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Genomic and proteomic characterization of “ Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean
Open accessAbstract
Thaumarchaeota are among the most abundant microbial cells in the ocean, but difficulty in cultivating marine Thaumarchaeota has hindered investigation into the physiological and evolutionary basis of their success. We report here a closed genome assembled from a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon CN25, originating from the open ocean. The CN25 genome exhibits strong evidence of genome streamlining, including a 1.23-Mbp genome, a high coding density, and a low number of paralogous genes. Proteomic analysis recovered nearly 70% of the predicted proteins encoded by the genome, demonstrating that a high fraction of the genome is translated. In contrast to other minimal marine microbes that acquire, rather than synthesize, cofactors, CN25 encodes and expresses near-complete biosynthetic pathways for multiple vitamins. Metagenomic fragment recruitment indicated the presence of DNA sequences >90% identical to the CN25 genome throughout the oligotrophic ocean. We propose the provisional name "Candidatus Nitrosopelagicus brevis" str. CN25 for this minimalist marine thaumarchaeon and suggest it as a potential model system for understanding archaeal adaptation to the open ocean.
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“These tradeoffs include the replacement of a Fe-containing superoxide dismutase with a Nicontaining version (Dupont et al., 2012), exchanging an Fe protein with a Cu protein in the electron transport chains in photosynthesis (Peers and Price, 2006) and ammonia oxidation (Santoro et al., 2015), and using B12 instead of Fe for ribonucleotide reductase.”
From Trace elements at the intersection of marine biological and geochemical evolution (2016) · cites this paper as Santoro et al., 2015
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Metadata
- Authors
- Santoro, A. E., Dupont, C. L., Richter, R. A., Craig, M. T., Carini, P., McIlvin, M. R., Yang, Y., Orsi, W. D., Moran, D. M., & Saito, M. A.
- Affiliations
- University of Maryland Center for Environmental Science (US)
- Microbial and Environmental Genomics and
- J. Craig Venter Institute (US)
- University of San Diego (US)
- Woods Hole Oceanographic Institution (US)
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2015-01-13
- Volume
- 112
- Issue
- 4
- Pages
- 1173-1178
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC4313803
- OpenAlex
- W2032670022
- Cited by
- 268
- References
- 64
- Citations by year
- 2026: 12 · 2025: 22 · 2024: 23 · 2023: 23 · 2022: 26 · 2021: 25 · 2020: 30 · 2019: 31 · 2018: 21 · 2017: 18 · 2016: 25 · 2015: 12
- FWCI
- 22.97
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Gordon and Betty Moore Foundation (GBMF3307, GBMF3782, GBMF2724)
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Pollution › Wastewater Treatment and Nitrogen Removal
- Keywords
- ammonia-oxidizing archaea, Thaumarchaeota, marine archaea, genome streamlining, minimal genome, vitamin biosynthesis, cofactor biosynthesis, proteome, genome assembly
- MeSH terms
- Amino Acid Sequence, Archaea, Molecular Sequence Data, Oceans and Seas, Water Microbiology, Archaeal Proteins, Gene Expression Regulation, Archaeal, Proteome, Proteomics, Metagenomics
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