期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2016
卷号：113
期号：49
页码：E7937-E7946
DOI：10.1073/pnas.1601212113
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：SignificanceAmmonia-oxidizing archaea (AOA), key players in global biogeochemical cycles, represent a heterogeneous group with a broad environmental distribution. Understanding their activity and physiology is of great importance due to the impact of the overuse of agricultural fertilizers on the N cycle and the production of the greenhouse gas N2O during nitrification. Despite their prominent ecological role, little is known about the fundamental metabolic processes of AOA. Here, we show that AOA of marine and terrestrial environments share unique and well-conserved pathways of carbon and nitrogen metabolism, and we raise hypotheses about missing steps in these pathways. Our approach also highlights the extensive environmental adaptations of the soil clade, including the capacity for cell surface modifications, carbohydrate conversions, detoxification, and biofilm formation. 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.
