Microbial Ecology

, Volume 70, Issue 3, pp 809–818 | Cite as

Coupling Between and Among Ammonia Oxidizers and Nitrite Oxidizers in Grassland Mesocosms Submitted to Elevated CO2 and Nitrogen Supply

  • Marie Simonin
  • Xavier Le Roux
  • Franck Poly
  • Catherine Lerondelle
  • Bruce A. Hungate
  • Naoise Nunan
  • Audrey Niboyet
Soil Microbiology


Many studies have assessed the responses of soil microbial functional groups to increases in atmospheric CO2 or N deposition alone and more rarely in combination. However, the effects of elevated CO2 and N on the (de)coupling between different microbial functional groups (e.g., different groups of nitrifiers) have been barely studied, despite potential consequences for ecosystem functioning. Here, we investigated the short-term combined effects of elevated CO2 and N supply on the abundances of the four main microbial groups involved in soil nitrification: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (belonging to the genera Nitrobacter and Nitrospira) in grassland mesocosms. AOB and AOA abundances responded differently to the treatments: N addition increased AOB abundance, but did not alter AOA abundance. Nitrobacter and Nitrospira abundances also showed contrasted responses to the treatments: N addition increased Nitrobacter abundance, but decreased Nitrospira abundance. Our results support the idea of a niche differentiation between AOB and AOA, and between Nitrobacter and Nitrospira. AOB and Nitrobacter were both promoted at high N and C conditions (and low soil water content for Nitrobacter), while AOA and Nitrospira were favored at low N and C conditions (and high soil water content for Nitrospira). In addition, Nitrobacter abundance was positively correlated to AOB abundance and Nitrospira abundance to AOA abundance. Our results suggest that the couplings between ammonia and nitrite oxidizers are influenced by soil N availability. Multiple environmental changes may thus elicit rapid and contrasted responses between and among the soil ammonia and nitrite oxidizers due to their different ecological requirements.


Global change Grasslands Nitrification Ammonia oxidizers Nitrite oxidizers Niche differentiation 



The authors thank the two anonymous reviewers for their constructive comments that helped to improve the article. We would like to thank the people involved in the initial experimentation from which the soil samples used in the present study were obtained, and in particular Annick Ambroise, Laure Barthes, Juliette Bloor, Sandrine Fontaine and Paul Leadley from the Laboratoire Ecologie, Systématique, Evolution (UMR 8079). Quantitative PCR were performed at the Microbial Ecology Centre (UMR 5557, USC 1364) and DTAMB platform (FR 41, University Lyon 1). This study was funded by AgroParisTech support of the Institute of Ecology and Environmental Sciences - Paris (UMR 7618), and CNRS and INRA supports of UMR 5557 / USC 1364.

Supplementary material

248_2015_604_MOESM1_ESM.doc (80 kb)
ESM 1 (DOC 79 kb)


