Nitrification is a key process in the nitrogen cycle of terrestrial, wastewater and marine systems. The first step in the process is the oxidation of ammonia, mediated by the ammonia-oxidizing bacteria. The genome sequence of the soil ammonia-oxidizing bacterium Nitrosospira multiformis (ATCC 25196) has recently been completed and offers a unique opportunity for comparison to the complete genome sequences of Nitrosomonas europaea (Chain et al 2003), Nitrosomonas eutropha and Nitrosococcus oceani (Joint Genome Institute-DOE). These proteobacteria are all chemolithoautotrophs using ammonia oxidation as their source for energy and reducing equivalents but these type cultures were isolated from a variety of habitats. Their close taxonomic and core physiological similarity allows for a targeted analysis of their differences in specific metabolic functions including ammonia oxidation, urea hydrolysis and nitrite metabolism. Interpretations in relations to the distinct ecological niche of N. multiformis versus N. europaea and the role of genome fluidity in the evolution and functional diversity of the ammonia oxidizing bacteria will be presented. Examples of the use of genomic data to inform soil ecology research and links between habitat and functional diversity in enzyme encoding genes will be explored.