Assessment of nitrogen and oxygen isotopic fractionation during nitrification and its expression in the marine environment

Methods in Enzymology

Volumn 486, Issue C, 2011, Pages 253-280

  Casciotti, Karen L ^a   Buchwald, Carolyn ^a   Santoro, Alyson E ^a   Frame, Caitlin ^a  

^a WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; NITRATE; NITRITE; NITROGEN; OXYGEN; STABLE ISOTOPE;

ARTICLE; BIOACCUMULATION; FRACTIONATION; ISOTOPIC FRACTIONATION; KINETICS; MARINE ENVIRONMENT; NITRIFICATION; NITROGEN CYCLE; OXIDATION; PRIORITY JOURNAL;

EID: 78650943349     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-381294-0.00011-0     Document Type: Chapter

References (93)

1. A. Abeliovich The nitrite-oxidizing bacteria The Prokaryotes 5 2006 861 872
2. 15N records Biogeosciences 4 2007 75 86
3. 15N-NMR evidence FEBS Lett. 164 1983 236 240
4. J. Bigeleisen Chemistry of Isotopes Science 147 1965 463 471
5. J. Bigeleisen, and M. Wolfsberg Theoretical and experimental aspects of isotope effects in chemical kinetics Adv. Chem. Phys. 1 1958 15 76
6. E. Bock, H.-P. Koops, and H. Harms Nitrifying bacteria H.G. Schelgel, B. Bowien, Autotrophic bacteria 1989 Springer-Verlag Berlin 81 96
7. J.K. Bhlke, S.J. Mroczkowski, and T.B. Coplen Oxygen isotopes in nitrate: new reference materials for O-18: O-17: O-16 measurements and observations on nitrate-water equilibration Rapid Commun. Mass Spectrom. 17 2003 1835 1846
8. 2O Anal. Chem. 79 2007 5888 5895
9. J.A. Brandes, and A.H. Devol A global marine fixed nitrogen isotopic budget: Implications for Holocene nitrogen cycling Glob. Biogeochem. Cycles 16 2002 1120
10. C. Buchwald, and K.L. Casciotti Oxygen isotopic fractionation and exchange during bacterial nitrite oxidation Limnol. Oceanogr. 55 2010 1064 1074
11. 2O of the West Pacific and East Indian Oceans during the El-Nino Southern Oscillation event of 1987 J. Geophys. Res. Atmos. 94 1989 14865 14877
12. A.F. Carlucci, and P.M. McNally Nitrification by marine bacteria at low concentrations of substrate and oxygen Limnol. Oceanogr. 14 1969 736 739
13. K.L. Casciotti Inverse kinetic isotope fractionation during bacterial nitrite oxidation Geochim. Cosmochim. Acta 73 2009 2061 2076
14. K.L. Casciotti, and M.R. McIlvin Isotopic analyses of nitrate and nitrite from reference mixtures and application to Eastern Tropical North Pacific waters Mar. Chem. 107 2007 184 201
15. K.L. Casciotti, D.M. Sigman, M. Galanter Hastings, J.K. Bhlke, and A. Hilkert Measurement of the oxygen isotopic composition of nitrate in seawater and freshwater using the denitrifier method Anal. Chem. 74 2002 4905 4912
16. K.L. Casciotti, D.M. Sigman, and B.B. Ward Linking diversity and stable isotope fractionation in ammonia-oxidizing bacteria Geomicrobiol. J. 20 2003 335 353
17. K.L. Casciotti, J.K. Bhlke, M.R. McIlvin, S.J. Mroczkowski, and J.E. Hannon Oxygen isotopes in nitrite: Analysis, calibration, and equilibration Anal. Chem. 79 2007 2427 2436
18. K.L. Casciotti, M.R. McIlvin, and C. Buchwald Oxygen isotopic exchange and fractionation during bacterial ammonia oxidation Limnol. Oceanogr. 55 2010 753 762
19. P. Chain Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea J. Bact 185 2003 2759 2773
20. L.A. Cifuentes, M.L. Fogel, J.R. Pennock, and J.H. Sharp Biogeochemical factors that influence the stable nitrogen isotope ratio of dissolved ammonium in the Delaware Estuary Geochim. Cosmochim. Acta 53 1989 2713 2721
21. W.W. Cleland The use of isotope effects in the detailed analysis of catalytic mechanisms of enzymes Bioinorg. Chem. 15 1987 283 302
22. Y. Cohen, and L.I. Gordon Nitrous oxide in the oxygen minimum of the eastern tropical North Pacific: Evidence for its consumption during denitrification and possible mechanisms for its production Deep Sea Res. 6 1978 509 525
