SOIL MICROBIOLOGY Influence of Land Use Intensity on the Diversity of Ammonia Oxidizing Bacteria and Archaea in Soils from Grassland Ecosystems Annabel Meyer & Andreas Focks & Viviane Radl & Gerhard Welzl & Ingo Schöning & Michael Schloter Received: 30 July 2013 /Accepted: 3 October 2013 # Springer Science+Business Media New York 2013 Abstract In the present study, the influence of the land use intensity on the diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in soils from different grassland ecosystems has been investigated in spring and summer of the season (April and July). Diversity of AOA and AOB was studied by TRFLP fingerprinting of amoA amplicons. The diversity from AOB was low and dominated by a peak that could be assigned to Nitrosospira . The obtained profiles for AOB were very stable and neither influenced by the land use intensity nor by the time point of sampling. In contrast, the obtained patterns for AOA were more complex although one peak that could be assigned to Nitrosopumilus was dominat- ing all profiles independent from the land use intensity and the sampling time point. Overall, the AOA profiles were much more dynamic than those of AOB and responded clearly to the land use intensity. An influence of the sampling time point was again not visible. Whereas AOB profiles were clearly linked to potential nitrification rates in soil, major TRFs from AOA were negatively correlated to DOC and ammonium availability and not related to potential nitrification rates. Introduction Since 2004, when the first evidence was provided that also organisms belonging to the kingdom of archaea are involved in ammonium oxidation [1–3], there is an ongoing debate to what extent these organisms contribute to nitrification and which factors drive their abundance, diversity, and activity in the environment. Today, it is generally acknowledged that ammonia oxidizing archaea (AOA) are ubiquitous [4] and several recently published studies assume a niche separation of AOA and their bacterial counterpart (AOB), which cannot be explained by a single environmental factor like ammonia availability, temperature or soil type [5–7]. Several studies based on the so far obtained isolates have also indicated a potential for the ammonia oxidation of AOA [ 8–11]. However, the turnover rates for ammonia do not only differ among AOB but also for the so far isolated AOA different ammonia oxidation rates have been measured. For AOB, ammonia oxidation rates between 21 and 43 fmol NO 2 - cell -1 h -1 have been described [12, 13]. For AOA, the ammo- nia oxidation rates, which have been reported, were lower and ranged from 1.2-15 fmol NO 2 - cell -1 h -1 [3, 10]. Thus, there is a need to measure not only the abundance of AOA and AOB in a particular environment, as it was done in a large number of studies in the last years, but also to monitor the Electronic supplementary material The online version of this article (doi:10.1007/s00248-013-0310-4) contains supplementary material, which is available to authorized users. A. Meyer Chair for Soil Ecology, Technische Universität München, Ingolstädter Landstr 1, 85764 Neuerberg, Germany A. Focks Department for Aquatic Ecology and Water Quality Management, P.O. Box 47, 6700 AA Wageningen, The Netherlands V. Radl : G. Welzl : M. Schloter (*) German Research Centre for Environmental Health; Environmental Genomics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuerberg, Germany e-mail: Schloter@helmholtz-muenchen.de I. Schöning Institute of Ecology, University of Jena, Dornburgerstr.159, 07743 Jena, Germany Microb Ecol DOI 10.1007/s00248-013-0310-4