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Biochemical cycling in the rhizosphere having an impact on global change

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Abstract

Changes in chemical properties in soil around plant roots influence many microbial processes, including those having an impact on greenhouse gas emissions. To potentially mitigate these emissions according to the Kyoto protocol, knowledge about how and where these gases are produced and consumed in soils is required. In this review, we focus on the greenhouse gases nitrous oxide and methane, which are produced by nitrifying and denitrifying prokaryotes and methanogenic archaea, respectively. After describing the microbial processes involved in production and consumption of nitrous oxide and methane and how they can be affected in the rhizosphere, we give an overview of nitrous oxide and methane emissions from the rhizosphere and soils and sediments with plants. We also discuss strategies to mitigate emissions from the rhizosphere and consider possibilities for carbon sequestration.

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References

  • Alm J, Shrupali NJ, Minkinen K, Aro L, Hytönen J, Laurila T, Lohila A, Maljanen M, Martikainen PJ, Mäkiranta P, Penttilä T, Saarnio S, Silvan N, Tuittila ES, Laine J (2007) Emission factors and their uncertainty for the exchange of CO2, CH4 and N2O in Finnish managed peatlands. Boreal Environ Res 12:191–209

    CAS  Google Scholar 

  • Angeloni LA, Jankowski KJ, Tuchmann NC, Kelly JJ (2006) Effects of an invasive cattail species (Typha × glauca) on sediment nitrogen and microbial community structure composition in a freshwater wetland. FEMS Microbiol Lett 263:86–92 doi:10.1111/j.1574-6968.2006.00409.x

    Article  PubMed  CAS  Google Scholar 

  • Arah JRM, Smith KA (1989) Steady-state denitrification in aggregated soils—a mathematical model. J Soil Sci 40:139–149 doi:10.1111/j.1365-2389.1989.tb01262.x

    Article  CAS  Google Scholar 

  • Armstrong W (1971) Radial oxygen losses from intact rice roots as affected by distance from the apex, respiration and waterlogging. Physiol Plant 25:192–197 doi:10.1111/j.1399-3054.1971.tb01427.x

    Article  Google Scholar 

  • Arth I, Frenzel P (2000) Nitrification and denitrification in the rhizosphere of rice: the detection of processes by a new multi-channel electrode. Biol Fertil Soils 31:427–435 doi:10.1007/s003749900190

    Article  CAS  Google Scholar 

  • Arth I, Frenzel P, Conrad R (1998) Denitrification coupled to nitrification in the rhizosphere of rice. Soil Biol Biochem 4:509–515 doi:10.1016/S0038-0717(97)00143-0

    Article  Google Scholar 

  • Aulakh MS, Wassmann R, Bueno C, Rennenberg H (2001a) Impact of root exudates of different cultivars and plant development stages of rice (Oryza sativa L.) on methane production in a paddy soil. Plant Soil 230:77–86 doi:10.1023/A:1004817212321

    Article  CAS  Google Scholar 

  • Aulakh MS, Wassmann R, Rennenberg H (2001b) Methane emission from rice fields—quantification, mechanisms, role of management, and mitigation options. Adv Agron 91:193–260 doi:10.1016/S0065-2113(01)70006-5

    Article  Google Scholar 

  • Baggs EM, Blum H (2004) CH4 oxidation and CH4 and N2O emissions from Lolium perenne swards under elevated atmospheric CO2. Soil Biol Biochem 36:713–723 doi:10.1016/j.soilbio.2004.01.008

    Article  CAS  Google Scholar 

  • Baggs EM, Richter M, Cadish G, Hartwig UA (2003) Denitrification in grass swards is increased under elevated atmospheric CO2. Soil Biol Biochem 35:729–732 doi:10.1016/S0038-0717(03)00083-X

    Article  CAS  Google Scholar 

  • Baggs EM, Chebii J, Ndufa JK (2006) A short-term investigation of trace gas emissions following tillage and no-tillage of agroforestry residues in western Kenya. Soil Tillage Res 90:69–76 doi:10.1016/j.still.2005.08.006

    Article  Google Scholar 

  • Bakken LR (1988) Denitrification under different cultivated plants: effects of soil moisture tension, nitrate concentration, and photosynthetic activity. Biol Fertil Soils 6:271–278 doi:10.1007/BF00261011

    Article  Google Scholar 

  • Bateman EJ, Baggs EM (2005) Contributions of nitrification and denitrification to N2O emissions from soils at different water-filled pore space. Biol Fertil Soils 41:379–388 doi:10.1007/s00374-005-0858-3

    Article  CAS  Google Scholar 

  • Beck H, Christensen S (1987) The effect of grass maturing and root decay on nitrous oxide production in soil. Plant Soil 103:269–273 doi:10.1007/BF02370399

    Article  CAS  Google Scholar 

  • Bending GD, Lincoln SD (1999) Characterization of volatile sulphur compounds from soils treated with sulfur-containing organic materials. Soil Biol Biochem 31:695–703 doi:10.1016/S0038-0717(98)00163-1

    Article  CAS  Google Scholar 

  • Bending GD, Lincoln SD (2000) Inhibition of soil nitrifying bacteria communities and their activities by glucosinolate hydrolysis products. Soil Biol Biochem 32:1261–1269 doi:10.1016/S0038-0717(00)00043-2

    Article  CAS  Google Scholar 

  • Bijay-Singh JC, Ryden A, Whitchhead DC (1988) Some relationships between denitrification potential and fractions of organic carbon in air-dried and field-moist soils. Soil Biol Biochem 20:737–741 doi:10.1016/0038-0717(88)90160-5

    Article  Google Scholar 

  • Blackmer AM, Bremner JM (1978) Inhibitory effect of nitrate on reduction of N2O to N2 by soil microorganisms. Soil Biol Biochem 10:187–191 doi:10.1016/0038-0717(78)90095-0

    Article  CAS  Google Scholar 

  • Bodelier PLE, Frenzel P (1999) Contribution of methanotrophic and nitrifying bacteria to CH4 and NH4 + oxidation in the rhizosphere of rice plants as determined by new methods of discrimination. Appl Environ Microbiol 65:1826–1833

    PubMed  CAS  Google Scholar 

  • Bodelier PLE, Libochant J, Blom C, Laanbroek H (1996) Dynamics of nitrification and denitrification in root-oxygenated sediments and adaptation of ammonia-oxidizing bacteria to low oxygen or anoxic habitats. Appl Environ Microbiol 62:4100–4107

    PubMed  CAS  Google Scholar 

  • Bosse U, Frenzel P (1997) Activity and distribution of methane-oxidizing bacteria in flooded rice soil microcosms and in rice plants (Oryza sativa). Appl Environ Microbiol 63:1199–1207

    PubMed  CAS  Google Scholar 

  • Bosse U, Frenzel P (1998) Methane emissions from rice microcosms: the balance of production, accumulation and oxidation. Biogeochem 41:199–214 doi:10.1023/A:1005909313026

    Article  CAS  Google Scholar 

  • Bouwman AF (1996) Direct emission of nitrous oxide from agricultural soils. Nutr Cycl Agroecosyst 45:53–70 doi:10.1007/BF00210224

    Article  Google Scholar 

  • Bowman JP (1999) The methanotrophs—the families Methylococcaceae and Methylocystaceae. In: Dorwin M (ed) The prokaryotes. Springer, New York, pp 266–289

    Google Scholar 

  • Brejda JJ, Kremer RJ, Brown JR (1994) Indication of associative nitrogen fixation in eastern grama grass. J Range Manage 47:192–196 doi:10.2307/4003014

