To assess links between the diversity of nitrite-oxidizing bacteria (NOB) in agricultural grassland soils and inorganic N fertilizer management, NOB communities in fertilized and unfertilized soils were characterized by analysis of clone libraries and denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Previously uncharacterized Nitrospira-like sequences were isolated from both long-term-fertilized and unfertilized soils, but DGGE migration patterns indicated the presence of additional sequence types in the fertilized soils. Detailed phylogenetic analysis of Nitrospira-like sequences suggests the existence of one newly described evolutionary group and of subclusters within previously described sublineages, potentially representing different ecotypes; the new group may represent a lineage of noncharacterized Nitrospira species. Clone libraries of Nitrobacter-like sequences generated from soils under different long-term N management regimes were dominated by sequences with high similarity to the rhizoplane isolate Nitrobacter sp. strain PJN1. However, the diversity of Nitrobacter communities did not differ significantly between the two soil types. This is the first cultivation-independent study of nitrite-oxidizing bacteria in soil demonstrating that nitrogen management practices influence the diversity of this bacterial functional group.Nitrogen fertilization is the most important management strategy for the improvement of agricultural crops. However, up to 60% of N fertilizer applied can be lost through leaching of mobile N compounds (NO 3 Ϫ ) and transformation into N 2 O and N 2 (53), leading to water pollution and contributing to global warming. The key process during natural N cycling is microbial chemolithoautotrophic nitrification, the conversion of NH 4 ϩ to NO 3 Ϫ via NO 2 Ϫ . Autotrophic nitrification is carried out by two distinct groups, ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), and it is generally assumed that the first step is rate-limiting (50). This assumption is based mainly on observations that NO 2 Ϫ concentrations are low or negligible in most natural systems. Consequently, with the exception of high-N-load sewage-processing systems, where nitrite concentrations are high (NO 2 Ϫ -N up to 70 mg liter Ϫ1 ) (17, 22) and nitrite washout is of concern (41, 63), research into community composition, activity, and environmental responses of nitrifying bacteria has focused on AOB (37). These studies have demonstrated the influence of land use management regimes on the diversity and activity of AOB, as well as links to changes in ammonia oxidation rates (4, 9, 11, 49, 70), but a comprehensive understanding of soil nitrification also requires characterization of NOB.Analysis of NOB in natural environments has been limited by reliance on traditional, cultivation-based methods. In contrast to AOB, for which most 16S rRNA gene sequences of cultured organisms and related environmental clones fall within a monophyletic group (51, 66), NOB are classified into...