea'. Science 321: 342c.
    • (2008) Science , vol.321
    • Berg, I.A.1    Kockelkorn, D.2    Buckel, W.3    Fuchs, G.4
  • 7
    • 39149118031 scopus 로고    scopus 로고
    • Mesophilic crenarchaeota: proposal for a third phylum, the Thaumarchaeota
    • Brochier-Armanet, C., Boussau, B., Gribaldo, S., and Forterre, P. (2008) Mesophilic crenarchaeota: proposal for a third phylum, the Thaumarchaeota. Nat Rev Microbiol 6: 245-252.
    • (2008) Nat Rev Microbiol , vol.6 , pp. 245-252
    • Brochier-Armanet, C.1    Boussau, B.2    Gribaldo, S.3    Forterre, P.4
  • 8
    • 35948999268 scopus 로고    scopus 로고
    • Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia
    • Caffrey, J.M., Bano, N., Kalanetra, K., and Hollibaugh, J.T. (2007) Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia. ISME J 1: 660-662.
    • (2007) ISME J , vol.1 , pp. 660-662
    • Caffrey, J.M.1    Bano, N.2    Kalanetra, K.3    Hollibaugh, J.T.4
  • 9
    • 18444372956 scopus 로고    scopus 로고
    • Nested PCR-denaturing gradient gel electrophoresis approach to determine the diversity of sulfate-reducing bacteria in complex microbial communities
    • Dar, S.A., Kuenen, J.G., and Muyzer, G. (2005) Nested PCR-denaturing gradient gel electrophoresis approach to determine the diversity of sulfate-reducing bacteria in complex microbial communities. Appl Environ Microbiol 71: 2325-2330.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 2325-2330
    • Dar, S.A.1    Kuenen, J.G.2    Muyzer, G.3
  • 10
    • 38549131184 scopus 로고    scopus 로고
    • Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol
    • De la Torre, J.R., Walker, C.B., Ingalls, A.E., Könneke, M., and Stahl, D.A. (2008) Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol 10: 810-818.
    • (2008) Environ Microbiol , vol.10 , pp. 810-818
    • De la Torre, J.R.1    Walker, C.B.2    Ingalls, A.E.3    Könneke, M.4    Stahl, D.A.5
  • 11
    • 47749111672 scopus 로고    scopus 로고
    • Comment on 'A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in archaea'
    • Ettema, T.J.G., and Andersson, S.G.E. (2008) Comment on 'A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in archaea'. Science 321: 342b.
    • (2008) Science , vol.321
    • Ettema, T.J.G.1    Andersson, S.G.E.2
  • 12
    • 0000122573 scopus 로고
    • PHYLIP - phylogeny inference package (version 3.2)
    • Felsenstein, J. (1989) PHYLIP - phylogeny inference package (version 3.2). Cladistics 5: 164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 13
    • 26844541457 scopus 로고    scopus 로고
    • Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean
    • Francis, C.A., Roberts, K.J., Beman, J.M., Santoro, A.E., and Oakley, B.B. (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
  • 14
    • 0034468557 scopus 로고    scopus 로고
    • Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition
    • Griffiths, R.I., Whiteley, A.S., O'Donnell, A.G., and Bailey, M.J. (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microbiol 66: 5488-5491.
    • (2000) Appl Environ Microbiol , vol.66 , pp. 5488-5491
    • Griffiths, R.I.1    Whiteley, A.S.2    O'Donnell, A.G.3    Bailey, M.J.4
  • 15
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon, S., and Gascuel, O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
    • (2003) Syst Biol , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 16
    • 0002051540 scopus 로고    scopus 로고
    • BioEdit: a user-friendly tbiological sequence alignment editor and analysis program for Windows 95/98/NT
    • Hall, T.A. (1999) BioEdit: a user-friendly tbiological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
    • (1999) Nucleic Acids Symp Ser , vol.41 , pp. 95-98
    • Hall, T.A.1
  • 18
    • 33646260901 scopus 로고    scopus 로고
    • Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota
    • Hallam, S.J., Mincer, T.J., Schleper, C., Preston, C.M., Roberts, K., Richardson, P.M., and DeLong, E.F. (2006b) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 4: 520-536.
    • (2006) PLoS Biol , vol.4 , pp. 520-536
    • 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
  • 21
    • 45549103517 scopus 로고    scopus 로고
    • A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis
    • Huber, H., Gallenberger, M., Jahn, U., Eylert, E., Berg, I.A., Kockelkorn, D., etal. (2008) A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis. Proc Natl Acad Sci USA 105: 7851-7856.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 7851-7856
    • Huber, H.1    Gallenberger, M.2    Jahn, U.3    Eylert, E.4    Berg, I.A.5    Kockelkorn, D.6
  • 22
    • 0018159772 scopus 로고
    • Inhibition by acetylene of ammonia oxidation in Nitrosomonas europaea
    • Hynes, R.K., and Knowles, R. (1978) Inhibition by acetylene of ammonia oxidation in Nitrosomonas europaea. FEMS Microbiol Lett 4: 319-321.
