title: Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers.
abstract: Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms and key players in the global nitrogen and carbon cycles. They share a common energy metabolism but represent a heterogeneous group with respect to their environmental distribution and adaptions, growth requirements, and genome contents. We report here the genome and proteome of Nitrososphaera viennensis EN76, the type species of the archaeal class Nitrososphaeria of the phylum Thaumarchaeota encompassing all known AOA. N. viennensis is a soil organism with a 2.52-Mb genome and 3,123 predicted protein-coding genes. Proteomic analysis revealed that nearly 50% of the predicted genes were translated under standard laboratory growth conditions. Comparison with genomes of closely related species of the predominantly terrestrial Nitrososphaerales as well as the more streamlined marine Nitrosopumilales [Candidatus (Ca.) order] and the acidophile "Ca. Nitrosotalea devanaterra" revealed a core genome of AOA comprising 860 genes, which allowed for the reconstruction of central metabolic pathways common to all known AOA and expressed in the N. viennensis and "Ca Nitrosopelagicus brevis" proteomes. Concomitantly, we were able to identify candidate proteins for as yet unidentified crucial steps in central metabolisms. In addition to unraveling aspects of core AOA metabolism, we identified specific metabolic innovations associated with the Nitrososphaerales mediating growth and survival in the soil milieu, including the capacity for biofilm formation, cell surface modifications and cell adhesion, and carbohydrate conversions as well as detoxification of aromatic compounds and drugs.
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria.
authors.forename: Melina
authors.initials: M
authors.lastname: Kerou
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria.
authors.forename: Pierre
authors.initials: P
authors.lastname: Offre
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria.
authors.forename: Luis
authors.initials: L
authors.lastname: Valledor
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria.
authors.forename: Sophie S
authors.initials: SS
authors.lastname: Abby
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria.
authors.forename: Michael
authors.initials: M
authors.lastname: Melcher
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria.
authors.forename: Matthias
authors.initials: M
authors.lastname: Nagler
authors.affiliation: Vienna Metabolomics Center, University of Vienna, A-1090 Vienna, Austria wolfram.weckwerth@univie.ac.at Christa.Schleper@univie.ac.at.
authors.forename: Wolfram
authors.initials: W
authors.lastname: Weckwerth
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria; wolfram.weckwerth@univie.ac.at Christa.Schleper@univie.ac.at.
authors.forename: Christa
authors.initials: C
authors.lastname: Schleper
mesh_terms: D000220:Adaptation, Biological; D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000235:genetics* / Q000378:metabolism; D018441:Biofilms; D002244:Carbon / Q000378:metabolism; D002352:Carrier Proteins; D002448:Cell Adhesion; D004260:DNA Repair; D004734:Energy Metabolism; D020745:Genome, Archaeal; D010084:Oxidation-Reduction; D051922:PII Nitrogen Regulatory Proteins; D000071696:Proteogenomics; D020543:Proteome
chemical_list: D002352:Carrier Proteins; D051922:PII Nitrogen Regulatory Proteins; D020543:Proteome; D002244:Carbon; D000641:Ammonia
keywords: ammonia oxidation; archaea; biofilm; comparative genomics; proteomics