메뉴 건너뛰기




Volumn 8, Issue 3, 2005, Pages 234-239

Finding the missing link between diversity and activity using denitrifying bacteria as a model functional community

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; NITRITE REDUCTASE; RNA 16S;

EID: 20444448894     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mib.2005.04.003     Document Type: Review
Times cited : (192)

References (50)
  • 1
    • 0002137823 scopus 로고
    • Ecology of denitrification and dissimilatory nitrate reduction to ammonium
    • A.J.B. Zehnder John Wiley & Sons; Inc. New York
    • J.M. Tiedje Ecology of denitrification and dissimilatory nitrate reduction to ammonium A.J.B. Zehnder Biology of anaerobic microorganisms 1988 John Wiley & Sons; Inc. New York 179 244
    • (1988) Biology of Anaerobic Microorganisms , pp. 179-244
    • Tiedje, J.M.1
  • 2
    • 0031456471 scopus 로고    scopus 로고
    • Cell biology and molecular basis of denitrification
    • W.G. Zumft Cell biology and molecular basis of denitrification Microbiol Mol Biol Rev 61 1997 533 536
    • (1997) Microbiol Mol Biol Rev , vol.61 , pp. 533-536
    • Zumft, W.G.1
  • 3
    • 0037184270 scopus 로고    scopus 로고
    • Denitrifying genes in bacterial and archeal genomes
    • L. Philippot Denitrifying genes in bacterial and archeal genomes Biochim Biophys Acta 1577 2002 355 376
    • (2002) Biochim Biophys Acta , vol.1577 , pp. 355-376
    • Philippot, L.1
  • 4
    • 0033765459 scopus 로고    scopus 로고
    • Molecular analysis of ammonia oxidation and denitrification in natural environments
    • H. Bothe, G. Jost, M. Schloter, B.B. Ward, and K.-P. Witzel Molecular analysis of ammonia oxidation and denitrification in natural environments FEMS Microbiol Rev 24 2000 673 690
    • (2000) FEMS Microbiol Rev , vol.24 , pp. 673-690
    • Bothe, H.1    Jost, G.2    Schloter, M.3    Ward, B.B.4    Witzel, K.-P.5
  • 5
    • 4344685944 scopus 로고    scopus 로고
    • Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE
    • I. Throbäck, K. Enwall, Å. Jarvis, and S. Hallin Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE FEMS Microbiol Ecol 49 2004 401 417 Re-evaluation of PCR primers targeting the nirK, nirS and nosZ genes for DGGE analysis improved the detection of denitrifying bacteria in the environment and demonstrated substantial diversity of nirS denitrifiers in soil.
    • (2004) FEMS Microbiol Ecol , vol.49 , pp. 401-417
    • Throbäck, I.1    Enwall, K.2    Jarvis, Å.3    Hallin, S.4
  • 6
    • 0031687820 scopus 로고    scopus 로고
    • Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples
    • G. Braker, A. Fesefeldt, and K.P. Witzel Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples Appl Environ Microbiol 64 1998 3769 3775
    • (1998) Appl Environ Microbiol , vol.64 , pp. 3769-3775
    • Braker, G.1    Fesefeldt, A.2    Witzel, K.P.3
  • 7
    • 0032964425 scopus 로고    scopus 로고
    • PCR detection of genes encoding nitrite reductase in denitrifying bacteria
    • S. Hallin, and P.E. Lindgren PCR detection of genes encoding nitrite reductase in denitrifying bacteria Appl Environ Microbiol 65 1999 1652 1657
    • (1999) Appl Environ Microbiol , vol.65 , pp. 1652-1657
    • Hallin, S.1    Lindgren, P.E.2
  • 8
    • 0034016758 scopus 로고    scopus 로고
    • Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in pacific northwest marine sediment communities
    • G. Braker, J. Zhou, L. Wu, A.H. Devol, and J.M. Tiedje Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in pacific northwest marine sediment communities Appl Environ Microbiol 66 2000 1096 1104
    • (2000) Appl Environ Microbiol , vol.66 , pp. 1096-1104
    • Braker, G.1    Zhou, J.2    Wu, L.3    Devol, A.H.4    Tiedje, J.M.5
  • 9
    • 0036203309 scopus 로고    scopus 로고
    • Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils
    • A. Prieme, G. Braker, and J.M. Tiedje Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils Appl Environ Microbiol 68 2002 1893 1900
    • (2002) Appl Environ Microbiol , vol.68 , pp. 1893-1900
