Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE
Tài liệu tham khảo
Palys, 1997, Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data, Int. J. Syst. Bacteriol., 47, 1145, 10.1099/00207713-47-4-1145
Zumft, 1997, Cell biology and molecular basis of denitrification, Microbiol. Mol. Biol. R, 61, 533, 10.1128/.61.4.533-616.1997
Conrad, 1996, Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O and NO), Microbiol. Rev., 60, 609, 10.1128/MMBR.60.4.609-640.1996
Bothe, 2000, Molecular analysis of ammonia oxidation and denitrification in natural environments, FEMS Microbiol. Rev., 24, 673, 10.1111/j.1574-6976.2000.tb00566.x
Braker, 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, 2096, 10.1128/AEM.66.5.2096-2104.2000
Scala, 1999, Diversity of nitrous oxide reductase (nosZ) genes in continental shelf sediments, Appl. Environ. Microbiol., 65, 1681, 10.1128/AEM.65.4.1681-1687.1999
Braker, 2003, Nitric oxide reductase (norB) genes from pure cultures and environmental samples, Appl. Environ. Microbiol., 69, 3476, 10.1128/AEM.69.6.3476-3483.2003
Ward, 1995, Diversity of culturable denitrifying bacteria, Arch. Microbiol., 163, 167
Braker, 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, 3769, 10.1128/AEM.64.10.3769-3775.1998
Hallin, 1999, PCR detection of genes encoding nitrite reductase in denitrifing bacteria, Appl. Environ. Microbiol., 65, 1652, 10.1128/AEM.65.4.1652-1657.1999
Michotey, 2000, Comparison of methods for quantification of cytochrome cd1-denitrifying bacteria in marine samples, Appl. Environ. Microbiol., 66, 1564, 10.1128/AEM.66.4.1564-1571.2000
Casciotti, 2001, Dissimilatory nitrite reductase genes from autotrophic ammonia-oxidizing bacteria, Appl. Environ. Microbiol., 67, 2213, 10.1128/AEM.67.5.2213-2221.2001
Rösch, 2002, Biodiversity of denitrifying and dinitrogen-fixing bacteria in an Acid forest soil, Appl. Environ. Microbiol., 68, 3818, 10.1128/AEM.68.8.3818-3829.2002
Mergel, 2001, Relative abundance of denitrifying and dinitrogen-fixing bacteria in layers of a forest soil, FEMS Microbiol. Ecol., 36, 33, 10.1111/j.1574-6941.2001.tb00823.x
Yan, 2003, Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater, Environ. Microbiol., 5, 13, 10.1046/j.1462-2920.2003.00393.x
Scala, 1998, Nitrous oxide reductase (nosZ) gene-specific PCR primers for detection of denitrifiers and three nosZ genes from marine sediments, FEMS Microbiol. Lett., 162, 61, 10.1111/j.1574-6968.1998.tb12979.x
Nogales, 2002, Detection and diversity of expressed denitrification genes in estuarine sediments after reverse transcription-PCR amplification from mRNA, Appl. Environ. Microbiol., 68, 5017, 10.1128/AEM.68.10.5017-5025.2002
Kloos, 2001, Denitrification within the genus Azospirillum and other associative bacteria, Aust. J. Plant. Physiol., 28, 991
Braker, 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, 1893, 10.1128/AEM.67.4.1893-1901.2001
Scala, 2000, Horizontal heterogeneity of denitrifying bacterial communities in marine sediments by terminal restriction fragment length polymorphism analysis, Appl. Environ. Microbiol., 66, 1980, 10.1128/AEM.66.5.1980-1986.2000
Wu, 2001, Development and evaluation of functional gene arrays for detection of selected genes in the environment, Appl. Environ. Microbiol., 67, 5780, 10.1128/AEM.67.12.5780-5790.2001
Liu, 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, 3549, 10.1128/AEM.69.6.3549-3560.2003
Tuomainen, 2003, Baltic sea cyanobacterial bloom contains denitrification and nitrification genes, but has negligible denitrification activity, FEMS Microbiol. Ecol., 45, 83, 10.1016/S0168-6496(03)00131-4
Chèneby, 1998, Diversity of denitrifying microflora and ability to reduce N2O in two soils, Biol. Fert. Soils., 28, 19, 10.1007/s003740050458
Avrahami, 2002, Effect of soil ammonium concentration on N2O release and on the community structure of ammonia oxidizers and denitrifiers, Appl. Environ. Microbiol., 68, 5685, 10.1128/AEM.68.11.5685-5692.2002
Stres, 2004, Nitrous oxide reductase (nosZ) gene fragments differ between native and cultivated Michigan soils, Appl. Environ. Microbiol., 70, 301, 10.1128/AEM.70.1.301-309.2004
Mounier, 2004, Influence of maize mucilage on the diversity and activity of the denitrifying community, Environ. Microbiol., 6, 301, 10.1111/j.1462-2920.2004.00571.x
Priemé, 2002, Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetlands soils, Appl. Environ. Microbiol., 68, 1893, 10.1128/AEM.68.4.1893-1900.2002
Rich, 2003, Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils, Appl. Environ. Microbiol., 69, 5974, 10.1128/AEM.69.10.5974-5982.2003
Sakano, 2002, Spatial distribution of total, ammonia-oxidizing, and denitrifying bacteria in biological wastewater treatment reactors for bioregenerative life support, Appl. Environ. Microbiol., 68, 2285, 10.1128/AEM.68.5.2285-2293.2002
Noda, 2003, Effects of SRT and DO on N2O reductase activity in an anoxic-oxic activated sludge system, Water Sci. Technol., 48, 363, 10.2166/wst.2004.0881
Muyzer, 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, 10.1128/AEM.59.3.695-700.1993
Myers, 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, 3131, 10.1093/nar/13.9.3131
Smalla, 2001, Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed, Appl. Environ. Microbiol., 67, 4742, 10.1128/AEM.67.10.4742-4751.2001
Novick, 1967, Properties of a cryptic high-frequency transducing phage in Staphylococcus aureus, Virology, 33, 155, 10.1016/0042-6822(67)90105-5
Peer, 1994, TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment, Comput. Appl. Biosci., 10, 569
Saitou, 1987, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 4, 406
Delorme, 2003, Comparative genetic diversity of the narG, nosZ, and 16S rRNA genes in fluorescent pseudomonads, Appl. Environ. Microbiol., 69, 1004, 10.1128/AEM.69.2.1004-1012.2003
Kisand, 2003, Limited resolution of 16S rDNA DGGE caused by melting properties and closely related DNA sequences, J. Microbiol. Methods, 54, 183, 10.1016/S0167-7012(03)00038-1
Vallaeys, 1997, Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs, FEMS Microbiol. Ecol., 24, 279, 10.1111/j.1574-6941.1997.tb00445.x
Nubel, 1996, Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis, J. Bacteriol., 178, 5636, 10.1128/jb.178.19.5636-5643.1996
Sekiguchi, 2001, A single band does not always represent single bacterial strains in denaturing gradient gel electrophoresis analysis, Biotechnol. Lett., 23, 1205, 10.1023/A:1010517117046
Green, 2004, Similarity of bacterial communities in sawdust- and straw-amended cow manure composts, FEMS Microbiol. Lett., 233, 115, 10.1016/j.femsle.2004.01.049
Avrahami, 2003, Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers, Environ. Microbiol., 5, 691, 10.1046/j.1462-2920.2003.00457.x