PCR detection of genes encoding nitrite reductase in denitrifying bacteria

Applied and Environmental Microbiology

Volumn 65, Issue 4, 1999, Pages 1652-1657

  Hallin, Sara ^a   Lindgren, Per Eric ^b  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b LINKÖPING UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOLOGY; DENITRIFICATION; DNA; ENZYMES; GENES;

NITRITE REDUCTASE; NONDENITRIFYING STRAINS;

ACTIVATED SLUDGE PROCESS;

NITRITE REDUCTASE;

ARTICLE; BACTERIAL GENE; DENITRIFICATION; GENE ISOLATION; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION;

BACTERIA (MICROORGANISMS); PARACOCCUS DENITRIFICANS;

EID: 0032964425     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.4.1652-1657.1999     Document Type: Article

References (33)

1. Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
2. Berks, B. C., S. J. Ferguson, J. W. B. Moir, and D. J. Richardson. 1995. Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions. Biochim. Biophys. Acta 1232:97-173.
3. Borneman, J., P. W. Skroch, K. M. O'Sullivan, J. A. Palus, N. G. Rumjanek, J. L. Jansen, J. Nienhuis, and E. W. Triplett. 1996. Molecular microbial diversity of an agricultural soil in Wisconsin. Appl. Environ. Microbiol. 62: 1935-1943.
4. Braker, G., A. Fesefeldt, and K.-P. Witzel. 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. 64:3769-3775.
5. Brittain, T., R. Blackmore, C. Greenwood, and A. J. Thomson. 1992. Bacterial nitrite-reducing enzymes. Eur. J. Biochem. 209:793-802.
6. 1 and nonheme copper nitrite reductases in denitrifying bacteria. Appl. Environ. Microbiol. 55:2924-2931.
7. de Boer, A. P. N., W. N. M. Reijnders, J. G. Kuenen, A. H. Stouthamer, and R. J. M. van Spanning. 1994. Isolation, sequencing and mutational analysis of a gene cluster involved in nitrite reduction in Paracoccus denitrificans. Antonie van Leeuwenhoek 66:111-127.
8. Fesefeldt, A., K. Kloos, H. Bothe, H. Lemmer, and C. G. Gliesche. 1998. Distribution of denitrification and nitrogen fixation genes in Hyphomicrobium spp. and other budding bacteria. Can. J. Microbiol. 44:181-186.
9. Förster, E. 1994. Rapid generation of internal primers for competitive PCR by low stringency primer annealing. BioTechniques 16:1006-1008.
10. Fries, M. R., J. Zhou, J. Chee-Sandford, and J. M. Tiedje. 1994. Isolation, characterization, and distribution of denitrifying toluene degraders from a variety of habitats. Appl. Environ. Microbiol. 60:2802-2810.
11. -) of Pseudomonas stutzeri. Arch. Microbiol. 160:18-26.
12. Higgins, D. G., A. J. Bleasby, and R. Fuchs. 1991. CLUSTAL V: improved software for multiple sequence alignment. Comp. Appl. Biosci. 8:189-191.
13. Hochstein, L. I., and G. A. Tomlinson. 1988. The enzymes associated with denitrification. Annu. Rev. Microbiol. 42:231-261.
14. 1-dependent nitrite respiration of Pseudomonas stutzeri consists of a cluster of mono-, di-, and tetraheme proteins. FEBS Lett. 279:205-209.
15. Kloos, K., A. Fesefeldt, C. G. Gliesche, and H. Bothe. 1995. DNA-probing indicates the occurrence of denitrification and nitrogen fixation genes in Hypohomicrobium. Distribution of denitrifying and nitrogen fixing isolates of Hypohomicrobium in a sewage treatment plant. FEMS Microbiol. Ecol. 18: 205-213.
16. Linne von Berg, K.-H., and H. Bothe. 1992. The distribution of denitrifying bacteria in soils monitored by DNA-probing. FEMS Microbiol. Ecol. 86:331-340.
17. Magnusson, G., H. Edin, and G. Dahlhammar. 1998. Characterisation of efficient denitrifying bacterial strains isolated from activated sludge by 16S-rDNA analysis. Water Sci. Technol. 38:63-68.
18. Myers, E. W., and W. Miller. 1988. Optimal alignments in linear space. Comp. Appl. Biosci. 4:11-17.
19. Nishiyama, M., J. Suzuki, M. Kukimoto, T. Ohnuki, S. Horinouchi, and T. Beppu. 1993. Cloning and characterization of a nitrite reductase gene from Alcaligenes faecalis and its expression in Escherichia coli. J. Gen. Microbiol. 139:725-733.
20. Novick, R. P. 1967. Properties of a cryptic high-frequency transducing phage in Staphylococcus aureus. Virology 33:155-156.
21. Ohkubo, S., H. Iwasaki, H. Hori, and S. Osawa. 1986. Evolutionary relationship of denitrifying bacteria as deduced from 5S rRNA sequences. J. Biochem. 100:1261-1267.
22. 1 nitrite reductase of Alcaligenes eutrophus H16. Appl. Environ. Microbiol. 63:800-802.
23. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
24. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual. 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
25. 1-type nitrite reductase mediates the first step of denitrification in Alcaligenes eutrophus H16. Arch. Microhiol. 161:453-459.
26. Silvestrini, M. C., C. L. Galeotti, M. Gervais, E. Schininà, D. Barra, F. Bossa, and M. Brunori. 1989. Nitrite reductase from Pseudomonas aeruginosa: sequence of the gene and the protein. FEBS Lett. 254:33-38.
27. Smith, G. B., and J. M. Tiedje. 1992. Isolation and characterization of a nitrite reductase gene and its use as a probe for denitrifying bacteria. Appl. Environ. Microbiol. 58:376-384.
28. Toffanin, A., Q. Wu, M. Maskus, S. Caselia, H. D. Abruna, and J. P. Shapleigh. 1996. Characterization of the gene encoding nitrite reductase and the physiological consequences of its expression in the nondenitrifying Rhizo-bium "hedysari" strain HCNT1. Appl. Environ. Microbiol. 62:4019-4025.
29. Tosques, I. E., A. V. Kwiatkowski, J. Shi, and J. P. Shapleigh. 1997. Characterization and regulation of the gene encoding nitrite reductase in Rhodobacter sphaeroides 2.4.3. J. Bacteriol. 179:1090-1095.
30. Ward, B. B. 1995. Diversity of culturable denitrifying bacteria. Arch. Microbiol. 163:167-175.
31. Ward, B. B., A. R. Cockcroft, and K. A. Kilpatrick. 1993. Antibody and DNA probes for detection of nitrite reductase in seawater. J. Gen. Microbiol. 139: 2285-2293.
32. Ye, R. W., M. R. Fries, S. G. Bezborodnikov, B. A. Averill, and J. M. Tiedje. 1993. Characterization of the structural gene encoding a copper-containing nitrite reductase and homology of this gene to DNA of other denitrifiers. Appl. Environ. Microbiol. 59:250-254.
33. Zumft, W. G. 1992. The denitrifying procaryotes, p. 554-582. In A. Balows, H. G. Trüper, M. Dworkin, W. Harder, and K.-H. Schleifer (ed.), The procaryotes. Springer Verlag, New York, N.Y.