  1. 1.
    Barnard RL, Leadley PW, Hungate BA (2005) Global change, nitrification and denitrification: a review. Glob Biogeochem Cycles. doi: 10.1029/2004GB002282 Google Scholar
  2. 2.
    Cantarel AAM, Bloor JMG, Pommier T, Guillaumaud N, Moirot C, Soussana JF, Poly F (2012) Four years of experimental climate change modifies the microbial drivers of N2O fluxes in an upland grassland ecosystem. Glob Chang Biol 18:2520–2531CrossRefGoogle Scholar
  3. 3.
    Gutknecht JLM, Field CB, Balser TC (2012) Microbial communities and their responses to simulated global change fluctuate greatly over multiple years. Glob Chang Biol 18:2256–2269CrossRefGoogle Scholar
  4. 4.
    Henry HAL, Juarez JD, Field CB, Vitousek PM (2005) Interactive effects of elevated CO2 N deposition and climate change on extracellular enzyme activity and soil density fractionation in a California annual grassland. Glob Chang Biol 11:1808–1815CrossRefGoogle Scholar
  5. 5.
    Kandeler E, Mosier AR, Morgan JA, Milchunas DG, King JY, Rudolph S, Tscherko D (2008) Transient elevation of carbon dioxide modifies the microbial community composition in a semi-arid grassland. Soil Biol Biochem 40:162–171CrossRefGoogle Scholar
  6. 6.
    Galloway JN, Townsend AR, Erisman JW, Bekunda M, Cai Z, Freney JR, Martinelli LA, Seitzinger SP, Sutton MA (2008) Transformation of the nitrogen cycle: recent trends questions and potential solutions. Science 320:889–892CrossRefPubMedGoogle Scholar
  7. 7.
    IPCC et al (2007) Climate change 2007: the physical science basis. In: Solomon S, Qin D, Manning M, Chen Z, Marquis M (eds) Contribution of working group I to the fourth assessment report of the IPCC. Cambridge University Press, Cambridge, p 1009Google Scholar
  8. 8.
    Schimel JP, Schaeffer SM (2012) Microbial control over carbon cycling in soil. Front Microbiol. doi: 10.3389/fmicb.2012.00348 PubMedCentralPubMedGoogle Scholar
  9. 9.
    Griffiths BS, Philippot L (2012) Insights into the resistance and resilience of the soil microbial community. FEMS Microbiol Rev 37:112–129CrossRefPubMedGoogle Scholar
  10. 10.
    Wertz S, Degrange V, Prosser JI, Poly F, Commeaux C, Guillaumaud N, Le Roux X (2007) Decline of soil microbial diversity does not influence the resistance and resilience of key soil microbial functional groups following a model disturbance. Environ Microbiol 9:2211–2219CrossRefPubMedGoogle Scholar
  11. 11.
    Boudsocq S, Niboyet A, Lata JC, Raynaud X, Loeuille N, Mathieu J, Blouin M, Abbadie L, Barot S (2012) Plant preference for ammonium versus nitrate: a neglected determinant of ecosystem functioning? Am Nat 180:60–69CrossRefPubMedGoogle Scholar
  12. 12.
    Hodge A, Robinson D, Fitter A (2000) Are microorganisms more effective than plants at competing for nitrogen? Trends Plant Sci 5:304–308CrossRefPubMedGoogle Scholar
  13. 13.
    Wrage N, Velthof GL, Van Beusichem ML, Oenema O (2001) Role of nitrifier denitrification in the production of nitrous oxide. Soil Biol Biochem 33:1723–1732CrossRefGoogle Scholar
  14. 14.
    Hayatsu M, Tago K, Saito M (2008) Various players in the nitrogen cycle: diversity and functions of the microorganisms involved in nitrification and denitrification. Soil Sci Plant Nutr 54:33–45CrossRefGoogle Scholar
  15. 15.
    Freitag TE, Chang L, Clegg CD, Prosser JI (2005) Influence of inorganic nitrogen management regime on the diversity of nitrite-oxidizing bacteria in agricultural grassland soils. Appl Environ Microbiol 71:8323–8334PubMedCentralCrossRefPubMedGoogle Scholar
