Abstract
Soil nitrogen (N) is in a constant state of flux, moving and changing chemical forms. Nitrification and denitrification are the main processes to remove reactive N (Nr) from the environment. Both are predominantly microbial processes that provide energy to specialized groups of microorganisms. Nitrification oxidizes reduced N, generally NH3 or NH +4 to NO −3 via nitrite under aerobic conditions. Denitrification is the process under which oxidized N is reduced back into N2 under anaerobic conditions. Autotrophic nitrification and heterotrophic denitrification are the major N2O forming processes in terrestrial and aquatic forming in terrestrial and aquatic ecosystems. Major factors regulating nitrification and denitrification are the availability of reactive N, the availability of reductant (mostly labile organic carbon compounds), and oxygen concentration. These three factors are in turn governed by many other factors such as water content, pH, porosity, and the presence of inhibitory compounds, which may act to cause accumulation of ionic (nitrite) or gaseous (nitric oxide, nitrous oxide) intermediates. It has been estimated that soils under terrestrial ecosystems denitrify ~124 Tg N year−1 or about 35–40% of total land based reactive N. Arable soils receiving high inputs of N are hot spots for denitrification and dominant sources of anthropogenic N2O emissions.
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- ATP:
-
adenosine triphosphate
- AMO:
-
ammonia monooxygenase
- HAO:
-
hydroxylamine oxidoreductase
- NADPH:
-
nicotinamide adenine dinucleotide phosphate oxidase
- OM:
-
organic matter
- SOM:
-
soil organic matter
- DNRA:
-
dissimilatory nitrate reduction to ammonium
- CEC:
-
cation exchange capacity
- SOC:
-
soil organic carbon
- AOB:
-
ammonia oxidizing bacteria
- WHO:
-
World Health Organization of the United Nations
- US EPA:
-
U.S. Environmental Protection Agency
- NT:
-
no tillage
References
Arp, D.J., Sayavedra-Soto, L.A., Hommes, N.G. (2002) Molecular biology and biochemistry of ammonia oxidation byNitrosomonas europaea. Arch. Microbiol.178(4), 250–255. doi:10.1007/s00203-002-0452-0
Averill, B.A., Tiedje, J.M. (1982) The chemical mechanism of microbial denitrification. Febs Lett.138(1), 8–12
Balderston, W.L., Sherr, B., Payne, W.J. (1976) Blockage by acetylene of nitrous oxide reduction inPseudomonas perfectomarinus. Appl. Environ. Microbiol.31(4), 504–508
Barton, L., McLay, C.D.A., Schipper, L.A., Smith, C.T. (1999) Annual denitrification rates in agricultural and forest soils: a review. Aus. J. Soil Res.37(6), 1073–1093. doi:10.1071/sr99009
Bartosch, S., Hartwig, C., Spieck, E., Bock, E. (2002) Immunological detection of nitrospira-like bacteria in various soils. Microbial Ecol.43(1), 26–33. doi:10.1007/s00248-001-0037-5
Basu, P., Katterle, B., Andersson, K.K., Dalton, H. (2003) The membrane-associated form of methane mono-oxygenase fromMethylococcus capsulatus (Bath) is a copper/iron protein. Biochem. J.369, 417–427. doi:10.1042/bj20020823
Bateman, E.J., Baggs, E.M. (2005) Contributions of nitrification and denitrification to N2O emissions from soils at different water-filled pore space. Biol. Fert. Soils41(6), 379–388. doi:10.1007/s00374-005-0858-3
Bedard-Haughn, A., Matson, A.L., Pennock, D.J. (2006) Land use effects on gross nitrogen mineralization, nitrification, and N2O emissions in ephemeral wetlands. Soil Biol. Biochem.38(12), 3398–3406. doi:10.1016/j.soilbio.2006.05.010
Belser, L.W. (1979) Population ecology of nitrifying bacteria. Annu. Rev. Microbiol.33, 309–333
Blagodatskiy, S.A., Avksent'ev, A.A., Davydova, M.A., Blagodatskaya, E.V., Kurakov, A.V. (2008) Nitrous oxide production in soils and the ratio of the fungal to bacterial biomass. Eurasian Soil Sci.41(13), 1448–1455. doi:10.1134/s1064229308130140
Bleakley, B.H., Tiedje, J.M. (1982) NIitrous oxide production by organisms other than nitrifiers or denitrifiers. Appl. Environ. Microbiol.44(6), 1342–1348
Bollmann, A., Conrad, R. (1997) Acetylene blockage technique leads to underestimation of denitrification rates in oxic soils due to scavenging of intermediate nitric oxide. Soil Biol. Biochem.29(7), 1067–1077
Bowden, W.B. (1986) Gaseous nitrogen emissions from undisturbed terrestrial ecosystems: An assessment of their impacts on local and global nitrogen budgets. Biogeochemistry2(3), 249–279
Bremner, J.M. (1997) Sources of nitrous oxide in soils. Nutr. Cycl. Agroecosys.49(1–3), 7–16. doi:10.1023/a:1009798022569
Butterbach-Bahl, K., Kock, M., Willibald, G., Hewett, B., Buhagiar, S., Papen, H., Kiese, R. (2004) Temporal variations of fluxes of NO, NO2, N2O, CO2, and CH4 in a tropical rain forest ecosystem. Glob. Biogeochem. Cycles18(3), GB3012. doi:10.1029/2004gb002243
Butterbach-Bahl, K., Willibald, G., Papen, H. (2002) Soil core method for direct simultaneous determination of N2 and N2O emissions from forest soils. Plant Soil240(1), 105–116
Casciotti, K.L., Bohlke, J.K., McIlvin, M.R., Mroczkowski, S.J., Hannon, J.E. (2007) Oxygen isotopes in nitrite: Analysis, calibration, and equilibration. Anal. Chem.79(6), 2427–2436. doi:10.1021/ac061598h
Chain, P., Lamerdin, J., Larimer, F., Regala, W., Lao, V., Land, M., Hauser, L., Hooper, A., Klotz, M., Norton, J., Sayavedra-Soto, L., Arciero, D., Hommes, N., Whittaker, M., Arp, D. (2003) Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea (vol 185, pg 2759, 2003). J. Bacteriol.185(21), 6496–6496. doi:10.1128/jb.185.21.2003.6496
Chalk, P.M., Smith, C.J. (1983) Chemodenitrification. In: Freney, J.R., Simpson, J.R. (eds.) Gaseous loss of nitrogen from plant-soil systems. Development in plant soil sciences9. 65–89.
