Microbial Ecology

, Volume 69, Issue 4, pp 879–883 | Cite as

pH as a Driver for Ammonia-Oxidizing Archaea in Forest Soils

  • Barbara Stempfhuber
  • Marion Engel
  • Doreen Fischer
  • Ganna Neskovic-Prit
  • Tesfaye Wubet
  • Ingo Schöning
  • Cécile Gubry-Rangin
  • Susanne Kublik
  • Brigitte Schloter-Hai
  • Thomas Rattei
  • Gerhard Welzl
  • Graeme W. Nicol
  • Marion Schrumpf
  • Francois Buscot
  • James I. Prosser
  • Michael Schloter
Soil Microbiology

Abstract

In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected, the ratio of archaeal (AOA) to bacterial (AOB) ammonia oxidizers’ amoA genes increased sharply with decreasing soil pH. The diversity of AOA differed significantly between sites with ultra-acidic soil pH (<3.5) and sites with higher pH values. The major OTUs from soil samples with low pH could be detected at each site with a soil pH <3.5 but not at sites with pH >4.5, regardless of geographic position and vegetation. These OTUs could be related to the Nitrosotalea group 1.1 and the Nitrososphaera subcluster 7.2, respectively, and showed significant similarities to OTUs described from other acidic environments. Conversely, none of the major OTUs typical of sites with a soil pH >4.6 could be found in the ultra- and extreme acidic soils. Based on a comparison with the amoA gene sequence data from a previous study performed on agricultural soils, we could clearly show that the development of AOA communities in soils with ultra-acidic pH (<3.5) is mainly triggered by soil pH and is not influenced significantly by the type of land use, the soil type, or the geographic position of the site, which was observed for sites with acido-neutral soil pH.

Keywords

Ammonia-oxidizing archaea amoA Soil pH Forest soil 454 pyrosequencing 

Notes

Acknowledgments

We thank Theresa Klötzung for her excellent technical assistance with the laboratory work. We thank the managers of the three exploratories, Swen Renner, Sonja Gockel, Kerstin Wiesner, and Martin Gorke, for their work in maintaining the plot and project infrastructure; Simone Pfeiffer and Christiane Fischer 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, 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”. Fieldwork permits were issued by the responsible state environmental offices of Baden-Württemberg, Thüringen, and Brandenburg (according to § 72 BbgNatSchG).

Supplementary material

248_2014_548_MOESM1_ESM.doc (4.1 mb)
ESM 1 (DOC 4.08 mb)

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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Barbara Stempfhuber
    • 1
  • Marion Engel
    • 1
  • Doreen Fischer
    • 1
  • Ganna Neskovic-Prit
    • 1
  • Tesfaye Wubet
    • 2
  • Ingo Schöning
    • 3
  • Cécile Gubry-Rangin
    • 4
  • Susanne Kublik
    • 1
  • Brigitte Schloter-Hai
    • 1
  • Thomas Rattei
    • 5
  • Gerhard Welzl
    • 1
  • Graeme W. Nicol
    • 4
  • Marion Schrumpf
    • 3
  • Francois Buscot
    • 2
    • 6
    • 7
  • James I. Prosser
    • 4
  • Michael Schloter
    • 1
  1. 1.Environmental Genomics, Helmholtz Zentrum MünchenGerman Research Centre for Environmental HealthNeuherbergGermany
  2. 2.Department of Soil EcologyHelmholtz Centre for Environmental Research, UFZHalleGermany
  3. 3.Max-Planck-Institute for BiogeochemistryJenaGermany
  4. 4.Institute of Biological and Environmental SciencesUniversity of AberdeenAberdeenUK
  5. 5.Department of Microbiology and Ecosystem ScienceUniversity of ViennaWienAustria
  6. 6.Institute of Biology, Chair of Soil EcologyUniversity of LeipzigLeipzigGermany
  7. 7.German Centre for Integrative Biodiversity Research (iDiv)LeipzigGermany

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