  16. 16.
    Horz HP, Barbrook A, Field CB, Bohannan BJM (2004) Ammonia-oxidizing bacteria respond to multifactorial global change. Proc Natl Acad Sci USA 101:15136–15141PubMedCentralCrossRefPubMedGoogle Scholar
  17. 17.
    Regan K, Kammann C, Hartung K, Lenhart K, Muller C, Philippot L, Kandeler E, Marhan S (2011) Can differences in microbial abundances help explain enhanced N2O emissions in a permanent grassland under elevated atmospheric CO2? Glob Chang Biol 17:3176–3186CrossRefGoogle Scholar
  18. 18.
    Chen YL, Hu HW, Han HY, Du Y, Wan SQ, Xu ZW, Chen BD (2014) Abundance and community structure of ammonia‐oxidizing archaea and bacteria in response to fertilization and mowing in a temperate steppe in Inner Mongolia. FEMS Microbiol Ecol. doi: 10.1111/1574-6941.12336 Google Scholar
  19. 19.
    Daebeler A, Abell GC, Bodelier PL, Bodrossy L, Frampton DM, Hefting MM, Laanbroek HJ (2012) Archaeal dominated ammonia-oxidizing communities in Icelandic grassland soils are moderately affected by long-term N fertilization and geothermal heating. Front Microbiol. doi: 10.3389/fmicb.2012.00352 PubMedCentralPubMedGoogle Scholar
  20. 20.
    Dai Y, Di HJ, Cameron KC, He JZ (2013) Effects of nitrogen application rate and a nitrification inhibitor dicyandiamide on ammonia oxidizers and N2O emissions in a grazed pasture soil. Sci Total Environ 465:125–135CrossRefPubMedGoogle Scholar
  21. 21.
    Di HJ, Cameron KC, Shen JP, Winefield CS, O’Callaghan M, Bowatte S, He JZ (2010) Ammonia‐oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions. FEMS Microbiol Ecol 72:386–394CrossRefPubMedGoogle Scholar
  22. 22.
    Docherty KM, Balser TC, Bohannan BJM, Gutknecht JLM (2012) Soil microbial responses to fire and interacting global change factors in a California annual grassland. Biogeochemistry 109:63–83CrossRefGoogle Scholar
  23. 23.
    Hartmann AA, Barnard RL, Marhan S, Niklaus PA (2013) Effects of drought and N-fertilization on N cycling in two grassland soils. Oecologia 171:705–717CrossRefPubMedGoogle Scholar
  24. 24.
    O’Callaghan M, Gerard EM, Carter PE, Lardner R, Sarathchandra U, Burch G et al (2010) Effect of the nitrification inhibitor dicyandiamide (DCD) on microbial communities in a pasture soil amended with bovine urine. Soil Biol Biochem 42:1425–1436CrossRefGoogle Scholar
  25. 25.
    Shen XY, Zhang LM, Shen JP, Li LH, Yuan CL, He JZ (2011) Nitrogen loading levels affect abundance and composition of soil ammonia oxidizing prokaryotes in semiarid temperate grassland. J Soils Sediments 11:1243–1252CrossRefGoogle Scholar
  26. 26.
    Tian XF, Hu HW, Ding Q, Song MH, Xu XL, Zheng Y, Guo LD (2013) Influence of nitrogen fertilization on soil ammonia oxidizer and denitrifier abundance microbial biomass and enzyme activities in an alpine meadow. Biol Fertil Soils. doi: 10.1007/s00374-013-0889-0 Google Scholar
  27. 27.
    Zhang X, Liu W, Schloter M, Zhang G, Chen Q, Huang J, Li L, Elser JJ, Han X (2013) Response of the abundance of key soil microbial nitrogen-cycling genes to multi-factorial global changes. PLoS One. doi: 10.1371/journal.pone.0076500 Google Scholar
  28. 28.
    Kowalchuk GA, Stephen JR (2001) Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu Rev Microbiol 55:485–529CrossRefPubMedGoogle Scholar
  29. 29.
    Burns LC, Stevens RJ, Laughlin RJ (1996) Production of nitrite in soil by simultaneous nitrification and denitrification. Soil Biol Biochem 28:609–616CrossRefGoogle Scholar
