Nitrogen compounds in dissolved and solid environmental samples

Developments in Soil Science

Volumn 34, Issue , 2010, Pages 255-288

  Leinweber, Peter ^a   Kruse, Jens ^a   Walley, Fran ^b   Gillespie, Adam ^b   Eckhardt, Kai Uwe ^a   Blyth, Robert I R ^c   Regier, Tom Z ^c  

^a UNIVERSITY OF ROSTOCK   (Germany)

^b UNIVERSITY OF SASKATCHEWAN   (Canada)

^c CANADIAN LIGHT SOURCE INC   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77955804901     PISSN: 01660918     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Book

References (108)

1. Abe, T., Watanabe, A., 2004. X-ray photoelectron spectroscopy of nitrogen functional groups in soil humic acids. Soil Sci. 169, 35-43.
2. Allison, F.E., Doestch, J.H., Roller, E.M., 1953. Availability of fixed ammonium in soils containing different clay minerals. Soil Sci. 75, 373-381.
3. Apen, E., Hitchcock, A.P., Gland, J.L., 1993. Experimental studies of the core excitation of imidazole, 4,5-Dicyanoimidazole, and S-Triazine. J. Phys. Chem. 97, 6859-6866.
4. Ascone, I., Meyer-Klaucke, W., Murphy, L., 2003. Experimental aspects of biological X-ray absorption spectroscopy. J. Synchrotron Radiat. 10, 16-22.
5. Bozack, M.J., Zhou, Y., Worley, S.D., 1994. Structural modifications in the amino-acid lysine induced by soft-X-Ray irradiation. J. Chem. Phys. 100, 8392-8398.
6. Bronner, H., Bachler, W., 1979. Der hydrolysierbare stickstoff als hilfsmittel für die schätzung des stickstoffnachlieferungsvermögens von zuckerrüben. Landwirtschaftliche Forschung 32, 255-261.
7. Burdon, J., 2001. Are the traditional concepts of the structures of humic substances realistic? Soil Sci. 166, 752-769.
8. Carniato, S., Taieb, R., Kukk, E., Luo, Y., Brena, B., 2005. N-K near-edge X-ray-absorption fine structures of acetonitrile in gas phase. J. Chem. Phys. 123, 214301, 1-12.
9. Catroux, G., Schnitzer, M., 1987. Chemical, spectroscopic, and biological characteristics of the organic matter in particle-size fractions separated from an Aquoll. Soil Sci. Soc. Am. J. 51, 1200-1207.
10. Chen, C.T., Sette, F., 1988. Performance of the dragon soft X-ray beamline. Rev. Sci. Instrum. 60, 1616-1621.
11. Cherezov, V., Riedl, K.M., Caffrey, M., 2002. Too hot to handle? Synchrotron X-ray damage of lipid membranes and mesophases. J. Synchrotron Radiat. 9, 333-341.
12. Chong, D.P., 2005. Density functional calculation of K-shell spectra of small molecules. J. Electron Spectros. Relat. Phenomena 148, 115-121.
13. Cutler, J., Hallin, E., de Jong, M., Thomlinson, W., Ellis, T., 2007. The Canadian Light Source: the newest synchrotron in the Americas. Nucl. Instrum. Methods Phys. Res. A 582, 11-13.
14. Coffey, T., Urquhart, S.G., Ade, H., 2002. Characterization of the effects of soft X-ray irradiation on polymers. J. Electron Spectros. Relat. Phenomena 122, 65-78.
15. Cooper, G., Gordon, M., Tulumello, D., Turci, C., Kaznatcheev, K., Hitchcock, A.R., 2004. Inner shell excitation of glycine, glycyl-glycine, alanine and phenylalanine. J. Electron Spectros. Relat. Phenomena 137-40, 795-799.
16. Curl, E.A., Truelove, B., 1986. The Rhizosphere. Springer-Verlag, Berlin.
17. 15N-CPMAS nuclear magnetic resonance spectroscopy and biological stability of soil organic nitrogen in whole soil and particle-sized fractions. Org. Geochem. 34, 1635-1650.
