Contribution of Bacteria to Initial Input and Cycling of Nitrogen in Soils

  • Laurent Philippot
  • J.C. Germon
Part of the Soil Biology book series (SOILBIOL, volume 3)


Soil Biol Ammonia Oxidizer nifH Gene Initial Input Appl Environ 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Amarger N (2001) Rhizobia in the field. Adv Agron 73: 109–167Google Scholar
  2. Anthonisen A, Loehr R, Prakasam T, Srinath E (1976) Inhibition of nitrification by ammonia and nitrous acid. J Water Pollut Control Fed 48:835–852Google Scholar
  3. Atlas R, Bartha R (1993) Microbial ecology. Benjamin/Cummings, Redwood City, CA, 563 ppGoogle Scholar
  4. Aulack M, Doran J, Mosier A (1992) Soil denitrification: significance, measurements and effect of management. Adv Soil Sci 18:1–57Google Scholar
  5. Baldani J, Oliveira A, Guimaraes S, Baldani V, Reis F, Silva L, Reis V, Teixera K, Döberiner J (2000) Biological nitrogen fixation (BNF) in nonleguminous plants, the role of endophytic diatozotrophs. In: Pedrosa F, Hungria H, Yates G, Newton W (eds) Nitrogen fixation: from molecules to crop productivity. Kluwer, Dordrecht, pp 397–400Google Scholar
  6. Bartosch S, Hartwig C, Spieck E, Bock E (2002) Immunological detection of Nitrospira-like bacteria in various soils. Microb Ecol 43: 26–33CrossRefGoogle Scholar
  7. Beauchamp E, Trevors J, Paul J (1998) Carbon sources for bacterial denitrification. Adv Soil Sci 10:113–142Google Scholar
  8. Berg P, Klemedtsson L, Roswall T (1982) Inhibitory effect of low partial pressures of acetylene on nitrification. Soil Biol Biochem 14: 301–303CrossRefGoogle Scholar
  9. Bothe H, Jost G, Schloter M, Ward B, Witzel K (2000) Molecular analysis of ammonia oxidation and denitrification in natural environments. FEMS Microbiol Rev 24:673–690CrossRefGoogle Scholar
  10. Braker G, Tiedje JM (2003) Nitric oxide reductase (norB) genes from pure cultures and environmental samples. Appl Environ Microbiol 69: 3476–3483CrossRefGoogle Scholar
  11. Braker G, Fesefeldt A, Witzel KP (1998) Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl Environ Microbiol 64:3769–3775Google Scholar
  12. Bruns MA, Stephen JR, Kowalchuk GA, Prosser JI, Paul EA (1999) Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled, and successional soils. Appl Environ Microbiol 65: 2994–3000Google Scholar
  13. Cavigelli MA, Robertson GP (2001) Role of denitrifiers diversity in rates of nitrous oxide consumption in a terrestrial ecosystem. Soil Biol Biochem 33:297–310CrossRefGoogle Scholar
  14. Cheneby D, Philippot L, Hartmann A, Hénault C, Germon JC (2000) 16S rDNA analysis for characterization of denitrifying bacteria isolated from three agricultural soils. FEMS Microbiol Ecol 34:121–128Google Scholar
  15. Cole JA (1990) Physiology, biochemistry and genetics of nitrate dissimilation to ammonia. In: Revsbech NP, Sorensen J (eds) Denitrification in soil and sediment. Plenum Press, New York, pp 57–76Google Scholar
  16. Cole JA, Brown CM (1980) Nitrite reduction to ammonia by fermentative bacteria: a short circuit in the biological nitrogen cycle. FEMS Microbiol Lett 7:65–72Google Scholar
  17. DeBoer W, Kowalchuk G (2001) Nitrification in acid soils: micro-organisms and mechanisms. Soil Biol Biochem 33:853–866Google Scholar
  18. DeBoer W, Tietema A, Gunnewiek PJAK, Lannbroek HJ (1992) The chemolithotrophic ammonium-oxidizing community in a nitrogen-saturated acid forest soil in relation to pH-dependent nitrifying activity. Soil Biol Biochem 24:229–234CrossRefGoogle Scholar
