메뉴 건너뛰기




Volumn 53, Issue 3, 2007, Pages 456-470

A nifH-based oligonucleotide microarray for functional diagnostics of nitrogen-fixing microorganisms

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; NITROGENASE REDUCTASE; OXIDOREDUCTASE; UNCLASSIFIED DRUG;

EID: 34248172325     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-006-9126-9     Document Type: Conference Paper
Times cited : (42)

References (46)
  • 1
    • 2942527326 scopus 로고    scopus 로고
    • Oligonucleotide microarrays in microbial diagnostics
    • Bodrossy, L, Sessitsch, A (2004) Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol 7: 246-255
    • (2004) Curr Opin Microbiol , vol.7 , pp. 246-255
    • Bodrossy, L.1    Sessitsch, A.2
  • 4
    • 51249169259 scopus 로고
    • A simple and efficient method for isolating RNA from pine trees
    • Chang, S, Puryear, J, Cairney, J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Reporter 11: 113-116
    • (1993) Plant Mol Biol Reporter , vol.11 , pp. 113-116
    • Chang, S.1    Puryear, J.2    Cairney, J.3
  • 5
    • 0027988426 scopus 로고
    • Cloning, DNA sequencing, and characterization of a nifD-homologous gene from the archaeon Methanosarcina barkeri 227 which resembles nifD1 from the eubacterium Clostridium pasteurianum
    • Chien, YT, Zinder, SH (1994) Cloning, DNA sequencing, and characterization of a nifD-homologous gene from the archaeon Methanosarcina barkeri 227 which resembles nifD1 from the eubacterium Clostridium pasteurianum. J Bacteriol 176: 6590-6598
    • (1994) J Bacteriol , vol.176 , pp. 6590-6598
    • Chien, Y.T.1    Zinder, S.H.2
  • 6
    • 0141564886 scopus 로고    scopus 로고
    • Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities
    • Denef, VJ, Park, J, Rodrigues, JL, Tsoi, TV, Hashsham, SA, Tiedje, JM (2003) Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ Microbiol 5: 933-943
    • (2003) Environ Microbiol , vol.5 , pp. 933-943
    • Denef, V.J.1    Park, J.2    Rodrigues, J.L.3    Tsoi, T.V.4    Hashsham, S.A.5    Tiedje, J.M.6
  • 7
    • 0034548840 scopus 로고    scopus 로고
    • Preferential occurrence of diazotrophic endophytes, Azoarcus spp., in wild rice species and land races of Oryza sativa in comparison with modern races
    • Engelhard, M, Hurek, T, Reinhold-Hurek, B (2000) Preferential occurrence of diazotrophic endophytes, Azoarcus spp., in wild rice species and land races of Oryza sativa in comparison with modern races. Environ Microbiol 2: 131-141
    • (2000) Environ Microbiol , vol.2 , pp. 131-141
    • Engelhard, M.1    Hurek, T.2    Reinhold-Hurek, B.3
  • 9
    • 0036007438 scopus 로고    scopus 로고
    • Microarrays in ecology and evolution: A preview
    • Gibson, G (2002) Microarrays in ecology and evolution: A preview. Mol Ecol 11: 17-24
    • (2002) Mol Ecol , vol.11 , pp. 17-24
    • Gibson, G.1
  • 10
    • 27444441081 scopus 로고    scopus 로고
    • 2-fixing microbes associated with graminaceous plants
    • Werner, D, Newton, WE Eds, Kluwer Academic Publishers, Dordrecht, The Netherlands, pp
    • 2-fixing microbes associated with graminaceous plants. In: Werner, D, Newton, WE (Eds.) Agriculture, Forestry, Ecology and the Environment. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp. 173-198
    • (2005) Agriculture, Forestry, Ecology and the Environment , pp. 173-198
    • Hurek, T.1    Reinhold-Hurek, B.2
  • 11
    • 0030814221 scopus 로고    scopus 로고
    • Divergence in nitrogenases of Azoarcus spp., Proteobacteria of the β-subclass
    • Hurek, T, Egener, T, Reinhold-Hurek, B (1997) Divergence in nitrogenases of Azoarcus spp., Proteobacteria of the β-subclass. J Bacteriol 179: 4172-4178
    • (1997) J Bacteriol , vol.179 , pp. 4172-4178
    • Hurek, T.1    Egener, T.2    Reinhold-Hurek, B.3
  • 12
    • 0027430312 scopus 로고
    • 16S rRNA-targeted polymerase chain reaction and oligonucleotide hybridization to screen for Azoarcus spp., grass-associated diazotrophs