    Article  Google Scholar 

  • Bremer C, Braker G, Matthies D, Reuter A, Engels C, Conrad R (2007) Impact of plant functional group, plant species, and sampling time on the composition of nirK-type denitrifier communities in soil. Appl Environ Microbiol 73:6876–6884 doi:10.1128/AEM.01536-07

    Article  PubMed  CAS  Google Scholar 

  • Briones AM, Okabe S, Umemiya Y, Ramsing N-B, Reichardt W, Okuyama H (2002) Influence of different cultivars on populations of ammonia-oxidizing bacteria in the root environment of rice. Appl Environ Microbiol 68:3067–3075 doi:10.1128/AEM.68.6.3067-3075.2002

    Article  PubMed  CAS  Google Scholar 

  • Brix H, Sorrell BK, Lorenzen B (2001) Are Phragmites-dominated wetlands a net source or net sink of greenhouse gases. Aquat Bot 69:313–324 doi:10.1016/S0304-3770(01)00145-0

    Article  CAS  Google Scholar 

  • Buresh RJ, Austin RA (1988) Direct measurement of dinitrogen and nitrous oxide flux in flooded rice fields. Soil Sci Soc Am J 52:681–687

    Article  CAS  Google Scholar 

  • Buresh RJ, DeDatta SK (1990) Denitrification losses from puddled rice soils in the tropics. Biol Fertil Soils 9:1–13 doi:10.1007/BF00335854

    Article  Google Scholar 

  • Butterbach-Bahl K, Papen H, Rennenberg H (1997) Impact of gas transport through rice cultivars on methane emission from paddy fields. Plant Cell Environ 20:1175–1183 doi:10.1046/j.1365-3040.1997.d01-142.x

    Article  CAS  Google Scholar 

  • Cassman KG, Kropf MJ, Gaunt J, Peng S (1993) Nitrogen use efficiency of rice reconsidered: what are the key constraints. Plant Soil 155–156:359–362 doi:10.1007/BF00025057

    Article  Google Scholar 

  • Chanton JP (2005) The effect of gas transport on the isotope signature of methane in wetlands. Org Geochem 36:753–768 doi:10.1016/j.orggeochem.2004.10.007

    Article  CAS  Google Scholar 

  • Chanton JP, Bauer JE, Glaser PA, Siegel DI, Kelley CA, Tyler SC, Romanowicz EH, Lazrus A (1995) Radiocarbon evidence for the substrates supporting methane formation within northern Minnesota peatlands. Geochim Cosmochim Acta 59:3663–3668 doi:10.1016/0016-7037(95)00240-Z

    Article  CAS  Google Scholar 

  • Chen DL, Chalk PM, Freney JR, Luo QX (1998) Nitrogen transformations in a flooded soil int the presence and absence of rice plants: 1. Nitrification. Nutr Cycl Agroecosyst 51:259–267 doi:10.1023/A:1009736729518

    Article  Google Scholar 

  • Chèneby D, Hartmann A, Hénault C, Topp E, Germon JC (1998) Diversity of denitrifying microflora and ability to reduce N2O in two soils. Biol Fertil Soils 28:19–26 doi:10.1007/s003740050458

    Article  Google Scholar 

  • Chèneby D, Hallet S, Mondon M, Martin-Laurent F, Germon JC, Philippot L (2003) Genetic characterization of the nitrate reducing community based on narG nucleotide sequence analysis. Microb Ecol 46:113–121 doi:10.1007/s00248-002-2042-8

    Article  PubMed  CAS  Google Scholar 

  • Chèneby D, Perrez S, Devroe C, Hallet S, Couton Y, Bizouard F, Iuretig G, Germon JC, Philippot L (2004) Denitrifying bacteria in bulk and maize-rhizospheric soil: diversity and N2O-reducing abilities. Can J Microbiol 50:469–474 doi:10.1139/w04-037

    Article  PubMed  Google Scholar 

  • Chin K-J, Lueders T, Friedrich MW, Klose M, Conrad R (2004) Archaeal community structure and pathway of methane formation on rice roots. Microb Ecol 47:59–67 doi:10.1007/s00248-003-2014-7

    Article  PubMed  CAS  Google Scholar 

  • Christensen TR, Panikov N, Mastepanov M, Joabsson A, Stewart A, Öquist M, Sommerkorn M, Reynaud S, Svensson B (2003) Biotic controls on CO2 and CH4 exchange in wetlands—a closed environment study. Biogeochem 64:337–354 doi:10.1023/A:1024913730848

    Article  CAS  Google Scholar 

  • Cicerone RJ, Oremland RS (1988) Biochemical aspects of atmospheric methane. Global Biogeochem Cycles 2:299–327 doi:10.1029/GB002i004p00299

    Article  CAS  Google Scholar 

  • Cicerone RJ, Shetter JD (1981) Sources of atmospheric methane: measurements in rice paddies and a discussion. J Geophys Res 86:7203–7209 doi:10.1029/JC086iC08p07203

    Article  CAS  Google Scholar 

  • Cole C, Duxbury J, Freney J, Heinemeyer O, Minami K, Mosier A, Paustian K, Rosenberg N, Sampson N, Sauerbeck D, Zhao Q (1997) Global estimates of potential mitigation of greenhouse gas emissions by agriculture. Nutr Cycl Agroecosyst 49:221–228 doi:10.1023/A:1009731711346

    Article  CAS  Google Scholar 

  • Colmer TD (2003) Long-distance transport of gases in plants: a perspective on internal aeration and radial oxygen loss from roots. Plant Cell Environ 26:17–36 doi:10.1046/j.1365-3040.2003.00846.x

    Article  CAS  Google Scholar 

  • Conrad R (1996) Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microbiol Rev 60:609–640

    PubMed  CAS  Google Scholar 

  • Conrad R (2002) Control of microbial methane production in wetalnd rice fields. Nutr Cycl Agroecosyst 64:59–69 doi:10.1023/A:1021178713988

    Article  CAS  Google Scholar 

  • Conrad R (2007) Microbial ecology of methanogens and methanotrophs. Adv Agron 96:1–63 doi:10.1016/S0065-2113(07)96005-8

    Article  CAS  Google Scholar 

  • Crutzen P (1991) Methane’s sinks and sources. Nature 350:380–381 doi:10.1038/350380a0

    Article  Google Scholar 

  • Dannenberg S, Conrad R (1999) Effect of rice plants on methane production and rhizospheric metabolism in paddy soil. Biochem 45:53–71

    Google Scholar 

  • Davidson EA (1991) Fluxes of nitrous oxide and nitric oxide from terrestrial ecosystems. A global inventory of nitric oxide emissions from soils. In: Rogers J, Whitman W (eds) Microbial production and consumption of greenhouse gases: methane, nitrogen oxides, and halomethanes. American Society for Microbiology, Washington DC, pp 219–235

    Google Scholar 

  • DeBoer W, Kowalchuk GA (2001) Nitrification in acid soils: micro-organisms and mechanisms. Soil Biol Biochem 33:853–866 doi:10.1016/S0038-0717(00)00247-9

    Article  CAS  Google Scholar 

  • Deiglmayr K, Philippot L, Hartwig UA, Kandeler E (2004) Structure and activity of the nitrate-reducing community in the rhizosphere of Lolium perenne and Trifolium repens under long-term elevated atmospheric pCO2. FEMS Microbiol Ecol 49:445–454 doi:10.1016/j.femsec.2004.04.017

    Article  CAS  PubMed  Google Scholar 

  • Di HJ, Cameron KC, Sherlock RR (2007) Comparison of the effectiveness of a nitrification inhibitor, dicyandiamide, in reducing nitrous oxide emissions in four different soils under different climatic and management conditions. Soil Use Manage 23:1–9 doi:10.1111/j.1475-2743.2006.00057.x

