SOILS, SEC 5 • SOIL AND LANDSCAPE ECOLOGY • RESEARCH ARTICLE Nitrification activity and putative ammonia-oxidizing archaea in acidic red soils Rong Huang & Yucheng Wu & Jinbo Zhang & Wenhui Zhong & Zhongjun Jia & Zucong Cai Received: 1 July 2011 /Accepted: 9 November 2011 /Published online: 6 December 2011 # Springer-Verlag 2011 Abstract Purpose Acidic red soils account for 21% of land area in China and contain low ammonia concentration due to ionization to ammonium. The unusual high affinity for ammonia of marine Nitrosopumilus maritimus and acido- philic soil Nitrosotalea devanaterra has suggested that ammonia-oxidizing archaea (AOA) may have greater selective advantage over ammonia-oxidizing bacteria (AOB) in ammonia-limited environment because ammonia rather than ammonium is thought to be the actual substrate for oxidation. The aim of this study was to assess whether nitrification activity can be attributed to AOA and/or AOB by relating community structures of AOA and AOB to nitrification activity in acidic red soils in southern China. Materials and methods In this study, the composition and abundance of AOA community were investigated in acidic red soils of coniferous Pinus forest, broad-leaf Cinnamomum forest, bush forest (BF), and a 30-year agricultural field converted from bush forest (BFA). The composition of AOA based on archaeal amoA genes were analyzed by denaturant gradient gel electrophoresis, and the abundances of AOA communities were deter- mined by real-time quantitative polymerase chain reaction, while soil nitrification activity was measured using 15 N pool enrichment technique. Results and discussion 15 N pool enrichment technique indicated nitrification activity in acidic red soils, but AOB were not detected. The absence of AOB in acidic red soils could be well explained by the low ammonia concentration ranging from 17.8 to 34.3 nM, which is far below the known threshold values required to support the growth of AOB in culture. Nitrification activity change coupled well with abundance and composition changes of archaeal amoA genes, particularly for acidic BF and BFA soils. Phylogenetic analysis demonstrated that the putatively active AOA were related to amoA transcripts in a hot spring within the soil Crenarchaeota group 1.1b lineage. Conclusions These results suggest that AOA play important roles in ammonia oxidation in acidic red soils tested in this study. Keywords 15 N pool enrichment technique . Acidic red soils . Archaeal ammonia oxidation . Crenarchaeota-specific 16S rRNA gene 1 Introduction Nitrification is one of the central processes in the global nitrogen cycle (Gruber and Galloway 2008). It has long been thought that only two monophyletic bacterial groups within β- and γ-Proteobacteria catalyze ammonia oxida- tion, the first and rate-limiting step of autotrophic nitrifica- tion (Koops and Pommerening-Röser 2001). However, recent discoveries have expanded the known ammonia oxidizers from the domain Bacteria to Archaea (Könneke et al. 2005; Treusch et al. 2005). The widespread presence of archaeal amoA genes and of their transcripts clearly Responsible editor: Ji-Zheng He R. Huang : Y. Wu : J. Zhang : Z. Jia : Z. Cai (*) State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu Province, People’ s Republic of China e-mail: zccai@issas.ac.cn R. Huang e-mail: rhuang@issas.ac.cn W. Zhong College of Chemistry and Environmental Science, Nanjing Normal University, Nanjing 210097, Jiangsu Province, People’ s Republic of China J Soils Sediments (2012) 12:420–428 DOI 10.1007/s11368-011-0450-4