The alphaproteobacterium Nitrobacter winogradskyi (ATCC 25391) is a gram-negative facultative chemolithoautotroph capable of extracting energy from the oxidation of nitrite to nitrate. Sequencing and analysis of its genome revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. There were extensive similarities to genes in two alphaproteobacteria, Bradyrhizobium japonicum USDA110 (1,300 genes) and Rhodopseudomonas palustris CGA009 CG (815 genes). Genes encoding pathways for known modes of chemolithotrophic and chemoorganotrophic growth were identified. Genes encoding multiple enzymes involved in anapleurotic reactions centered on C 2 to C 4 metabolism, including a glyoxylate bypass, were annotated. The inability of N. winogradskyi to grow on C 6 molecules is consistent with the genome sequence, which lacks genes for complete Embden-Meyerhof and Entner-Doudoroff pathways, and active uptake of sugars. Two gene copies of the nitrite oxidoreductase, type I ribulose-1,5-bisphosphate carboxylase/oxygenase, cytochrome c oxidase, and gene homologs encoding an aerobictype carbon monoxide dehydrogenase were present. Similarity of nitrite oxidoreductases to respiratory nitrate reductases was confirmed. Approximately 10% of the N. winogradskyi genome codes for genes involved in transport and secretion, including the presence of transporters for various organic-nitrogen molecules. The N. winogradskyi genome provides new insight into the phylogenetic identity and physiological capabilities of nitrite-oxidizing bacteria. The genome will serve as a model to study the cellular and molecular processes that control nitrite oxidation and its interaction with other nitrogen-cycling processes.Nitrification, the microbiological process by which ammonia is converted to nitrate, is a major component of the global nitrogen cycle, plays a crucial role in transformation of fertilizer nitrogen in agricultural systems, and is a key component of nitrogen removal in wastewater treatment. Excess production of soluble nitrogen by nitrification results in the contamination of potable water and eutrophication of aquatic and terrestrial ecosystems, while the gaseous by-products of nitrification, nitric oxide and nitrous oxide, are two of the most potent greenhouse gases. As anthropogenic inputs of fixed nitrogen continue to expand to meet the demands of a growing global population, intimate knowledge of the nitrification process and the microorganisms that control this process will be necessary to address environmental nitrogen imbalances.Nitrobacter winogradskyi Nb-255 and other nitrite-oxidizing bacteria participate in nitrification by converting nitrite, the end product of ammonia oxidation, into nitrate according to the reaction NO 2 Ϫ ϩ H 2 O 3 NO 3 Ϫ ϩ 2H ϩ ϩ 2e Ϫ . Nitrite functions as an electron donor for the reduction of NAD via reverse electron flow and the generation of ATP by oxidative phosphorylation (36).As a facultative chemolithoautotroph, N. winogradskyi gains energy from nitrite oxidation, and fix...