Applied Microbiology and Biotechnology

, Volume 97, Issue 12, pp 5507–5515 | Cite as

Nitrogen cycling and relationships between ammonia oxidizers and denitrifiers in a clay-loam soil

  • N. V. Paranychianakis
  • M. Tsiknia
  • G. Giannakis
  • N. P. Nikolaidis
  • N. Kalogerakis
Applied microbial and cell physiology


This study investigated the effect of municipal solid waste (MSW) compost (0, 50, and 100 t/ha) on N cycling and the microorganisms involved in it, in a clay-loam soil. After a release of nitrates (NO3 -N) in the first 6 days after compost incorporation, soil NO3 -N content remained constant in all the treatments until day 62, suggesting N immobilization induced by the soil used in this study. Then, soil NO3 -N content increased in all treatments and especially in the highest compost dose, providing evidence that immobilization effect has been at least partially relieved. amoA gene copies of ammonia-oxidizing archaea (AOA) and bacteria (AOB) followed the overall pattern of soil NO3 -N content; however, no differences were found in amoA gene copies among treatments, except in the last sampling, an effect attributed to the slight differences in the potential nitrification rate among them. Ammonia oxidizer pattern provided evidence that both groups were involved in ammonia oxidation and changes in their abundance can be used as ‘indicator’ to predict changes in soil nitrification status. Moreover, the strong correlation between AOA and AOB amoA copies (R 2 = 0.94) and the high slope (13) of the curve suggest that AOA had probably an important role on ammonia oxidation. Denitrifying genes (nirS, nirK, nosZ) also followed the general pattern of soil NO3 -N, and they were strongly correlated with both groups of ammonia oxidizers, and particularly AOA, suggesting strong interrelationships among them. Losses of N through denitrification, as they were estimated by total nitrogen, were inversely related to soil NO3 -N content. Similar to ammonia oxidizers, denitrifying gene copies did not differ among compost treatments an effect that could be probably explained by the low availability of organic-C in the MSW compost and hence the competition with aerobic heterotrophs.


Ammonia-oxidizing archaea Ammonia-oxidizing bacteria Nitrification Immobilization 



This work was founded from the EU FP7 Collaborative Project “Soil Transformations in European Catchments” (SoilTrEC) (Grant Agreement no. 244118).