    • Prieme, A.1    Braker, G.2    Tiedje, J.M.3
  • 10
    • 0035656126 scopus 로고    scopus 로고
    • Development and evaluation of functional gene arrays for detection of selected genes in the environment
    • L. Wu, D.K. Thompson, G. Li, R.A. Hurt, J.M. Tiedje, and J. Zhou Development and evaluation of functional gene arrays for detection of selected genes in the environment Appl Environ Microbiol 67 2001 5780 5790
    • (2001) Appl Environ Microbiol , vol.67 , pp. 5780-5790
    • Wu, L.1    Thompson, D.K.2    Li, G.3    Hurt, R.A.4    Tiedje, J.M.5    Zhou, J.6
  • 12
    • 0042285618 scopus 로고    scopus 로고
    • Genetic characterization of the nitrate-reducing community based on narG nucleotide sequence analysis
    • D. Cheneby, S. Hallet, M. Mondon, F. Martin-Laurent, J.C. Germon, and L. Philippot Genetic characterization of the nitrate-reducing community based on narG nucleotide sequence analysis Microb Ecol 46 2003 113 121
    • (2003) Microb Ecol , vol.46 , pp. 113-121
    • Cheneby, D.1    Hallet, S.2    Mondon, M.3    Martin-Laurent, F.4    Germon, J.C.5    Philippot, L.6
  • 14
    • 0032080514 scopus 로고    scopus 로고
    • Nitrous oxide reductase (nosZ) gene-specific PCR primers for detection of denitrifiers and three nosZ genes from marine sediments
    • D.J. Scala, and L.J. Kerkhof Nitrous oxide reductase (nosZ) gene-specific PCR primers for detection of denitrifiers and three nosZ genes from marine sediments FEMS Microbiol Lett 162 1998 61 68
    • (1998) FEMS Microbiol Lett , vol.162 , pp. 61-68
    • Scala, D.J.1    Kerkhof, L.J.2
  • 15
    • 0037978972 scopus 로고    scopus 로고
    • Nitric oxide reductase (norB) genes from pure cultures and environmental samples
    • G. Braker, and J.M. Tiedje Nitric oxide reductase (norB) genes from pure cultures and environmental samples Appl Environ Microbiol 69 2003 3476 3483 The nitric oxide reductase gene (norB) was the last gene for which primers were lacking. The development of these primers allows detection of all steps in the denitrification pathway in the environment.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 3476-3483
    • Braker, G.1    Tiedje, J.M.2
  • 16
    • 0035319656 scopus 로고    scopus 로고
    • Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes
    • G. Braker, H.L. Ayala-del-Rio, A.H. Devol, A. Fesefeldt, and J.M. Tiedje Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes Appl Environ Microbiol 67 2001 1893 1901
    • (2001) Appl Environ Microbiol , vol.67 , pp. 1893-1901
    • Braker, G.1    Ayala-Del-Rio, H.L.2    Devol, A.H.3    Fesefeldt, A.4    Tiedje, J.M.5
  • 17
    • 0034071156 scopus 로고    scopus 로고
    • Horizontal heterogeneity of denitrifying bacterial communities in marine sediments by terminal restriction fragment length polymorphism analysis
    • D.J. Scala, and L.J. Kerkhof Horizontal heterogeneity of denitrifying bacterial communities in marine sediments by terminal restriction fragment length polymorphism analysis Appl Environ Microbiol 66 2000 1980 1986
    • (2000) Appl Environ Microbiol , vol.66 , pp. 1980-1986
    • Scala, D.J.1    Kerkhof, L.J.2
  • 18
    • 0036330611 scopus 로고    scopus 로고
    • Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil
    • C. Rosch, A. Mergel, and H. Bothe Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil Appl Environ Microbiol 68 2002 3818 3829
    • (2002) Appl Environ Microbiol , vol.68 , pp. 3818-3829
    • Rosch, C.1    Mergel, A.2    Bothe, H.3
  • 21
    • 0037316061 scopus 로고    scopus 로고
    • Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment
    • G. Taroncher-Oldenburg, E.M. Griner, C.A. Francis, and B.B. Ward Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment Appl Environ Microbiol 69 2003 1159 1171 In this study, a 70-mer oligonucleotide DNA micro-array was developed to achieve similar hybridization conditions across the array. This substantially improved the detection and quantification of the denitrifying nitrite reductase.