Chapuis-Lardy, L., Wrage, N., Metay, A., Chotte, J.L., Bernoux, M. (2007) Soils, a sink for N2O? A review. Global Change Biol.13, 1–17
Codispoti, L.A., Brandes, J.A., Christensen, J.P., Devol, A.H., Naqvi, S.W.A., Paerl, H.W., Yoshinari, T. (2001) The oceanic fixed nitrogen and nitrous oxide budgets: Moving targets as we enter the anthropocene? Sci. Mar.65, 85–105
Codispoti, L.A., Yoshinari, T., Devol, A.H. ( 2005) Suboxic respiration in the oceanic water-column. In: del Giorgio, P.A., Williams, P.J.l.B. (eds.) Respiration in Aquatic Ecosystems. pp. 225–247. Oxford University Press, Oxford, U.K.
Conen, F., Neftel, A. (2007) Do increasingly depleted delta N-15 values of atmospheric N2O indicate a decline in soil N2O reduction? Biogeochemistry82(3), 321–326. doi:10.1007/s10533-006-9066-y
Conrad, R. (1990) Flux of NOx between soil and atmosphere: Importance and soil microbial metabolism. In: Revsbech, N.P., Sorensen, J. (eds.) Denitrification in Soil and Sediments. pp. 105–128. Plenum, New York
Conrad, R. (1995) Soil microbial processes involved in production and consumption of atmospheric trace gases. Adv. Microb. Ecol.14, 207–250
Conrad, R. (1996) Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microbiol. Rev.60(4), 609–640
Conrad, R. (2002) Microbial and biogeochemical background of production and consumption of NO and N2O in soil. In: Gasche, R., Papen, H., Rennenberg, H. (eds.) Trace Gas Exchange in Forest Ecosystem. pp. 3–33. Springer, New York, USA
Cookson, W.R., Cornforth, I.S., Rowarth, J.S. (2002) Winter soil temperature (2-4 °C) effects on nitrogen transformations in clover green manure amended or unamended soils; a laboratory and field study. Soil Biol. Biochem.34(10), 1401–1415
Coyne, M.S., Tiedje, J.M. (1990) Induction of denitrifying enzymes in oxygen-limitedAchromobacter cycloclastes continuous culture. Fems Microbiol. Ecol.73(3), 263–270. doi:10.1111/j.1574-6968.1990.tb03949.x
Coyne, M.S. (2008) Biological denitrification. In: Schepers, J.S., Raun, W.R. (eds.) Nitrogen in agricultural soils. Agronomy Monograph No. 49, pp. 201–253. ASA-CSSA-SSSA, Madison, WI
Dambreville, C., Hallet, S., Nguyen, C., Morvan, T., Germon, J.C., Philippot, L. (2006) Structure and activity of the denitrifying community in a maize-cropped field fertilized with composted pig manure or ammonium nitrate. Fems Microbiol. Ecol.56(1), 119–131. doi:10.1111/j.1574-6941.2006.00064.x
Davidson, E.A., Myrold, D.D., Groffman, P.M. (1990) Denitrification in temperate forest ecosystems. In: Gessel, S.P., Lacate, D.S., Weetam, G.F., Powers, R.F. (eds.) Sustained productivity of forest soils. Proceedings of 7th North America Forest Soils Conference. pp. 196–220. University of British Columbia, Vancouver, Britis Columbia
Davidson, E.A., Vitousek, P.M., Matson, P.A., Riley, R., Garciamendez, G., Maass, J.M. (1991) Soil emissions of nitric-oxide in a seasonally dry tropical forest of Mexico. J. Geophys. Res.-Atmos.96(D8), 15439–15445
De Boer, W., Kowalchuk, G.A. (2001) Nitrification in acid soils: microorganisms and mechanisms. Soil Biol. Biochem.33(7–8), 853–866
Devol, A.H. (2008) Denitrification inluding anammox. In: Capone, D.G., Bronk, D.A., Muholland, M.R., Carpenter, E.J. (eds.) Nitrogen in the Marine Environment. pp. 263–301. Elsevier Amsterdam, The Netherland
Dutch, J., Ineson, P. (1990) Denitrification of an upland forest site. Forestry63(4), 363–377. doi:10.1093/forestry/63.4.363
Duxbury, J.M., McConnaughey, P.K. (1986) Effect of fertilizer source on denitrification and nitrous oxide emissions in a maize field. Soil Sci. Soc. Am. J.50(3), 644–648
Enwall, K., Philippot, L., Hallin, S. (2005) Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization. Appl. Environ. Microbiol.71(12), 8335–8343. doi:10.1128/aem.71.12.8335-8343.2005
Firestone, M.K., Davidson, E.A. (1989) Microrbiolgical basis of NO and N2O production and consumption in soil. In: Andreae, M.O., Schimel, D.S. (eds.) Exchange of Trace Gases between Terrestrial Ecosystems and the Atmosphere, Life Sciences Research Report47, 7–21.
