Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 113, Issue 49, Pages E7937-E7946Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1601212113
Keywords
ammonia oxidation; proteomics; archaea; comparative genomics; biofilm
Categories
Funding
- Austrian Science Fund [P27017, W1257, P26342]
- European Research Council [ERC-ADG 695192]
- Marie Sklodowska-Curie Grants [FP7-PEOPLE-2009-IEF-255109, H2020-MSCA-IF-2017:701981]
- Austrian Science Fund (FWF) [P26342, P27017] Funding Source: Austrian Science Fund (FWF)
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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 organismwith 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.
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