  30. 30.
    Gelfand I, Yakir D (2008) Influence of nitrite accumulation in association with seasonal patterns and mineralization of soil nitrogen in a semi-arid pine forest. Soil Biol Biochem 40:415–424CrossRefGoogle Scholar
  31. 31.
    Roux-Michollet D, Czarnes S, Adam B, Berry D, Commeaux C, Guillaumaud N, Le Roux X, Clays-Josserand A (2008) Effects of steam disinfestation on community structure abundance and activity of heterotrophic denitrifying and nitrifying bacteria in an organic farming soil. Soil Biol Biochem 40:1836–1845CrossRefGoogle Scholar
  32. 32.
    Niboyet A, Le Roux X, Dijkstra P, Hungate BA, Barthes L, Blankinship JC, Brown JR, Field CB, Leadley PW (2011) Testing interactive effects of global environmental changes on soil nitrogen cycling. Ecosphere 2:1–24CrossRefGoogle Scholar
  33. 33.
    Zhang L-M, Offre PR, He J-Z, Verhamme DT, Nicol GW, Prosser JI (2010) Autotrophic ammonia oxidation by soil thaumarchaea. Proc Natl Acad Sci U S A 107:17240–17245PubMedCentralCrossRefPubMedGoogle Scholar
  34. 34.
    Degrange V, Lensi R, Bardin R (1997) Activity size and structure of a Nitrobacter community as affected by organic carbon and nitrite in sterile soil. FEMS Microbiol Ecol 24:173–180CrossRefGoogle Scholar
  35. 35.
    Hatzenpichler R (2012) Diversity physiology and niche differentiation of ammonia-oxidizing archaea. Appl Environ Microbiol 78:7501–7510PubMedCentralCrossRefPubMedGoogle Scholar
  36. 36.
    Prosser JI, Nicol GW (2012) Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol 20:523–531CrossRefPubMedGoogle Scholar
  37. 37.
    Xie Z, Le Roux X, Wang C, Gu Z, An M, Nan H, Li F, Du G, Feng H, Ma X (2014) Identifying response groups of soil nitrifiers and denitrifiers to grazing and associated soil environmental drivers in Tibetan alpine meadows. Soil Biol Biochem 77:89–99CrossRefGoogle Scholar
  38. 38.
    Attard E, Poly F, Commeaux C, Laurent F, Terada A, Smets BF, Recous S, Le Roux X (2010) Shifts between Nitrospira- and Nitrobacter-like nitrite oxidizers underlie the response of soil potential nitrite oxidation to changes in tillage practices. Environ Microbiol 12:315–326CrossRefPubMedGoogle Scholar
  39. 39.
    Niboyet A, Barthes L, Hungate BA, Le Roux X, Bloor JMG, Ambroise A, Fontaine S, Price PM, Leadley PW (2010) Responses of soil nitrogen cycling to the interactive effects of elevated CO2 and inorganic N supply. Plant Soil 327:35–47CrossRefGoogle Scholar
  40. 40.
    Bloor JM, Niboyet A, Leadley PW, Barthes L (2009) CO2 and inorganic N supply modify competition for N between co-occurring grass plants, tree seedlings and soil microorganisms. Soil Biol Biochem 41:544–552CrossRefGoogle Scholar
  41. 41.
    Bardgett RD, Mawdsley JL, Edwards S, Hobbs PJ, Rodwell JS, Davies WJ (1999) Plant species and nitrogen effects on soil biological properties of temperate upland grasslands. Funct Ecol 13:650–660CrossRefGoogle Scholar
  42. 42.
    Holland EA, Braswell B, Lamarque J-F, Townsend A, Sulzman J, Müller J-F, Dentener F, Brasseur G, Levy H II, Penner JE (1997) Variations in the predicted spatial distribution of atmospheric nitrogen deposition and their impact on carbon uptake by terrestrial ecosystems. J Geophys Res 102:15849–15815CrossRefGoogle Scholar
  43. 43.
    Tourna M, Freitag TE, Nicol GW, Prosser JI (2008) Growth activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ Microbiol 10:1357–1364CrossRefPubMedGoogle Scholar
  44. 44.