Focht, D.D., Verstraete, W. (1977) Biochemical ecology of nitrification and denitrification. In: Alexander, M. (ed.) Advances in Microbial Ecology1, 135–214. Plenum Press, New York
Forrest, W.W., Walker, D.J. (1971) The generation and utilization of energy during growth. Adv. Microb. Physiol.5, 213–274
Freney, J.R. (1997) Emission of nitrous oxide from soils used for agriculture. Nutr. Cycl. Agroecosys.49(1–3), 1–6
Galloway, J.N., Aber, J.D., Erisman, J.W., Seitzinger, S.P., Howarth, R.W., Cowling, E.B., Cosby, B.J. (2003) The nitrogen cascade. Bioscience53(4), 341–356
Gasche, R., Papen, H. (1999) A 3-year continuous record of nitrogen trace gas fluxes from untreated and limed soil of a N-saturated spruce and beech forest ecosystem in Germany. 2. NO and NO2 fluxes. J. Geophys. Res.-Atmos.104(D15), 18505–18520
Godde, M., Conrad, R. (2000) Influence of soil properties on the turnover of nitric oxide and nitrous oxide by nitrification and denitrification at constant temperature and moisture. Biol. Fert. Soils32(2), 120–128
Groffman, P.M., Altabet, M.A., Böhlke, J.K., Butterbach-Bahl, K., David, M.B., Firestone, M.K., Giblin, A.E., Kana, T.M., Nielsen, L.P., Voytek, M.A. (2006) Methods for measuring denitrification: Diverse approaches to a difficult problem. Ecol. Appl.16(6), 2091–2122
Groffman, P.M., Rice, C.W., Tiedje, J.M. (1993) Denitrification in a tallgrass Prairie landscape. Ecology74(3), 855–862. doi:10.2307/1940811
Haynes, R.J. (1995) Nitrous oxide budget Enc. Environ. Biol.2, 579–585
Henrich, M., Haselwandter, K. (1997) Denitrification and gaseous nitrogen losses from an acid spruce forest soil. Soil Biol. Biochem.29(9–10), 1529–1537. doi:10.1016/s0038-0717(97)00010-2
Henry, S., Baudoin, E., Lopez-Gutierrez, J.C., Martin-Laurent, F., Baumann, A., Philippot, L. (2004) Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR. J. Microbiol. Meth.59(3), 327–335. doi:10.1016/j.mimet.2004.07.002
Henry, S., Bru, D., Stres, B., Hallet, S., Philippot, L. (2006) Quantitative detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils. Appl. Environ. Microbiol.72(8), 5181–5189. doi:10.1128/aem.00231-06
Hofstra, N., Bouwman, A.F. (2005) Denitrification in agricultural soils: Summarizing published data and estimating global annual rates. Nutr. Cycl. Agroecosys.72(3), 267–278. doi:10.1007/s10705-005-3109-y
Hooper, A.B.. (1968) A nitrite-reducing enzyme fromNitrosomonas europaea: preliminary characterization with hydroxylamine as electron donor. Biochim. Biophys. Acta162(1), 49–65
Hooper, A.B.., Vannelli, T., Bergmann, D.J., Arciero, D.M. (1997) Enzymology of the oxidation of ammonia to nitrite by bacteria. Ant. Leew. Int. J. G. Mol. Microb.71(1–2), 59–67
Jarvis, S.C. (1996) Future trends in nitrogen research. Plant Soil181(1), 47–56
Jetten, M.S.M., Logemann, S., Muyzer, G., Robertson, L.A., deVries, S., vanLoosdrecht, M.C.M., Kuenen, J.G. (1997) Novel principles in the microbial conversion of nitrogen compounds. Ant. Leew. Int. J. G. Mol. Microb.71(1–2), 75–93
Johansson, C., Sanhueza, E. (1988) Emission of NO from savanna soils during rainy season. J. Geophys. Res.-Atmos.93(D11), 14193–14198
Kelly, D.P. (1978) Bioenergetics of chemolithotrophic bacteria. In: Bull, Meadow (eds.) Companion to microbiology. pp. 363–386. Longman, London
Killham, K. (1990) Nitrification in coniferous forest soils. Plant Soil128(1), 31–44
Kim, D.Y., Burger, J.A. (1997) Nitrogen transformations and soil processes in a wastewater-irrigated, mature Appalachian hardwood forest. Forest Ecol. Manag.90(1), 1–11. doi:10.1016/s0378-1127(96)03889-3
Knowles, R. (1982) Denitrification. Microbiol. Rev.46(1), 43–70
Knowles, R. (1996) Denitrification: microbiology and ecology. Life Support Bioph. Sci.3(1–2), 31–34
Konneke, M., Bernhard, A.E., de la Torre, J.R., Walker, C.B., Waterbury, J.B., Stahl, D.A. (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature437(7058), 543–546. doi:10.1038/nature03911