    Article  Google Scholar 

  • Ding W, Cai Z, Tsuruta H (2004) Summertime variation of methane oxidation in the rhizosphere of a Carex dominated freshwater marsh. Atmos Environ 38:4165–4173 doi:10.1016/j.atmosenv.2004.04.022

    Article  CAS  Google Scholar 

  • Ding W, Cai Z, Tsurutua H (2005) Plant species effects on methane emissions from freshwater marshes. Atmos Environ 39:3199–3207 doi:10.1016/j.atmosenv.2005.02.022

    Article  CAS  Google Scholar 

  • Dobbie KE, Smith KA (2006) The effect of water table depth on emissions of N2O from a grassland soil. Soil Use Manage 22:22–28 doi:10.1111/j.1475-2743.2006.00002.x

    Article  Google Scholar 

  • Dobbie K, Taggart I, Smith K (1999) Nitrous oxide emissions from intensive agricultural systems: Variations between crops and seasons, key driving variables, and mean emission factors. J Geo Res 104:891–899

    Google Scholar 

  • Duxbury JM, Bouldin DR, Terry RE, Tate RL (1982) Emissions of nitrous oxide from soils. Nature 298:462–464 doi:10.1038/298462a0

    Article  CAS  Google Scholar 

  • Eichner MJ (1990) Nitrous oxide emission from fertilized soils: Summary of available data. J Environ Qual 19:272–280

    Google Scholar 

  • Eller G, Frenzel P (2001) Changes in activity and community structure of methane-oxidizing bacteria over the growth period of rice. Appl Environ Microbiol 67:2395–2403 doi:10.1128/AEM.67.6.2395-2403.2001

    Article  PubMed  CAS  Google Scholar 

  • Engelaar WHMG, Symens JC, Lanbroek HJ, Blom CWPM (1995) Preservation of nitrifying capacity and nitrate availability in waterlogged soils by radial oxygen loss from roots of wetland plants. Biol Fertil Soils 20:243–248 doi:10.1007/BF00336084

    Article  Google Scholar 

  • Enwall K, Nyberg K, Bertilsson S, Cederlund H, Stenström J, Hallin S (2007) Long-term impact of fertilization on activity and composition of bacterial communities and metabolic guilds in agricultural soil. Soil Biol Biochem 39:106–115 doi:10.1016/j.soilbio.2006.06.015

    Article  CAS  Google Scholar 

  • Eswaran H, Van den Berg E, Reich P, Kimble JM (1995) Global soil C ressources. In: Lal R, Kimble J, Levine E (eds) Soils and global change. Lewis, Boca Raton, FL, pp 27–43

    Google Scholar 

  • Fillery IRP (2007) Plant-based manipulation of nitrification in soil: a new approach to managing N loss. Plant Soil 294:1–4 doi:10.1007/s11104-007-9263-z

    Article  CAS  Google Scholar 

  • Firestone MK, Firestone RB, Tiedje JM (1980) Nitrous oxide from soil denitrification: factors controlling its biological production. Science 208:749–751 doi:10.1126/science.208.4445.749

    Article  PubMed  CAS  Google Scholar 

  • Fontaine S, Barot S, Barré P, Bdioui N, Mary B, Rumpel C (2007) Stability of organic carbon in deep soil layers controlled by fresh carbon supply. Nature 450:277–281 doi:10.1038/nature06275

    Article  PubMed  CAS  Google Scholar 

  • Freibauer A, Rounsevell MDA, Smith P, Verhagen J (2004) Carbon sequestration in the agricultural soils of Europe. Geoderma 122:1–23 doi:10.1016/j.geoderma.2004.01.021

    Article  CAS  Google Scholar 

  • Freney JR (1997) Emission of nitrous oxide from soils used for agriculture. Nutr Cycl Agroecosyst 49:1–6 doi:10.1023/A:1009702832489

    Article  CAS  Google Scholar 

  • Frenzel P (2000) Plant-associated methane oxidation in rice fields and wetlands. Adv Microb Ecol 16:85–114

    CAS  Google Scholar 

  • Frenzel, P, Bosse, U (1996) Methyl fluoride, an inhibitor of methane oxidation and methane production. FEMS Microbiol Ecol 21:25–36

    Article  CAS  Google Scholar 

  • Frenzel P, Rudolph J (1998) Methane emission from a wetland plant: the role of CH4 oxidation in Eriophorum. Plant Soil 202:27–32 doi:10.1023/A:1004348929219

    Article  CAS  Google Scholar 

  • Frenzel P, Rothfuss F, Conrad R (1992) Oxygen profiles and methane turnover in a flooded rice microcosm. Biol Fertil Soils 14:84–89 doi:10.1007/BF00336255

    Article  CAS  Google Scholar 

  • Gersberg RM, Elkins BV, Goldman CR (1986) Role of aquatic plants in wastewater treatment by artifical wetlands. Water Res 20:363–368 doi:10.1016/0043-1354(86)90085-0

    Article  CAS  Google Scholar 

  • Gilbert B, Frenzel P (1995) Methanotrophic bacteria in the rhizosphere of rice microcosms and their effect on porewater methane concentration and methane emission. Biol Fertil Soils 20:93–100 doi:10.1007/BF00336586

    Article  CAS  Google Scholar 

  • Gilbert B, Frenzel P (1998) Rice roots and CH4 oxidation: the activity of bacteria, their distribution and the microenvironment. Soil Biol Biochem 30:1903–1916 doi:10.1016/S0038-0717(98)00061-3

    Article  CAS  Google Scholar 

  • Giles J (2005) Nitrogen study fertilizes fears of pollution. Nature 433:791 doi:10.1038/433791a

    Article  PubMed  CAS  Google Scholar 

  • Godbold DL, Hoosebeek MR, Lukac M, Cotrufo MF, Janssens IA, Ceulemans R, Polle A, Velthorst EJ, Scarascia-Mugnozza G, DeAngelis P, Miglietta F, Peressottu A (2006) Mycorrhizal hyphal turnover as a dominant process for carbon input into soil organic matter. Plant Soil 281:15–24 doi:10.1007/s11104-005-3701-6

    Article  CAS  Google Scholar 

  • Goodroad LL, Keeney DR (1984) Nitrous oxide production in aerobic soils under varying pH, temperature and water content. Soil Biol Biochem 16:39–43 doi:10.1016/0038-0717(84)90123-8

    Article  CAS  Google Scholar 

  • Gosh P, Kashyap AK (2003) Effect of rice on rate of N-mineralization, nitrification and nitrifier population size in an irrigated rice ecosystem. Appl Soil Ecol 24:27–41 doi:10.1016/S0929-1393(03)00068-4

    Article  Google Scholar 

  • Gosh S, Majumdar D, Jain MC (2003) Methane and nitrous oxide emissions from an irrigated rice of North India. Chemosphere 51:181–195 doi:10.1016/S0045-6535(02)00822-6

    Article  Google Scholar 

  • Greenup AL, Bradford MA, McMamara NP, Ineson P, Lee JA (2000) The role of Eriophorum vaginatum in CH4 flux from ombotrophic peatland. Plant Soil 227:265–272 doi:10.1023/A:1026573727311

    Article  CAS  Google Scholar 

  • Haider K, Mosier AR, Heinemeyer O (1987) Effect of growing plants on denitrification at high nitrate concentrations. Soil Sci Soc Am J 51:97–102

    CAS  Google Scholar 

  • Haller T, Stolp H (1985) Quantitative estimation of root exudation of maize plant. Plant Soil 86:207–216 doi:10.1007/BF02182895