  19. Degrange V, Coûteaux M, Anderson J, Berg M, Lensi R (1998) Nitrification and occurrence of Nitrobacter by MPN-PCR in low and high nitrifying coniferous forest soils. Plant Soil 198:201–208CrossRefGoogle Scholar
  20. Dommergues Y (1997) Contribution of actinorhizal plants to tropical soil productivity and rehabilitation. Soil Biol Biochem 6:931–941Google Scholar
  21. Donaldson JM, Henderson GS (1990) Nitrification potential of secondary-succession upland oak forest. II. Regulation of ammonium-oxidizing bacteria populations. Soil Sci Soc Am J 54:898–902Google Scholar
  22. Fazzolari E, Mariotti A, Germon J (1990) Nitrate reduction to ammonia:a dissimilatory process in Enterobacter amnigenus. Can J Microbiol 36:779–785Google Scholar
  23. Fazzolari E, Nicolardot B, Germon J (1998) Simultaneous effects of increasing levels of glucose and oxygen partial pressures on denitrification and dissimilatory nitrate reduction to ammonium in repacked soil cores. Eur J Soil Biol 34:47–52Google Scholar
  24. Flanagan D, Gregory L, Carter J, Karakas-Sen A, Richardson D, Spiro S (1999) Detection of genes for periplasmic nitrate reductase in nitrate respiring bacteria and in community DNA. FEMS Microbiol Lett 177: 263–270CrossRefGoogle Scholar
  25. Galloway J (1998) The global nitrogen cycle: changes and consequences. Environ Pollut 102:15–24CrossRefGoogle Scholar
  26. Gamble T, Betlach H, Tiedje J (1977) Numerically dominant denitrifying bacteria from world soils. Appl Environ Microbiol 33:926–939Google Scholar
  27. Garrido F, Hénault C, Gaillard H, Pérez S, Germon J (2002) N2O and NO emissions by agricultural soils with low hydraulic potentials. Soil Biol Biochem 34:559–575CrossRefGoogle Scholar
  28. Germon J, Jacques D (1990) Denitrifying activity measurement by soil core method. Effect of depth and characterisation of N2O/N2 ratio in different soils. Mitt Dtsch Bodenkd Ges 60:51–58Google Scholar
  29. Hallin S, Lindgren P (1999) PCR detection of genes encoding nitrite reductase in denitrifying bacteria. Appl Environ Microbiol 65:1652–1657Google Scholar
  30. Hastings R, Butler C, Singleton I, Saunders J (2000) Analysis of ammonia-oxidizing bacteria populations in acid forest soil during conditions of moisture limitation. Lett Appl Microbiol 30:14–18CrossRefGoogle Scholar
  31. Hauck R (1983) Agronomic and technological approaches to minimize gaseous nitrogen losses from croplands. In: Freney JR, Simpson JR (eds) Gaseous loss of nitrogen from plant-soil systems. Nijhoff/Junk, The Hague, pp 285–312Google Scholar
  32. Head IM, Saunders JR, Pickup RW (1998) Microbial evolution, diversity and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb Ecol 35:1–21CrossRefGoogle Scholar
  33. Hénault C, Germon J (2000) Nemis, a predictive model of denitrification on the field. Eur J Soil Sci 51:257–270Google Scholar
  34. Hénault C, Chèneby D, Heurlier K, Garrido F, Perez S, Germon JC (2001) Laboratory kinetics of soil denitrification are useful to discriminate soils with potentially high levels of N2O emission on the field scale. Agronomie 21:713–723Google Scholar
  35. Holtan-Hartwig L, Dörsch P, Bakken L (2000) Comparison of denitrifying communities in organic soils: kinetics of NO- 3 and N2O reduction. Soil Biol Biochem 32:833–843CrossRefGoogle Scholar
  36. IPCC (2001) Climate change, the scientific basis. Cambridge Univ Press, Cambridge, 881 ppGoogle Scholar
  37. Keeney D (1986) Inhibition of nitrification in soils. In: Prosser J (ed) Nitrification. IRL Press, Oxford, pp 99–115Google Scholar
  38. Kowalchuk G, Stephen J (2001) Ammonia-oxidizing bacteria: a model for molecular biology. Annu Rev Microbiol 55:485–529CrossRefGoogle Scholar