Kool, D.M., Wrage, N., Oenema, O., Harris, D., Van Groenigen, J.W. (2009) The O-18 signature of biogenic nitrous oxide is determined by O exchange with water. Rapid Comm. Mass Sp.23(1), 104–108. doi:10.1002/rcm.3859
Koops, H.P., Bottcher, B., Moller, U.C., Pommereningroser, A., Stehr, G. (1991) Classification of 8 new species of ammonia-oxidizing bacteria:Nitrosomonas communis sp-novNitrosomonas ureae sp-novNitrosomonas aestuarii sp-novNitrosomonas marina sp-novNitrosomonas nitrosa sp-novNitrosomonas eutropha sp-novNitrosomonas oligotropha sp-nov andNitrosomonas halophila sp-nov. J. Gen. Microbiol.137, 1689–1699
Koops, H.P., Moller, U.C. (1992) The lithotropic ammonia-oxidizing bacteria. In: Ballows (ed.) Prokaryotes111,2625–2637. Springer, New York
Kowalchuk, G.A., Stephen, J.R. (2001) Ammonia oxidizing bacteria: A model for molecular microbial ecology. Annu. Rev. Microbiol.55, 485–529. doi:10.1146/annurev.micro.55.1.485
Laanbroek, H.J., Gerards, S. (1993) Competition for limiting amounts of oxygen betweenNitrosomonas europaea andNitrobacter winogradskyi grown in mixed continuous cultures. Arch. Microbiol.159(5), 453–459
Laughlin, R.J., Stevens, R.J. (2002) Evidence for fungal dominance of denitrification and codenitrification in a grassland soil. Soil Sci. Soc. Am. J.66(5), 1540–1548
Laughlin, R.J., Stevens, R.J., Muller, C., Watson, C.J. (2008) Evidence that fungi can oxidize NH +4 to NO −3 in a grassland soil. Eur. J. Soil Sci.59(2), 285–291. doi:10.1111/j.1365-2389.2007.00995.x
Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G.W., Prosser, J.I., Schuster, S.C., Schleper, C. (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature442, 806–809. doi:10.1038/nature04983
Li, D., Wang, X. (2008) Nitrogen isotopic signature of soil-released nitric oxide (NO) after fertilizer application. Atmos. Environ.42(19), 4747–4754. doi:10.1016/j.atmosenv.2008.01.042
Linn, D.M., Doran, J.W. (1984) Effect of water-filled pore space on carbon dioxide and nitrous oxide production in tilled and nontilled soils. Soil Sci. Soc. Am. J.48(6), 1267–1272
Luther, G.W., Brendel, P.J., Lewis, B.L., Sundby, B., Lefrancois, L., Silverberg, N., Nuzzio, D.B. (1998) Simultaneous measurement of O2, Mn, Fe, I-, and S(-II) in marine pore waters with a solid state voltammetric microelectrode. Limnol. Oceanogr.43(2), 325–333
Mahne, I., Tiedje, J.M. (1995) Criteria and methodology for identifying respiratory denitrifiers. Appl. Environ. Microbiol.61(3), 1110–1115
Mogge, B., Kaiser, E.A., Munch, J.C. (1999) Nitrous oxide emissions and denitrification N-losses from agricultural soils in the Bornhöved Lake region: influence of organic fertilizers and land-use. Soil Biol. Biochem.31(9), 1245–1252
Morley, N., Baggs, E.M., Dorsch, P., Bakken, L. (2008) Production of NO, N2O and N2 by extracted soil bacteria, regulation by NO −2 and O2 concentrations. Fems Microbiol. Ecol.65(1), 102–112. doi:10.1111/j.1574-6941.2008.00495.x
Mosier, A.R. (1998) Soil processes and global change. Biol. Fert. Soils27(3), 221–229
Mosier, A.R., Duxbury, J.M., Freney, J.R., Heinemeyer, O., Minami, K. (1996) Nitrous oxide emissions from agricultural fields: Assessment, measurement and mitigation. Plant Soil181(1), 95–108. doi:10.1007/bf00011296
Mulvaney, R.L., Khan, S.A., Mulvaney, C.S. (1997) Nitrogen fertilizers promote denitrification. Biol. Fert. Soils24(2), 211–220
Myers, R.J.K. (1975) Temperature effects on ammonification and nitrification in a tropical soil. Soil Biol. Biochem.7(2), 83–86. doi:10.1016/0038-0717(75)9-6
Myrold, D.D., Tiedje, J.M. (1985) Diffusional constraints on denitrification in soil. Soil Sci. Soc. Am. J.49(3), 651–657
Norton, J.M. (2008) Nitrification in agricultural soils. In: Schepers, J.S., Raun, W.R. (eds.) Nitrogen in agricultural soils. Agronomy Monograph No. 49, pp. 173–199. ASA-CSSA-SSSA, Madison, WI
