• [1]
    Palys, T., Nakamura, L.K., Cohan, F.M. (1997) Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int. J. Syst. Bacteriol. 47, 11451156.
  • [2]
    Zumft, W.G. (1997) Cell biology and molecular basis of denitrification. Microbiol. Mol. Biol. R 61, 533616.
  • [3]
    Conrad, R. (1996) Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O and NO). Microbiol. Rev. 60, 609640.
  • [4]
    Bothe, H., Jost, G., Schloter, M., Ward, B.B., Witzel, K.-P. (2000) Molecular analysis of ammonia oxidation and denitrification in natural environments. FEMS Microbiol. Rev. 24, 673690.
  • [5]
    Braker, G., Zhou, J., Wu, L., Devol, A.H., Tiedje, J.M. (2000) 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, 20962104.
  • [6]
    Scala, D.J., Kerkhof, L.J. (1999) Diversity of nitrous oxide reductase (nosZ) genes in continental shelf sediments. Appl. Environ. Microbiol. 65, 16811687.
  • [7]
    Braker, G., Tiedje, J.M. (2003) Nitric oxide reductase (norB) genes from pure cultures and environmental samples. Appl. Environ. Microbiol. 69, 34763483.
  • [8]
    Ward, B.B. (1995) Diversity of culturable denitrifying bacteria. Arch. Microbiol. 163, 167175.
  • [9]
    Braker, G., Fesefeldt, A., Witzel, K.-P. (1998) 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, 37693775.
  • [10]
    Hallin, S., Lindgren, P.-E. (1999) PCR detection of genes encoding nitrite reductase in denitrifing bacteria. Appl. Environ. Microbiol. 65, 16521657.
  • [11]
    Michotey, V., Mejean, V., Bonin, P. (2000) Comparison of methods for quantification of cytochrome cd1-denitrifying bacteria in marine samples. Appl. Environ. Microbiol. 66, 15641571.
  • [12]
    Casciotti, K.L., Ward, B.B. (2001) Dissimilatory nitrite reductase genes from autotrophic ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 67, 22132221.
  • [13]
    Rösch, C., Mergel, A., Bothe, H. (2002) Biodiversity of denitrifying and dinitrogen-fixing bacteria in an Acid forest soil. Appl. Environ. Microbiol. 68, 38183829.
  • [14]
    Mergel, A., Schmitz, O., Mallmann, T., Bothe, H. (2001) Relative abundance of denitrifying and dinitrogen-fixing bacteria in layers of a forest soil. FEMS Microbiol. Ecol. 36, 3342.
  • [15]
    Yan, T., Fields, M.W., Wu, L., Zu, Y., Tiedje, J.M., Zhou, J. (2003) Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater. Environ. Microbiol. 5, 1324.
  • [16]
    Scala, D.J., Kerkhof, L.J. (1998) Nitrous oxide reductase (nosZ) gene-specific PCR primers for detection of denitrifiers and three nosZ genes from marine sediments. FEMS Microbiol. Lett. 162, 6168.
  • [17]
    Nogales, B., Timmis, K.N., Nedwell, D.B., Osborn, A.M. (2002) Detection and diversity of expressed denitrification genes in estuarine sediments after reverse transcription-PCR amplification from mRNA. Appl. Environ. Microbiol. 68, 50175025.
  • [18]
    Kloos, K., Mergel, A., Rosch, C., Bothe, H. (2001) Denitrification within the genus Azospirillum and other associative bacteria. Aust. J. Plant. Physiol. 28, 991998.
  • [19]
    Braker, G., Ayala, H.L., Devol, A.H., Fesefeldt, A., Tiedje, J.M. (2001) Community structure of denitrifiers, bacteria, 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, 18931901.
  • [20]
    Scala, D.J., Kerkhof, L.J. (2000) Horizontal heterogeneity of denitrifying bacterial communities in marine sediments by terminal restriction fragment length polymorphism analysis. Appl. Environ. Microbiol. 66, 19801986.
  • [21]
    Wu, L., Thompson, D.K., Li, G., Hurt, R.A., Tiedje, J.M., Zhou, J. (2001) Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl. Environ. Microbiol. 67, 57805790.
  • [22]
    Liu, X., Tiquia, S.M., Holguin, G., Wu, L., Nold, S.C., Devol, A.H., Luo, K., Palumbo, A.V., Tiedje, J.M., Zhou, J. (2003) Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico. Appl. Environ. Microbiol. 69, 35493560.
  • [23]
    Tuomainen, J., Hietanen, S., Kuparinen, J., Martikainen, P., Servomaa, K. (2003) Baltic sea cyanobacterial bloom contains denitrification and nitrification genes, but has negligible denitrification activity. FEMS Microbiol. Ecol. 45, 8396.