    • (1978) FEMS Microbiol Lett , vol.4 , pp. 319-321
    • Hynes, R.K.1    Knowles, R.2
  • 23
    • 0019982491 scopus 로고
    • Effect of acetylene on autotrophic and heterotrophic nitrification
    • Hynes, R.K., and Knowles, R. (1982) Effect of acetylene on autotrophic and heterotrophic nitrification. Can J Microbiol 28: 334-340.
    • (1982) Can J Microbiol , vol.28 , pp. 334-340
    • Hynes, R.K.1    Knowles, R.2
  • 25
    • 67649939034 scopus 로고    scopus 로고
    • Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil
    • Jia, Z., and Conrad, R. (2009) Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol 11: 1658-1671.
    • (2009) Environ Microbiol , vol.11 , pp. 1658-1671
    • Jia, Z.1    Conrad, R.2
  • 26
    • 0035945618 scopus 로고    scopus 로고
    • Archaeal dominance in the mesopelagic zone of the Pacific Ocean
    • Karner, M.B., DeLong, E.F., and Karl, D.M. (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
  • 27
    • 0027075258 scopus 로고
    • Leaching of genetically modified Pseudomonas fluorescens through organic soils: influence of temperature, soil pH, and roots
    • Kemp, J.S., Paterson, E., Gammack, S.M., Cresser, M.S., and Killham, K. (1992) Leaching of genetically modified Pseudomonas fluorescens through organic soils: influence of temperature, soil pH, and roots. Biol Fertil Soils 13: 218-224.
    • (1992) Biol Fertil Soils , vol.13 , pp. 218-224
    • Kemp, J.S.1    Paterson, E.2    Gammack, S.M.3    Cresser, M.S.4    Killham, K.5
  • 29
    • 53849115701 scopus 로고    scopus 로고
    • Genomic patterns of recombination, clonal divergence and environment in marine microbial populations
    • Konstantinidis, K.T., and DeLong, E.F. (2008) Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. ISME J 2: 1052-1065.
    • (2008) ISME J , vol.2 , pp. 1052-1065
    • Konstantinidis, K.T.1    DeLong, E.F.2
  • 31
    • 70449090074 scopus 로고    scopus 로고
    • Soil pH regulates the abundance and diversity of Group 1.1c Crenarchaeota
    • Lehtovirta, L.E., Prosser, J.I., and Nicol, G.W. (2009) Soil pH regulates the abundance and diversity of Group 1.1c Crenarchaeota. FEMS Microbiol Ecol 70: 367-376.
    • (2009) FEMS Microbiol Ecol , vol.70 , pp. 367-376
    • Lehtovirta, L.E.1    Prosser, J.I.2    Nicol, G.W.3
  • 32
    • 33747479446 scopus 로고    scopus 로고
    • Archaea predominate among ammonia-oxidising prokaryotes in soils
    • Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G.W., etal. (2006) Archaea predominate among ammonia-oxidising prokaryotes in soils. Nature 442: 806-809.
    • (2006) Nature , vol.442 , pp. 806-809
    • Leininger, S.1    Urich, T.2    Schloter, M.3    Schwark, L.4    Qi, J.5    Nicol, G.W.6
  • 33
    • 8144230590 scopus 로고    scopus 로고
    • Crystal structure of 4-hydroxybutyryl-Coa dehydratase: radical catalysis involving a [4Fe-4S] cluster and flavin
    • Martins, B.M., Dobbek, H., Çinkaya, I., Buckel, W., and Messerschmidt, A. (2004) Crystal structure of 4-hydroxybutyryl-Coa dehydratase: radical catalysis involving a [4Fe-4S] cluster and flavin. Proc Natl Acad Sci USA 101: 15645-15649.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 15645-15649
    • Martins, B.M.1    Dobbek, H.2    Çinkaya, I.3    Buckel, W.4    Messerschmidt, A.5
  • 34
    • 0027460328 scopus 로고
    • Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
    • Muyzer, G., De Waal, E.C., and Uitterlinden, A.G. (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
    • (1993) Appl Environ Microbiol , vol.59 , pp. 695-700
    • Muyzer, G.1    De Waal, E.C.2    Uitterlinden, A.G.3
  • 35
    • 33646497904 scopus 로고    scopus 로고
    • Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle?
    • Nicol, G.W., and Schleper, C. (2006) Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle? Trends Microbiol 14: 207-212.