Norton, J.M., Alzerreca, J.J., Suwa, Y., Klotz, M.G. (2002) Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Arch. Microbiol.177(2), 139–149. doi:10.1007/s00203-001-0369-z
O'hara, G.W., Daniel, R.M. (1985) Rhizobial denitrification: A review. Soil Biol. Biochem.17(1), 1–9
Odu, C.T.I., Adeoye, K.B. (1970) Heterotrophic nitrification in soils - a preliminary investigation. Soil Biol. Biochem.2, 41–45
Papen, H., Vonberg, R., Hinkel, I., Thoene, B., Rennenberg, H. (1989) Heterotrophic nitrification byAlcaligenes faecalis: NO −2 , NO −3 , N2O, and NO production in exponentially growing cultures. Appl. Environ. Microbiol.55(8), 2068–2072
Patureau, D., Zumstein, E., Delgenes, J.P., Moletta, R. (2000) Aerobic denitrifiers isolated from diverse natural and managed ecosystems. Microbial Ecol.39(2), 145–152. doi:10.1007/s002480000009
Payne, W.J. (1973) Reduction of nitrogenous oxides by microorganisms. Becterial. Reviews37(4), 409–452
Perez, T., Trumbore, S.E., Tyler, S.C., Matson, P.A., Ortiz-Monasterio, I., Rahn, T., Griffith, D.W.T. (2001) Identifying the agricultural imprint on the global N2O budget using stable isotopes. J. Geophys. Res.-Atmos.106(D9), 9869–9878
Philippot, L. (2002) Denitrifying genes in bacterial and Archaeal genomes. Bioch. Biophys. Acta1577(3), 355–376
Philippot, L., Hallin, S., Borjesson, G., Baggs, E.M. (2009) Biochemical cycling in the rhizosphere having an impact on global change. Plant Soil321(1–2), 61–81. doi:10.1007/s11104-008-9796-9
Philippot, L., Hallin, S., Schloter, M. (2007) Ecology of denitrifying prokaryotes in agricultural soil. Adv. Agron.96, 249–305. doi:10.1016/s0065-2113(07)96003-4
Philippot, L., Piutti, S., Martin-Laurent, F., Hallet, S., Germon, J.C. (2002) Molecular analysis of the nitrate-reducing community from unplanted and maize-planted soils. Appl. Environ. Microbiol.68(12), 6121–6128. doi:10.1128/aem.68.12.6121-6128.2002
Pina-Ochoa, E., Hogslund, S., Geslin, E., Cedhagen, T., Revsbech, N.P., Nielsen, L.P., Schweizer, M., Jorissen, F., Rysgaard, S., Risgaard-Petersen, N. (2010) Widespread occurrence of nitrate storage and denitrification among Foraminifera and Gromiida. Proc. Natl. Acad. Sci. USA107(3), 1148–1153. doi:10.1073/pnas.0908440107
Poth, M., Focht, D.D. (1985) N-15 Kinetic analysis of N2O production by Nitrosomonas europaea: an examination of nitrifier denitrification. Appl. Environ. Microbiol.49(5), 1134–1141
Prendergast-Miller, M.T., Baggs, E.M., Johnson, D. (2011) Nitrous oxide production by the ectomycorrhizal fungiPaxillus involutus andTylospora fibrillosa. Fems Microbiol. Lett.316(1), 31–35. doi:10.1111/j.1574-6968.2010.02187.x
Prosser, J.I. (1989) Autotrophic nitrification in bacteria. Adv. Microb. Physiol.30, 125–181
Prosser, J.I. (2005) Nitrification. In: Hillel, D. (ed.) Encyclopedia of soils in the environment, vol. 3. pp. 31–39. Elsevier Academic Press, Oxford
Purkhold, U., Wagner, M., Timmermann, G., Pommerening-Roser, A., Koops, H.P. (2003) 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads. Int. J. Syst. Evol. Micr.53, 1485–1494. doi:10.1099/ijs.0.02638-0
Ravishankara, A.R., Daniel, J.S., Portmann, R.W. (2009) Nitrous oxide (N2O): The oominant ozone-depleting substance emitted in the 21st Century. Science326(5949), 123–125. doi:10.1126/science.1176985
Ritchie, G.A.F., Nicholas, D.J. (1972) Identification of sources of nitrous oxide produced by oxidative and reductive processes inNitrosomonas europaea. Biochem. J.126(5), 1181–1191
Robertson, G.P., Tiedje, J.M. (1987) Nitrous oxide sources in aerobic soils: Nitrification, denitrification and other biological processes. Soil Biol. Biochem.19(2), 187–193
Robertson, L.A., Kuenen, J.G. (1990) Combined heterotrophic nitrification and aerobic denitrification inThiosphaera pantotropha and other bacteria. Ant. Leew. Int. J. G. Mol. Microb.57(3), 139–152
