Phylogenetic analysis of nitric oxide reductase gene homologues from aerobic ammonia-oxidizing bacteria

FEMS Microbiology Ecology

Volumn 52, Issue 2, 2005, Pages 197-205

  Casciotti, Karen L ^a,b   Ward, Bess B ^a  

^a PRINCETON UNIVERSITY   (United States)

^b WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

Author keywords

Ammonia oxidizing bacteria; Nitric oxide reductase; Nitrifier denitrification; Nitrite reductase; Nitrous oxide

Indexed keywords

AMMONIA; FUNCTIONAL GROUP; NITRIC OXIDE REDUCTASE; PROTEIN SUBUNIT;

AMMONIA; BACTERIUM; DENITRIFICATION; NITRIC OXIDE; OXIDATION; PHYLOGENETICS;

ARTICLE; BACTERIAL STRAIN; CONTROLLED STUDY; GENE EXPRESSION; GENE SEQUENCE; METABOLISM; NITROSOMONAS; NITROSOSPIRA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL;

NITROSOCOCCUS; NITROSOMONADALES; NITROSOMONAS; NITROSOMONAS EUROPAEA; NITROSOSPIRA; PROTEOBACTERIA;

EID: 15244339396     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.femsec.2004.11.002     Document Type: Article

References (48)