  • [24]
    Chèneby, D., Hartmann, A., Henault, C., Topp, E., Germon, J.-C. (1998) Diversity of denitrifying microflora and ability to reduce N2O in two soils. Biol. Fert. Soils. 28, 1926.
  • [25]
    Avrahami, S., Conrad, R., Braker, G. (2002) Effect of soil ammonium concentration on N2O release and on the community structure of ammonia oxidizers and denitrifiers. Appl. Environ. Microbiol. 68, 56855692.
  • [26]
    Stres, B., Mahne, I., Avgustin, G., Tiedje, J.M. (2004) Nitrous oxide reductase (nosZ) gene fragments differ between native and cultivated Michigan soils. Appl. Environ. Microbiol. 70, 301309.
  • [27]
    Mounier, E., Hallet, S., Cheneby, D., Benizri, E., Gruet, Y., Nguyen, C., Piutti, S., Robin, C., Slezack-Deschaumes, S., Martin-Laurent, F., Germon, J.C., Philippot, L. (2004) Influence of maize mucilage on the diversity and activity of the denitrifying community. Environ. Microbiol. 6, 301312.
  • [28]
    Priemé, A., Braker, G., Tiedje, J.M. (2002) Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetlands soils. Appl. Environ. Microbiol. 68, 18931900.
  • [29]
    Rich, J.J., Heichen, R.S., Bottomley, P.J., Cromack Jr K. Jr., Myrold, D.D. (2003) Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils. Appl. Environ. Microbiol. 69, 59745982.
  • [30]
    Sakano, Y., Pickering, K.D., Strom, P.F., Kerkhof, L.J. (2002) Spatial distribution of total, ammonia-oxidizing, and denitrifying bacteria in biological wastewater treatment reactors for bioregenerative life support. Appl. Environ. Microbiol. 68, 22852293.
  • [31]
    Noda, N., Kaneko, N., Mikami, M., Kimochi, Y., Tsuneda, S., Hirata, A., Mizuochi, M., Inamori, Y. (2003) Effects of SRT and DO on N2O reductase activity in an anoxic-oxic activated sludge system. Water Sci. Technol. 48, 363370.
  • [32]
    Muyzer, G., de Waal, E.C., 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, 695700.
  • [33]
    Myers, R.M., Fischer, S.G., Lerman, L.S., Maniatis, T. (1985) Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res. 13, 31313145.
  • [34]
    Smalla, K., Wieland, G., Buchner, A., Zock, A., Parzy, J., Kaiser, S., Roskot, N., Heuer, H., Berg, G. (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl. Environ. Microbiol. 67, 47424751.
  • [35]
    Vincent, J.M. (1970) A Manual for the Practical Study of the Root-nodule Bacteria. Blackwell Scientific Publications, Oxford..
  • [36]
    Sambrook, J., Fritsch, E.F., Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd Edn. Cold Spring Harbor Laboratory Press, New York..
  • [37]
    Novick, R.P. (1967) Properties of a cryptic high-frequency transducing phage in Staphylococcus aureus. Virology 33, 155156.
  • [38]
    van de Peer, Y., de Wachter, R. (1994) TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Appl. Biosci. 10, 569570.
  • [39]
    Jukes, T.H., Cantor, C.R. Evolution of protein molecules. Munro, H.N., Ed. Mammalian Protein Metabolism Vol. III. (1969) Academic Press, New York. 21–132.
  • [40]
    Saitou, N., Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406425.
  • [41]
    Delorme, S., Philippot, L., Edel-Hermann, V., Deulvot, C., Mougel, C., Lemanceau, P. (2003) Comparative genetic diversity of the narG, nosZ, and 16S rRNA genes in fluorescent pseudomonads. Appl. Environ. Microbiol. 69, 10041012.
  • [42]
    Kisand, V., Wikner, J. (2003) Limited resolution of 16S rDNA DGGE caused by melting properties and closely related DNA sequences. J. Microbiol. Methods 54, 183191.
  • [43]
    Vallaeys, T., Topp, E., Muyzer, G., Laguerre, G., Soulas, G. (1997) Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs. FEMS Microbiol. Ecol. 24, 279285.
  • [44]
    Nubel, U., Engelen, B., Felske, A., Snaidr, J., Wieshuber, A., Amann, R.I., Ludwig, W., Backhaus, H. (1996) Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 178, 56365643.
  • [45]
    Sekiguchi, H., Tomioka, N., Nakahara, T., Yuchiyama, H. (2001) A single band does not always represent single bacterial strains in denaturing gradient gel electrophoresis analysis. Biotechnol. Lett. 23, 12051208.
  • [46]
    Green, S.J., Michel F.C. Jr., Hadar, Y., Minz, D. (2004) Similarity of bacterial communities in sawdust- and straw-amended cow manure composts. FEMS Microbiol. Lett. 233, 115123.
  • [47]
    Avrahami, S., Liesack, W., Conrad, R. (2003) Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers. Environ. Microbiol. 5, 691705.