Robertson, L.A., Vanniel, E.W.J., Torremans, R.A.M., Kuenen, J.G. (1988) Simultaneous nitrification and denitrification in aerobic chemostat cultures ofThiosphaera pantotropha. Appl. Environ. Microbiol.54(11), 2812–2818
Rotthauwe, J.H., Witzel, K.P., Liesack, W. (1997) The ammonia monooxygenase structural gene amoA as a functional marker: Molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol.63(12), 4704–4712
Rutting, T., Huygens, D., Muller, C., Cleemput, O., Godoy, R., Boeckx, P. (2008) Functional role of DNRA and nitrite reduction in a pristine south ChileanNothofagus forest. Biogeochemistry90(3), 243–258. doi:10.1007/s10533-008-9250-3
Rutting, T., Clough, T.J., Muller, C., Lieffering, M., Newton, P.C.D. (2010) Ten years of elevated atmospheric carbon dioxide alters soil nitrogen transformations in a sheep-grazed pasture. Global Change Biol.16(9), 2530–2542. doi:10.1111/j.1365-2486.2009.02089.x
Ryden, J.C., Lund, L.J. (1980) Nature and extent of directly measured denitrification losses from some irrigated vegetable crop production units. Soil Sci. Soc. Am. J.44(3), 505–511
Sahrawat, K.L. (1982) Nitrification in some tropical soils. Plant Soil65(2), 281–286
Sahrawat, K.L. (1996) Nitrification inhibitors, with emphasis on natural products, and the persistence of nitrogen in the soil. In: Ahmad, N. (ed.) Nitrogen economy in tropical soils. pp. 379–388. Kluwer Academic Publishers, Dordrecht
Schipper, L.A., Vojvodić-Vuković, M. (2000) Nitrate removal from groundwater and denitrification rates in a porous treatment wall amended with sawdust. Ecol. Engn.14(3), 269–278
Schjonning, P., Thomsen, I.K., Moldrup, P., Christensen, B.T. (2003) Linking soil microbial activity to water- and air-phase contents and diffusivities. Soil Sci. Soc. Am. J.67(1), 156–165
Schleper, C., Jurgens, G., Jonuscheit, M. (2005) Genomic studies of uncultivated archaea. Nat. Rev. Microbiol.3(6), 479–488. doi:10.1038/nrmicro1159
Schmidt, I., van Spanning, R.J.M., Jetten, M.S.M. (2004) Denitrification and ammonia oxidation by Nitrosomonas europaea wild-type, and NirK- and NorB-deficient mutants. Microbiol.-SGM150, 4107–4114. doi:10.1099/mic.0.27382-0
Schmidt, C.S., Richardson, D.J., Baggs, E.M. (2011) Constraining the conditions conducive to dissimilatory nitrate reduction to ammonium in temperate arable soils. Soil Biol. Biochem.43(7), 1607–1611. doi:10.1016/j.soilbio.2011.02.015
Scholefield, D., Hawkins, J.M.B., Jackson, S.M. (1997) Use of a flowing helium atmosphere incubation technique to measure the effects of denitrification controls applied to intact cores of a clay soil. Soil Biol. Biochem.29(9–10), 1337–1344
Seitzinger, S., Harrison, J.A., Bohlke, J.K., Bouwman, A.F., Lowrance, R., Peterson, B., Tobias, C., Van Drecht, G. (2006) Denitrification across landscapes and waterscapes: A synthesis. Ecol. Appl.16(6), 2064–2090
Shaw, L.J., Nicol, G.W., Smith, Z., Fear, J., Prosser, J.I., Baggs, E.M. (2006) Nitrosospira spp. can produce nitrous oxide via a nitrifier denitrification pathway. Environ. Microbiol.8(2), 214–222. doi:10.1111/j.1462-2920.2005.00882.x
Shi, W., Norton, J.M. (2000) Effect of long-term, biennial, fall-applied anhydrous ammonia and nitrapyrin on soil nitrification. Soil Sci. Soc. Am. J.64(1), 228–234
Shoun, H., Kim, D.H., Uchiyama, H., Sugiyama, J. (1992) Dinitrification by fungi. Fems Microbiol. Lett.94(3), 277–281. doi:10.1111/j.1574-6968.1992.tb05331.x
Silver, W.L., Herman, D.J., Firestone, M.K. (2001) Dissimilatory Nitrate Reduction to Ammonium in Upland Tropical Forest Soils. Ecology82(9), 2410–2416
Skiba, U., Smith, K.A. (2000) The control of nitrous oxide emissions from agricultural and natural soils. Chemosphere2(3–4), 379–386
Smith, J.H., Gilbert, R.G., Miller, J.B. (1976) Redox potentials and denitrification in a cropped potato processing waste-water disposal field. J. Environ. Qual.5(4), 397–399
Smith, K.A. (1980) A model of the extent of anaerobic zones in aggregated soils and its potential application to estimates of denitrification. J. Soil Sci.31(2), 263–277
