메뉴 건너뛰기




Volumn 2014, Issue , 2014, Pages

A comprehensive aligned nifH gene database: A multipurpose tool for studies of nitrogen-fixing bacteria

Author keywords

[No Author keywords available]

Indexed keywords

NITROGENASE REDUCTASE; OXIDOREDUCTASE; RNA 16S;

EID: 84906556405     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bau001     Document Type: Article
Times cited : (204)

References (46)
  • 1
    • 0030612951 scopus 로고    scopus 로고
    • Human alteration of the global nitrogen cycle: Sources and consequences
    • Vitousek, P.M., Aber, J.D., Howarth, R.W. et al. (1997) Human alteration of the global nitrogen cycle: sources and consequences. Ecol. Appl., 7, 737-750.
    • (1997) Ecol. Appl. , vol.7 , pp. 737-750
    • Vitousek, P.M.1    Aber, J.D.2    Howarth, R.W.3
  • 3
    • 0027079485 scopus 로고
    • Biological nitrogen fixation: Investments, expectations and actual contributions to agriculture
    • Peoples, M.B. and Craswell, E.T. (1992) Biological nitrogen fixation: investments, expectations and actual contributions to agriculture. Plant Soil, 141, 13-39.
    • (1992) Plant Soil , vol.141 , pp. 13-39
    • Peoples, M.B.1    Craswell, E.T.2
  • 4
    • 0035019301 scopus 로고    scopus 로고
    • The current and potential contribution of asymbiotic nitrogen fixation to nitrogen requirements on farms: A review
    • Kennedy, I.R. and Islam, N. (2001) The current and potential contribution of asymbiotic nitrogen fixation to nitrogen requirements on farms: a review. Aust. J. Exp. Agric., 41, 447-457.
    • (2001) Aust. J. Exp. Agric. , vol.41 , pp. 447-457
    • Kennedy, I.R.1    Islam, N.2
  • 6
  • 7
    • 79955742866 scopus 로고    scopus 로고
    • Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria
    • Farnelid, H., Andersson, A.F., Bertilsson, S. et al. (2011) Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria. Plos One, 6, e19223.
    • (2011) Plos One , vol.6
    • Farnelid, H.1    Andersson, A.F.2    Bertilsson, S.3
  • 8
    • 29144514574 scopus 로고    scopus 로고
    • Diazotrophic diversity and distribution in the tropical and subtropical Atlantic ocean
    • Langlois, R.J., LaRoche, J. and Raab, P.A. (2005) Diazotrophic diversity and distribution in the tropical and subtropical Atlantic ocean. Appl. Environ. Microbiol., 71, 7910-7919.
    • (2005) Appl. Environ. Microbiol. , vol.71 , pp. 7910-7919
    • Langlois, R.J.1    LaRoche, J.2    Raab, P.A.3
  • 9
    • 0031664504 scopus 로고    scopus 로고
    • New nitrogen-fixing microorganisms detected in oligotrophic oceans by amplification of nitrogenase (nifH) genes
    • Zehr, J.P., Mellon, M.T. and 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
  • 10
    • 37749001498 scopus 로고    scopus 로고
    • Biodiversity of diazotrophic bacteria within the soil, root and stem of field-grown maize
    • Roesch, L.F.W., Camargo, F.A.O., Bento, F.M. et al. (2008) Biodiversity of diazotrophic bacteria within the soil, root and stem of field-grown maize. Plant Soil, 302, 91-104.
    • (2008) Plant Soil , vol.302 , pp. 91-104
    • Roesch, L.F.W.1    Camargo, F.A.O.2    Bento, F.M.3
  • 11
    • 33745491299 scopus 로고    scopus 로고
    • Distribution of extensive nifH gene diversity across physical soil microenvironments
    • Izquierdo, J.A. and Nusslein, K. (2006) Distribution of extensive nifH gene diversity across physical soil microenvironments. Microb. Ecol., 51, 441-452.
    • (2006) Microb. Ecol. , vol.51 , pp. 441-452
    • Izquierdo, J.A.1    Nusslein, K.2
  • 12
    • 0036330611 scopus 로고    scopus 로고
    • Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil
    • Rosch, C., Mergel, A. and Bothe, H. (2002) Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. Appl. Environ. Microbiol., 68, 3818-3829.
    • (2002) Appl. Environ. Microbiol. , vol.68 , pp. 3818-3829
    • Rosch, C.1    Mergel, A.2    Bothe, H.3
  • 13
    • 0346195660 scopus 로고    scopus 로고
    • Phylogenetic diversity of nitrogenase (nifH) genes in deep-sea and hydrothermal vent environments of the juan de fuca ridge