    Rotthauwe JH, Witzel KP, 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 63:4704–4712PubMedCentralPubMedGoogle Scholar
  45. 45.
    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 442:806–809CrossRefPubMedGoogle Scholar
  46. 46.
    Poly F, Wertz S, Brothier E, Degrange V (2008) First exploration of Nitrobacter diversity in soils by a PCR cloning-sequencing approach targeting functional gene nxrA. FEMS Microbiol Ecol 63:132–140CrossRefPubMedGoogle Scholar
  47. 47.
    Wertz S, Poly F, Le Roux X, Degrange V (2008) Development and application of a PCR‐denaturing gradient gel electrophoresis tool to study the diversity of Nitrobacter‐like nxrA sequences in soil. FEMS Microbiol Ecol 63:261–271CrossRefPubMedGoogle Scholar
  48. 48.
    Graham DW, Knapp CW, Van Vleck ES, Bloor K, Lane TB, Graham CE (2007) Experimental demonstration of chaotic instability in biological nitrification. ISME J 1:385–393CrossRefPubMedGoogle Scholar
  49. 49.
    Erguder TH, Boon N, Wittebolle L, Marzorati M, Verstraete W (2009) Environmental factors shaping the ecological niches of ammonia‐oxidizing archaea. FEMS Microbiol Rev 33:855–869CrossRefPubMedGoogle Scholar
  50. 50.
    Zhalnina K, de Quadros PD, Camargo FA, Triplett EW (2012) Drivers of archaeal ammonia-oxidizing communities in soil. Front Microbiol. doi: 10.3389/fmicb.2012.00210 PubMedCentralPubMedGoogle Scholar
  51. 51.
    Martens-Habbena W, Berube PM, Urakawa H, José R, Stahl DA (2009) Ammonia oxidation kinetics determine niche separation of nitrifying archaea and bacteria. Nature 461:976–979CrossRefPubMedGoogle Scholar
  52. 52.
    Taylor AE, Zeglin LH, Wanzek TA, Myrold DD, Bottomley PJ (2012) Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials. ISME J 6:2024–2032PubMedCentralCrossRefPubMedGoogle Scholar
  53. 53.
    Verhamme DT, Prosser JI, Nicol GW (2011) Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms. ISME J 5:1067–1071PubMedCentralCrossRefPubMedGoogle Scholar
  54. 54.
    Blackburne R, Vadivelu VM, Yuan Z, Keller J (2007) Kinetic characterisation of an enriched Nitrospira culture with comparison to Nitrobacter. Water Res 41:3033–3042CrossRefPubMedGoogle Scholar
  55. 55.
    Schramm A, de Beer D, van den Heuvel JC, Ottengraf S, Amann R (1999) Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifying bioreactor: quantification by in situ hybridization and the use of microsensors. Appl Environ Microbiol 65:3690–3696PubMedCentralPubMedGoogle Scholar
  56. 56.
    Wertz S, Leigh AK, Grayston SJ (2012) Effects of long‐term fertilization of forest soils on potential nitrification and on the abundance and community structure of ammonia oxidizers and nitrite oxidizers. FEMS Microbiol Ecol 79:142–154CrossRefPubMedGoogle Scholar
  57. 57.
    Nicol GW, Leininger S, Schleper C, Prosser JI (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol 10:2966–2978CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Marie Simonin
    • 1
    • 2
  • Xavier Le Roux
    • 2
  • Franck Poly
    • 2
  • Catherine Lerondelle
    • 2
  • Bruce A. Hungate
    • 3
  • Naoise Nunan
    • 1
  • Audrey Niboyet
    • 1
  1. 1.Institute of Ecology and Environmental Sciences - ParisUMR 7618 Université Pierre et Marie Curie/CNRS/AgroParisTechThiverval GrignonFrance
  2. 2.Microbial Ecology CenterUniversité de Lyon/Université Lyon 1/CNRS/INRA, UMR CNRS 5557, USC INRA 1364VilleurbanneFrance
  3. 3.Center for Ecosystem Science and Society and Department of Biological SciencesNorthern Arizona UniversityFlagstaffUSA

Personalised recommendations