23. R.D. Cox Determination of nitrate and nitrite at the parts per billion level by chemiluminescence Anal. Chem. 52 1980 332 335
24. J.R. De La Torre, C.B. Walker, A.E. Ingalls, M. Konneke, and D.A. Stahl Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol Environ. Microbiol. 10 2008 810 818
25. J. Detmers, V. Bruchert, K.S. Habicht, and J. Kuever Diversity of sulfur isotope fractionations by sulfate-reducing prokaryotes Appl. Environ. Microbiol. 67 2001 888 894
26. C. Deutsch, D.M. Sigman, R.C. Thunell, A.N. Meckler, and G.H. Haug Isotopic constraints on glacial/interglacial changes in the oceanic nitrogen budget Global Biogeochem. Cycles 18 2004 ARTN GB4012
27. A.A. Dispirito, and A.B. Hooper Oxygen exchange between nitrate molecules during nitrite oxidation by Nitrobacter J. Biol. Chem. 261 1986 10534 10537
28. 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
29. 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
30. R.D. Dua, B. Bhandari, and D.J.D. Nicholas Stable isotope studies on the oxidation of ammonia to hydroxylamine by Nitrosomonas europaea FEBS Lett. 106 1979 401 404
31. 18 content of waters from natural sources Geochim. Cosmochim. Acta 4 1953 213 224
32. C.H. Frame, and K.L. Casciotti Biogeochemical controls and isotopic signatures of nitrous oxide production by a marine ammonia-oxidizing bacterium Biogeosci. Discuss. 7 2010 3019 3059
33. S.H. Friedman, W. Massefski, and T.C. Hollocher Catalysis of intermolecular oxygen atom transfer by nitrite dehydrogenase of Nitrobacter agilis J. Biol. Chem. 261 1986 10538 10543
34. C. Garside A chemiluminescent technique for the determination of nanomolar concentrations of nitrate, nitrite, or nitrite alone in seawater Mar. Chem. 11 1982 159 167
35. L. Gianfrani, G. Gagliardi, M. Van Burgel, and E.R. Kerstel Isotope analysis of water by means of near-infrared dual-wavelength diode laser spectroscopy Opt. Express 11 2003 1566 1576
36. R. Goericke, J.P. Montoya, and B. Fry Physiology of isotope fractionation in algae and cyanobacteria K. Lakitha, B. Michener, Stable Isotopes in Ecology and Environmental Science 1994 Blackwell Scientific Oxford
37. J. Granger, and D.M. Sigman Removal of nitrite with sulfamic acid for nitrate N and O isotope analysis with the denitrifier method Rapid Commun. Mass Spectrom. 23 2009 3753 3762
38. J. Granger, D.M. Sigman, J.A. Needoba, and P.J. Harrison Coupled nitrogen and oxygen isotope fractionation of nitrate during assimilation by cultures of marine phytoplankton Limnol. Oceanogr. 49 2004 1763 1773
39. J. Granger, D.M. Sigman, M.M. Rohde, M.T. Maldonado, and P.D. Tortell N and O isotope effects during nitrate assimilation by unicellular prokaryotic and eukaryotic plankton cultures Geochim. Cosmochim. Acta 74 2010 1030 1040
40. R. Hatzenpichler A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring Proc. Natl. Acad. Sci. USA 105 2008 2134 2139
41. J.D. Hermes, P.M. Weiss, and W.W. Cleland Use of nitrogen-15 and deuterium isotope effects to determine the chemical mechanism of phenylalanine ammonia-lyase Biochemistry 24 1985 2959 2967
42. T.C. Hollocher, M.E. Tate, and D.J.D. Nicholas Oxidation of ammonia by Nitrosomonas europaea J. Biol. Chem. 256 1981 10834 10836
43. + in marine, estuarine, and fresh waters: an adaptation of the ammonium diffusion method for samples with low-ammonium concentrations Mar. Chem. 60 1998 235 243
44. S.G. Horrigan, J.P. Montoya, J.L. Nevins, and J.J. Mccarthy Natural isotopic composition of dissolved inorganic nitrogen in the Chesapeake Bay Estuar. Coast. Shelf Sci. 30 1990 393 410