    Article  CAS  Google Scholar 

  • Hansen S, Maehlum JE, Bakken LR (1993) N2O and CH4 fluxes in soil influenced by fertilization and tractor traffic. Soil Biol Biochem 25:621–630 doi:10.1016/0038-0717(93)90202-M

    Article  CAS  Google Scholar 

  • Hanson RS, Hanson TE (1996) Methanogenic bacteria. Microbiol Rev 60:439–471

    PubMed  CAS  Google Scholar 

  • Henry S, Texier S, Hallet S, Bru D, Dambreville C, Chèneby D, Bizouard F, Germon JC, Philippot L (2008) Disentangling the rhizosphere effect on nitrate reducers and denitrifiers: insight into the role of root exudates. Environ Microbiol 10(11):3082–3092

    Article  PubMed  CAS  Google Scholar 

  • Herman DJ, Johnson KK, Jaeger CH III, Schwartz E, Firestone MK (2006) Root influence on nitrogen mineralization and nitrification in Avena barbata rhizosphere soil. Soil Sci Soc Am J 70:1504–1511 doi:10.2136/sssaj2005.0113

    Article  CAS  Google Scholar 

  • Hojberg O, Binnerup SJ, Sorensen J (1996) Potential rates of ammonium oxidation, nitrate reduction and denitrification in the young barley rhizosphere. Soil Biol Biochem 28:47–54 doi:10.1016/0038-0717(95)00119-0

    Article  Google Scholar 

  • Holtzapfel-Pschorn A, Conrad R, Seiler W (1985) Production, oxidation and emission of methane in rice paddies. FEMS Microbiol Ecol 31:343–351 doi:10.1111/j.1574-6968.1985.tb01170.x

    Article  Google Scholar 

  • Holtzapfel-Pschorn A, Conrad R, Seiler W (1986) Effects of vegetation of the emission of methane from submerged paddy soil. Plant Soil 92:223–231 doi:10.1007/BF02372636

    Article  Google Scholar 

  • Hoogendorn CJ, Klein CAMd, Rutheford AJ, Letica S, Devantier BP (2008) The effect of increasing rates of nitrogen fertilizer and a nitrification inhibitor on nitrous oxide emissions from urine patches on sheep grazed hill country pasture. Aust J Exp Agric 48:147–151 doi:10.1071/EA07238

    Article  Google Scholar 

  • Hou AX, Chen GX, Wang ZP, Van Cleemput O, Partick WH Jr (2000) Methane and nitrous oxide emissions from a rice field in relation to soil redox and microbiological processes. Soil Sci Am J 64:2180–2186

    CAS  Google Scholar 

  • Huang B, Jonhson JW, Nesmith S, Bridges DC (1994) Growth, physiological and anatomical responses of two wheat genotypes to waterlogging and nutrient supply. J Exp Bot 45:193–202 doi:10.1093/jxb/45.2.193

    Article  Google Scholar 

  • Iizumi T, Mizumoto M, Nakamura K (1998) A bioluminescence assay using Nitrosomonas europaea for rapid and sensitive detection of nitrification inhibitors. Appl Environ Microbiol 64:3656–3662

    PubMed  CAS  Google Scholar 

  • Inubishi K, Naganuma H, Kitahara S (1996) Contribution of denitrification and autotrophic and heterotrophic nitrification to nitrous oxide production in andosols. Biol Fertil Soils 23:292–298 doi:10.1007/BF00335957

    Article  Google Scholar 

  • IPCC (2007) Climate Change 2007: Synthesis Report. Contribution of Working Groups I, II and III to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change [Core Writing Team, Pachauri RK, Reisinger A (eds.)]. IPCC, Geneva, Switzerland, p 104

    Google Scholar 

  • Ishikawa I, Subbarao GV, Ito O, Okado K (2003) Suppresion of nitrification and nitrous oxide emission by the tropical grass Brachiaria humidicola. Plant Soil 255:413–419 doi:10.1023/A:1026156924755

    Article  CAS  Google Scholar 

  • Jarecki MK, Lal R (2003) Crop management for soil carbon sequestration. Crit Rev Plant Sci 22:471–502 doi:10.1080/713608318

    Article  Google Scholar 

  • Jia ZJ, Cai ZC, Xu H, Tsuruta H (2002) Effect of rice cultivars on methane fluxes in a paddy soil. Nutr Cycl Agroecosyst 64:87–94 doi:10.1023/A:1021102915805

    Article  CAS  Google Scholar 

  • Jiao ZH, Hou AX, Shi Y, Huang GH, Wang YH, Chen X (2006) Water management influencing methane and nitrous oxide emissions from rice field in relation to soil redox and microbial community. Commun Soil Sci Plant Anal 37:1889–1903 doi:10.1080/00103620600767124

    Article  CAS  Google Scholar 

  • Jing L, Mingxing W, Yao H, Yuesci W (2002) New estimates of methane emissions from Chinese rice paddies. Nutr Cycl Agroecosyst 64:33–42 doi:10.1023/A:1021184314338

    Article  Google Scholar 

  • Joabsson A, Christensen TR, Wallén B (1999) Vascular plant controls on methane emissions from northern peatforming wetlands. Trends Ecol Evol 14:385–388 doi:10.1016/S0169-5347(99)01649-3

    Article  PubMed  Google Scholar 

  • Jones DL, Hodge A (1999) Biodegradation kinetics ans sorption reactions of three differently charged amino acids in soil and their effect on plant organic nitrogen availability. Soil Biol Biochem 31:1331–1342 doi:10.1016/S0038-0717(99)00056-5

    Article  CAS  Google Scholar 

  • Kallner-Bastviken S, Eriksson PG, Martins I, Neto JM, Leonardson L, Tonderski K (2003) Potential nitrification and denitrification on different surfaces in a constructed treatment wetland. J Environ Qual 32:2414–2420

    PubMed  Google Scholar 

  • Kallner-Bastviken S, Eriksson PG, Premrov A, Tonderski K (2005) Potential denitrification in wetland sediments with different plant species detritus. Ecol Eng 25:183–190 doi:10.1016/j.ecoleng.2005.04.013

    Article  Google Scholar 

  • Kankaala P, Bergström I (2004) Emission and oxidation of methane in Equisetum fluviatile stands growing on organic sediment and sand bottoms. Biogeochemistry 67:21–37 doi:10.1023/B:BIOG.0000015277.17288.7a

    Article  CAS  Google Scholar 

  • Kern JS, Gong ZT, Zhang GL, Zhuo HZ, Luo GB (1997) Spatial analysis of methane emission from paddy soil in China and the potential for emission reduction. Nutr Cycl Agroecosyst 49:181–195 doi:10.1023/A:1009710425295

    Article  CAS  Google Scholar 

  • Kilian S, Werner D (1996) Enhanced denitrification in plots of N2-fixing faba beans compared to plots of a non-fixing legume and non-legumes. Biol Fertil Soils 21:77–83 doi:10.1007/BF00335996

    Article  Google Scholar 

  • Killham K (1986) Heterotrophic nitrification. In: Prosser J (ed) Nitrification. IRL Press, Oxford

    Google Scholar 

  • King GM (1996) In situ analyses of methane oxidation associated with the roots and rhizomes of a bur reed, Sparganium eurycarpum, in a marine wetland. Appl Environ Microbiol 62:4548–4555

    PubMed  CAS  Google Scholar 

  • Klemedtsson L, Svensson BH, Rosswall T (1987) Dinitrogen and nitrous oxide produced by denitrification and nitrification in soil with and without barley plants. Plant Soil 99:303–310 doi:10.1007/BF02370877