  39. Kowalchuk GA, Stienstra AW, Heilig GH, Stephen JR, Woldendorp JW (2000) Molecular analysis of ammonia-oxidising bacteria in soil of successional grasslands of the Dreentsche A (The Netherlands). FEMS Microbial Ecol 31:207–215Google Scholar
  40. Lashof D, Ahuja D (1990) Relative contributions of greenhouse gas emissions to global warming. Nature 344:529–531CrossRefGoogle Scholar
  41. Lovel C, Friez M, Longshore J, Bagwell C (2001) Recovery and phylogenetic analysis of nifH sequences from diazotrophic bacteria associated with dead aboveground biomass of Spartina alterniflora. Appl Environ Microbiol 67:5308–5314Google Scholar
  42. MacDonald R (1986) Nitrification in soil: an introductory history. In: Prosser J (ed) Nitrification. IRL Press, Oxford, pp 1–16Google Scholar
  43. Mahne I, Tiedje JM (1995) Criteria and methodology for identifying respiratory denitrifiers. Appl Environ Microbiol 61:1110–1115Google Scholar
  44. Mendum TA, Sockett RE, Hirsch PR (1999) Use of molecular and isotopic techniques to monitor the response of autotrophic ammonia-oxidizing populations of the beta subdivisons of the class Proteobateria in arable soils to nitrogen fertilizer. Appl Environ Microbiol 65:4155–4162Google Scholar
  45. Moreno-Vivian C, Ferguson S (1998) Definition and distinction between assimilatory, dissimilatory and respiratory pathways. Mol Microbiol 29:661–669CrossRefGoogle Scholar
  46. Newton WE (2000) Nitrogen fixation in perspective. In: Pedrosa F, Hungria M, Yates G, Newton W (eds) Nitrogen fixation: from molecules to crop productivity. Kluwer, Dordrecht, pp 3–8Google Scholar
  47. O’Hara G, Daniel R (1985) Rhizobial denitrification. Annu Rev Soil Biol Biochem 17:1–9Google Scholar
  48. Pennington PI, Ellis RC (1993) Autotrophic and heterotrophic nitrification in acidic forest and native grassland soils. Soil Biol Biochem 25:1399–1408CrossRefGoogle Scholar
  49. Philippot L, Piutti S, Martin-Laurent F, Hallet S, Germon J (2002) Molecular analysis of the nitrate-reducing community from unplanted and maize planted soil. Appl Environ Microbiol 68:6121–6128CrossRefGoogle Scholar
  50. Pinay G, Rogues L, Fabre A (1993) Spatial and temporal pattern of denitrification in a riparian forest. J Appl Biol 30:581–591Google Scholar
  51. Poly F, Ranjard L, Nazaret S, Gourbiere F, Monrozier L (2001) Comparison of nifH gene pools in soils and soil microenvironments with contrasting properties. Appl Environ Microbiol 67:2255–2262CrossRefGoogle Scholar
  52. Pratt P, Barber J, Corrin M, Goering J, Hauck R, Johnston H, Klute A, Knowles R, Nelson D, Pickett R, Stephens E (1997) Effect of increased nitrogen fixation on stratospheric ozone. Climate Change 1: 109–135Google Scholar
  53. Roberston GP (1982) Factors regulating nitrification in primary and secondary succession. Ecology 63:1561–1573Google Scholar
  54. Robertson GP, Tiedje JM (1987) Nitrous oxide sources in aerobic soils: Nitrification, denitrification and other biological processes. Soil Biol Biochem 19:187–193CrossRefGoogle Scholar
  55. Rosch C, Mergel A, Bothe H (2002) Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. Appl Environ Microbiol 68:3818–3829CrossRefGoogle Scholar
  56. Rotthauwe J-H, Witzel K-P, Liesack W (1997) The ammonia monoxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammoniaoxidizing populations. Appl Environ Microbiol 63(12):4704–4712Google Scholar
  57. Ryden J, Lund L (1980) Nature and extent of directly measured denitrification losses from some irrigated vegetable crop production units. Soil Sci Soc Am J 49:505–511Google Scholar