45. S.G. Horrigan Nitrogenous nutrient transformations in the spring and fall in the Chesapeake Bay Estuar. Coast. Shelf Sci. 30 1990 369 391
46. IPCC Climate change 2007: Synthesis report 2007 p. 104. Contribution of working groups I, II, and III to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change
47. - produced by nitrification in aqueous samples Limnol. Oceanogr. 37 1992 900 907
48. 2O in the Pacific Ocean and constraints on its origin in deep water Nature 347 1990 58 61
49. M.G. Klotz Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707 Appl. Env. Microbiol. 72 2006 6299 6315
50. M.G. Klotz, M.C. Schmid, M. Strous, H.J.M. Op Den Camp, M.S.M. Jetten, and A.B. Hooper Evolution of an octahaem cytochrome c protein family that is key to aerobic and anaerobic ammonia oxidation by bacteria Environ. Microbiol. 10 2008 3150 3163
51. S. Kumar, D.J.D. Nicholas, and E.H. Williams Definitive N-15 NMR evidence that water serves as a source of O during nitrite oxidation by Nitrobacter agilis FEBS Lett. 152 1983 71 74
52. 2 concentration on carbon isotopic fractionation by the marine diatom Phaeodactylum tricornutum Limnol. Oceanogr. 42 1997 1552 1560
53. A. Mariotti Experimental determination of nitrogen kinetic isotope fractionation: Some principles; Illustration for the denitrification and nitrification processes Plant Soil 62 1981 413 430
54. A. Mariotti, C. Lancelot, and G. Billen Natural isotopic composition of nitrogen as a tracer of origin for suspended organic-matter in the Scheldt Estuary Geochim. Cosmochim. Acta 48 1984 549 555
55. W. Martens-Habbena, P.M. Berube, H. Urakawa, J.R. De La Torre, and D.A. Stahl Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria Nature 461 2009 976 U234
56. B. Mayer, S.M. Bollwerk, T. Mansfeldt, B. Hutter, and J. Veizer The oxygen isotope composition of nitrate generated by nitrification in acid forest floors Geochim. Cosmochim. Acta 65 2001 2743 2756
57. M.R. McIlvin, and M.A. Altabet Chemical conversion of nitrate and nitrite to nitrous oxide for nitrogen and oxygen isotopic analysis in freshwater and seawater Anal. Chem. 77 2005 5589 5595
58. 18O in Water Anal. Chem. 78 2006 2377 2381
59. M.R. McIlvin, and K.L. Casciotti Fully automated system for stable isotopic analyses of dissolved nitrous oxide at natural abundance levels Limnol. Oceanogr. Methods 8 2010 54 66
60. Y. Miyake, and E. Wada The isotope effect on the nitrogen in biochemical oxidation-reduction reactions Rec. Oceanogr. Works Japan 11 1971 1 6
61. J.A. Needoba, D.M. Sigman, and P.J. Harrison The mechanism of isotope fractionation during algal nitrate assimilation as illuminated by the N-15/N-14 of intracellular nitrate J. Phycol. 40 2004 517 522
62. D.B. Northrop The expression of isotope effects on enzyme-catalyzed reactions Annu. Rev. Biochem. 50 1981 103 131
63. J.M. Norton Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil enviroment Appl. Env. Microbiol. 74 2008 3559 3572
64. M.H. O'leary Carbon isotope fractionations in plants Phytochemistry 20 1981 553 567
65. 15N tracer studies of the primary nitrite maximum J. Mar. Res. 39 1981 203 226
66. 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. ChemosphereGlobal Change Science 2 2000 281 290
67. 2O in the oligotrophic subtropical North Pacific gyre Global Biogeochem. Cycles 16 2002 1064
68. 2O): The dominant ozone-depleting substance emitted in the 21st Century Science 326 2009 123 125
69. 18O measurements in nitrate by different combustion techniques Anal. Chem. 74 2002 5410 5413
70. 13C of the clam-chemoautotroph symbiosis Solemya velum Environ. Microbiol. 6 2004 1210 1219