18. Doram, D.R., Evans, L.J., 1983. Native fixed ammonium and fixation of added ammonium in relation to clay mineralogy in some Ontario soils. Can. J. Soil Sci. 63, 631-639.
19. Fan, T.W.M., Lane, A.N., Shenker, M., Bartley, J.P., Crowley, D., Higashi, R.M., 2001. Comprehensive chemical profiling of gramineous plant root exudates using high-resolution. NMR MS Phytochem. 57, 209-221.
20. Franke, R., Bender, S., Hormes, J., 1995. N K-shell absorptionspectra of ionic and molecular-crystals. Physica B 209, 293-294.
21. Fujii, K., Akamatsu, K., Yokoya, A., 2004. Near-edge X-ray absorption fine structure of DNA nucleobases thin film in the nitrogen and oxygen K-edge region. J. Phys. Chem. B 108, 8031-8035.
22. Garman, E.F., McSweeney, S.M., 2007. Progress in research into radiation damage in cryocooled macromolecular crystals. J. Synchrotron Radiat. 14, 1-3.
23. Gillespie, A.W., Walley, F.L., Farrell, R.E., Regier, T.Z., Blyth, R.I.R., 2008. Calibration method at the N K-edge using interstitial nitrogen gas in solid-state nitrogen-containing inorganic compounds. J. Synchrotron Radiat. 15, 532-534.
24. Gillespie, A.W., Walley, F.L., Farrell, R.E., Leinweber, P., Schlichting, A., Eckhardt, K.U., et al., 2009. Profiling rhizosphere chemistry: evidence from C & N K-edge XANES and Py-FIMS. Soil Sci. Soc. Am. J. 73, 2002-2012.
25. Gordon, M.L., Cooper, G., Morin, C., Araki, T., Turci, C.C., Kaznatcheev, K., et al., 2003. Inner-shell excitation spectroscopy of the peptide bond: comparison of the C 1s, N 1s, and O 1s spectra of glycine, glycyl-glycine, and glycyl-glycyl-glycine. J. Phys. Chem. A 107, 6144-6159.
26. Grayston, S.J., Wang, S., Campbell, C.D., Edwards, A.C., 1998. Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol. Biochem. 30, 369-378.
27. Gregorich, E.G., Beare, M.H., Stoklas, U., St-Georges, P., 2003. Biodegradability of soluble organic matter in maize-cropped soils. Geoderma 113, 237-252.
28. Harada, Y., Takeuchi, T., Kino, H., Fukushima, A., Takakura, K., Hieda, K., et al., 2006. Electronic structure of DNA nucleobases and their dinucleotides explored by soft X-ray spectroscopy. J. Phys. Chem. A 110, 13227-13231.
29. Hennig, C., Hallmeier, K.H., Bach, A., Bender, S., Franke, R., Hormes, J., et al., 1996. Influence of substituents on the N K X-ray absorption near-edge structure of pyrrole derivatives. Spectrochim. Acta A 52, 1079-1083.
30. Hermann, K., Pettersson, L.G.M., Casida, M.E., Daul, C., Goursot, A., Koester, A., et al., 2007. StoBe-deMon version 3.0.
31. 2. J. Electron Spectros. Relat. Phenomena 18, 1-21.
32. 3NCS. J. Phys. Chem. 93, 3068-3077.
33. Jeff, J.C., Chappin, F.S., Vitousek, P.M., 2003. Breaks in the cycle: dissolved organic nitrogen in terrestrial ecosystems. Front. Ecol. Environ. 1, 205-211.
34. 15N-ammonium sulphate for five years. Biol. Fertil. Soils 8, 298 302.
35. Jokic, A., Schulten, H.R., Cutler, J.N., Schnitzer, M., Huang, P.M., 2004a. A significant abiotic pathway for the formation of unknown nitrogen in nature. Geophys. Res. Lett. L05502 doi:10.1029/2003GL018520.
