Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 107, Issue 19, Pages 8818-8823Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0913533107
Keywords
ammonia oxidation; marine microbiology; archaea; nitroxyl
Categories
Funding
- Department of Energy
- National Science Foundation [MCB-0604448, MCB-0920741, OCE-0623174, OCE-0623908, EF-0412129]
- University of Louisville VP Research office
- Deutsche Forschungsgemeinschaft
- US Department of Agriculture [2010-65115-20380]
- Salk Institute Innovation
- NIFA [2010-65115-20380, 581274] Funding Source: Federal RePORTER
- Direct For Biological Sciences
- Div Of Molecular and Cellular Bioscience [0920741] Funding Source: National Science Foundation
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Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling. The isolation of Candidatus Nitrosopumilus maritimus strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory of the globally distributed archaea. Here we report the 1,645,259-bp closed genome of strain SCM1, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria. Consistent with in situ isotopic studies of marine archaea, the genome sequence indicates N. maritimus grows autotrophically using a variant of the 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon assimilation, while maintaining limited capacity for assimilation of organic carbon. This unique instance of archaeal biosynthesis of the osmoprotectant ectoine and an unprecedented enrichment of multicopper oxidases, thioredoxin-like proteins, and transcriptional regulators points to an organism responsive to environmental cues and adapted to handling reactive copper and nitrogen species that likely derive from its distinctive biochemistry. The conservation of N. maritimus gene content and organization within marine metagenomes indicates that the unique physiology of these specialized oligophiles may play a significant role in the biogeochemical cycles of carbon and nitrogen.
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