    • Hurek, T, Burggraf, S, Woese, CR, Reinhold-Hurek, B (1993) 16S rRNA-targeted polymerase chain reaction and oligonucleotide hybridization to screen for Azoarcus spp., grass-associated diazotrophs. Appl Environ Microbiol 59: 3816-3824
    • (1993) Appl Environ Microbiol , vol.59 , pp. 3816-3824
    • Hurek, T.1    Burggraf, S.2    Woese, C.R.3    Reinhold-Hurek, B.4
  • 13
    • 0035987085 scopus 로고    scopus 로고
    • Azoarcus grass endophytes contribute fixed nitrogen to the plant in an unculturable state
    • Hurek, T, Handley, L, Reinhold-Hurek, B, Piché, Y (2002) Azoarcus grass endophytes contribute fixed nitrogen to the plant in an unculturable state. Mol Plant-Microbe Interact 15: 233-242
    • (2002) Mol Plant-Microbe Interact , vol.15 , pp. 233-242
    • Hurek, T.1    Handley, L.2    Reinhold-Hurek, B.3    Piché, Y.4
  • 14
    • 1642321120 scopus 로고    scopus 로고
    • Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray
    • Jenkins, BD, Steward, GF, Short, SM, Ward, BB, Zehr, JP (2004) Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray. Appl Environ Microbiol 70: 1767-1776
    • (2004) Appl Environ Microbiol , vol.70 , pp. 1767-1776
    • Jenkins, B.D.1    Steward, G.F.2    Short, S.M.3    Ward, B.B.4    Zehr, J.P.5
  • 15
    • 27444441768 scopus 로고    scopus 로고
    • Influence of different Oryza cultivars on expression of nifH gene pools in roots of rice
    • Knauth, S, Hurek, T, Brar, D, Reinhold-Hurek, B (2005) Influence of different Oryza cultivars on expression of nifH gene pools in roots of rice. Environ Microbiol 7: 1725-1733
    • (2005) Environ Microbiol , vol.7 , pp. 1725-1733
    • Knauth, S.1    Hurek, T.2    Brar, D.3    Reinhold-Hurek, B.4
  • 16
    • 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
  • 17
    • 0036795787 scopus 로고    scopus 로고
    • Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment
    • Loy, A, Lehner, A, Lee, N, Adamczyk, J, Meier, H, Ernst, J et al. (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68: 5064-5081
    • (2002) Appl Environ Microbiol , vol.68 , pp. 5064-5081
    • Loy, A.1    Lehner, A.2    Lee, N.3    Adamczyk, J.4    Meier, H.5    Ernst, J.6
  • 20
    • 0033426953 scopus 로고    scopus 로고
    • Evaluation of single-stranded nucleic acids as carriers in the DNA-directed assembly of macromolecules
    • Niemeyer, CM, Boldt, L, Ceyhan, B, Blohm, D (1999) Evaluation of single-stranded nucleic acids as carriers in the DNA-directed assembly of macromolecules. J Biomol Struct Dyn 17: 527-538
    • (1999) J Biomol Struct Dyn , vol.17 , pp. 527-538
    • Niemeyer, C.M.1    Boldt, L.2    Ceyhan, B.3    Blohm, D.4
  • 21
    • 0032755033 scopus 로고    scopus 로고
    • Culture-independent characterization of a gene responsible for nitrogen fixation in the symbiotic microbial community in the gut of the termite Neotermes koshunensis
    • Noda, S, Ohkuma, M, Usami, R, Horikoshi, K, Kudo, T (1999) Culture-independent characterization of a gene responsible for nitrogen fixation in the symbiotic microbial community in the gut of the termite Neotermes koshunensis. Appl Environ Microbiol 65: 4935-4942
    • (1999) Appl Environ Microbiol , vol.65 , pp. 4935-4942
    • Noda, S.1    Ohkuma, M.2    Usami, R.3    Horikoshi, K.4    Kudo, T.5
  • 22
    • 0032748070 scopus 로고    scopus 로고
    • Phylogenetic diversity of nitrogen fixation genes in the symbiotic microbial community in the gut of diverse termites
    • Ohkuma, M, Noda, S, Kudo, T (1999) Phylogenetic diversity of nitrogen fixation genes in the symbiotic microbial community in the gut of diverse termites. Appl Environ Microbiol 65: 4926-4934
    • (1999) Appl Environ Microbiol , vol.65 , pp. 4926-4934
    • Ohkuma, M.1    Noda, S.2    Kudo, T.3
  • 23
    • 0037335692 scopus 로고    scopus 로고
    • Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes
    • Peplies, J, Glöckner, FO, Amann, R (2003) Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl Environ Microbiol 69: 1397-1407
