Detection methods for the expression of the dissimilatory copper-containing nitrite reductase gene (DnirK) in environmental samples

Journal of Microbiological Methods

Volumn 55, Issue 1, 2003, Pages 41-50

  Metz, Sigrun ^a   Beisker, Wolfgang ^a   Hartmann, Anton ^a   Schloter, Michael ^a  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

Confocal laser scanning microscopy; Copper nitrite reductase (DnirK); Denitrification; Flow cytometry; Immunoassay; In situ gene expression

Indexed keywords

ANTIBODY; BACTERIAL ENZYME; COPPER; NITRATE REDUCTASE; NITROUS OXIDE; OLIGONUCLEOTIDE;

ARTICLE; BACTERIAL CELL; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; CELL LABELING; CELL SELECTION; CONFOCAL LASER MICROSCOPY; CONTROLLED STUDY; DENITRIFICATION; ENVIRONMENT; FLOW CYTOMETRY; FLUORESCENCE ACTIVATED CELL SORTING; GENE EXPRESSION; GENE EXPRESSION SYSTEM; IMMUNOASSAY; IMMUNOHISTOCHEMISTRY; NONHUMAN; OCHROBACTRUM ANTHROPI; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL; PROMOTER REGION; RHIZOSPHERE; SEWAGE TREATMENT; WASTE WATER MANAGEMENT;

BACTERIA (MICROORGANISMS); OCHROBACTRUM; OCHROBACTRUM ANTHROPI; TRITICUM AESTIVUM;

EID: 0142060254     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-7012(03)00089-7     Document Type: Article

References (25)

1. Aβmus B., Schloter M., Kirchhof G., Hutzler P., Hartmann A. Improved in situ tracking of rhizosphere bacteria using dual staining with fluorescence-labeled antibodies and rRNA-targeted oligonucleotides. Microb. Ecol. 33:1997;32-40.
2. Amann R.I., Krumholtz L., Stahl D. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic and environmental studies in microbiology. J. Bacteriol. 172:1990;762-770.
3. Amann R.I., Ludwig W., Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:1995;143-169.
4. Bach H.-J. Bakterielle Populationen und Stoffumsatzpotentiale in Acker-, Grünland-und Waldböden einer Jungmoränenlandschaft in Schleswig-Holstein. EcoSys. Suppl. 15:1996;1-128.
5. Bartosch S., Wolgast L., Spieck E., Bock E. Identification of nitrite-oxidizing bacteria with monoclonal antibodies recognizing the nitriteoxidoreductase. Appl. Environ. Microbiol. 65:1999;4126-4133.
6. Baumann B., Snozzi M., Tehnder A.J.B., van der Meer J.R. Dynamics of denitrification activity of Paracoccus denitrificans in continuous culture during aerobic-anaerobic changes. J. Bacteriol. 178:1996;4367-4374.
7. Braker G., Fesefeldt A., Witzel K.P. 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.
8. Conrad R. Soil microorganisms as controllers of atmospheric trace gases. Microbiol. Rev. 60:1996;609-640.
9. Coyne M.S., Arunakumari A., Averill B.A., Tiedje J.M. Immunological identification and distribution of dissimilatory heme cd1 and nonheme copper nitrite reductases in denitrifying bacteria. Appl. Environ. Microbiol. 55:1989;2924-2931.
10. Dendooven L., Anderson J.M. Dynamics of reduction enzymes involved in the denitrification process in pasture soil. Soil Biol. Biochem. 26:1994;1501-1506.
11. Hartig E., Zumft W.G. Kinetics of nirS expression (cytochrome cd1 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.
12. Killham K. Soil Ecology. 1994;University Press, Cambridge.
13. Knowles R. Dentrification. Microbial. Rev. 46:1982;43-70.
14. Lebuhn M., Achouak W., Schloter M., Berge O., Meier H., Barakat M., Hartmann A., Heulin T. Taxonomic characterization of Ochrobactrum sp. isolates from soil samples and wheat roots, and description of Ochrobactrum tritici sp. nov. and Ochrobactrum grignonense sp. nov. J. Syst. Evol. Microbiol. 50:2000;2207-2223.
15. Lin H.J., Nixon S., Taylor D.I., Granger D., Buckley B.A. Responses of epiphytes on eelgrass, Zostera marina L., to separate and combined nitrogen and phosphorus enrichment. Aquat. Bot. 52:1996;243-258.
16. Loftfield N., Flessa H., Augustin J., Beese F. Automated gas chromatographic system for rapid analyses of the atmospheric trace gases methane, carbon dioxide, and nitrous oxide. J. Environ. Qual. 26:1997;560-564.
17. Metz S., Hartmann A., Schloter M. Development and characterization of murine monoclonal antibodies specific for dissimilatoric copper nitrite reductase. Hybridoma Hybridomics. 21:2002;351-357.
18. Porter K.G., Feig Y.S. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25:1980;943-948.
19. Porter J., Edwards C., Morgan A.W., Pickup R.W. Rapid automated separation of specific bacteria from lake water and sewage by flow cytometry and cell sorting. Appl. Environ. Microbiol. 59:1993;3327-3333.
20. Ryden J.C., Lund L.J., Focht D.D. Direct in-field measurement of nitrous oxide flux from soils. J. Am. Soil Sci. 42:1978;731-737.
21. Schloter M., Wiehe W., Assmus B., Steindl H., Becke H., Höflich G., Hartmann A. Root colonization of different plants by plant-growth-promoting Rhizobium leguminosarum bv. trifolii R39 studied with monospecific polyclonal antisera. Appl. Environ. Microbiol. 63:1997;2038-2046.
22. Tolker-Nielsen T., Holmstrom K., Molin S. Visualization of specific gene expression in individual Salmonella typhimurium cells by in situ PCR. Appl. Environ. Microbiol. 63:1997;4196-4203.
23. Van Schie P.M., Young L.Y. Isolation and characterization of phenoldegrading denitrifying bacteria. Appl. Environ. Microbiol. 64:1998;2432-2438.
24. Ye R.W., Fries M.R., Bezborodnikov S.G., Averill B.A., Tiedje J.M. Characterization of the structural gene encoding a copper-containing nitrite reductase and homology of this gene to DNA of other denitrifiers. Appl. Environ. Microbiol. 59:1993;250-254.
25. Zumft W.G. Cell biology and molecular basis of denitrification. Microbiol. Biol. Rev. 61:1997;533-616.