    Article  CAS  Google Scholar 

  • Klemedtsson L, Jiang Q, Klemedtsson AK, Bakken L (1999) Autotrophic ammonium-oxidising bacteria in Swedish mor humus. Soil Biol Biochem 31:839–847 doi:10.1016/S0038-0717(98)00183-7

    Article  CAS  Google Scholar 

  • Kludze HK, DeLaune RD (1994) Methane emissions and growth of Spartina patens in response to soil redox intensity. Soil Sci Soc Am J 58:1838–1845

    CAS  Google Scholar 

  • Kludze HK, Delaune RD, Patrick WH Jr (1993) Aerenchyma formation and methane and oxygen-exchange in rice. Soil Sci Soc Am J 57:386–391

    CAS  Google Scholar 

  • Kowalchuk GA, Stephen JR (2001) Ammonia-oxidizing bacteria: a model for molecular biology. Annu Rev Microbiol 55:485–529 doi:10.1146/annurev.micro.55.1.485

    Article  PubMed  CAS  Google Scholar 

  • Krüger M, Frenzel P, Kemnitz D, Conrad R (2005) Activity, structure and dynamics of the methanogenic archaeal community in a flooded Italian rice field. FEMS Microbiol Ecol 51:323–331 doi:10.1016/j.femsec.2004.09.004

    Article  PubMed  CAS  Google Scholar 

  • Kumar R, Pandey S, Pendey A (2006) Plant roots and carbon sequestration. Curr Sci 91:885–890

    CAS  Google Scholar 

  • Kuzyakov Y, Demin V (1998) CO2 efflux by rapid decomposition of low molecular organic substances in soils. Sci Soils 3:1–12 doi:10.1007/s10112-998-0002-2

    Article  Google Scholar 

  • Laan P, Berrevoets MJ, Lythe S, Armstrong W, Blom CWPM (1989) Root morphology and aerenchyma formation as indicators of the flooded-tolerance of Rumex species. J Ecol 77:693–703 doi:10.2307/2260979

    Article  Google Scholar 

  • Lal R (2004) Agricultural activities and the global carbon cycle. Nutr Cycl Agroecosyst 70:103–116 doi:10.1023/B:FRES.0000048480.24274.0f

    Article  CAS  Google Scholar 

  • Lata JC, Degrange V, Abbadie L, Lensi R (2000) Relationships between root density of the African grass Hyparrhenia diplandra and nitrification at the decimetric scale: an inhibition–stimulation balance hypothesis. Proc R Soc Lond B. Biol Sci 276:1–6

    Google Scholar 

  • Lata JC, Degrange V, Raynaud X, Maron P, Lensi R, Abbadie L (2004) Grass population control nitrification in savanna soils. Funct Ecol 18:605–611 doi:10.1111/j.0269-8463.2004.00880.x

    Article  Google Scholar 

  • Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806–809 doi:10.1038/nature04983

    Article  PubMed  CAS  Google Scholar 

  • LeMer J, Roger P (2001) Production, oxidation and consumption of methane by soils: a review. Eur J Soil Biol 37:25–50 doi:10.1016/S1164-5563(01)01067-6

    Article  CAS  Google Scholar 

  • Lensi R, Domenach AM, Abbadie L (1992) Field study of nitrification and denitrification in a wet savanna of west africa (Lamto, Côte d’ivoire). Plant Soil 147:107–113 doi:10.1007/BF00009376

    Article  CAS  Google Scholar 

  • Letey J, Valoras N, Hadas A, Focht DD (1980) Effect of air-filled porosity, nitrate concentration and time on the ratio of N2O/N2 evolution during denitrification. J Environ Qual 9:227–231

    CAS  Google Scholar 

  • Li YL, Zhang YL, Hu J, Shen QR (2004) Contribution of nitrification happened in rhizospheric soil growing with different rice cultivars to N nutrition. Biol Fertil Soils 43:417–425 doi:10.1007/s00374-006-0119-0

    Article  CAS  Google Scholar 

  • Li CS, Frolking S, Butterbach-Bahl K (2005) Carbon sequestration in arable soils is likely to increase nitrous oxide emissions, offsetting reductions in climate radiative forcing. Clim Change 72:321–338 doi:10.1007/s10584-005-6791-5

    Article  CAS  Google Scholar 

  • Lindau CW, DeLaune RD, Patrick WHJ, Bollich PK (1990) Fertilizer effects on dinitrogen, nitrous oxide, and methane emissions from lowland rice. Soil Sci Soc Am J 54:1789–1794

    CAS  Google Scholar 

  • Linn DM, Doran JW (1984) Effect of water-filled pore space on carbon dioxide and nitrous oxide production in tilled and nontilled soils. Soil Sci Soc Am J 48:1267–1272

    CAS  Google Scholar 

  • Lu Y, Conrad R (2005) In situ stable isotope probing of methanogenic Archaea in the rice rhizosphere. Science 309:1088–1090 doi:10.1126/science.1113435

    Article  PubMed  CAS  Google Scholar 

  • Lynch JM (1990) The rhizosphere. Wiley, Chichester

    Google Scholar 

  • Martikainen PJ, DeBoer W (1993) Nitrous oxide production and nitrification in acidic soil from a Dutch coniferous forest. Soil Biol Biochem 25:343–347 doi:10.1016/0038-0717(93)90133-V

    Article  CAS  Google Scholar 

  • Mary B, Mariotti A, Morel JL (1992) Use of 13C variations at natural abundance for studying the biodegradation of root mucilage, roots and glucose in soil. Soil Biol Biochem 24:1065–1072 doi:10.1016/0038-0717(92)90037-X

    Article  Google Scholar 

  • Mary B, Fresneau C, Morel JL, Mariotti A (1993) C and N cycling during decomposition of root mucilage, roots and glucose in soil. Soil Biol Biochem 25:1005–1014 doi:10.1016/0038-0717(93)90147-4

    Article  CAS  Google Scholar 

  • McCarty GW, Bremner JM (1993) Factors affecting the availability of organic-carbon for denitrification of nitrate in subsoils. Biol Fertil Soils 15:132–136 doi:10.1007/BF00336431

    Article  CAS  Google Scholar 

  • McLauchlan KL, Hobbie SE, Post WM (2006) Conversion from agriculture to grassland buils soil organic matter on decadal timescales. Ecol Appl 16:143–153 doi:10.1890/04-1650

    Article  PubMed  Google Scholar 

  • McTaggart IP, Tsuruta H (2003) The influence of controlled release fertilisers and the form of applied nitrogen on nitrous oxide emissions from an andosol. Nutr Cycl Agroecosyst 67:47–54 doi:10.1023/A:1025108911676

    Article  CAS  Google Scholar 

  • Menyailo M, Hungate BA (2003) Interactive effects of tree species and soil moisture on methane consumption. Soil Biol Biochem 35:73–79 doi:10.1016/S0038-0717(03)00018-X

    Article  CAS  Google Scholar 

  • Minkkinen K, Laine J (2006) Vegetation heterogeneity and ditches create spatial variability in methane fluxes from peatlands drained for forestry. Plant Soil 285:289–304 doi:10.1007/s11104-006-9016-4

    Article  CAS  Google Scholar 

  • Minoda T, Kimura M (1994) Contribution of photosynthesized carbon to methane emitted from paddy fields. Geophys Res Lett 21:2007–2010 doi:10.1029/94GL01595

    Article  CAS  Google Scholar 

  • Minoda T, Kimura M, Wada E (1996) Photosynthates as dominant source of CH4 and CO2 in soil water and CH4 emitted to the atmosphere from paddy fields. J Geo Res 101:21091–21097 doi:10.1029/96JD01710