Smith, K.A., McTaggart, I.P., Tsuruta, H. (1997) Emissions of N2O and NO associated with nitrogen fertilization in intensive agriculture, and the potential for mitigation. Soil Use Manage.13(4), 296–304
Smith, M.S., Tiedje, J.M. (1979) Phases of denitrification following oxygen depletion in soil. Soil Biol. Biochem.11(3), 261–267. doi:10.1016/0038-0717(79)90071-3
Smith, P., Goulding, K.W., Smith, K.A., Powlson, D.S., Smith, J.U., Falloon, P., Coleman, K. (2001) Enhancing the carbon sink in European agricultural soils: including trace gas fluxes in estimates of carbon mitigation potential. Nutr. Cycl. Agroecosys.60(1–3), 237–252. doi:10.1023/a:1012617517839
Sorai, M., Yoshida, N., Ishikawa., M. (2007) Biogeochemical simulation of nitrous oxide cycle based on the major nitrogen processes. J. Geophys. Res.-Biogeo.112, G01006 doi:10.1029/2005JG000109
Sorokin, D., Tourova, T., Schmid, M.C., Wagner, M., Koops, H.P., Kuenen, J.G., Jetten, M. (2001) Isolation and properties of obligately chemolithoautotrophic and extremely alkali-tolerant ammonia-oxidizing bacteria from Mongolian soda lakes. Arch. Microbiol.176(3), 170–177
Spieck, E., Muller, S., Engel, A., Mandelkow, E., Patel, H., Bock, E. (1996) Two-dimensional structure of membrane-bound nitrite oxidoreductase from Nitrobacter hamburgensis. J. Struct. Biol.117(2), 117–123
Stark, J.M., Firestone, M.K. (1995) Mechanisms for soil moisture effects on activity of nitrifying bacteria. Appl. Environ. Microbiol.61(1), 218–221
Stein, L.Y., Arp, D.J., Hyman, M.R. (1997) Regulation of the synthesis and activity of ammonia monooxygenase in Nitrosomonas europaea by altering pH to affect NH3 availability. Appl. Environ. Microbiol.63(11), 4588–4592
Stevens, R.J., Laughlin, R.J., Malone, J.P. (1998) Soil pH affects the processes reducing nitrate to nitrous oxide and di-nitrogen. Soil Biol. Biochem.30(8–9), 1119–1126
Strong, D.T., Sale, P.W.G., Helyar, K.R. (1999) The influence of the soil matrix on nitrogen mineralisation and nitrification. IV. Texture. Aus. J. Soil Res.37(2), 329–344
Subbarao, G.V., Ito, O., Sahrawat, K.L., Berry, W.L., Nakahara, K., Ishikawa, T., Watanabe, T., Suenaga, K., Rondon, M., Rao, I.M. (2006) Scope and strategies for regulation of nitrification in agricultural systems-challenges and opportunities. Crit. Rev. Plant Sci.25(4), 303–335. doi:10.1080/07352680600794232
Sutka, R.L., Ostrom, N.E., Ostrom, P.H., Gandhi, H., Breznak, J.A. (2003) Nitrogen isotopomer site preference of N2O produced by Nitrosomonas europaea and Methylococcus capsulatus Bath. Rapid Comm. Mass Sp.17(7), 738–745. doi:10.1002/rcm.968
Suwa, Y., Imamura, Y., Suzuki, T., Tashiro, T., Urushigawa, Y. (1994) Ammonia-oxidizing bacteria with different sensitivities to (NH4)2SO4 in activated sludges. Water Res.28(7), 1523–1532
Suzuki, I., Dular, U., Kwok, S.C. (1974) Ammonia or ammonium ion as substrate for oxidation byNitrosomonas europaea cells and extracts. J. Bacteriol.120(1), 556–558
Takaya, N. (2009) Response to hypoxia, reduction of electron acceptors, and subsequent survival by Filamentous fungi. Biosci. Biotechnol. Biochem.73(1), 1–8. doi:10.1271/bbb.80487
Tenuta, M., Beauchamp, E.G. (1996) Denitrification following herbicide application to a grass sward. Can.J. Soil Sci.76(1), 15–22
Tiedje, J.M. (1988) Ecology of denitrification and the dissimilatory nitrate reduction to ammonium. In: Zehnder, J.B. (ed.) Biology of anaerobic microorganisms. pp. 179–244. Wiley, New York
Treusch, A.H., Leininger, S., Kletzin, A., Schuster, S.C., Klenk, H.P., Schleper, C. (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ. Microbiol.7(12), 1985–1995. doi:10.1111/j.1462-2920.2005.00906.x
U.S. Environmental Protection Agency (US EPA) (2009) National Primary Drinking Water Regulations. Report No. EPA 816-F-09-0004. United States Enveronmental Protection Agency.
