title: Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira.
abstract: Nitrospira are a diverse group of nitrite-oxidizing bacteria and among the environmentally most widespread nitrifiers. However, they remain scarcely studied and mostly uncultured. Based on genomic and experimental data from Nitrospira moscoviensis representing the ubiquitous Nitrospira lineage II, we identified ecophysiological traits that contribute to the ecological success of Nitrospira. Unexpectedly, N. moscoviensis possesses genes coding for a urease and cleaves urea to ammonia and CO2. Ureolysis was not observed yet in nitrite oxidizers and enables N. moscoviensis to supply ammonia oxidizers lacking urease with ammonia from urea, which is fully nitrified by this consortium through reciprocal feeding. The presence of highly similar urease genes in Nitrospira lenta from activated sludge, in metagenomes from soils and freshwater habitats, and of other ureases in marine nitrite oxidizers, suggests a wide distribution of this extended interaction between ammonia and nitrite oxidizers, which enables nitrite-oxidizing bacteria to indirectly use urea as a source of energy. A soluble formate dehydrogenase lends additional ecophysiological flexibility and allows N. moscoviensis to use formate, with or without concomitant nitrite oxidation, using oxygen, nitrate, or both compounds as terminal electron acceptors. Compared with Nitrospira defluvii from lineage I, N. moscoviensis shares the Nitrospira core metabolism but shows substantial genomic dissimilarity including genes for adaptations to elevated oxygen concentrations. Reciprocal feeding and metabolic versatility, including the participation in different nitrogen cycling processes, likely are key factors for the niche partitioning, the ubiquity, and the high diversity of Nitrospira in natural and engineered ecosystems.
authors: Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, 1090 Vienna, Austria;
authors: Hanna
authors: H
authors: Koch
authors: Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, 1090 Vienna, Austria;
authors: Sebastian
authors: S
authors: Lücker
authors: Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark;
authors: Mads
authors: M
authors: Albertsen
authors: Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, 1090 Vienna, Austria;
authors: Katharina
authors: K
authors: Kitzinger
authors: Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, 1090 Vienna, Austria;
authors: Craig
authors: C
authors: Herbold
authors: Biozentrum Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany.
authors: Eva
authors: E
authors: Spieck
authors: Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark;
authors: Per Halkjaer
authors: PH
authors: Nielsen
authors: Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, 1090 Vienna, Austria;
authors: Michael
authors: M
authors: Wagner
authors: Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, 1090 Vienna, Austria; daims@microbial-ecology.net.
authors: Holger
authors: H
authors: Daims
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001419:Bacteria / Q000235:genetics / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D017753:Ecosystem; D005560:Formate Dehydrogenases / Q000235:genetics / Q000378:metabolism; D005561:Formates / Q000378:metabolism; D005618:Fresh Water / Q000382:microbiology; D016680:Genome, Bacterial / Q000235:genetics; D054892:Metagenome / Q000235:genetics; D008969:Molecular Sequence Data; D009566:Nitrates / Q000378:metabolism; D009573:Nitrites / Q000378:metabolism*; D058458:Nitrogen Cycle; D010084:Oxidation-Reduction; D010100:Oxygen / Q000378:metabolism; D017422:Sequence Analysis, DNA; D012722:Sewage / Q000382:microbiology; D012988:Soil Microbiology; D014508:Urea / Q000378:metabolism*; D014510:Urease / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D005561:Formates; D009566:Nitrates; D009573:Nitrites; D012722:Sewage; D000641:Ammonia; D014508:Urea; D005560:Formate Dehydrogenases; D014510:Urease; D010100:Oxygen
keywords: Nitrospira; formate; genome; nitrification; urease