    Article  CAS  Google Scholar 

  • Molina JAE, Rovira AD (1964a) Influence of plant roots on autotrophic nitrifying bacteria. Can J Microbiol 10:249–255

    Article  Google Scholar 

  • Molina JAE, Rovira AD (1964b) The influence of plant roots on autotrophic nitrifying bacteria. Can J Microbiol 10:249–247

    Google Scholar 

  • Monteny GJ, Bannink A, Chadwick D (2006) Greenhouse gas abatement strategies for animal husbandry. Agric Ecosyst Environ 112:163–170 doi:10.1016/j.agee.2005.08.015

    Article  CAS  Google Scholar 

  • Moore DRE, Waid JS (1971) The influence of washings of living roots on nitrification. Soil Biol Biochem 3:69–83 doi:10.1016/0038-0717(71)90032-0

    Article  CAS  Google Scholar 

  • Mosier AR (1994) Nitrous oxide emissions from agricultural soils. Fertil Res 37:191–200 doi:10.1007/BF00748937

    Article  CAS  Google Scholar 

  • Mounier E, Hallet S, Chèneby D, Benizri E, Gruet Y, Nguyen C, Piutti S, Robin C, Slezack-Deschaumes S, Martin-Laurent F, Germon JC, Philippot L (2004) Influence of maize mucilage on the diversity and activity of the denitrifying community. Environ Microbiol 6:301–312 doi:10.1111/j.1462-2920.2004.00571.x

    Article  PubMed  CAS  Google Scholar 

  • Munro PE (1966) Inhibition of nitrite-oxidizers by roots of grass. J Appl Ecol 3:227–229 doi:10.2307/2401247

    Article  Google Scholar 

  • Nägele W, Conrad R (1990) Influence of pH on the release of NO and N2O from fertilized and unfertilized soil. Biol Fertil Soils 10:139–144

    Google Scholar 

  • Neue HU (1993) Methane emission from rice fields. Bioscience 43:466–474 doi:10.2307/1311906

    Article  Google Scholar 

  • Nguyen C (2003) Rhizodeposition of organic C by plants: mechanisms and controls. Agronomie 23:375–396 doi:10.1051/agro:2003011

    Article  CAS  Google Scholar 

  • Nieder R, Schollmayer G, Richter J (1989) Denitrification in the rooting zone of cropped soils with regard to methodology and climate: A review. Biol Fertil Soils 8:219–226 doi:10.1007/BF00266482

    Article  CAS  Google Scholar 

  • Nielsen LP, Christensen PB, Revsbech NP, Sorensen J (1990) Denitrification and oxygen respiration in biofilms studied with microsensor for nitrous oxide and oxygen. Microb Ecol 19(1):63–72

    Article  CAS  Google Scholar 

  • Nijburg JW, Coolen MJL, Gerards S, Klein Gunnewiek PJA, Laanbroek HJ (1997) Effect of nitrate availability and the presence of Glyceria maxima on the composition and activity of the dissimilatory nitrate-reducing bacterial community. Appl Environ Microbiol 63:931–937

    PubMed  CAS  Google Scholar 

  • Nilsson M, Bohlin E (1993) Methane and carbon dioxide concentrations in bogs and fens—with special reference to the effects of the botanical composition of the peat. J Ecol 81:615–625 doi:10.2307/2261660

    Article  CAS  Google Scholar 

  • Nilsson M, Mikkelä C, Sundh I, Granberg G, Svensson BH, Ranneby B (2001) Methane emission from Swedish mires: National and regional budgets and dependence on mire vegetation. J Geophys Res 106:20,847–820,860

    CAS  Google Scholar 

  • Norton J, Firestone M (1996) N dynamics in the rhizosphere of Pinus ponderosa seedlings. Soil Biol Biochem 28:351–362 doi:10.1016/0038-0717(95)00155-7

    Article  CAS  Google Scholar 

  • Nouchi I, Mariko S, Aoki K (1990) Mechanism of methane transport from the rhizosphere to the atmosphere through rice plants. Plant Physiol 94:59–66

    Article  PubMed  CAS  Google Scholar 

  • Parkin TB, Tiedje JM (1984) Application of a soil core method to investigate the effect of oxygen concentration on denitrification. Soil Biol Biochem 16:331–334 doi:10.1016/0038-0717(84)90027-0

    Article  CAS  Google Scholar 

  • Patra A, Abbadie L, Clays-Josserand A, Degrange V, Grayston SJ, Guillaumaud N, Loiseau P, Louault F, Mahmood S, Nazaret S, Philippot L, Poly F, Prosser JI, Le Roux X (2006) Effects of management regime and plant species on the enzyme activity and genetic structure of N-fixing, denitrifying and nitrifying bacterial communities in grassland soils. Environ Microbiol 8:1005–1016 doi:10.1111/j.1462-2920.2006.00992.x

    Article  PubMed  CAS  Google Scholar 

  • Paul JW, Beauchamp EG (1989) Denitrification and fermentation in plant-residue-amended soil. Biol Fertil Soils 7:303–309 doi:10.1007/BF00257824

    Article  CAS  Google Scholar 

  • Philippot L (1999) Dissimilatory nitrate reductases in bacteria. Biochim Biophys Acta 1446:1–23

    PubMed  CAS  Google Scholar 

  • Philippot L, Piutti S, Martin-Laurent F, Hallet S, Germon JC (2002) Molecular analysis of the nitrate-reducing community from unplanted and maize-planted soil. Appl Environ Microbiol 68:6121–6128 doi:10.1128/AEM.68.12.6121-6128.2002

    Article  PubMed  CAS  Google Scholar 

  • Philippot L, Kufner M, Chèneby D, Depret G, Laguerre G, Martin-Laurent F (2006) Genetic structure and activity of the nitrate-reducers community in the rhizosphere of different cultivars of maize. Plant Soil 287:177–186 doi:10.1007/s11104-006-9063-x

    Article  CAS  Google Scholar 

  • Philippot L, Hallin S, Schloter M (2007) Ecology of denitrifying prokaryotes in agricultural soil. Adv Agron 96:135–190

    Google Scholar 

  • Popp TJ, Chanton JP, Whiting GJ, Grant N (2000) Evaluation of methane oxidation in the rhizosphere of a Carex dominated fen in north central Alberta. Biogeochemistry 51:259–281 doi:10.1023/A:1006452609284

    Article  CAS  Google Scholar 

  • Post W, Izzaurralde R, Jastrow J, McCarl B, Amonette J, Bailey V, Jardine P, West T, Zhou J (2004) Enhencement of carbon sequestration in US soils. Bioscience 54:895–908 doi:10.1641/0006-3568(2004)054[0895:EOCSIU]2.0.CO;2

    Article  Google Scholar 

  • Prade K, Trolldenier G (1988) Effect of wheat roots on denitrification at varying soil air-filled porosity and organic-carbon content. Biol Fertil Soils 7:1–6 doi:10.1007/BF00260723

    Article  Google Scholar 

  • Priha O, Grayston SJ, Pennanen T, Smolander A (1999) Microbial activities related to C and N cycling and microbial community structure in the rhizospheres of Pinus sylvestris, Picea abies and Betula pendula seedlings in an organic and mineral soil. FEMS Microbiol Ecol 30:187–199 doi:10.1111/j.1574-6941.1999.tb00647.x

    Article  PubMed  CAS  Google Scholar 

  • Qian JH, Doran JW, Walters DT (1997) Maize plant contributions to root zone available carbon and nitrogen transformations of nitrogen. Soil Biol Biochem 29:1451–1462 doi:10.1016/S0038-0717(97)00043-6