  1. Bouyoucos GJ (1962) Hydrometer method improved for making particle and size analysis of soils. Agron J 54:464–465CrossRefGoogle Scholar
  2. Braker G, Conrad R (2011) Diversity, structure, and size of N2O-producing microbial communities in soils—what matters for their functioning? Adv Appl Microbiol 75:33–70CrossRefGoogle Scholar
  3. Busby RR, Allen Torbert H, Gebhart DL (2007) Carbon and nitrogen mineralization of non-composted and composted municipal solid waste in sandy soils. Soil Biol Biochem 39:1277–1283CrossRefGoogle Scholar
  4. Cordovil CMDS, Coutinho J, Goss M, Cabral F (2005) Potentially mineralizable nitrogen from organic materials applied to a sandy soil: fitting the one-pool exponential model. Soil Use Manage 21:65–72CrossRefGoogle Scholar
  5. Dandie CE, Burton DL, Zebarth BJ, Henderson SL, Trevors JT, Goyer C (2008) Changes in bacterial denitrifier community abundance over time in an agricultural field and their relationship with denitrification activity. Appl Environ Microbiol 74:5997–6005CrossRefGoogle Scholar
  6. Dandie CE, Wertz S, Leclair CL, Goyer C, Burton DL, Patten CL, Zebarth BJ, Trevors JT (2011) Abundance, diversity and functional gene expression of denitrifier communities in adjacent riparian and agricultural zones. FEMS Microbiol Ecol 77:69–82CrossRefGoogle Scholar
  7. Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci U S A 102:14683–14688CrossRefGoogle Scholar
  8. García-Gil JC, Plaza C, Soler-Rovira P, Polo A (2000) Long-term effects of municipal solid waste compost application on soil enzyme activities and microbial biomass. Soil Biol Biochem 32:1907–1913CrossRefGoogle Scholar
  9. Gomez-Munoz B, Hatch DJ, Bol R, Dixon ER, Garcia-Ruiz R (2011) Gross and net rates of nitrogen mineralisation in soil amended with composted olive mill pomace. Rapid Commun Mass spectrom: RCM 25:1472–1478CrossRefGoogle Scholar
  10. Gubry-Rangin C, Nicol GW, Prosser JI (2010) Archaea rather than bacteria control nitrification in two agricultural acidic soils. FEMS Microbiol Ecol 74:566–574CrossRefGoogle Scholar
  11. Hargreaves JC, Adl MS, Warman PR (2008) A review of the use of composted municipal solid waste in agriculture. Agric Ecosyst Environ 123:1–14CrossRefGoogle Scholar
  12. Henry S, Baudoin E, López-Gutiérrez JC, Martin-Laurent F, Brauman A, Philippot L (2004) Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR. J Microbiol Methods 59:327–335CrossRefGoogle Scholar
  13. 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 72:5181–5189CrossRefGoogle Scholar
  14. Höfferle Š, Nicol GW, Pal L, Hacin J, Prosser JI, Mandić-Mulec I (2010) Ammonium supply rate influences archaeal and bacterial ammonia oxidizers in a wetland soil vertical profile. FEMS Microbiol Ecol 74:302–315CrossRefGoogle Scholar
  15. Ishikawa K, Ohmori T, Miyamoto H, Ito T, Kumagai Y, Sonoda M, Matsumoto J, Kodama H (2012) Denitrification in soil amended with thermophile-fermented compost suppresses nitrate accumulation in plants. Appl Microbiol Biotechnol 1–11Google Scholar
  16. Kelly JJ, Policht K, Grancharova T, Hundal LS (2011) Distinct responses in ammonia-oxidizing archaea and bacteria after addition of biosolids to an agricultural soil. Appl Environ Microbiol 77:6551–6558CrossRefGoogle Scholar
  17. Kim I, Deurer M, Sivakumaran S, Huh KY, Green S, Clothier B (2011) The impact of soil carbon management and environmental conditions on N mineralization. Biol Fertil Soils 47:709–714CrossRefGoogle Scholar
  18. Könneke M, Bernhard AE, De La Torre JR, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543–546CrossRefGoogle Scholar
  19. Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW (2011) Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc Natl Acad Sci U S A 108:15892–15897CrossRefGoogle Scholar
  20. Levicnik-Hofferle S, Nicol GW, Ausec L, Mandic-Mulec I, Prosser JI (2012) Stimulation of thaumarchaeal ammonia oxidation by ammonia derived from organic nitrogen but not added inorganic nitrogen. FEMS Microbiol Ecol 80:114–123CrossRefGoogle Scholar
  21. Madrid F, López R, Cabrera F, Murillo JM (2011) Nitrogen mineralization of immature municipal solid waste compost. J Plant Nutr 34:324–336CrossRefGoogle Scholar
  22. Methods of Soil Analysis (1982) American Society of Agronomy. In: Soil Science Society of America, Inc. Madison, 2nd edn. Chemical and microbiological properties, Wisconsin, USAGoogle Scholar
  23. Miller MN, Zebarth BJ, Dandie CE, Burton DL, Goyer C, Trevors JT (2008) Crop residue influence on denitrification, N < sub > 2</sub > O emissions and denitrifier community abundance in soil. Soil Biol Biochem 40:2553–2562CrossRefGoogle Scholar
  24. Miller MN, Zebarth BJ, Dandie CE, Burton DL, Goyer C, Trevors JT (2009) Influence of liquid manure on soil denitrifier abundance, denitrification, and nitrous oxide emissions. Soil Sci Soc Am J 73:760–768CrossRefGoogle Scholar
  25. Mkhabela MS, Warman PR (2005) The influence of municipal solid waste compost on yield, soil phosphorus availability and uptake by two vegetable crops grown in a Pugwash sandy loam soil in Nova Scotia. Agric Ecosyst Environ 106:57–67CrossRefGoogle Scholar
  26. Prosser JI, Nicol GW (2012) Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol 20:523–531CrossRefGoogle Scholar
  27. 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 63:4704–4712Google Scholar
  28. Sanford RA, Wagner DD, Wu Q, Chee-Sanford JC, Thomas SH, Cruz-García C, Rodríguez G, Massol-Deyá A, Krishnani KK, Ritalahti KM, Nissen S, Konstantinidis KT, Löffler FE (2012) Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils. Proc Natl Acad Sci 109:19709–19714CrossRefGoogle Scholar
  29. Shoun H, Fushinobu S, Jiang L, Kim SW, Wakagi T (2012) Fungal denitrification and nitric oxide reductase cytochrome P450nor. Philosophical Transactions of the Royal Society B. Biol Sci 367:1186–1194CrossRefGoogle Scholar
  30. Stopnisek N, Gubry-Rangin C, Hofferle S, Nicol GW, Mandic-Mulec I, Prosser JI (2010) Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by ammonium amendment. Appl Environ Microbiol 76:7626–7634CrossRefGoogle Scholar
  31. Throbäck IN, Enwall K, Jarvis Å, Hallin S (2004) Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiol Ecol 49:401–417CrossRefGoogle Scholar
  32. Tognetti C, Mazzarino MJ, Laos F (2008) Compost of municipal organic waste: effects of different management practices on degradability and nutrient release capacity. Soil Biol Biochem 40:2290–2296CrossRefGoogle Scholar
  33. Tourna M, Stieglmeier M, Spang A, Konneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter A, Schleper C (2011) Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci USA 108:8420–8425CrossRefGoogle Scholar
  34. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74CrossRefGoogle Scholar
  35. Verhamme DT, Prosser JI, Nicol GW (2011) Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms. ISME J 5:1067–1071CrossRefGoogle Scholar
  36. Wu L, Osmond D, Graves A, Burchell M, Duckworth O (2012) Relationships between nitrogen transformation rates and gene abundance in a riparian buffer soil. Environ Manag 50:861–874CrossRefGoogle Scholar
  37. Xu Y, Yu W, Ma Q, Zhou H (2012) Responses of bacterial and archaeal ammonia oxidisers of an acidic luvisols soil to different nitrogen fertilization rates after 9 years. Biol Fertil Soils 1–11Google Scholar
  38. Yamamoto N, Asano R, Yoshii H, Otawa K, Nakai Y (2011) Archaeal community dynamics and detection of ammonia-oxidizing archaea during composting of cattle manure using culture-independent DNA analysis. Appl Microbiol Biotechnol 90:1501–1510CrossRefGoogle Scholar
  39. Zhang LM, Hu HW, Shen JP, He JZ (2012) Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils. ISME J 6:1032–1045CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • N. V. Paranychianakis
    • 1
  • M. Tsiknia
    • 1
  • G. Giannakis
    • 1
  • N. P. Nikolaidis
    • 1
  • N. Kalogerakis
    • 1
  1. 1.Department of Environmental EngineeringTechnical University of CreteChaniaGreece

Personalised recommendations