Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils Kristina Schauss, 1† Andreas Focks, 2† Sven Leininger, 3† Anja Kotzerke, 4 Holger Heuer, 5 Sören Thiele-Bruhn, 6 Shilpi Sharma, 1 Berndt-Michael Wilke, 4 Michael Matthies, 2 Kornelia Smalla, 5 Jean Charles Munch, 1 Wulf Amelung, 7 Martin Kaupenjohann, 8 Michael Schloter 1 * † and Christa Schleper 3 ** †‡ 1 Helmholtz Zentrum München, German Research Center for Environmental Health, Institute for Soil Ecology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany. 2 University of Osnabrück, Institute of Environmental Systems Research, Barbarastr. 12, 49069 Osnabrück, Germany. 3 University of Bergen, Institute for Biology, Jahnebakken 5, 5020 Bergen, Norway. 4 Berlin University of Technology, Institute of Ecology, Franklinstr. 29, 10587 Berlin, Germany. 5 Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany. 6 University of Trier, Department of Soil Science, Behringstr. 21, 54286 Trier, Germany. 7 University of Bonn, Institute of Crop Science and Resource Conservation – Soil Science and Soil Ecology, Nussallee 13, 53115 Bonn, Germany. 8 Berlin University of Technology, Institute of Ecology, Salzufer 11-12, 10587 Berlin, Germany. Summary Crucial steps in geochemical cycles are in many cases performed by more than one group of microorgan- isms, but the significance of this functional redun- dancy with respect to ecosystem functioning is poorly understood. Ammonia-oxidizing archaea (AOA) and their bacterial counterparts (AOB) are a perfect system to address this question: although performing the same transformation step, they belong to well- separated phylogenetic groups. Using pig manure amended with different concentrations of sulfadiazine (SDZ), an antibiotic that is frequently used in veteri- nary medicine, it was possible to affect AOB and AOA to different degrees. Addition of manure stimulated growth of AOB in both soils and, interestingly, also growth of AOA was considerably stimulated in one of the soils. The antibiotic treatments decreased the manure effect notably on AOB, whereas AOA were affected to a lower extent. Model calculations concern- ing the respective proportions of AOA and AOB in ammonia oxidation indicate a substantial contribution of AOA in one of the soils that further increased under the influence of SDZ, hence indicating functional redundancy between AOA and AOB. Introduction Microbial communities in terrestrial environments are extremely complex, both with respect to their phylogeny and with respect to their physiology (Gans et al., 2005; O’Donnell et al., 2007). However, the significance of this diversity for stability and functioning of these ecosystems remains poorly understood (Prosser et al., 2007). The application of models in soil microbial ecology combining process data and abundance data of functional groups has been suggested to address such questions (Rittmann et al., 2006; Prosser et al., 2007), but has been rarely applied so far (Garnier et al., 2003; Dassonville et al., 2004; Khalil et al., 2005). Oxidation of ammonia, which is the first step in nitrifi- cation, a key process in the global nitrogen cycle resulting in the formation of nitrate, is an interesting process to be studied in this respect. Despite the huge phylogenetic and physiological diversity that is found in the two domains of bacteria and archaea, only a few selected groups seem to be able to transform ammonia into nitrite. Therefore, this step has been described as ‘pinhole’ in microbial nitrogen turnover. For almost five decades two specific groups of b- and g-proteobacteria have been considered as most important contributors to ammonia oxidation (Bock and Wagner, 2006). However recently, ammonia oxidizers of the domain archaea were identified through metagenomic and cultivation studies from terrestrial and marine ecosystems (Könneke et al., 2005; Schleper et al., 2005; Treusch et al., 2005; Hallam et al., 2006). Quantification Received 14 December, 2007; accepted 23 August, 2008. For corre- spondence. *E-mail schloter@gsf.de; Tel. (+49) 89 3178 2304; Fax (+49) 89 3178 3376; **E-mail christa.schleper@univie.ac.at; Tel. (+43) 1 4277 57320; Fax (+43) 1 4277 9578. † These authors contrib- uted equally to this work. ‡ Present address: University of Vienna, Faculty of Life Sciences, Althanstr. 14, A-1090 Vienna, Austria. Environmental Microbiology (2009) 11(2), 446–456 doi:10.1111/j.1462-2920.2008.01783.x © 2008 The Authors Journal compilation © 2008 Society for Applied Microbiology and Blackwell Publishing Ltd