    • (2003) Appl Environ Microbiol , vol.69 , pp. 1397-1407
    • Peplies, J.1    Glöckner, F.O.2    Amann, R.3
  • 25
    • 0034023558 scopus 로고    scopus 로고
    • Reassessment of the taxonomic structure of the diazotrophic genus Azoarcus sensu lato and description of three new genera and species, Azovibrio restrictus gen. nov., sp. nov., Azospira oryzae gen. nov., sp. nov, and Azonexus funguphilus gen. nov., sp. nov
    • Reinhold-Hurek, B, Hurek, T (2000) Reassessment of the taxonomic structure of the diazotrophic genus Azoarcus sensu lato and description of three new genera and species, Azovibrio restrictus gen. nov., sp. nov., Azospira oryzae gen. nov., sp. nov, and Azonexus funguphilus gen. nov., sp. nov. Int J Syst Evol Microbiol 50: 649-659
    • (2000) Int J Syst Evol Microbiol , vol.50 , pp. 649-659
    • Reinhold-Hurek, B.1    Hurek, T.2
  • 26
    • 0027169610 scopus 로고
    • Azoarcus gen. nov., nitrogen-fixing proteobacteria associated with roots of Kallar grass (Leptochloa fusca (L.) Kunth) and description of two species Azoarcus indigens sp. nov. and Azoarcus communis sp. nov
    • Reinhold-Hurek, B, Hurek, T, Gillis, M, Hoste, B, Vancanneyt, M, Kersters, K, De Ley, J (1993) Azoarcus gen. nov., nitrogen-fixing proteobacteria associated with roots of Kallar grass (Leptochloa fusca (L.) Kunth) and description of two species Azoarcus indigens sp. nov. and Azoarcus communis sp. nov. Int J Syst Bacteriol 43: 574-584
    • (1993) Int J Syst Bacteriol , vol.43 , pp. 574-584
    • Reinhold-Hurek, B.1    Hurek, T.2    Gillis, M.3    Hoste, B.4    Vancanneyt, M.5    Kersters, K.6    De Ley, J.7
  • 28
    • 0033990048 scopus 로고    scopus 로고
    • Primer3 on the WWW for general users and for biologist programmers
    • Rozen, S, Skaletsky, H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386
    • (2000) Methods Mol Biol , vol.132 , pp. 365-386
    • Rozen, S.1    Skaletsky, H.2
  • 29
    • 2442766122 scopus 로고    scopus 로고
    • Spreadsheet software for thermodynamic melting point prediction of oligonucleotide hybridization with and without mismatches
    • Schütz, E, von Ahsen, N (1999) Spreadsheet software for thermodynamic melting point prediction of oligonucleotide hybridization with and without mismatches. BioTechniques 27: 1218-1222
    • (1999) BioTechniques , vol.27 , pp. 1218-1222
    • Schütz, E.1    von Ahsen, N.2
  • 30
    • 0030862620 scopus 로고    scopus 로고
    • Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays
    • Shchepinov, MS, Case-Green, SC, Southern, EM (1997) Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res 25: 1155-1161
    • (1997) Nucleic Acids Res , vol.25 , pp. 1155-1161
    • Shchepinov, M.S.1    Case-Green, S.C.2    Southern, E.M.3
  • 32
    • 84984934354 scopus 로고    scopus 로고
    • Molecular interactions on microarrays
    • Southern, E, Mir, K, Shchepinov, M (1999) Molecular interactions on microarrays. Nat Genet 21: 5-9
    • (1999) Nat Genet , vol.21 , pp. 5-9
    • Southern, E.1    Mir, K.2    Shchepinov, M.3
  • 33
    • 1642330746 scopus 로고    scopus 로고
    • Development and testing of a DNA macroarray to assess nitrogenase (nifH) gene diversity
    • Steward, GF, Jenkins, BD, Ward, BB, Zehr, JP (2004) Development and testing of a DNA macroarray to assess nitrogenase (nifH) gene diversity. Appl Environ Microbiol 70: 1455-1465
    • (2004) Appl Environ Microbiol , vol.70 , pp. 1455-1465
    • Steward, G.F.1    Jenkins, B.D.2    Ward, B.B.3    Zehr, J.P.4
  • 34
    • 0034687124 scopus 로고    scopus 로고
    • Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes
    • Sugimoto, N, Nakano, M, Nakano, S (2000) Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes. Biochemistry 39: 11270-11281
    • (2000) Biochemistry , vol.39 , pp. 11270-11281
    • Sugimoto, N.1    Nakano, M.2    Nakano, S.3
  • 35
    • 0141788244 scopus 로고    scopus 로고
    • Effect of N-fertilization, plant genotype and environmental conditions on nifH gene pools in roots of rice