36. Jokic, A., Cutler, J.N., Anderson, D.W., Walley, F.L., 2004b. Detection of heterocyclic N compounds in whole soils using N-XANES spectroscopy. Can. J. Soil Sci. 84, 291-293.
37. Kalbitz, K., Solinger, S., Park, H.J., Michalzik, B., Matzner, E., 2000. Controls on the dynamics of dissolved organic matter in soils: a review. Soil Sci. 165, 277-304.
38. Kaneko, F., Tanaka, M., Narita, S., Kitada, T., Matsui, T., Nakagawa, K., et al., 2005. Chemical evolution of amino acid induced by soft X-ray with synchrotron radiation. J. Electron Spectros. Relat. Phenomena 144, 291-294.
39. 15N NMR study of nitrogen forms in carbonaceous solids. Energy Fuels 16, 1507-1515.
40. 15N NMR spectroscopy. J. Environ. Qual. 29, 715-723.
41. Knicker, H., Gonzalez-Vila, F.J., Polvillo, O., Gonzalez, J.A., Almendros, G., 2005. Fire-induced transformation of C- and N-forms in different organic soil fractions from a dystric cambisol under a Mediterranean pine forest (Pinus pinaster). Soil Biol. Biochem. 37, 701-718.
42. Kolczewski, C., Puttner, R., Plashkevych, O., Agren, H., Staemmler, V., Martins, M., et al., 2001. Detailed study of pyridine at the C1s and N1s ionization thresholds: the influence of the vibrational fine structure. J. Chem. Phys. 115, 6426-6437.
43. 15N. Can. J. Soil Sci. 60, 61-70.
44. Körschens, M., Weigel, A., Schulz, E., 1998. Turnover of soil organic matter (SOM) and long-term balances: tools for evaluating sustainable productivity of soils. J. Plant Nutr. Soil Sci. 161, 409-424.
45. Kuzyakov, Y., Leinweber, P., Sapronov, D., Eckardt, K.U., 2003. Qualitative assesment of rhizodeposits in nosterile soil by analytical pyrolysis. J. Plant Nutr. Soil Sci. 166, 719-723.
46. Lehmann, J., Solomon, D., 2008. Nitrogen speciation in soils by near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and scanning transmission X-ray microscopy (STXM). CLS-Report 2008.
47. Leinweber, P., Schulten, H.R., 1998. Nonhydrolyzable organic nitrogen in soil size separates from long-term agricultural experiments. Soil Sci. Soc. Am. J. 62, 383-393.
48. Leinweber, P., Schulten, H.R., 2000. Nonhydrolyzable forms of soil organic nitrogen: extractability and composition. J. Plant Nutr. Soil Sci. 163, 433-439.
49. Leinweber, P., Schulten, H.R., Körschens, M., 1995. Hot water-extracted organic matter: chemical composition and temporal variations in a long-term field experiment. Biol. Fertil. Soils 20, 17-23.
50. Leinweber, P., Kruse, J., Walley, F.L., Gillespie, A., Eckhardt, K.U., Blyth, R.I.R., et al., 2007. Nitrogen K-edge XANES: an overview of reference compounds used to identify 'unknown' organic nitrogen in environmental samples. J. Synchrotron Radiat. 15, 500-511.
51. Leinweber, P., Jandl, G., Baum, C., Eckhardt, K.U., Kandeler, E., 2008. Stability and composition of soil organic matter control respiration and soil enzyme activities. Soil Biol. Biochem. 40, 1496-1505.
52. Leinweber, P., Walley, F.L., Kruse, J., Jandl, G., Eckhardt, K.U., Blyth, R., et al., 2009. Cultivation affects soil organic nitrogen: pyrolysis-mass spectrometry and N K-edge XANES evidence. Soil Sci. Soc. Am. J. 73, 82-92.
