Short-term population dynamics of ammonia oxidizing bacteria in an agricultural soil T.R. Cavagnaro a, *, L.E. Jackson b , K. Hristova b , K.M. Scow b a School of Biological Sciences and Australian Centre for Biodiversity, Monash University, Clayton, Victoria 3800, Australia b Department of Land, Air and Water Resources, University of California Davis, One Shields Avenue, Davis, CA 95616-8627, United States 1. Introduction Application of inorganic N fertilizers and tillage are two components of intensive agricultural management that can cause environmental degradation via promotion of nitrate (NO 3 À ) leaching, nitrous oxide (N 2 O) production, and reduction of soil C content (Matson et al., 1998; Riley et al., 2001; Johnson et al., 2005). Rates of key steps of the soil N cycle, i.e., mineralization, nitrification, and denitrification, increase when N inputs are high (Mendum et al., 1999; Burger and Jackson, 2003; Okano et al., 2004) and tillage is frequent (Doran, 1982; Jackson et al., 2003). Nitrification and the ammonia oxidizing bacteria (AOB) are particularly important to consider in managing N cycles because they produce NO 3 À , which in turn can be lost through leaching or produce N 2 O during denitrification. Nitrification is also a significant source of N 2 O emissions from soils, especially under aerobic conditions. AOB population sizes increase in response to N fertilization in arable soils (Hermansson and Lindgren, 2001; Okano et al., 2004) and soil disturbance, and are generally higher in applied soil ecology 40 (2008) 13–18 article info Article history: Received 1 November 2007 Received in revised form 31 January 2008 Accepted 16 February 2008 Keywords: Agriculture Ammonia oxidizing bacteria (AOB) Ammonia monooxygenase (amoA) Nitrification Quantitative realtime PCR abstract Ammonia oxidizing bacteria (AOB) control the rate limiting step of nitrification, the con- version of ammonia (NH 4 + ) to nitrite (NO 2 À ). The AOB therefore have an important role to play in regulating soil nitrogen cycling. Tillage aerates the soil, stimulating rapid changes in soil N cycling and microbial communities. Here we report results of a study of the short term responses of AOB and net nitrification to simulated tillage and NH 4 + addition to soil. The intensively farmed vegetable soils of the Salinas Valley, California, provide the context for this study. These soils are cultivated frequently, receive large N fertilizer inputs and there are regional concerns about groundwater N concentrations. An understanding of N dynamics in these systems is therefore important. AOB population sizes were quantified using a real-time PCR approach. In a 15 day experiment AOB populations, increased rapidly following tillage and NH 4 + addition and persisted after the depletion of soil NH 4 + . AOB population sizes increased to a similar degree, over a 1.5-day period, irrespective of the amount of NH 4 + supplied. These data suggest selection of an AOB community in this intensively farmed and C-limited soil, that rapidly uses NH 4 + that becomes available. These data also suggest that mineralization may play an especially important role in regulating AOB populations where NH 4 + pool sizes are very low. Methodological considerations in the study of soil AOB communities are also discussed. # 2008 Elsevier B.V. All rights reserved. * Corresponding author. Tel.: +61 3 9905 5793; fax: +61 3 9905 5613. E-mail address: tim.cavagnaro@sci.monash.edu.au (T.R. Cavagnaro). available at www.sciencedirect.com journal homepage: www.elsevier.com/locate/apsoil 0929-1393/$ – see front matter # 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.apsoil.2008.02.006