    • (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
  • 22
    • 1842579620 scopus 로고    scopus 로고
    • Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples
    • S.M. Tiquia, L. Wu, S.C. Chong, S. Passovets, D. Xu, T. Xu, and J. Zhou Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples Biotechniques 36 2004 664 670
    • (2004) Biotechniques , vol.36 , pp. 664-670
    • Tiquia, S.M.1    Wu, L.2    Chong, S.C.3    Passovets, S.4    Xu, D.5    Xu, T.6    Zhou, J.7
  • 23
    • 2942525588 scopus 로고    scopus 로고
    • Molecular microbial ecology: Land of the one-eyed king
    • L.J. Forney, X. Zhou, and C.J. Brown Molecular microbial ecology: land of the one-eyed king Curr Opin Microbiol 7 2004 210 220
    • (2004) Curr Opin Microbiol , vol.7 , pp. 210-220
    • Forney, L.J.1    Zhou, X.2    Brown, C.J.3
  • 24
    • 0027427692 scopus 로고
    • Kinetics of the persistence of chromosomal DNA from genetically engineered Escherichia coli introduced into soil
    • G. Recorbet, C. Picard, P. Normand, and P. Simonet Kinetics of the persistence of chromosomal DNA from genetically engineered Escherichia coli introduced into soil Appl Environ Microbiol 59 1993 4289 4294
    • (1993) Appl Environ Microbiol , vol.59 , pp. 4289-4294
    • Recorbet, G.1    Picard, C.2    Normand, P.3    Simonet, P.4
  • 25
    • 0035001349 scopus 로고    scopus 로고
    • Relative abundance of denitrifying and dinitrogen-fixing bacteria in layers of a forest soil
    • A. Mergel, O. Schmitz, T. Mallmann, and H. Bothe Relative abundance of denitrifying and dinitrogen-fixing bacteria in layers of a forest soil FEMS Microbiol Ecol 36 2001 33 42
    • (2001) FEMS Microbiol Ecol , vol.36 , pp. 33-42
    • Mergel, A.1    Schmitz, O.2    Mallmann, T.3    Bothe, H.4
  • 26
    • 0036193078 scopus 로고    scopus 로고
    • Quantitative detection of microbial genes by using DNA microarrays
    • J.-C. Cho, and J.M. Tiedje Quantitative detection of microbial genes by using DNA microarrays Appl Environ Microbiol 68 2002 1425 1430
    • (2002) Appl Environ Microbiol , vol.68 , pp. 1425-1430
    • Cho, J.-C.1    Tiedje, J.M.2
  • 28
    • 14244256656 scopus 로고    scopus 로고
    • Stratification of activity and bacterial community structure in biofilms grown on membranes transferring oxygen
    • A.C. Cole, M.J. Semmens, and T.M. LaPara Stratification of activity and bacterial community structure in biofilms grown on membranes transferring oxygen Appl Environ Microbiol 70 2004 1982 1989
    • (2004) Appl Environ Microbiol , vol.70 , pp. 1982-1989
    • Cole, A.C.1    Semmens, M.J.2    Lapara, T.M.3
  • 29
    • 0035146327 scopus 로고    scopus 로고
    • Pseudomonas stutzeri nitrite reductase gene abundance in environmental samples measured by real-time PCR
    • V. Grüntzig, S.C. Nold, J. Zhou, and J.M. Tiedje Pseudomonas stutzeri nitrite reductase gene abundance in environmental samples measured by real-time PCR Appl Environ Microbiol 67 2001 760 768
    • (2001) Appl Environ Microbiol , vol.67 , pp. 760-768
    • Grüntzig, V.1    Nold, S.C.2    Zhou, J.3    Tiedje, J.M.4
  • 30
    • 5644239930 scopus 로고    scopus 로고
    • Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR
    • S. Henry, E. Baudouin, J.C. López-Gutiérrez, F. Martin-Laurent, A. Brauman, and L. Philippot Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR J Microbiol Methods 59 2004 327 335 Corrigendum published in J Microbiol Methods 2005, 61:289-290 This study reports the first successful application of real-time PCR to quantify taxonomically diverse denitrifying bacteria in the environment. Specificity of the assay was verified by sequencing of the real-time PCR products from the different environments analyzed.
