Cited by 273Microbial Community Ecology and PhysiologyGenomics and Phylogenetic StudiesWastewater Treatment and Nitrogen Removal

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Genomic and proteomic characterization of “ Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean

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Santoro, Alyson E., Dupont, Christopher L., Richter, R. Alex, Craig, Matthew T., Carini, Paul, McIlvin, Matthew R., Yang, Youngik, Orsi, William D., Moran, Dawn M., Saito, Mak A.·2015·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.1416223112PMC PMC4313803

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Abstract

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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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: Santoro, Alyson E.
Dupont, Christopher L.
Craig, Matthew T.
Carini, Paul
McIlvin, Matthew R.
Yang, Youngik
Orsi, William D.
Moran, Dawn M.
Saito, Mak A.
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
DOI: 10.1073/pnas.1416223112
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
Licence: www.pnas.org/site/misc/userlicense.xhtml (vor)
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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Genomic and proteomic characterization of “ Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean

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