1. R.A. Kester, L. de Boer, and H.J. Laanbroek Short exposure to acetylene to distinguish between nitrifier and denitrifier nitrous oxide production in soil and sediment samples FEMS Microbiol. Ecol. 20 1996 111 120
2. K.-R. Kim, and H. Craig Nitrogen-15 and oxygen-18 characteristics of nitrous oxide: a global perspective Science 262 1993 1855 1857
3. 2O emissions from tropical forest soils Globe Biogeochem. Cyc. 14 2000 525 535
4. J.E. Dore, and D.M. Karl Nitrification in the euphotic zone as a source for nitrite, nitrate, and nitrous oxide at Station ALOHA Limnol. Oceanogr. 41 1996 1619 1628
5. J.E. Dore, B.N. Popp, D.M. Karl, and F.J. Sansone A large source of atmospheric nitrous oxide from subtropical North Pacific surface waters Nature 396 1998 63 66
6. 2O in the Pacific Ocean and constraints on its origin in deep water Nature 347 1990 58 61
7. N.E. Ostrom, M.E. Russ, B. Popp, T.M. Rust, and D.M. Karl Mechanisms of nitrous oxide production in the subtropical North Pacific based on determinations of the isotopic abundances of nitrous oxide and di-oxygen Chemosph. Glob. Change. Sci. 2 2000 281 290
8. T. Yoshinari Nitrous oxide in the sea Mar. Chem. 4 1976 189 202
9. P.J. Crutzen The influence of nitrogen oxides on the atmospheric ozone content Quart. J. Royal Met. Soc. 96 1970 320 325
10. Y.L. Yung, W.C. Wang, and A.A. Lacis Greenhouse effect due to atmospheric nitrous-oxide Geophys. Res. Lett. 3 1976 619 621
11. L.A. Codispoti, and J.P. Christensen Nitrification, denitrification, and nitrous oxide cycling in the eastern tropical Pacific Ocean Mar. Chem. 16 1985 277 300
12. 2O in the eastern tropical Pacific Ocean Nature 307 1984 442 444
13. 2O release and on the community structure of ammonia oxidizers and denitrifiers Appl. Environ. Microbiol. 68 2002 5685 5692
14. 2O by the ammonia-oxidizing nitrifiers Stacey Gresshoff Newton Nitrogen Fixation: Achievements and Objectives 1990 Chapman & Hall New York
15. 2O produced by Nitrosomonas europaea: an examination of nitrifier denitrification Appl. Environ. Microbiol. 49 1985 1134 1141
16. G.A.F. Ritchie, and D.J.D. Nicholas Identification of the sources of nitrous oxide produced by oxidative and reductive processes in Nitrosomonas europaea Biochem. J. 126 1972 1181 1191
17. A.B. Hooper A nitrite-reducing enzyme from Nitrosomonas europaea Biochim. Biophys. Acta 162 1968 49 65
18. D.J. Miller, and P.M. Wood The soluble cytochrome oxidase of Nitrosomonas europaea J. Gen. Microbiol. 129 1983 1645 1650
19. G.A.F. Ritchie, and D.J.D. Nicholas The partial characterization of purified nitrite reductase and hydroxylamine oxidase from Nitrosomonas europaea Biochem. J. 138 1974 471 480
20. P. Chain, J. Lamerdin, F. Larimer, W. Regala, V. Lao, M. Land, L. Hauser, A. Hooper, M. Klotz, J. Norton, L. Sayavedra-Soto, D. Arciero, N. Hommes, M. Whittaker, and D. Arp Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea J. Bacteriol. 185 2003 2759 2773
21. K.L. Casciotti, and B.B. Ward Dissimilatory nitrite reductase genes from autotrophic ammonia-oxidizing bacteria Appl. Environ. Microbiol. 67 2001 2213 2221
22. H.J.E. Beaumont, N.G. Hommes, L.A. Sayavedra-Soto, D.J. Arp, D.M. Arciero, A.B. Hooper, H.V. Westerhoff, and R.J.M. van Spanning Nitrite reductase of Nitrosomonas europaea is not essential for production of gaseous nitrogen oxides and confers tolerance to nitrite J. Bacteriol. 184 2002 2557 2560
23. H.J.E. Beaumont, B. van Schooten, S.I. Lens, H.V. Westerhoff, and R.J.M. van Spanning Nitrosomonas europaea expresses a nitric oxide reductase during nitrification J. Bacteriol. 186 2004 4417 4421
24. A. Busch, B. Friedrich, and R. Cramm Characterization of the norB gene, encoding nitric oxide reductase, in the nondenitrifying cyanobacterium Synechocystis sp. strain PCC6803 Appl. Environ. Microbiol. 68 2002 668 672
25. G. Braker, J.Z. Zhou, L.Y. 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 2096 2104
26. G. Braker, H.L. Alaya-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
27. 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
28. 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
29. B.B Ward, A.R. Cockroft, and K.A. Kilpatrick Antibody and DNA probes for detection of nitrite reductase in seawater J. Gen. Microbiol. 139 1993 2285 2293
30. J. van der Oost, A.P.N. de Boer, J.-W.L. de Gier, W.G. Zumft, A.H. Stouthamer, and R.J.M. van Spanning The heme-copper oxidase family consists of three distinct types of terminal oxidases and is related to nitric oxide reductase FEMS Microbiol. Lett. 121 1994 1 10
31. J. Hendriks, A. Oubrie, J. Castresana, A. Urbani, S. Gemeinhardt, and M. Saraste Nitric oxide reductases in bacteria Biochim. Biophys. Acta 1459 2000 266 273
32. J. Hendriks, A. Warne, and U. Gohlke The active site of the bacterial nitric oxide reductase is a dinuclear iron center Biochemistry 37 1998 13102 13109
33. T. Sakurai, N. Sakurai, H. Matsumoto, S. Hirota, and O. Yamauchi Roles of four iron centers in Paracoccus halodenitrificans nitric oxide reductase Biochem. Biophys. Res. Commun. 251 1998 248 251
34. R. Cramm, R.A. Siddiqui, and B. Friedrich Two isofunctional nitric oxide reductases in Alcaligenes eutrophus H16 J. Bacteriol. 179 1997 6769 6777
35. S. de Vries, M.J.F. Strampraad, and I. Schroder Biochemical characterization of the reductases involved in denitrification in the hyperthermophilic Pyrobaculum aerophilum and purification of the NO reductase J. Inorg. Biochem. 86 2001 199
36. R. Cramm, A. Pohlmann, and B. Friedrich Purification and characterization of the single-component nitric oxide reductase from Ralstonia eutropha H16 FEBS Lett. 460 1999 6 10
37. G. Braker, and J.M. Tiedje Nitric oxide reductase (norB) genes from pure cultures and environmental samples Appl. Environ. Microbiol. 69 2003 3476 3483
38. S. Soriano, and N. Walker Isolation of ammonia-oxidizing autotrophic bacteria J. Appl. Bacteriol. 31 1968 493 507
39. B.B. Ward Kinetic studies on ammonia and methane oxidation by Nitrosococcus oceanus Arch. Microbiol. 147 1987 126 133
40. F.M. Ausubel R. Brent R.E. Kingston E.E. Moore J.A. Smith J.G. Sideman K. Struhl Current Protocols in Molecular Biology 1987 John Wiley and Sons New York, NY
41. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680
42. G. Butland, S. Spiro, N.J. Watmough, and D.J. Richardson Two conserved glutamates in the bacterial nitric oxide reductase are essential for activity but not assembly of the enzyme J. Bacteriol. 183 2001 189 199
43. Y. Matsuda, K. Inamori, T. Osake, A. Eguchi, A. Wantabe, S. Kawabata, K. Iba, and H. Arata Nitric oxide reductase homologue that contains copper atom and has cytochrome c-oxidase activity from an aerobic phototrophic bacterium Roseobacter denitrificans J. Biochem. 131 2002 791 800
44. N. Bano, and J.T. Hollibaugh Diversity and distribution of DNA sequences with affinity to ammonia-oxidizing bacteria of the β subdivision of the class Proteobacteria in the Arctic Ocean Appl. Environ. Microbiol. 66 2000 1960 1969
45. J.T. Hollibaugh, N. Bano, and H. Ducklow Widespread distribution in polar oceans of a 16S rRNA gene sequence with affinity to Nitrosospira-like ammonia-oxidizing bacteria Appl. Environ. Microbiol. 68 2002 1478 1484
46. 2O by nitrifying bacteria at reduced concentrations of oxygen Appl. Environ. Microbiol. 40 1980 526 532
47. Q.-Q. Jiang, and L.R. Bakken Nitrous oxide production and methane oxidation by different ammonia-oxidizing bacteria 1999
48. N. Wrage, G.L. Velthof, O. Oenema, and H.J. Laanbroek Acetylene and oxygen as inhibitors of nitrous oxide production in Nitrosomonas europaea and Nitrosospira briensis: a cautionary tale FEMS Microbiol. Ecol. 47 2004 13 18