title: Complete nitrification by a single microorganism.
abstract: Nitrification is a two-step process where ammonia is first oxidized to nitrite by ammonia-oxidizing bacteria and/or archaea, and subsequently to nitrate by nitrite-oxidizing bacteria. Already described by Winogradsky in 1890, this division of labour between the two functional groups is a generally accepted characteristic of the biogeochemical nitrogen cycle. Complete oxidation of ammonia to nitrate in one organism (complete ammonia oxidation; comammox) is energetically feasible, and it was postulated that this process could occur under conditions selecting for species with lower growth rates but higher growth yields than canonical ammonia-oxidizing microorganisms. Still, organisms catalysing this process have not yet been discovered. Here we report the enrichment and initial characterization of two Nitrospira species that encode all the enzymes necessary for ammonia oxidation via nitrite to nitrate in their genomes, and indeed completely oxidize ammonium to nitrate to conserve energy. Their ammonia monooxygenase (AMO) enzymes are phylogenetically distinct from currently identified AMOs, rendering recent acquisition by horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. We also found highly similar amoA sequences (encoding the AMO subunit A) in public sequence databases, which were apparently misclassified as methane monooxygenases. This recognition of a novel amoA sequence group will lead to an improved understanding of the environmental abundance and distribution of ammonia-oxidizing microorganisms. Furthermore, the discovery of the long-sought-after comammox process will change our perception of the nitrogen cycle.
authors.affiliation: Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
authors.forename: Maartje A H J
authors.initials: MA
authors.lastname: van Kessel
authors.affiliation: Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
authors.forename: Daan R
authors.initials: DR
authors.lastname: Speth
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: 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, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
authors.forename: Huub J M
authors.initials: HJ
authors.lastname: Op den Camp
authors.affiliation: Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.|Laboratory for Microbiology, University of Gent, K. L. Ledeganckstraat 35, 9000 Gent, Belgium.
authors.forename: Boran
authors.initials: B
authors.lastname: Kartal
authors.affiliation: Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.|Department of Biotechnology, TU Delft, Julianalaan 67, 2628 BC Delft, the Netherlands.
authors.forename: Mike S M
authors.initials: MS
authors.lastname: Jetten
authors.affiliation: Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Lücker
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001419:Bacteria / Q000201:enzymology / Q000235:genetics / Q000378:metabolism*; D019143:Evolution, Molecular; D016680:Genome, Bacterial / Q000235:genetics; 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; C045582:ammonia monooxygenase