    Article  CAS  Google Scholar 

  • Reddy K, Patrick WJ (1986) Denitrification losses in flooded rice fields. Fertil Res 9:99–116 doi:10.1007/BF01048697

    Article  CAS  Google Scholar 

  • Reedy K, Patrick WJ, Lindau C (1989) Nitrification-denitrification at the plant root-sediment interface in wetlands. Limnol Oceanogr 34:241–302

    Google Scholar 

  • Rice C, Pancholy S (1972) Inhibition of nitrification by climax ecosystem. Am J Bot 59:1033–1040 doi:10.2307/2441488

    Article  Google Scholar 

  • Robertson G, Paul E, Harwood R (2000) Greenhouse gases in intensive agriculture: contributions of individual gases to the radiative forcing of the atmosphere. Science 289:1922–1925 doi:10.1126/science.289.5486.1922

    Article  PubMed  CAS  Google Scholar 

  • Robinson J (1972) Nitrification in a New Zealand grassland soil. Plant Soil 14:173–183

    Google Scholar 

  • Ruiz-Rueda O, Hallin S, Bañeras L (2008) Structure and function of denitrifying and nitrifying bacterial communities in relation to the plant species in a constructed wetland. FEMS Microbiol Ecol (in press)

  • Saarnio S, Wittenmayer L, Merbach W (2004) Rhizospheric exudation of Eriophorum vaginatum L.—potential link to methanogenesis. Plant Soil 267:343–355 doi:10.1007/s11104-005-0140-3

    Article  CAS  Google Scholar 

  • Sass RL, Fisher FM, Harcombe PA, Turner FT (1991) Methane emission from rice fields as influenced by solar radiation, temperature and straw incorporation. Glob Change Cycles 5:335–350 doi:10.1029/91GB02586

    Article  CAS  Google Scholar 

  • Scaglia J, Lensi R, Chalamet A (1985) Relationship between photosynthesis and denitrification in planted soil. Plant Soil 84:37–43 doi:10.1007/BF02197865

    Article  CAS  Google Scholar 

  • Schlesinger W (1984) Soil organic matter: a source of atmospheric CO2. In: Woodwell G (ed) The role of terrestrial vegetation in the global carbon cycle. Wiley, New York, pp 111–127

    Google Scholar 

  • Schütz H, Holzapfel-Pschorn A, Conrad R, Rennenberg H, Seiler W (1989) A three years continuous record on the influence of daytime, season and fertilizer treatment on methane emission rate from an Italian rice paddy field. J Geophys Res 94:16405–16416 doi:10.1029/JD094iD13p16405

    Article  Google Scholar 

  • Sehy U, Ruser R, Munch J (2003) Nitrous oxide fluxes from maize fields: relationship to yield, site-specific fertilization, and soil conditions. Agric Ecosyst Environ 99:97–111 doi:10.1016/S0167-8809(03)00139-7

    Article  CAS  Google Scholar 

  • Sextone A, Revsbech N, Parkin T, Tiedje J (1985) Direct measurement of oxygen profiles and denitrification rates in soil aggregates. Soil Sci Soc Am J 49:645–651

    Article  Google Scholar 

  • Sharma S, Aneja MK, Mayer J, Munch JC, Schloter M (2005) Diversity of transcripts of nitrite reductase genes (nirK and nirS) in rhizospheres of grain legumes. Appl Environ Microbiol 71:2001–2007 doi:10.1128/AEM.71.4.2001-2007.2005

    Article  PubMed  CAS  Google Scholar 

  • Shrestha M, Abraham W-R, Shrestha PM, Noll M, Conrad R (2008) Activity and composition of methanotrophic bacterial communities in planted rice soil studied by flux measurements, analyses of pmoA gene and stable isotope probing of phospholipid fatty acids. Environ Microbiol 10:400–412 doi:10.1111/j.1462-2920.2007.01462.x

    Article  PubMed  CAS  Google Scholar 

  • Šimek M, Cooper JE (2002) The influence of soil pH on denitrification: Progress towards the understanding of this interaction over the last 50 years. Eur J Soil Sci 53:345–354 doi:10.1046/j.1365-2389.2002.00461.x

    Article  Google Scholar 

  • Six J, Ogle S, Breidt F, Conant R, Mosier A, Paustian K (2004) The potential to mitigate global warming with no-tillage management is only realized when practiced in the long term. Glob Change Biol 10:155–160 doi:10.1111/j.1529-8817.2003.00730.x

    Article  Google Scholar 

  • Skiba U, Smith K (2000) The control of nitrous oxide emissions from agricultural and natural soils. Chemosphere Glob Chang Sci 2:379–386

    Article  CAS  Google Scholar 

  • Smith KA (1980) A model of the extent of anaerobic zones in aggregated soil and its potential application to estimates of denitrification. J Soil Sci 31:263–277 doi:10.1111/j.1365-2389.1980.tb02080.x

    Article  CAS  Google Scholar 

  • Smith MS, Tiedje JM (1979) The effect of roots on soil denitrification. Soil Sci Soc Am J 43:951–955

    CAS  Google Scholar 

  • Smith CJ, Brandon M, Patrick WJ (1982) Nitrous oxide emission following urea-N fertilization of wetland rice. Soil Sci Plant Nutr 28:161–171

    CAS  Google Scholar 

  • Smith P, Powlson D, Glendining M, Smith J (1998) Preliminary estimates of the potential for carbon mitigation in European soils through no-till farming. Glob Change Biol 4:679–685 doi:10.1046/j.1365-2486.1998.00185.x

    Article  Google Scholar 

  • Sørensen J (1997) The rhizosphere as a habitat for soil microorganisms. In: Elsas JDV, Trevors JT, Wellington EMK (eds) Modern soil microbiology. Marcel Dekker, New York

    Google Scholar 

  • Sorrell BK, Downes MT, Stanger CL (2002) Methanotrophic bacteria and their activity on submerged aquatic macrophytes. Aquat Bot 72:107–119 doi:10.1016/S0304-3770(01)00215-7

    Article  Google Scholar 

  • Stams A, Flameling E, Marnette E (1990) The importance of autotrophic versus heterotrophic oxidation of atmospheric ammonium in forest ecosystems with acid soil. FEMS Microbiol Ecol 74:337–344 doi:10.1111/j.1574-6968.1990.tb04080.x

    Article  CAS  Google Scholar 

  • Steltzer H, Bowman W (1998) Differential influence of plant species on soil nitrogen transformation within moist meadow alpine toundra. Ecosystems (N Y, Print) 1:464–474 doi:10.1007/s100219900042

    Article  CAS  Google Scholar 

  • Ström L, Mastepanov M, Christensen TR (2005) Species-specific effects of vascular plants on carbon turnover and methane emissions from wetlands. Biogeochem 75:65–82 doi:10.1007/s10533-004-6124-1

    Article  CAS  Google Scholar 

  • Subbarao GV, Ishikawa I, Ito O, Nakahara K, Wang H, Berry WL (2006) A bioluminescence assay to detect nitrification inhibitors released from plant roots: a case study with Brachiaria humidicola. Plant Soil 288:101–112 doi:10.1007/s11104-006-9094-3

    Article  CAS  Google Scholar 

  • Subbarao GV, Rondon M, Ito O, Ishikawa I, Rao IM, Nakahara K, Lascano C, Berry WL (2007) Biological nitrification inhibition (BNI)—is it a widespread phenomenon. Plant Soil 294:5–18 doi:10.1007/s11104-006-9159-3