    • Mehta, M.P., Butterfield, D.A. and Baross, J.A. (2003) Phylogenetic diversity of nitrogenase (nifH) genes in deep-sea and hydrothermal vent environments of the Juan de Fuca ridge. Appl. Environ. Microbiol., 69, 960-970.
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 960-970
    • Mehta, M.P.1    Butterfield, D.A.2    Baross, J.A.3
  • 14
    • 0038234799 scopus 로고    scopus 로고
    • Nitrogenase gene diversity and microbial community structure: A cross-system comparison
    • Zehr, J.P., Jenkins, B.D., Short, S.M. et al. (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
  • 15
    • 79959816953 scopus 로고    scopus 로고
    • A global census of nitrogenase diversity
    • Gaby, J.C. and Buckley, D.H. (2011) A global census of nitrogenase diversity. Environ. Microbiol., 13, 1790-1799.
    • (2011) Environ. Microbiol. , vol.13 , pp. 1790-1799
    • Gaby, J.C.1    Buckley, D.H.2
  • 16
    • 0027988426 scopus 로고
    • Cloning, DNA-sequencing, and characterization of a nifD-homologous gene from the archaeon methanosarcina barkeri-227 which resembles nifD from the eubacterium clostridium pasteurianum
    • Chien, Y.T. and Zinder, S.H. (1994) Cloning, DNA-sequencing, and characterization of a nifD-homologous gene from the archaeon methanosarcina barkeri-227 which resembles nifD 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
  • 17
    • 0038740940 scopus 로고    scopus 로고
    • Alternative nitrogenases
    • Leigh, G.J. (ed). Elsevier Science B.V. Elsevier Science B.V., Amsterdam, Netherlands
    • Masepohl, B., Schneider, K., Drepper, T. et al. (2002) Alternative nitrogenases. In: Leigh, G.J. (ed). Elsevier Science B.V., Nitrogen Fixation at the Millennium. Elsevier Science B.V., Amsterdam, Netherlands, pp. 191-222.
    • (2002) Nitrogen Fixation at the Millennium , pp. 191-222
    • Masepohl, B.1    Schneider, K.2    Drepper, T.3
  • 18
    • 0023683589 scopus 로고
    • Nucleotide sequence of regions homologous to nifH (nitrogenase fe protein) from the nitrogen-fixing archaebacteria methanococcus thermolithotrophicus and methanobacterium ivanovii: Evolutionary implications
    • Souillard, N., Magot, M., Possot, O. et al. (1988) Nucleotide sequence of regions homologous to nifH (nitrogenase fe protein) from the nitrogen-fixing archaebacteria Methanococcus thermolithotrophicus and Methanobacterium ivanovii: evolutionary implications. J. Mol. Evol., 27, 65-76.
    • (1988) J. Mol. Evol. , vol.27 , pp. 65-76
    • Souillard, N.1    Magot, M.2    Possot, O.3
  • 19
    • 35048881646 scopus 로고    scopus 로고
    • Expression and association of group IV nitrogenase nifD and nifH homologs in the non-nitrogen-fixing archaeon methanocaldococcus jannaschii
    • Staples, C.R., Lahiri, S., Raymond, J. et al. (2007) Expression and association of group IV nitrogenase nifD and nifH homologs in the non-nitrogen-fixing archaeon Methanocaldococcus jannaschii. J. Bacteriol., 189, 7392-7398.
    • (2007) J. Bacteriol. , vol.189 , pp. 7392-7398
    • Staples, C.R.1    Lahiri, S.2    Raymond, J.3
  • 20
    • 33744959925 scopus 로고    scopus 로고
    • A second nitrogenase-like enzyme for bacteriochlorophyll biosynthesis-reconstitution of chlorophyllide a reductase with purified x-protein (bchX) and yz-protein (bchY-bchZ) from rhodobacter capsulatus
    • Nomata, J., Mizoguchi, T., Tamiaki, H. et al. (2006) A second nitrogenase-like enzyme for bacteriochlorophyll biosynthesis-reconstitution of chlorophyllide a reductase with purified x-protein (bchX) and yz-protein (bchY-bchZ) from Rhodobacter capsulatus. J. Biol. Chem., 281, 15021-15028.
    • (2006) J. Biol. Chem. , vol.281 , pp. 15021-15028
    • Nomata, J.1    Mizoguchi, T.2    Tamiaki, H.3
  • 21
    • 0001916527 scopus 로고
    • The nifH-like (frxC) gene is involved in the biosynthesis of chlorophyll in the filamentous cyanobacterium plectonema boryanum
    • Fujita, Y., Takahashi, Y., Chuganji, M. et al. (1992) The nifH-like (frxC) gene is involved in the biosynthesis of chlorophyll in the filamentous cyanobacterium Plectonema boryanum. Plant. Cell. Physiol., 33, 81-92.
