Biology and Fertility of Soils

, Volume 53, Issue 6, pp 691–700 | Cite as

Soil pH and plant diversity drive co-occurrence patterns of ammonia and nitrite oxidizer in soils from forest ecosystems

  • Barbara Stempfhuber
  • Tim Richter-Heitmann
  • Lisa Bienek
  • Ingo Schöning
  • Marion Schrumpf
  • Michael Friedrich
  • Stefanie Schulz
  • Michael Schloter
Original Paper


In this study, we investigated how co-occurrence patters of ammonia and nitrite oxidizers, which drive autotrophic nitrification, are influenced by tree species composition as well as soil pH in different forest soils. We expected that a decline of ammonia oxidizers in coniferous forests, as a result of excreted nitrification inhibitors and at acidic sites with low availability of ammonia, would reduce the abundance of nitrite-oxidizing bacteria (NOB). To detect shifts in co-occurrence patterns, the abundance of key players was measured at 50 forest plots with coniferous respectively deciduous vegetation and different soil pH levels in the region Schwäbische Alb (Germany). We found ammonia-oxidizing archaea (AOA) and Nitrospira-like NOB (NS) to be dominating in numbers over their counterparts across all forest types. AOA co-occurred mostly with NS, while bacterial ammonia oxidizers (AOB) were correlated with Nitrobacter-like NOB (NB). Co-occurrence patterns changed from tight significant relationships of all ammonia and nitrite oxidizers in deciduous forests to a significant relationship of AOB and NB in coniferous forests, where AOA abundance was reduced. Surprisingly, no co-occurrence structures between ammonia and nitrite oxidizers could be determined at acidic sites, although abundances were correlated to the respective nitrogen pools. This raises the question whether interactions with heterotrophic nitrifiers may occur, which needs to be addressed in future studies.


Forest ecosystem Nitrification Nitrogen cycle Soil pH Ammonia oxidation Nitrite oxidation Interactions qPCR Co-occurrence 



We thank the managers of the three Exploratories, Kirsten Reichel-Jung, Swen Renner, Katrin Hartwich, Sonja Gockel, Kerstin Wiesner, and Martin Gorke for their work in maintaining the plot and project infrastructure, Christiane Fischer and Simone Pfeiffer for giving support through the central office, Michael Owonibi for managing the central data base, and Markus Fischer, Eduard Linsenmair, Dominik Hessenmöller, Jens Nieschulze, Daniel Prati, Ingo Schöning, François Buscot, Ernst-Detlef Schulze, Wolfgang W. Weisser, and the late Elisabeth Kalko for their role in setting up the Biodiversity Exploratories project. The work has been (partly) funded by the DFG Priority Program 1374 “Infrastructure-Biodiversity-Exploratories.” Field work permits were issued by the responsible state environmental offices of Baden-Württemberg, Thüringen, and Brandenburg (according to § 72 BdgNatSchG).

Supplementary material

374_2017_1215_MOESM1_ESM.doc (86 kb)
ESM 1 (DOC 85 kb)