53. MacNaughton, J., Moewes, A., Kurmaev, E.Z., 2005. Electronic structure of the nucleobases. J. Phys. Chem. B 109, 7749-7757.
54. Mengel, K., 1996. Turnover of organic nitrogen in soils and its availability to crops. Plant Soil 181, 83-93.
55. Mitra-Kirtley, S., Mullins, O.C., Chen, J., Vanelp, J., George, S.J., Chen, C.T., et al., 1992. Nitrogen chemical-structure in DNA and related molecules by X-Ray absorption-spectroscopy. Biochim. Biophys. Acta 1132, 249-254.
56. Mitra-Kirtley, S., Mullins, O.C., Vanelp, J., George, S., Chen, J., Cramer, S.P., 1993. Determination of the nitrogen chemical structures in petroleum asphaltenes using @ spectroscopy. J. Am. Chem. Soc. 115, 252-258.
57. Mullins, O.C., Mitrakirtley, S., Vanelp, J., Cramer, S.P., 1993. Molecular structure of nitrogen in coal from XANES spectroscopy. Appl. Spectrosc. 47, 1268-1275.
58. O'Neill, P., Stevens, D.L., Garman, E.F., 2002. Physical and chemical considerations of damage induced in protein crystals by synchrotron radiation: a radiation chemical perspective. J. Synchrotron Radiat. 9, 329-332.
59. Palm, C.A., Sanchez, P.A., 1991. Nitrogen release from the leaves of some tropical legumes as affected by their lignin and polyphenolic contents. Soil Biol. Biochem. 23, 83-88.
60. Paul, A.E., Clark, F.E., 1996. Soil Microbiology and Biochemistry, 2nd ed Academic Press, Orlando.
61. Petravic, M., Gao, Q., Llewellyn, D., Deenapanray, P.N.K., Macdonald, D., Crotti, C., 2006. Broadening of vibrational levels in X-ray absorption spectroscopy of molecular nitrogen in compound semiconductors. Chem. Phys. Lett. 425, 262-266.
62. Pinton, R., Varanini, Z., Nannipieri, P., 2007. The Rhizosphere: Biochemistry and Organic Substances at the Soil-Plant Interface, second ed. Marcel Dekker, New York, NY.
63. 3 observed by X-ray absorption and resonant Auger spectroscopy. Phys. Rev. B 65, 205116.
64. Ravel, B., Newville, M., 2005. ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectroscopy using IFEFFIT. J. Synchrotron Radiat. 12, 537-541.
65. Regier, T., Krochak, J., Sham, T.K., Hu, Y.F., Thompson, J., Blyth, R.I.R., 2007a. Performance and capabilities of the Canadian Dragon: the SGM beamline at the Canadian Light Source. Nucl. Instrum. Methods A 582, 93-95.
66. Regier, T., Paulsen, J., Wright, G., Coulthard, I., Tan, K., Sham, T.K., et al., 2007b. Commissioning of the spherical grating monochromator (SGM) soft X-ray spectroscopy beamline at the Canadian Light Source. AIP Conf. Proc. 879, 473-476.
67. 3. J. Chem. Phys. 112, 9929-9939.
68. Rosier, C.L., Hoye, A.T., Rillig, M.C., 2006. Glomalin-related soil protein: assessment of current detection and quantification tools. Soil Biol. Biochem. 38, 2205-2211.
69. Samuel, N.T., Lee, C.Y., Gamble, L.J., Fischer, D.A., Castner, D.G., 2006. NEXAFS characterization of DNA components and molecular-orientation of surface-bound DNA oligomers. J. Electron Spectros. Relat. Phenomena 152, 134-142.
70. Schirmer, J., Trofimov, A.B., Randall, K.J., Feldhaus, J., Bradshaw, A.M., Ma, Y., et al., 1993. K-shell excitation of the water, ammonia, and methane molecules using high-resolution photoabsorption spectroscopy. Phys. Rev. A 47, 1136-1147.