    Article  CAS  Google Scholar 

  • Svensson BH, Klemedtsson L, Simkins S, Paustin K, Rosswall T (1991) Soil denitrification in three cropping systems characterized by differences in nitrogen and carbon supply. I. Rate-distribution frequencies, comparison between systems and seasonal N losses. Plant Soil 138:257–271 doi:10.1007/BF00012253

    Article  CAS  Google Scholar 

  • Sylvester-Bradley R, Mosquera D, Mendez J (1988) Inhibition of nitrate accumulation in tropical grassland soils: effect of nitrogen fertilization and soil disturbance. J Soil Sci 39:407–416 doi:10.1111/j.1365-2389.1988.tb01226.x

    Article  CAS  Google Scholar 

  • Thomsen J, Geest T, Cox R (1994) Mass spectrometric studies of the effect of pH on the accumulation of intermediates in denitrification in Paracoccus denitrificans. Appl Environ Microbiol 60:536–541

    PubMed  CAS  Google Scholar 

  • Tiedje JM (1988) Ecology of denitrification and dissimilatory nitrate reduction to ammonium. In: Zehnder AJB (ed) Biology of anaerobic microorganisms. Wiley, New York, pp 179–244

    Google Scholar 

  • van Veen JA, Merckx R, van de Geijn SC (1989) Plant- and soil-related controls of the flow of carbon from roots through soil microbial biomass. Plant Soil 115:179–188 doi:10.1007/BF02202586

    Article  Google Scholar 

  • VanCleemput O, Vermoesen A, DeGroot C, VanRyckeghem K (1994) Nitrous oxide emission out of grassland. Environ Monit Assess 31:145–152 doi:10.1007/BF00547190

    Article  CAS  Google Scholar 

  • Verburg P, Gorissen A, Arp W (1998) Carbon allocation and decomposition of root-derived organic matter in a plant–soil system of Calluna vulgaris as affected by elevated CO2. Soil Biol Biochem 30:1251–1258 doi:10.1016/S0038-0717(98)00055-8

    Article  CAS  Google Scholar 

  • Verhagen F, Hageman P, Woldendorp JM, Laanbroek H (1994) Competition for ammonium between nitrifying bacteria and plant roots in soil in pots—effects of grazing by flagellates and fertilization. Soil Biol Biochem 26:89–96 doi:10.1016/0038-0717(94)90199-6

    Article  CAS  Google Scholar 

  • Voesenek LACJ, Colmer TD, Pieril R, Milenaar FF, Peeters AJM (2006) How plants cope with complete submergence. New Phytol 170:213–226 doi:10.1111/j.1469-8137.2006.01692.x

    Article  PubMed  CAS  Google Scholar 

  • Wassmann R, Aulakh MS (2000) The role of rice plants in regulating mechanisms of methane emissions. Biol Fertil Soils 31:20–29 doi:10.1007/s003740050619

    Article  CAS  Google Scholar 

  • Wassmann R, Neue HU, Lantin RS, Aduna JB, Alberto MCR, Andales MJ, Tan MJ, Vandergon HACD, Hoffmann H, Papen H, Rennberg H, Seiler W (1999) Temporal patterns of methane emissions from wetland ricefields treated by different modes of N-application. J Geophys Res Atmo 99:16457–16462 doi:10.1029/94JD00017

    Article  Google Scholar 

  • Watanabe A, Takeda T, Kimura M (1999) Evaluation of origins of CH4 carbon emitted rice paddies. J Geo Res 104:23623–23629 doi:10.1029/1999JD900467

    Article  CAS  Google Scholar 

  • Wheatley R, Ritz K, Griffiths B (1990) Microbial biomass and mineral N transformations in soil planted with barley, ryegrass, pea or turnip. Plant Soil 127:157–167 doi:10.1007/BF00014422

    Article  Google Scholar 

  • Woldendorp JM (1962) The quantitative influence of the rhizosphere on denitrification. Plant Soil 17:267–270 doi:10.1007/BF01376229

    Article  CAS  Google Scholar 

  • Wollersheim R, Trolldenier G, Beringer H (1987) Effect of bulk density and soil water tension on denitrification in the rhizosphere of spring wheat (Triticum vulgare). Biol Fertil Soils 5:181–187 doi:10.1007/BF00256898

    Article  Google Scholar 

  • Xing GX (1998) N2O emission from ropland in China. Nutr Cycl Agroecosyst 52:249–254 doi:10.1023/A:1009776008840

    Article  CAS  Google Scholar 

  • Xing GX, Cao YC, Shi SL, Sun GQ, Du LJ, Zhu JG (2002a) Denitrification in underground saturated soil in a rice paddy region. Soil Biol Biochem 34:1593–1598 doi:10.1016/S0038-0717(02)00143-8

    Article  CAS  Google Scholar 

  • Xing GX, Shi SL, Shen GY, Du LJ, Xiong ZQ (2002b) Nitrous oxide emissions from paddy soil in three rice-based cropping system in china. Nutr Cycl Agroecosyst 64:135–143 doi:10.1023/A:1021131722165

    Article  CAS  Google Scholar 

  • Xiong ZQ, Xing GX, Tsuruta H, Shen GY, Shi SL, Du LJ (2002) Measurement of nitrous oxide emissions from two rice-based cropping systems in china. Nutr Cycl Agroecosyst 64:125–133 doi:10.1023/A:1021179605327

    Article  CAS  Google Scholar 

  • Yang L, Cai Z (2006) Effects of shading soybean plants on N2O emission from soil. Plant Soil 283:265–274 doi:10.1007/s11104-006-0017-0

    Article  CAS  Google Scholar 

  • Zaman M, Nguyen M, Matheson F, Blennerhassett J, Quin B (2007) Can soil amendments (zeolite or lime) shift the balance between nitrous oxide and dinitrogen emissions from pasture and wetland soils receiving urine or urea-N. Aust J Soil Res 45:543–553 doi:10.1071/SR07034

    Article  CAS  Google Scholar 

  • Zhu J, Liu G, Han Y, Zhang Y, Xing G (2003) Nitrate distribution and denitrification in the saturated zone of a paddy field under rice/wheat rotation. Chemosphere 50:725–732 doi:10.1016/S0045-6535(02)00212-6

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

The Environment and Agronomy research division and the International Relations Department of the INRA and the Department of Microbiology of the Swedish University of Agricultural Sciences in Uppsala are gratefully acknowledged for supporting and hosting L. Philippot’s long-term mission in Sweden. E.M. Baggs is supported by an Advanced Research Fellowship awarded by the Natural Environment Research Council (NERC), U.K. S. Halin is supported by the Formas financed Uppsala Microbiomics Center.

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Authors and Affiliations

  1. INRA, UMR 1229, 21000, Dijon, France

    L. Philippot

  2. University of Burgundy, UMR 1229, 21000, Dijon, France

    L. Philippot

  3. Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, 750 07, Uppsala, Sweden

    S. Hallin & G. Börjesson

  4. Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK

    E. M. Baggs

  5. Soil and Environmental Microbiology, UMR 1229, 17 rue Sully, 21065, Dijon Cedex, France

    L. Philippot

Authors
  1. L. Philippot
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  2. S. Hallin
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  3. G. Börjesson
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  4. E. M. Baggs
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Corresponding author

Correspondence to L. Philippot.

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Responsible Editor: Philippe Lemanceau.

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Philippot, L., Hallin, S., Börjesson, G. et al. Biochemical cycling in the rhizosphere having an impact on global change. Plant Soil 321, 61–81 (2009). https://doi.org/10.1007/s11104-008-9796-9

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  • DOI: https://doi.org/10.1007/s11104-008-9796-9

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