  1. Aubert M, Bureau F, Vinceslas-Akpa M (2005) Sources of spatial and temporal variability of inorganic N in pure and mixed deciduous temperate forests. Soil Biol Biochem 37:67–79. doi: 10.1016/j.soilbio.2004.07.025 CrossRefGoogle Scholar
  2. Bannert A, Kleineidam K, Wissing L, Müller-Niggemann C, Vogelsang V, Welzl G, Cao Z, Schloter M (2011) Changes in diversity and functional gene abundances of microbial communities involved in N fixation, nitrification and denitrification in a tidal wetland versus paddy soils cultivated for different time periods. Appl Environ Microbiol 77:6109–6116. doi: 10.1128/aem.01751-10 CrossRefPubMedPubMedCentralGoogle Scholar
  3. Bartosch S, Hartwig C, Spieck E, Bock E (2002) Immunological detection of Nitrospira-like bacteria in various soils. Microb Ecol 43:26–33. doi: 10.1007/s00248-001-0037-5 CrossRefPubMedGoogle Scholar
  4. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc 57:289–300. doi: 10.2307/2346101 Google Scholar
  5. Booth M, Tark J, Rastetter E (2005) Controls on nitrogen cycling in terrestrial ecosystems: a synthetic analysis of literature data. Ecol Monogr 75:130–157CrossRefGoogle Scholar
  6. Boring LR, Swank WT, Waide JB, Henderson GS (1988) Sources, fates, and impacts of N inputs to terrestrial ecosystems: review and synthesis. Biogeochem 6:119–159. doi: 10.1007/bf00003034 CrossRefGoogle Scholar
  7. Boyle-Yarwood SA, Bottomley PJ, Myrold DD (2008) Community composition of ammonia-oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon. Environ Microbiol 10:2956–2965. doi: 10.1111/j.1462-2920.2008.01600.x CrossRefPubMedGoogle Scholar
  8. Brierley EDR, Wood M (2001) Heterotrophic nitrification in an acid forest soil: isolation and characterisation of a nitrifying bacterium. Soil Biol Biochem 33:1403–1409. doi: 10.1016/S0038-0717(01)00045-1 CrossRefGoogle Scholar
  9. Burns LC, Stevens RJ, Smith RV, Cooper JE (1995) The occurrence and possible sources of nitrite in a grazed, fertilized, grassland soil. Soil Biol Biochem 27:47–59. doi: 10.1016/0038-0717(94)00130-S CrossRefGoogle Scholar
  10. Burton SAQ, Prosser JI (2001) Autotrophic ammonia oxidation at low pH through urea hydrolysis. Appl Environ Microbiol 67:2952–2957. doi: 10.1128/aem.67.7.2952-2957.2001 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Daebeler A, Bodelier PLE, Yan Z, Hefting MM, Jia Z, Laanbroek HJ (2014) Interactions between Thaumarchaea, Nitrospira and methanotrophs modulate autotrophic nitrification in volcanic grassland soil. ISME J. doi: 10.1038/ismej.2014.81
  12. Daims H, Nielsen JL, Nielsen PH, Schleifer K-H, Wagner M (2001) In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater rreatment plants. Appl Environ Microbiol 67:5273–5284. doi: 10.1128/aem.67.11.5273-5284.2001 CrossRefPubMedPubMedCentralGoogle Scholar
  13. Daims H, Lebedeva E, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard R, van Bergen M, Rattei T, Bendinger B, Nielsen P, Wagner M (2015) Complete nitrification by Nitrospira bacteria. Nature 528:504–509. doi: 10.1038/nature16461 PubMedPubMedCentralGoogle Scholar
  14. De Boer W, Kowalchuk GA (2001) Nitrification in acid soils: microorganisms and mechanisms. Soil Biol Biochem 33:853–866. doi: 10.1016/S0038-0717(00)00247-9 CrossRefGoogle Scholar
  15. De Boer W, Klein Gunnewiek PJA, Troelstra SR (1990) Nitrification in Dutch heathland soils. Plant Soil 127:193–200. doi: 10.1007/bf00014425 CrossRefGoogle Scholar
  16. De Boer W, Gunnewiek PJAK, Veenhuis M, Bock E, Laanbroek HJ (1991) Nitrification at low pH by aggregated chemolithotrophic bacteria. Appl Environ Microbiol 57:3600–3604PubMedPubMedCentralGoogle Scholar
  17. Degrange V, Couteaux 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 1998:201–208. doi: 10.1023/A:1004344631379 CrossRefGoogle Scholar
  18. Di HJ, Cameron KC, Shen JP, Winefield CS, O'Callaghan M, Bowatte S, He JZ (2009) Nitrification driven by bacteria and not archaea in N-rich grassland soils. Nat Geosci 2:621–624 doi: S1.htmlCrossRefGoogle Scholar
  19. Epskamp S, Cramer AOJ, Waldorp LJ, Schmittmann VD, Borsboom D (2012) Qgraph: network visualizations of relationships in psychometric data. J Stat Softw 48:1–18CrossRefGoogle Scholar
  20. Fischer M, Bossdorf O, Gocke S, Hänsel F, Hemp A, Hessenmöller D, Korte G, Nieschulze J, Pfeiffer S, Prati D, Renn S, Schöning I, Schumacher U, Wells K, Buscot F, Kalko E, Linsenmair K, Schulze E, Weiser W (2010) Implementing large-scale and long-term functional biodiversity research: the biodiversity exploratories. Basic Appl Ecol 11:473–485. doi: 10.1016/j.baae.2010.07.009 CrossRefGoogle Scholar