    • (2004) J Microbiol Methods , vol.59 , pp. 327-335
    • Henry, S.1    Baudouin, E.2    López-Gutiérrez, J.C.3    Martin-Laurent, F.4    Brauman, A.5    Philippot, L.6
  • 31
    • 5344270552 scopus 로고    scopus 로고
    • Detection and quantification of copper-denitrifying bacteria by quantitative competitive PCR
    • X.-Y. Qiu, R.A. Hurt, L.-Y. Wu, C.-H. Chen, J.M. Tiedje, and J.-Z. Zhou Detection and quantification of copper-denitrifying bacteria by quantitative competitive PCR J Microbial Methods 59 2004 199 210
    • (2004) J Microbial Methods , vol.59 , pp. 199-210
    • Qiu, X.-Y.1    Hurt, R.A.2    Wu, L.-Y.3    Chen, C.-H.4    Tiedje, J.M.5    Zhou, J.-Z.6
  • 33
    • 0031213942 scopus 로고    scopus 로고
    • Development of stable denitrifying cultures during repeated aerobic-anaerobic transient periods
    • B. Baumann, M. Snozzi, J.R. van der Meer, and A.J.B. Zehnder Development of stable denitrifying cultures during repeated aerobic-anaerobic transient periods Water Res 31 1997 1947 1954
    • (1997) Water Res , vol.31 , pp. 1947-1954
    • Baumann, B.1    Snozzi, M.2    Van Der Meer, J.R.3    Zehnder, A.J.B.4
  • 34
    • 0036793715 scopus 로고    scopus 로고
    • Detection and diversity of expressed denitrification genes in estuarine sediments after reverse transcription-PCR amplification from mRNA
    • B. Nogales, K.N. Timmis, D.B. Nedwell, and A.M. Osborn Detection and diversity of expressed denitrification genes in estuarine sediments after reverse transcription-PCR amplification from mRNA Appl Environ Microbiol 68 2002 5017 5025
    • (2002) Appl Environ Microbiol , vol.68 , pp. 5017-5025
    • Nogales, B.1    Timmis, K.N.2    Nedwell, D.B.3    Osborn, A.M.4
  • 35
    • 0032939521 scopus 로고    scopus 로고
    • MRNA degradation in bacteria
    • R. Rauhut, and G. Klug mRNA degradation in bacteria FEMS Microbiol Rev 23 1999 353 370
    • (1999) FEMS Microbiol Rev , vol.23 , pp. 353-370
    • Rauhut, R.1    Klug, G.2
  • 36
    • 0032934360 scopus 로고    scopus 로고
    • 1 nitrite reductase) in Pseudomonas stutzeri during the transition from aerobic respiration to denitrification: Evidence for a denitrification-specific nitrate- and nitrite-responsive regulatory system
    • 1 nitrite reductase) in Pseudomonas stutzeri during the transition from aerobic respiration to denitrification: evidence for a denitrification- specific nitrate- and nitrite-responsive regulatory system J Bacteriol 181 1999 161 166
    • (1999) J Bacteriol , vol.181 , pp. 161-166
    • Hartig, E.1    Zumft, W.G.2
  • 37
    • 0035895814 scopus 로고    scopus 로고
    • Characterization and transcriptional analysis of Pseudomonas fluorescens denitrifying clusters containing the nar, nir, nor and nos genes
    • L. Philippot, P. Mirleau, S. Mazurier, S. Siblot, A. Hartmann, P. Lemanceau, and J.C. Germon Characterization and transcriptional analysis of Pseudomonas fluorescens denitrifying clusters containing the nar, nir, nor and nos genes Biochim Biophys Acta 1517 2001 436 440
    • (2001) Biochim Biophys Acta , vol.1517 , pp. 436-440
    • Philippot, L.1    Mirleau, P.2    Mazurier, S.3    Siblot, S.4    Hartmann, A.5    Lemanceau, P.6    Germon, J.C.7
  • 38
    • 0029765614 scopus 로고    scopus 로고
    • Dynamics of denitrification activity of Paracoccus denitrificans in continuous culture during aerobic-anaerobic changes
    • B. Baumann, M. Snozzi, Zehnder AJB, and J.R.V.D. Meer Dynamics of denitrification activity of Paracoccus denitrificans in continuous culture during aerobic-anaerobic changes J Bacteriol 178 1996 4367 4374
    • (1996) J Bacteriol , vol.178 , pp. 4367-4374
    • Baumann, B.1    Snozzi, M.2    Zehnder, A.J.B.3    Meer, J.R.V.D.4
  • 39
    • 0142060254 scopus 로고    scopus 로고
    • Detection methods for the expression of the dissimilatory copper-containing nitrite reductase gene (DnirK) in environmental samples
    • S. Metz, W. Beisker, A. Hartmann, and M. Schloter Detection methods for the expression of the dissimilatory copper-containing nitrite reductase gene (DnirK) in environmental samples J Microbiol Methods 55 2003 41 50 This immunological approach enables the researcher to detect denitrifying bacteria that express the copper nitrite reductase in situ.