    • Tan, Z, Hurek, T, Reinhold-Hurek, B (2003) Effect of N-fertilization, plant genotype and environmental conditions on nifH gene pools in roots of rice. Environ Microbiol 5: 1009-1015
    • (2003) Environ Microbiol , vol.5 , pp. 1009-1015
    • Tan, Z.1    Hurek, T.2    Reinhold-Hurek, B.3
  • 36
    • 0037316061 scopus 로고    scopus 로고
    • Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment
    • Taroncher-Oldenburg, G, Griner, EM, Francis, CA, Ward, BB (2003) Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol 69: 1159-1171
    • (2003) Appl Environ Microbiol , vol.69 , pp. 1159-1171
    • Taroncher-Oldenburg, G.1    Griner, E.M.2    Francis, C.A.3    Ward, B.B.4
  • 37
    • 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
  • 38
    • 0036135264 scopus 로고    scopus 로고
    • Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses
    • Urakawa, H, Noble, PA, El Fantroussi, S, Kelly, JJ, Stahl, DA (2002) Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses. Appl Environ Microbiol 68: 235-244
    • (2002) Appl Environ Microbiol , vol.68 , pp. 235-244
    • Urakawa, H.1    Noble, P.A.2    El Fantroussi, S.3    Kelly, J.J.4    Stahl, D.A.5
  • 40
    • 0033916012 scopus 로고    scopus 로고
    • Expression of nifH genes in natural microbial assemblages in Lake George, New York, detected by reverse transcriptase PCR
    • Zani, S, Mellon, MT, Collier, JL, Zehr, JP (2000) Expression of nifH genes in natural microbial assemblages in Lake George, New York, detected by reverse transcriptase PCR. Appl Environ Microbiol 66: 3119-3124
    • (2000) Appl Environ Microbiol , vol.66 , pp. 3119-3124
    • Zani, S.1    Mellon, M.T.2    Collier, J.L.3    Zehr, J.P.4
  • 41
    • 0024746373 scopus 로고
    • Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii
    • Zehr, JP, McReynolds, LA (1989) Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol 55: 2522-2526
    • (1989) Appl Environ Microbiol , vol.55 , pp. 2522-2526
    • Zehr, J.P.1    McReynolds, L.A.2
  • 42
    • 0030303003 scopus 로고    scopus 로고
    • Problems and promises of assaying the genetic potential for nitrogen fixation in the marine environment
    • Zehr, JP, Capone, DG (1996) Problems and promises of assaying the genetic potential for nitrogen fixation in the marine environment. Microb Ecol 32: 263-281
    • (1996) Microb Ecol , vol.32 , pp. 263-281
    • Zehr, J.P.1    Capone, D.G.2
  • 43
    • 0031664504 scopus 로고    scopus 로고
    • New nitrogen-fixing microorganisms detected in oligotrophic oceans by amplification of nitrogenase (nifH) genes
    • Zehr, JP, Mellon, MT, Zani, S (1998) New nitrogen-fixing microorganisms detected in oligotrophic oceans by amplification of nitrogenase (nifH) genes. Appl Environ Microbiol 64: 3444-3450
    • (1998) Appl Environ Microbiol , vol.64 , pp. 3444-3450
    • Zehr, J.P.1    Mellon, M.T.2    Zani, S.3
  • 44
    • 0038234799 scopus 로고    scopus 로고
    • Nitrogenase gene diversity and microbial community structure: A cross-system comparison
    • Zehr, JP, Jenkins, BD, Short, SM, Steward, GF (2003) Nitrogenase gene diversity and microbial community structure: A cross-system comparison. Environ Microbiol 5: 539-554
    • (2003) Environ Microbiol , vol.5 , pp. 539-554
    • Zehr, J.P.1    Jenkins, B.D.2    Short, S.M.3    Steward, G.F.4
  • 45
    • 28544450415 scopus 로고    scopus 로고
    • Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridisations
    • Zhang, L, Hurek, T, Reinhold-Hurek, B (2005) Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridisations. Nucleic Acids Res 33: e166
    • (2005) Nucleic Acids Res , vol.33
    • Zhang, L.1    Hurek, T.2    Reinhold-Hurek, B.3
  • 46
    • 0037772204 scopus 로고    scopus 로고
    • Microarrays for bacterial detection and microbial community analysis
    • Zhou, JZ (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6: 288-294
    • (2003) Curr Opin Microbiol , vol.6 , pp. 288-294
    • Zhou, J.Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.