  21. Freitag TE, Chang L, Clegg CD, Prosser JI (2005) Influence of inorganic N management regime on the diversity of nitrite-oxidizing bacteria in agricultural grassland soils. Appl Environ Microbiol 71:8323–8334. doi: 10.1128/aem.71.12.8323-8334.2005 CrossRefPubMedPubMedCentralGoogle Scholar
  22. Gessler A, Schnieder S, von Sengbusch D, Weber P, Hanemann U, Huber C, Rothe A, Kreutzer K, Rennenberg H (1998) Field and laboratory experiments on net uptake of nitrate and ammonium by the roots of spruce (Picea abies) and beech (Fagus sylvatica) trees. New Phytol 138:275–285. doi: 10.1046/j.1469-8137.1998.00107.x CrossRefGoogle Scholar
  23. Gieseke A, Bjerrum L, Wagner M, Amann R (2003) Structure and activity of multiple nitrifying bacterial populations co-existing in a biofilm. Environ Microbiol 5:355–369. doi: 10.1046/j.1462-2920.2003.00423.x CrossRefPubMedGoogle Scholar
  24. Giles ME, Morley NJ, Baggs EM, Daniell TJ (2012) Soil nitrate reducing processes—drivers, mechanisms for spatial variation and significance for nitrous oxide production. Front Microbiol 3. doi: 10.3389/fmicb.2012.00407
  25. Gubry-Rangin C, Hai B, Quince C, Engel M, Thomson BC, James P, Schloter M, Griffiths R, Prosser J, Nicol GW (2011) Niche specialization of terrestrial archaeal ammonia oxidizers. PNAS 108:21206–21211. doi: 10.1073/pnas.1109000108 CrossRefPubMedPubMedCentralGoogle Scholar
  26. Hankinson TR, Schmidt EL (1988) An acidophilic and a neutrophilic nitrobacter strain isolated from the mumerically predominant nitrite-oxidizing population of an acid forest soil. Appl Environ Microbiol 54:1536–1540PubMedPubMedCentralGoogle Scholar
  27. Herberich E, Sikorski J, Hothorn T (2010) A robust procedure for comparing multiple means under heteroscedasticity in unbalanced designs. PLoS One 5:e9788. doi: 10.1371/journal.pone.0009788 CrossRefPubMedPubMedCentralGoogle Scholar
  28. Hothorn T, Bretz F, Westfall P (2008) Simultaneous inference in general parametric models. Biom Z 50:346–363. doi: 10.1002/bimj.200810425 Google Scholar
  29. Jia Z, Conrad R (2009) Bacteria rather than archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol 11:1658–1671. doi: 10.1111/j.1462-2920.2009.01891.x CrossRefPubMedGoogle Scholar
  30. Ke X, Angel R, Lu Y, Conrad R (2013) Niche differentiation of ammonia oxidizers and nitrite oxidizers in rice paddy soil. Environ Microbiol 15:2275–2292. doi: 10.1111/1462-2920.12098 CrossRefPubMedGoogle Scholar
  31. Keeney DR (1980) Prediction of soil nitrogen availability in forest ecosystems: a literature review. For Sci 26:159–171Google Scholar
  32. Killham K (1990) Nitrification in coniferous forest soils. Plant Soil 128:31–44. doi: 10.1007/BF00009394 CrossRefGoogle Scholar
  33. Knapp CW, Graham DW (2007) Nitrite-oxidizing bacteria guild ecology associated with nitrification failure in a continuous-flow reactor. FEMS Microbiol Ecol 62:195–201Google Scholar
  34. Koch H, Lückera S, Albersen M, Kitzingera K, Herbold C, Spieck E, Nielsen PH, Wagner M, Daims H (2015) Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. PNAS 112:11371–11376. doi: 10.1073/pnas.1506533112 CrossRefPubMedPubMedCentralGoogle Scholar
  35. Lebedeva EV, Hatzenpichler R, Pelletier E, Schuster N, Hauzmayer S, Bulaev A, Grigor’eva NV, Galushko A, Schmid M, Palatinszky M, Le Paslier D, Daims H, Wagner M (2013) Enrichment and genome sequence of the group I.1a ammonia-oxidizing archaeon “Ca. Nitrosotenuis uzonensis” representing a clade globally distributed in thermal habitats. PLoS ONE 8:e80835Google Scholar
  36. Lehtovirta-Morley LE, Sayavedra-Soto LA, Gallois N, Schouten S, Stein LY, Prosser JI, Nicol GW (2016) Identifying potential mechanisms enabling acidophily in the ammonia-oxidising archaeon ‘Candidatus Nitrosotalea devanaterra’. Appl Environ Microbiol. doi: 10.1128/aem.04031-15
  37. Lueders T, Manefield M, Friedrich MW (2004) Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ Microbiol 6:73–78. doi: 10.1046/j.1462-2920.2003.00536.x CrossRefPubMedGoogle Scholar
  38. Maixner F, Noguera DR, Anneser B, Stoecker K, Wegl G, Wagner M, Daims H (2006) Nitrite concentration influences the population structure of Nitrospira-like bacteria. Environ Microbiol 8:1487–1495. doi: 10.1111/j.1462-2920.2006.01033.x CrossRefPubMedGoogle Scholar
