Environmental Microbiology (2005) 7(1), 1–12 doi:10.1111/j.1462-2920.2004.00649.x © 2004 Society for Applied Microbiology and Blackwell Publishing Ltd Blackwell Science, LtdOxford, UKEMIEnvironmental Microbiology1462-2912Society for Applied Microbiology and Blackwell Publishing Ltd, 20047 1112Original ArticleAmmonium oxidation in soil crust communitiesS. L. Johnson et al . Received 29 October, 2003; revised 3 March, 2004; accepted 5 March, 2004. *For correspondence. E-mail ferran@asu.edu; Tel. (+1) 480 727 7534; Fax (+1) 480 965 0098. † Present address: Department of Marine Sciences, Marine Sciences Bldg, University of Georgia, Athens, GA 30602, USA. Relevance of ammonium oxidation within biological soil crust communities Shannon L. Johnson, 1 Charles R. Budinoff, 1† Jayne Belnap 2 and Ferran Garcia-Pichel 1* 1 School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA. 2 US Geological Survey, 2290 West Resource Blvd, Moab, UT 84532, USA. Summary Thin, vertically structured topsoil communities that become ecologically important in arid regions (bio- logical soil crusts or BSCs) are responsible for much of the nitrogen inputs into pristine arid lands. We studied N 2 fixation and ammonium oxidation (AO) at subcentimetre resolution within BSCs from the Colo- rado Plateau. Pools of dissolved porewater nitrate/ nitrite, ammonium and organic nitrogen in wetted BSCs were high in comparison with those typical of aridosoils. They remained stable during incubations, indicating that input and output processes were of similar magnitude. Areal N 2 fixation rates (6.5– 48 mmol C 2 H 2 m -2 h -1 ) were high, the vertical distribu- tion of N 2 fixation peaking close to the surface if populations of heterocystous cyanobacteria were present, but in the subsurface if they were absent. Areal AO rates (19–46 mmol N m -2 h -1 ) were commen- surate with N 2 fixation inputs. When considering oxy- gen availability, AO activity invariably peaked 2–3 mm deep and was limited by oxygen (not ammonium) supply. Most probable number (MPN)-enumerated ammonia-oxidizing bacteria (6.7–7.9 ¥ 10 3 cells g -1 on average) clearly peaked at 2–3 mm depth. Thus, AO (hence nitrification) is a spatially restricted but impor- tant process in the nitrogen cycling of BSC, turning much of the biologically fixed nitrogen into oxidized forms, the fate of which remains to be determined. Introduction Because nitrogen is second only to water as a limiting factor in the fertility of arid lands (Schlesinger, 1996; Evans and Lange, 2001), nitrogen inputs into desert eco- systems, either as deposition or as biological fixation, are crucial for their ecology and biogeochemistry. But high rates of nitrogen input resulting from biological fixation are not reflected in an increase in nitrogen content over the long term in arid soils (Peterjohn and Schlesinger, 1990). Clearly, our knowledge of nitrogen cycling and mass transport processes in these ecosystems is insufficient. Because much of the N 2 fixation in arid lands is carried out by microbes, particularly cyanobacteria, associated with topsoil communities known as biological soil crusts (Rychert and Skujins, 1974; Isichei, 1980; Jeffries et al., 1992; Steppe et al., 1996; Belnap, 2002), the study of nitrogen cycling in these communities may hold the key to unravelling this apparent nitrogen paradox. Biological soil crusts (BSCs) are millimetres to centime- tres thick microbial communities that typically cover large portions of the plant interspaces in arid lands (Belnap and Lange, 2001). BSCs have been referred to as microbiotic, microfloral, microphytic, cryptobiotic and cryptogamic crusts (West and Skujins, 1978; Harper and Marble, 1988) or as microbial earths (Retallack, 2001). They are driven by the autochthonous primary productivity of cyanobacte- ria and/or microalgae (Garcia-Pichel, 2002), either as free- living organisms or as partners in lichen symbioses; mosses may also be found in well-developed crusts (Johansen, 1993; Eldridge and Greene, 1994; Belnap et al., 2001). Highly diverse populations of both pho- totrophic and non-phototrophic microbes reside in a thin mantle some 1 cm deep, as has been determined by cultivation-independent molecular studies (Garcia-Pichel et al., 2001; 2003; Kuske et al., 2002); there, they attain large population densities compared with bulk desert soil and organize themselves in a vertically stratified manner (Garcia-Pichel et al., 2003), similar to that described for microbial mats (Cohen and Rosenberg, 1989) or biofilms (Doyle, 1999). The microbes remain desiccated, and thus inactive, for most of the time but, upon wetting, become quickly hydrated and active. During pulses of activity, high metabolic rates constrained within small spaces result in the rapid formation of steep chemical gradients and microenvironments, which include oxygen-supersaturated zones close to the surface and anoxic zones some 1– 3 mm deep (de Winder, 1990; Garcia-Pichel and Belnap, 1996; 2001). BSCs are important as agents in resisting soil erosion (Campbell, 1979; Schulten, 1985; Belnap, 1993).