71. D.M. Sigman, M.A. Altabet, R.H. Michener, D.C. Mccorkle, B. Fry, and R.M. Holmes Natural abundance-level measurement of the Nitrogen isotopic composition of oceanic nitrate: an adaptation of the ammonia diffusion method Mar. Chem. 57 1997 227 242
72. 15N of nitrate in the Southern Ocean: Consumption of nitrate in surface waters Glob. Biogeochem. Cycles 13 1999 1149 1166
73. D.M. Sigman, K.L. Casciotti, M. Andreani, C. Barford, M. Galanter, and J.K. Bhlke A bacterial method for the nitrogen isotopic analysis of nitrate in seawater and freshwater Anal. Chem. 73 2001 4145 4153
74. D.M. Sigman Coupled nitrogen and oxygen isotope measurements of nitrate along the eastern North Pacific margin Global Biogeochem. Cycles 19 2005 GB4022
75. D.M. Sigman, P.J. Difiore, M.P. Hain, C. Deutsch, and D.M. Karl Sinking organic matter spreads the nitrogen isotope signal of pelagic denitrification in the North Pacific Geophys. Res. Lett. 36 2009, L08605
76. D.M. Sigman, K.L. Karsh, and K.L. Casciotti Ocean process tracers: Nitrogen isotopes in the ocean Encyclopedia of Ocean Sciences 2009 Academic Press New York 4138 4153
77. S.R. Silva, C. Kendall, D.H. Wilkison, A.C. Ziegler, C.C.Y. Chang, and R.J. Avanzino A new method for collection of nitrate from fresh water and analysis of nitrogen and oxygen isotope ratios J. Hydrol. 228 2000 22 36
78. L. Solorzano Determination of ammonia in natural waters by the phenolhypochlorite method Limnol. Oceanogr. 14 1969 799 801
79. S. Soriano, and N. Walker Isolation of ammonia-oxidizing autotrophic bacteria J.Appl. Bacteriol. 31 1968 493 497
80. L.Y. Stein, and Y.L. Yung Production, isotopic composition and atmospheric fate of biologically produced nitrous oxide Annu. Rev. Earth Planet. Sci. 31 2003 329 356
81. J.D.H. Strickland, and T.R. Parsons A practical handbook of seawater analysis, 2nd ed Bull. Fish. Res. Bd. Canada 167 1972 1 310
82. E.K. Thornton, and E.R. Thornton Scope and limitations of the concept of the transition state R.D. Gandour, R.L. Schowen, Transition States of Biochemical Processes 1978 Plenum Press New York 3 75
83. D.J. Velinsky, J.R. Pennock, J.H. Sharp, L.A. Cifuentes, and M.L. Fogel Determination of the isotopic composition of ammonium nitrogen at the natural abundance level from estuarine waters Mar. Chem. 26 1989 351 361
84. C.B. Walker Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea Proc. Natl. Acad. Sci. USA 107 2010 8818 8823
85. S.D. Wankel, C. Kendall, J.T. Pennington, F.P. Chavez, and A. Paytan Nitrification in the euphotic zone as evidenced by nitrate dual isotopic composition: Observations from Monterey Bay, California Global Biogeochem. Cycles 21 2007 GB2009
86. B.B. Ward, and G.D. O'Mullan Community Level Analysis: Genetic and biogeochemical approaches to investigate community composition and function in aerobic ammonia oxidation Meth. Enzymol. 397 2005 395 413
87. S.W. Watson Characteristics of a marine nitrifying bacterium, Nitrosocystis oceanus sp. n Limnol. Oceanogr. 10 Suppl. 1965 R274 R289
88. M. Whittaker, D.J. Bergmann, D.M. Arciero, and A.B. Hooper Electron transfer during the oxidation of ammonia by the chemolithotrophic bacterium Nitrosomonas europaea Biochim. Biophys. Acta 1459 2000 346 355
89. H. Yamagishi Role of nitrification and denitrification on the nitrous oxide cycle in the eastern tropical North Pacific and Gulf of California J. Geophys. Res.Biogeosci. 112 2007 ARTN G02015
90. 2O in the eastern tropical Pacific Ocean Nature 307 1984 442 444
91. T. Yoshinari Nitrous oxide in the sea Mar. Chem. 4 1976 189 202
92. 2O from suboxic waters of the eastern tropical North Pacific and the Arabian Sea-measurement by continuous-flow isotope-ratio monitoring Mar. Chem. 56 1997 253 264
93. +) at natural abundance levels in fresh and saltwaters Anal. Chem. 79 2007 5297 5303