71. Schnitzer, M., 1991. Soil organic matter-the next 75 years. Soil Sci. 51, 41-58.
72. Schulten, H.R., Leinweber, P., 2000. New insights in organic-mineral particles: composition, properties and models of molecular structure. Biol. Fertil. Soils 30, 399-432.
73. Schulten, H.R., Schnitzer, M., 1998. The chemistry of soil organic nitrogen: a review. Biol. Fertil. Soils 26, 1-15.
74. Schulten, H.R., Sorge-Lewin, C., Schnitzer, M., 1997. Structure of "unknown" soil nitrogen investigated by analytical pyrolysis. Biol. Fertil. Soils 24, 249-254.
75. Schwarzkopf, O., Borchert, M., Eggenstein, F., Flechsig, U., Kalus, C., Lammert, H., et al., 1999. The BESSY constant length rowland circle monochromator. J. Electron Spectros. Relat. Phenomena 101-103, 997-1001.
76. (2+) formation controlled by vibrational motion in core-excited ammonia. J. Electron Spectros. Relat. Phenomena 144, 195-197.
77. Shen, S., Tu, S.I., Kemper, W.D., 1997. Equilibrium and kinetic study of ammonium absorption and fixation in sodium-treated vermiculite. Soil Sci. Soc. Am. J. 61, 1611-1618.
78. Siemens, J., Kaupenjohann, M., 2002. Contribution of dissolved organic nitrogen to N leaching from four German agricultural soils. J. Plant Nutr. Soil Sci. 165, 675-681.
79. Simakov, M.B., Kuzicheva, E.A., Malko, I.L., Dodonova, N.Y., 1996. Abiogenic synthesis of oligopeptides in solid state under action of vacuum ultraviolet light (100-200 nm). Life Sci. Space Mars Recent Results 18, 61-64.
80. Sims, G.K., 2006. Nitrogen starvation promotes biodegradation of N-heterocyclic compounds in soil. Soil Biol. Biochem. 38, 2478-2480.
81. 15N-enriched plant materials. Plant Soil 275, 271-283.
82. 15N NMR spectroscopy detect all soil organic nitrogen? Biogeochemistry 75, 507-528.
83. Smolander, A., Kitunen, V., 2002. Soil microbial activities and characteristics of dissolved organic C and N in relation to tree species. Soil Biol. Biochem. 34, 651-660.
84. Sparks, D.L., 2003. Environmental Soil Chemistry, Chap. 2, Academic Press, Amsterdam.
85. Sparling, G.P., Vojvodic-Vukovic, M., Schipper, L.A., 1998. Hot-water-soluble C as a simple measure of labile soil organic matter: the relationship with microbial biomass C. Soil Biol. Biochem. 30, 1469-1472.
86. Stankiewicz, B.A., van Bergen, P.F., 1998. Nitrogen and N-containing macromolecules in the bio- and geosphere: an Introduction. ACS Symp. Ser. 702, 1-12.
87. Stevenson, F.J., 1994. Humus Chemistry, Genesis, Composition, Reactions, second ed. John Wiley and Sons, New York.
88. Stewart-Ornstein, J., Hitchcock, A.P., Cruz, D.H., Henklein, P., Overhage, J., Hilpert, K., et al., 2007. Using intrinsic X-ray absorption spectral differences to identify and map peptides and proteins. J. Phys. Chem. B 111, 7691-7699.
89. Stöhr, J., 1992. NEXAFS Spectroscopy, Chap. 5, Springer-Verlag, Berlin.
90. 2 adsorption. J. Electron Spectros. Relat. Phenomena 150, 164-170.
91. Takahashi, O., Pettersson, L.G.M., 2004. Functional dependence of core-excitation energies. J. Chem. Phys. 121, 10339-10345.
92. Thorn, K.A., Mikita, M.A., 2000. Nitrite fixation by humic substances: nitrogen-15 nuclear magnetic resonance evidence for potential intermediates in chemodenitrification. Soil Sci. Soc. Am. J. 64, 568-582.