  58. Scala D, Kerkhof L (1998) Nitrous oxide reductase (nosZ) gene-specific PCR primers for detection of denitrifiers and three nosZ genes from marine sediments. FEMS Microbiol Lett 162:61–68CrossRefGoogle Scholar
  59. Shirey JJ, Sextone AJ (1989) Denitrification and nitrate-reducing bacterial populations in abandoned and reclaimed minesoils. FEMS Microbiol Ecol 62:59–70CrossRefGoogle Scholar
  60. Shrama E (1993) Nutrient dynamics in Himalayan alder plantations. Ann Bot 72:329–336Google Scholar
  61. Simon J (2002) Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiol Rev 26:285–309CrossRefGoogle Scholar
  62. Simonet P, Grosjean M, Misra A, Nazaret S, Cournoyer B, Normand P (1991) Frankia genusspecific characterization by polymerase chain reaction. Appl Environ Microbiol 57:3278–3286Google Scholar
  63. 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 74:337–344CrossRefGoogle Scholar
  64. Stephen JR, Kowalchuk GA, Bruns M-AV, McCaig AE, Philipps C, Embley TM, Prosser JI (1998) Analysis of β-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing. Appl Environ Microbiol 64:2958–2965Google Scholar
  65. Stevens R, Laughlin R, Burns L, Arah J, Hood R (1997) Measuring the contributions of nitrification and denitrification to the flux of nitrous oxide from soil. Soil Biol Biochem 29:139–151CrossRefGoogle Scholar
  66. Tiedje JM (1988) Ecology of denitrification and dissimilatory nitrate reduction to ammonium. In: Zehnder AJB (ed) Biology of anaerobic microorganisms. Wiley, New York, pp 179–244Google Scholar
  67. Ueda T, Suga Y, Yahiro N, Matsugushi T (1995) Remarkable N2 fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. J Bacteriol 177:1414–1417Google Scholar
  68. Vance C (1998) Legume symbiotic nitrogen fixation: agronomic aspects. In: Spaink H, Kondorosi A, Hooykaas P (eds) The Rhizobiaceae; molecular biology of plant-associated bacteria. Kluwer, Dordrecht, pp 509–503Google Scholar
  69. Vitousek P, Walker L (1989) Biological invasion by Myrica faya in Hawaii: plant demography, nitrogen fixation, ecosystems effects. Ecol Monogr 59:247–265Google Scholar
  70. Waibel A, Peter T, Carslaw K, Oelhaf H, Wetzel G, Crutzen P, Poschl U, Tsias A, Reimer E, Fischer H (1999) Arctic ozone loss due to denitrification. Science 283:2064–2069CrossRefGoogle Scholar
  71. Waterer J, Vessey J, Stobbe E, Soper R (1994) Yield and symbiotic nitrogen fixation in a peamustard intercrop as influenced by N fertilizer addition. Soil Biol Biochem 26:447–453CrossRefGoogle Scholar
  72. Webster EA, Hopkins DW (1996) Contributions from different microbial processes to N2O emission from soil under different moisture regimes. Biol Fertil Soils 22:3331–3335Google Scholar
  73. Weier KL, MacRae IC (1992) Denitrifying bacteria in the profile of a brigalow clay soil beneath a permanent pasture and a cultivated crop. Soil Biol Biochem 29:919–923Google Scholar
  74. Widmer F, Shaffer B, Porteous L, Seidler R (1999) Analysis of nifH gene pool complexity in soil and litter at a Douglas fir forest site in the Oregon cascade mountain range. Appl Environ Microbiol 65:374–380Google Scholar
  75. Yin S, Chen D, Chen L, Eddis R (2002) Dissimilatory nitrate reduction and responsible microorganisms in two Chinese and Australian paddy soils. Soil Biol Biochem 34:1131–1137CrossRefGoogle Scholar
  76. Zehr J, Jenkins B, Short S, Stewart G (2003) Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ Microbiol 5:539–554CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Laurent Philippot
    • 1
  • J.C. Germon
    • 1
  1. 1.Microbiologie et Geochimie des SolsINRA-University of BurgundyDijon CedexFrance

Personalised recommendations