title: Complete nitrification by Nitrospira bacteria.
abstract: Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira-contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.
authors.affiliation: Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
authors.forename: Holger
authors.initials: H
authors.lastname: Daims
authors.affiliation: Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia.
authors.forename: Elena V
authors.initials: EV
authors.lastname: Lebedeva
authors.affiliation: Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
authors.forename: Petra
authors.initials: P
authors.lastname: Pjevac
authors.affiliation: Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
authors.forename: Ping
authors.initials: P
authors.lastname: Han
authors.affiliation: Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
authors.forename: Craig
authors.initials: C
authors.lastname: Herbold
authors.affiliation: Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark.
authors.forename: Mads
authors.initials: M
authors.lastname: Albertsen
authors.affiliation: Helmholtz-Centre for Environmental Research - UFZ, Department of Proteomics, Permoserstrasse 15, 04318 Leipzig, Germany.
authors.forename: Nico
authors.initials: N
authors.lastname: Jehmlich
authors.affiliation: Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
authors.forename: Marton
authors.initials: M
authors.lastname: Palatinszky
authors.affiliation: Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
authors.forename: Julia
authors.initials: J
authors.lastname: Vierheilig
authors.affiliation: Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia.
authors.forename: Alexandr
authors.initials: A
authors.lastname: Bulaev
authors.affiliation: Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark.
authors.forename: Rasmus H
authors.initials: RH
authors.lastname: Kirkegaard
authors.affiliation: Helmholtz-Centre for Environmental Research - UFZ, Department of Proteomics, Permoserstrasse 15, 04318 Leipzig, Germany.|Helmholtz-Centre for Environmental Research - UFZ, Department of Metabolomics, Permoserstrasse 15, 04318 Leipzig, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: von Bergen
authors.affiliation: Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Rattei
authors.affiliation: DVGW-Forschungsstelle TUHH, Hamburg University of Technology, 21073 Hamburg, Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Bendinger
authors.affiliation: Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark.
authors.forename: Per H
authors.initials: PH
authors.lastname: Nielsen
authors.affiliation: Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
authors.forename: Michael
authors.initials: M
authors.lastname: Wagner
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001419:Bacteria / Q000201:enzymology / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D019143:Evolution, Molecular; D016680:Genome, Bacterial / Q000235:genetics; D008969:Molecular Sequence Data; D009566:Nitrates / Q000378:metabolism*; D058465:Nitrification / Q000235:genetics; D009573:Nitrites / Q000378:metabolism*; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny
chemical_list: D009566:Nitrates; D009573:Nitrites; D000641:Ammonia; D010088:Oxidoreductases; C021401:hydroxylamine dehydrogenase; C045582:ammonia monooxygenase