  39. Nadelhoffer KJ, Aber JD, Melillo JM (1984) Seasonal patterns of ammonium and nitrate uptake in nine temperate forest ecosystems. Plant Soil 80:321–335. doi: 10.1007/bf02140039 CrossRefGoogle Scholar
  40. 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 10:2966–2978. doi: 10.1111/j.1462-2920.2008.01701.x CrossRefPubMedGoogle Scholar
  41. Ollivier J, Töwe S, Bannert A, Hai B, Kastl EM, Meyer A, Su MX, Kleineidam K, Schloter M (2013) Effects of repeated application of sulfadiazine-contaminated pig manure on the abundance and diversity of ammonia and nitrite oxidizers in the root-rhizosphere complex of pasture plants under field conditions. Front Microbiol:4. doi: 10.3389/fmicb.2013.00022
  42. Paavolainen L, Smolander A (1998) Nitrification and denitrification in soil from a clear-cut norway spruce (Picea abies) stand. Soil Biol Biochem 30:775–781. doi: 10.1016/S0038-0717(97)00165-X CrossRefGoogle Scholar
  43. R Development Core Team (2015) R: a language and environment for statistical computing. R. Foundation for Statistical Computing, Vienna, AustriaGoogle Scholar
  44. Schramm A, de Beer D, Wagner M, Amann R (1998) Identification and activities in situ of Nitrosospira and Nitrospira spp. as dominant populations in a nitrifying fluidized bed reactor. Appl Environ Microbiol 64:3480–3485PubMedPubMedCentralGoogle Scholar
  45. 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 65:3690–3696PubMedPubMedCentralGoogle Scholar
  46. Spieck E, Bock E (2005) The lithoautotrophic nitrite-oxidizing bacteria. In: Brenner D, Krieg N, Staley J, Garrity G (eds) Bergey’s manual of systematic bacteriology. Springer, Berlin, pp 149–153. doi: 10.1007/0-387-28021-9_19 CrossRefGoogle Scholar
  47. Stark JM, Hart SC (1997) High rates of nitrification and nitrate turnover in undisturbed coniferous forests. Nature 385:61–64CrossRefGoogle Scholar
  48. Stempfhuber B, Engel M, Fischer D, Wubet T, Rangin C, Kublik S, Schloter-Hai B, Rattei T, Welzl G, Nicol G, Schrumpf M, Buscot F, Prosser J, Schloter M (2015) pH as a driver for ammonia-oxidizing archaea in forest soils. Microb Ecol 69:879–883. doi: 10.1007/s00248-014-0548-5 CrossRefPubMedGoogle Scholar
  49. Stempfhuber B, Richter-Heitmann T, Regan K, Kölbl A, Kaul P, Marhan S, Sikorski J, Overmann J, Friedrich M, Kandeler E, Schloter M (2016) Spatial interaction of archaeal ammonia-oxidizers and nitrite-oxidizing bacteria in an unfertilized grassland soil. Front Microbiol:6. doi: 10.3389/fmicb.2015.01567
  50. Strauss EA, Lamberti GA (2002) Effect of dissolved organic carbon quality on microbial decomposition and nitrification rates in stream sediments. Freshw Biol 47:65–74. doi: 10.1046/j.1365-2427.2002.00776.x CrossRefGoogle Scholar
  51. Trap J, Bureau F, Vinceslas-Akpa M, Chevalier R, Aubert M (2009) Changes in soil N mineralization and nitrification pathways along a mixed forest chronosequence. Forest Ecol Management 258:1284–1292. doi: 10.1016/j.foreco.2009.06.021 CrossRefGoogle Scholar
  52. van Kessel MAHJ, Speth D, Albertsen M, Nielsen P, Op den Camp H, Kartal B, Jettem M, Lücker S (2015) Complete nitrification by a single microorganism. Nature 528:555–559. doi: 10.1038/nature16459 PubMedPubMedCentralGoogle Scholar
  53. Verhamme DT, Prosser JI, Nicol GW (2011) Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms. ISME J 5:1067–1071CrossRefPubMedPubMedCentralGoogle Scholar
  54. White CS (1986) Volatile and water-soluble inhibitors of N mineralization and nitrification in a ponderosa pine ecosystem. Biol Fertil Soils 2:97–104. doi: 10.1007/bf00257586 Google Scholar
  55. Zeng W, Bai X, Zhang L, Wang A, Peng Y (2014) Population dynamics of nitrifying bacteria for nitritation achieved in Johannesburg (JHB) process treating municipal wastewater. Bioresource Tech 162:30–37. doi: 10.1016/j.biortech.2014.03.102 CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Barbara Stempfhuber
    • 1
  • Tim Richter-Heitmann
    • 2
  • Lisa Bienek
    • 1
  • Ingo Schöning
    • 3
  • Marion Schrumpf
    • 3
  • Michael Friedrich
    • 2
  • Stefanie Schulz
    • 1
  • Michael Schloter
    • 1
    • 4
  1. 1.Research Unit for Comparative Microbiome AnalysisHelmholtz Zentrum München, German Research Centre for Environmental Health, Environmental GenomicsNeuherbergGermany
  2. 2.Faculty of Biology/ChemistryUniversity of BremenBremenGermany
  3. 3.Max-Planck-Institute for BiogeochemistryJenaGermany
  4. 4.Chair of Soil ScienceTechnische Universität MünchenFreisingGermany

Personalised recommendations