    • (2003) J Microbiol Methods , vol.55 , pp. 41-50
    • Metz, S.1    Beisker, W.2    Hartmann, A.3    Schloter, M.4
  • 40
    • 2642585515 scopus 로고    scopus 로고
    • Immunological method for direct assessment of the functionality of a denitrifying strain of Pseudomonas fluorescens in soil
    • P.-A. Maron, A. Richaume, P. Potier, J.-C. Lata, and R. Lensi Immunological method for direct assessment of the functionality of a denitrifying strain of Pseudomonas fluorescens in soil J Microbiol Methods 58 2004 13 21
    • (2004) J Microbiol Methods , vol.58 , pp. 13-21
    • Maron, P.-A.1    Richaume, A.2    Potier, P.3    Lata, J.-C.4    Lensi, R.5
  • 42
    • 0036628867 scopus 로고    scopus 로고
    • Nitrous oxide emissions from an ultisol of the humid tropics under maize-groundnut rotation
    • M.I. Khalil, A.B. Rosenani, O. Van Cleemput, C.I. Fauziah, and J. Shamshuddin Nitrous oxide emissions from an ultisol of the humid tropics under maize-groundnut rotation J Environ Qual 31 2002 1071 1078
    • (2002) J Environ Qual , vol.31 , pp. 1071-1078
    • Khalil, M.I.1    Rosenani, A.B.2    Van Cleemput, O.3    Fauziah, C.I.4    Shamshuddin, J.5
  • 43
    • 0036084206 scopus 로고    scopus 로고
    • Nitrous oxide release from soils receiving N-rich crop residues and paper mill sludge in eastern Scotland
    • E.M. Baggs, R.M. Rees, K. Castle, A. Scott, K.A. Smith, and A.J.A. Vienten Nitrous oxide release from soils receiving N-rich crop residues and paper mill sludge in eastern Scotland Agi Ecost Environ 90 2002 109 123
    • (2002) Agi Ecost Environ , vol.90 , pp. 109-123
    • Baggs, E.M.1    Rees, R.M.2    Castle, K.3    Scott, A.4    Smith, K.A.5    Vienten, A.J.A.6
  • 44
    • 0033695777 scopus 로고    scopus 로고
    • The control of nitrous oxide emissions from agricultural and natural soils
    • U. Skiba, and K.A. Smith The control of nitrous oxide emissions from agricultural and natural soils Glob Change Sci 2 2000 379 386
    • (2000) Glob Change Sci , vol.2 , pp. 379-386
    • Skiba, U.1    Smith, K.A.2
  • 45
    • 0033939308 scopus 로고    scopus 로고
    • The functional significance of denitrifier community composition in a terrestrial ecosystem
    • M.A. Cavigelli, and G.P. Robertson The functional significance of denitrifier community composition in a terrestrial ecosystem Ecology 81 2000 1402 1414
    • (2000) Ecology , vol.81 , pp. 1402-1414
    • Cavigelli, M.A.1    Robertson, G.P.2
  • 46
    • 0035117250 scopus 로고    scopus 로고
    • Role of denitrifier diversity in rates of nitrous oxide consumption in a terrestrial ecosystem
    • M.A. Cavigelli, and G.P. Robertson Role of denitrifier diversity in rates of nitrous oxide consumption in a terrestrial ecosystem Soil Biol Biochem 33 2001 297 310
    • (2001) Soil Biol Biochem , vol.33 , pp. 297-310
    • Cavigelli, M.A.1    Robertson, G.P.2
  • 49
    • 0142040877 scopus 로고    scopus 로고
    • Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils
    • J.J. Rich, R.S. Heichen, P.J. Bottomley, K. Cromack Jr., and D.D. Myrold Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils Appl Environ Microbiol 69 2003 5974 5982
    • (2003) Appl Environ Microbiol , vol.69 , pp. 5974-5982
    • Rich, J.J.1    Heichen, R.S.2    Bottomley, P.J.3    Cromack Jr., K.4    Myrold, D.D.5
  • 50
    • 0346499634 scopus 로고    scopus 로고
    • Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community
    • M.P. Ginige, P. Hugenholtz, H. Daims, M. Wagner, J. Keller, and L.L. Blackall Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community Appl Environ Microbiol 70 2004 588 596 Proof of concept for using SIP together with FISH with microautoradiography to address the in vivo physiology of denitrifying bacteria in a mixed-population environment.
    • (2004) Appl Environ Microbiol , vol.70 , pp. 588-596
    • Ginige, M.P.1    Hugenholtz, P.2    Daims, H.3    Wagner, M.4    Keller, J.5    Blackall, L.L.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.