93. Török, S., Osan, J., Beckhoff, B., Ulm, G., 2004. Ultratrace speciation of nitrogen compounds in aerosols collected on silicon wafer surfaces by means of TXRF-NEXAFS. Powder Diffr. 19, 81-86.
94. Triguero, L., Pettersson, L.G.M., Agren, H., 1998. Calculations of near-edge X-ray-absorption spectra of gas-phase and chemisorbed molecules by means of density-functional and transition-potential theory. Phys. Rev. B 58, 8097-8110.
95. Uren, N.C., 2007. Types, amounts, and possible functions of compounds released into the rhizosphere by soil-grown plants. In: Pinton, et al., (Ed.), The Rhizosphere: Biochemistry and Organic Substances at the Soil-Plant Interface. second ed. Marcel Dekker, New York, pp. 1-21.
96. Vairavamurthy, A., Wang, S., 2002. Organic nitrogen in geomacromolecules: insights on speciation and transformation with K-edge XANES spectroscopy. Environ. Sci. Technol. 36, 3050-3056.
97. Vall-Ilosera, G., Gao, B., Kivimaki, A., Coreno, M., Ruiz, J.A., de Simone, M., et al., 2008. The C 1s and N 1s near edge X-ray absorption fine structure spectra of five azabenzenes in the gas phase. J. Chem. Phys. 128, 044316.
98. Vitousek, P.M., Howarth, R.W., 1991. Nitrogen limitation on land and in the sea: how can it occur? Biogeochemistry 13, 87-115.
99. Vitousek, P.M., Aber, J., Howarth, R.W., Likens, G.E., Matson, P.A., Schindler, D.W., et al., 1997. Human alteration of the global nitrogen cycle: sources and consequences. Ecol. Appl. 7, 737-750.
100. Watts, B., Thomsen, L., Dastoor, P.C., 2006. Methods in carbon K-edge NEXAFS: experiment and analysis. J. Electron Spectros. Relat. Phenomena 101, 105-120.
101. Wilson, C.C., 1994. Pulsed-neutron single-crystal study of the structure of 3-Deazauracil. J. Chem. Crystallogr. 24, 371-373.
102. Wright, S.F., Upadhyaya, A., 1998. A survey of soils for aggregate stability and glomalin, a glycoprotein produced by hyphae of arbuscular mycorrhizal fungi. Plant Soil 198, 97-107.
103. Zhuang, S., Xu, M., Hu, Z., 2006. Determination of forest soil organic nitrogen determination using technique of X-ray adsorption near-edge structure. J. For. Res. 17, 189-192.
104. Zubavichus, Y., Fuchs, O., Weinhardt, L., Heske, C., Umbach, E., Denlinger, J.D., et al., 2004a. Soft X-ray-induced decomposition of amino acids: an XPS, mass spectrometry, and NEXAFS study. Radiat. Res. 161, 346-358.
105. Zubavichus, Y., Zharnikov, M., Shaporenko, A., Fuchs, O., Weinhardt, L., Heske, C., et al., 2004b. Soft X-ray induced decomposition of phenylalanine and tyrosine: a comparative study. J. Phys. Chem. A 108, 4557-4565.
106. Zubavichus, Y., Zharnikov, M., Schaporenko, A., Grunze, M., 2004c. NEXAFS study of glycine and glycine-based oligopeptides. J. Electron Spectros. Relat. Phenomena 134, 25-33.
107. Zubavichus, Y., Shaporenko, A., Grunze, M., Zharnikov, M., 2005. Innershell absorption spectroscopy of amino acids at all relevant absorption edges. J. Phys. Chem. A 109, 6998-7000.
108. Zubavichus, Y., Shaporenko, A., Grunze, M., Zharnikov, M., 2006. Solid-state near-edge X-ray absorption fine structure spectra of glycine in various charge states. J. Phys. Chem. B 110, 3420-3427.