    • (2006) Trends Microbiol , vol.14 , pp. 207-212
    • Nicol, G.W.1    Schleper, C.2
  • 36
    • 14344252220 scopus 로고    scopus 로고
    • Primary succession of soil Crenarchaeota across a receding glacier foreland
    • Nicol, G.W., Tscherko, D., Embley, T.M., and Prosser, J.I. (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
  • 37
    • 52949137846 scopus 로고    scopus 로고
    • The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidising archaea and bacteria
    • Nicol, G.W., Leininger, S., Schleper, C., and Prosser, J.I. (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidising archaea and bacteria. Environ Microbiol 10: 2966-2978.
    • (2008) Environ Microbiol , vol.10 , pp. 2966-2978
    • Nicol, G.W.1    Leininger, S.2    Schleper, C.3    Prosser, J.I.4
  • 38
    • 0036242855 scopus 로고    scopus 로고
    • Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria
    • Nicolaisen, M.H., and Ramsing, N.B. (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
  • 39
    • 0042853314 scopus 로고    scopus 로고
    • Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S rRNA surveys and real time PCR
    • Ochsenreiter, T., Selezi, D., Quaiser, A., Bonch-Osmolovskaya, L., and Schleper, C. (2003) Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S rRNA 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
  • 40
    • 69949127231 scopus 로고    scopus 로고
    • Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene
    • Offre, P., Prosser, J.I., and Nicol, G.W. (2009) Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene. FEMS Microbiol Ecol 70: 99-108.
    • (2009) FEMS Microbiol Ecol , vol.70 , pp. 99-108
    • Offre, P.1    Prosser, J.I.2    Nicol, G.W.3
  • 41
    • 52949113790 scopus 로고    scopus 로고
    • Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment
    • Prosser, J.I., and Nicol, G.W. (2008) Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ Microbiol 10: 2931-2941.
    • (2008) Environ Microbiol , vol.10 , pp. 2931-2941
    • Prosser, J.I.1    Nicol, G.W.2
  • 42
    • 0033990048 scopus 로고    scopus 로고
    • Primer3 on the WWW for general users and for biologists programmers
    • Misener, S., and Krawetz, S. (eds). Totowa, NJ: Humana Press
    • Rozen, S., and Skaletsky, H. (2000) Primer3 on the WWW for general users and for biologists programmers. In Methods in Molecular Biology. vol. 132. Misener, S., and Krawetz, S. (eds). Totowa, NJ: Humana Press, pp. 365-386.
    • (2000) Methods in Molecular Biology , vol.132 , pp. 365-386
    • Rozen, S.1    Skaletsky, H.2
  • 43
    • 58549087182 scopus 로고    scopus 로고
    • Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils
    • Schauss, K., Focks, A., Leininger, S., Kotzerke, A., Heuer, H., Thiele-Bruhn, S., etal. (2009) Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils. Environ Microbiol 11: 446-456.
    • (2009) Environ Microbiol , vol.11 , pp. 446-456
    • Schauss, K.1    Focks, A.2    Leininger, S.3    Kotzerke, A.4    Heuer, H.5    Thiele-Bruhn, S.6
  • 44
    • 0000023099 scopus 로고
    • Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes
    • Sheffield, V.C., Cox, D.R., Lerman, L.S., and Myers, R.M. (1989) Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc Natl Acad Sci USA 86: 232-236.
    • (1989) Proc Natl Acad Sci USA , vol.86 , pp. 232-236
    • Sheffield, V.C.1    Cox, D.R.2    Lerman, L.S.3    Myers, R.M.4
  • 45
    • 77955273494 scopus 로고    scopus 로고
    • Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota
    • Spang, A., Hatzenpichler, R., Brochier-Armanet, C., Rattei, T., Tischler, P., Spieck, E., etal. (2010) Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol 18: 331-340.
    • (2010) Trends Microbiol , vol.18 , pp. 331-340
    • Spang, A.1    Hatzenpichler, R.2    Brochier-Armanet, C.3    Rattei, T.4    Tischler, P.5    Spieck, E.6
  • 46
    • 37249062588 scopus 로고    scopus 로고
    • A fifth pathway of carbon fixation
    • Thauer, R.K. (2007) A fifth pathway of carbon fixation. Science 318: 1732-1733.
    • (2007) Science , vol.318 , pp. 1732-1733
    • Thauer, R.K.1
  • 47
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994) CLUSTAL W: improving the the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 48
    • 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, A.H., Leininger, S., Kletzin, A., Schuster, S.C., Klenk, H.-P., and 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
    • 77952739182 scopus 로고    scopus 로고
    • Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea
    • Walker, C.B., Torre, J.R., Klotz, M.G., Urakawa, H., Pinel, N., Arp, D.J., etal. (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci USA 107: 8818-8823.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 8818-8823
    • Walker, C.B.1    Torre, J.R.2    Klotz, M.G.3    Urakawa, H.4    Pinel, N.5    Arp, D.J.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.