van Cleemput, O. (1998) Subsoils: chemo- and biological denitrification, N2O and N2 emissions. Nutr. Cycl. Agroecosys.52(2–3), 187–194
Vitousek, P.M., Gosz, J.R., Grier, C.C., Melillo, J.M., Reiners, W.A. (1982) A comparative analysis of potential nitrification and nitrate mobility in forest ecosystems. Ecol. Monogr.52(2), 155–177. doi:10.2307/1942609
Vitousek, P.M., Hattenschwiler, S., Olander, L., Allison, S. (2002) Nitrogen and nature. Ambio31(2), 97–101. doi:10.1639/0044-7447(2002)031[0097:nan]2.0.co;2
Wan, Y.J., Ju, X.T., Ingwersen, J., Schwarz, U., Stange, C.F., Zhang, F.S., Streck, T. (2009) Gross nitrogen transformations and related nitrous oxide emissions in an intensively used calcareous soil. Soil Sci. Soc. Am. J.73(1), 102–112. doi:10.2136/sssaj2007.0419
Wang, W.J., Dalal, R.C., Moody, P.W., Smith, C.J. (2003) Relationships of soil respiration to microbial biomass, substrate availability and clay content. Soil Biol. Biochem.35(2), 273–284
Ward, B.B. (1986) Nitrification in marine environments. In: Prosser, J.I. (ed.) Nitrification. pp. 157–184. IRL Press, Oxford
Ward, B.B. (2008) Nitrification in marine systems. In: Capone, D.G., Bronk, D.A., Muholland, M.R., Carpenter, E.J. (eds.) Nitrogen in the Marine Environment. vol. 5, pp. 199–261. Elsevier, Amsterdam, The Netherland
Ward, B.B., Zafiriou, O.C. (1988) Nitrification and nitric-oxide in the oxygen minimum of the eastern tropical north pacific. Deep Seas Res. Pt A35(7), 1127–1142
Watson, S.W., Bock, E., Valois, F.W., Waterbury, J.B., Schlosser, U. (1986) Nitrospira marina gen-nov sp-nov - a chemolithotrophic nitrite-oxidizing bacterium. Arch. Microbiol.144(1), 1–7
World Health Organization (WHO) (2007) Nitrate and nitrite in drinking-water. World Health Organization of the United Nations.
Wood, P.M. (1986) Nitrification as an energy source In: Prosser, J.I. (ed.) Nitrification. pp. 39–62. IRL Press, Oxford
Wrage, N., van Groenigen, J.W., Oenema, O., Baggs, E.M. (2005) A novel dual-isotope labelling method for distinguishing between soil sources of N2O. Rapid Comm. Mass Sp.19(22), 3298–3306. doi:10.1002/rcm.2191
Wrage, N., Velthof, G.L., van Beusichem, M.L., Oenema, O. (2001) Role of nitrifier denitrification in the production of nitrous oxide. Soil Biol. Biochem.33(12–13), 1723–1732
Wuchter, C., Abbas, B., Coolen, M.J.L., Herfort, L., van Bleijswijk, J., Timmers, P., Strous, M., Teira, E., Herndl, G.J., Middelburg, J.J., Schouten, S., Damste, J.S.S. (2006) Archaeal nitrification in the ocean. Proc. Natl. Acad. Sci. USA103, 12317–12322. doi:10.1073/pnas.0600756103
Wuebbles, D.J. (2009) Nitrous Oxide: No Laughing Matter. Science326(5949), 56–57. doi:10.1126/science.1179571
Xiong, Z.Q., Xing, G.X., Zhu, Z.L. (2007) Nitrous oxide and methane emissions as affected by water, soil and nitrogen. Pedosphere17(2), 146–155
Ye, R.W., Averill, B.A., Tiedje, J.M. (1994) Denitrification: Production and consumption of nitric oxide. Appl. Environ. Microbiol.60(4), 1053–1058
Yin, S.X., Chen, D., Chen, L.M., Edis, R. (2002) Dissimilatory nitrate reduction to ammonium and responsible microorganisms in two Chinese and Australian paddy soils. Soil Biol. Biochem.34(8), 1131–1137. doi:10.1016/s0038-0717(02)00049-4
Yoshida, T., Alexander, M. (1971) Hydroxylamine oxidation byNitrosomonas europea. Soil Sci.111(5), 307–312
Zart, D., Bock, E. (1998) High rate of aerobic nitrification and denitrification by Nitrosomonas eutropha grown in a fermentor with complete biomass retention in the presence of gaseous NO2 or NO. Arch. Microbiol.169(4), 282–286
Zumft, W.G. (1993) The biological role of nitric oxide in bacteria. Arch. Microbiol.160(4), 253–264
Zumft, W.G. (1997) Cell biology and molecular basis of denitrification. Microbiol. Mol. Biol. R.61(4), 533–616
Zumft, W.G., Korner, H. (1997) Enzyme diversity and mosaic gene organization in denitrification. Ant. Leew. Int. J. G. Mol. Microb.71(1–2), 43–58
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Ussiri, D., Lal, R. (2013). Formation and Release of Nitrous Oxide from Terrestrial and Aquatic Ecosystems. In: Soil Emission of Nitrous Oxide and its Mitigation. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5364-8_3
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