Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers

Author(s)
Melina Kerou, Pierre Offre, Luis Valledor, Sophie S. Abby, Michael Melcher, Matthias Nagler, Wolfram Weckwerth, Christa Schleper
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 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.

Organisation(s)
Department of Ecogenomics and Systems Biology, Large-Instrument Facility for Mass Spectrometry in Life Sciences, Research Platform Vienna Metabolomics Center
Journal
Proceedings of the National Academy of Sciences of the United States of America (PNAS)
Volume
113
Pages
E7937-E7946
No. of pages
10
ISSN
0027-8424
DOI
https://doi.org/10.1073/pnas.1601212113
Publication date
12-2016
Peer reviewed
Yes
Austrian Fields of Science 2012
Microbiology, Genomics, Proteomics
Keywords
Portal url
https://ucris.univie.ac.at/portal/en/publications/proteomics-and-comparative-genomics-of-nitrososphaera-viennensis-reveal-the-core-genome-and-adaptations-of-archaeal-ammonia-oxidizers(adcc0146-ad27-4872-8014-23782db12953).html