Genome Sequence of the Chemolithoautotrophic Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Nb-255

Abstract

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...

Comparison of Oxidation Kinetics of Nitrite-Oxidizing Bacteria: Nitrite Availability as a Key Factor in Niche Differentiation

“…One reason besides the kinetics of the NXR might be low affinities of the transporters that are needed to shuttle nitrite across the cytoplasmic membrane. There are narK homologs identified in the genomes of N. hamburgensis and N. winogradskyi that could function as nitrite/nitrate transporters (58,59), but their kinetics await experimental clarification. However, the K m values for nitrite indicate a great diversity of Nitrobacter ecotypes, which is consistent with a large genetic heterogeneity within Nitrobacter communities (60,61).…”

Oxidation kinetics and inverse isotope effect of marine nitrite-oxidizing isolates

“…In cytoplasmically oriented NXR (Nitrobacter and Nitrococcus), transporters shuttle nitrite into and nitrate out of the cell (Spieck et al 1996, Starkenburg et al 2006, Sorokin et al 2012) to avoid accumulation of nitrate in the cell and potential unfavourable conditions. This transport can potentially be a bottleneck for oxidation, depending on the substrate affinity and activity of the transporter (Daims et al 2016).…”

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

“…Members of Bradyrhizobiaceae include a number of nonsymbiotic bacteria with diverse biochemical functions such as photosynthesis (Molouba et al, 1999;Larimer et al, 2004;Giraud et al, 2007), oligotrophy (Saito et al, 1998;King, 2007), 2,4-dichlorophenoxyacetic acid degradation (Kamagata et al, 1997) and nitrification (Starkenburg et al, 2006).…”