    • (1992) Plant. Cell. Physiol. , vol.33 , pp. 81-92
    • Fujita, Y.1    Takahashi, Y.2    Chuganji, M.3
  • 22
    • 10344228215 scopus 로고    scopus 로고
    • Status of the microbial census
    • Schloss, P.D. and Handelsman, J. (2004) Status of the microbial census. Microbiol. Rev., 68, 686-691.
    • (2004) Microbiol. Rev. , vol.68 , pp. 686-691
    • Schloss, P.D.1    Handelsman, J.2
  • 24
    • 0036181778 scopus 로고    scopus 로고
    • Exploring prokaryotic diversity in the genomic era
    • Hugenholtz, P. (2002) Exploring prokaryotic diversity in the genomic era. Genome Biol., 3, reviews0003-reviews0003.8.
    • (2002) Genome Biol. , vol.3
    • Hugenholtz, P.1
  • 25
    • 84864691243 scopus 로고    scopus 로고
    • A comprehensive evaluation of PCR primers to amplify the nifH gene of nitrogenase
    • Gaby, J.C. and Buckley, D.H. (2012) A comprehensive evaluation of PCR primers to amplify the nifH gene of nitrogenase. Plos One, 7, e42149.
    • (2012) Plos One , vol.7
    • Gaby, J.C.1    Buckley, D.H.2
  • 26
    • 13444304367 scopus 로고    scopus 로고
    • The ribosomal database project (RDP-II): Sequences and tools for high-throughput rRNA analysis
    • Cole, J.R., Chai, B., Farris, R.J. et al. (2005) The ribosomal database project (RDP-ii): sequences and tools for high-throughput rRNA analysis. Nucleic Acid Res., 33, D294-D296.
    • (2005) Nucleic Acid Res. , vol.33 , pp. D294-D296
    • Cole, J.R.1    Chai, B.2    Farris, R.J.3
  • 28
    • 79960799888 scopus 로고    scopus 로고
    • Seasonal variations in the diversity and abundance of diazotrophic communities across soils
    • Pereira e Silva, M.C., Semenov, A.V., van Elsas, J.D. et al. (2011) Seasonal variations in the diversity and abundance of diazotrophic communities across soils. FEMS Microbiol. Ecol., 77, 57-68.
    • (2011) FEMS Microbiol. Ecol. , vol.77 , pp. 57-68
    • Pereira e Silva, M.C.1    Semenov, A.V.2    Van Elsas, J.D.3
  • 29
    • 27744511084 scopus 로고    scopus 로고
    • Quantitative analyses of nitrogen cycling genes in soils
    • Wallenstein, M.D. and Vilgalys, R.J. (2005) Quantitative analyses of nitrogen cycling genes in soils. Pedobiologia, 49, 665-672.
    • (2005) Pedobiologia , vol.49 , pp. 665-672
    • Wallenstein, M.D.1    Vilgalys, R.J.2
  • 30
    • 71249111574 scopus 로고    scopus 로고
    • Diazotrophic diversity, nifH gene expression and nitrogenase activity in a rice paddy field in fujian, China
    • Martensson, L., Diez, B., Wartiainen, I. et al. (2009) Diazotrophic diversity, nifH gene expression and nitrogenase activity in a rice paddy field in Fujian, China. Plant Soil, 325, 207-218.
    • (2009) Plant Soil , vol.325 , pp. 207-218
    • Martensson, L.1    Diez, B.2    Wartiainen, I.3
  • 31
    • 78650623430 scopus 로고    scopus 로고
    • Distribution of roseobacter RCA and SAR11 lineages in the north sea and characteristics of an abundant RCA isolate
    • Giebel, H.-A., Kalhoefer, D., Lemke, A. et al. (2011) Distribution of Roseobacter RCA and SAR11 lineages in the north sea and characteristics of an abundant RCA isolate. ISME J., 5, 8-19.
    • (2011) ISME J. , vol.5 , pp. 8-19
    • Giebel, H.-A.1    Kalhoefer, D.2    Lemke, A.3
  • 32
    • 37549027613 scopus 로고    scopus 로고
    • Silva: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    • Pruesse, E., Quast, C., Knittel, K. et al. (2007) Silva: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acid Res., 35, 7188-7196.
    • (2007) Nucleic Acid Res. , vol.35 , pp. 7188-7196
    • Pruesse, E.1    Quast, C.2    Knittel, K.3
  • 33
    • 58149200948 scopus 로고    scopus 로고
    • The ribosomal database project: Improved alignments and new tools for rRNA analysis
    • Cole, J.R., Wang, Q., Cardenas, E. et al. (2009) The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acid Res., 37, D141-D145.
    • (2009) Nucleic Acid Res. , vol.37 , pp. D141-D145
    • Cole, J.R.1    Wang, Q.2    Cardenas, E.3
  • 34
    • 33746061683 scopus 로고    scopus 로고
    • Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    • DeSantis, T.Z., Hugenholtz, P., Larsen, N. et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol., 72, 5069-5072.
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 5069-5072
    • DeSantis, T.Z.1    Hugenholtz, P.2    Larsen, N.3
  • 35
    • 2542523843 scopus 로고    scopus 로고
    • ARB: A software environment for sequence data
    • Ludwig, W., Strunk, O., Westram, R. et al. (2004) ARB: A software environment for sequence data. Nucleic Acid Res., 32, 1363-1371.
    • (2004) Nucleic Acid Res. , vol.32 , pp. 1363-1371
    • Ludwig, W.1    Strunk, O.2    Westram, R.3
  • 36
    • 75549090603 scopus 로고    scopus 로고
    • The pfam protein families database
    • Finn, R.D., Mistry, J., Tate, J. et al. (2010) The pfam protein families database. Nucleic Acid Res., 38, D211-D222.
    • (2010) Nucleic Acid Res. , vol.38 , pp. D211-D222
    • Finn, R.D.1    Mistry, J.2    Tate, J.3
  • 38
    • 84965039431 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing, Vienna, Austria
    • R Development Core Team. (2012) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN: 3-900051-07-0.
    • (2012) R: A Language and Environment for Statistical Computing
  • 39
    • 77953215386 scopus 로고    scopus 로고
    • NifH expression by five groups of phototrophs compared with nitrogenase activity in coastal micro-bial mats
    • Severin, I. and Stal, L.J. (2010) NifH expression by five groups of phototrophs compared with nitrogenase activity in coastal micro-bial mats. FEMS Microbiol. Ecol., 73, 55-67.
    • (2010) FEMS Microbiol. Ecol. , vol.73 , pp. 55-67
    • Severin, I.1    Stal, L.J.2
  • 40
    • 2342661195 scopus 로고    scopus 로고
    • Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method
    • Farahi, K., Pusch, G.D., Overbeek, R. et al. (2004) Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method. J. Mol. Evol., 58, 615-631.
    • (2004) J. Mol. Evol. , vol.58 , pp. 615-631
    • Farahi, K.1    Pusch, G.D.2    Overbeek, R.3
  • 41
    • 0028028182 scopus 로고
    • Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology
    • Stackebrandt, E. and Goebel, B.M. (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol., 44, 846-849.
    • (1994) Int. J. Syst. Bacteriol. , vol.44 , pp. 846-849
    • Stackebrandt, E.1    Goebel, B.M.2
  • 42
    • 79954994069 scopus 로고    scopus 로고
    • A late methanogen origin for molybdenum-dependent nitrogenase
    • Boyd, E.S., Anbar, A.D., Miller, S. et al. (2011) A late methanogen origin for molybdenum-dependent nitrogenase. Geobiology, 9, 221-232.
    • (2011) Geobiology , vol.9 , pp. 221-232
    • Boyd, E.S.1    Anbar, A.D.2    Miller, S.3
  • 43
    • 0021932595 scopus 로고
    • Structural and functional homology between the alpha-subunits and beta-subunits of the nitrogenase NifE protein as revealed by sequencing the rhizobium japonicum nifK gene
    • Thony, B., Kaluza, K. and Hennecke, H. (1985) Structural and functional homology between the alpha-subunits and beta-subunits of the nitrogenase NifE protein as revealed by sequencing the Rhizobium japonicum nifK gene. Mol. Gen. Genet., 198, 441-448.
    • (1985) Mol. Gen. Genet. , vol.198 , pp. 441-448
    • Thony, B.1    Kaluza, K.2    Hennecke, H.3
  • 44
    • 84875888093 scopus 로고    scopus 로고
    • Classifying the metal dependence of uncharacterized nitrogenases
    • McGlynn, S.E., Boyd, E.S., Peters, J.W. et al. (2012) Classifying the metal dependence of uncharacterized nitrogenases. Front. Microbiol., 3, 419-419.
    • (2012) Front. Microbiol. , vol.3 , pp. 419
    • McGlynn, S.E.1    Boyd, E.S.2    Peters, J.W.3
  • 45
    • 0034658817 scopus 로고    scopus 로고
    • Biogeographical diversity among marine bacterioplankton
    • Hagstrom, A., Pinhassi, J. and Zweifel, U.L. (2000) Biogeographical diversity among marine bacterioplankton. Aquat. Microb. Ecol., 21, 231-244.
    • (2000) Aquat. Microb. Ecol. , vol.21 , pp. 231-244
    • Hagstrom, A.1    Pinhassi, J.2    Zweifel, U.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.