The DOI matches its Crossref record; 64 of the 64 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“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
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Cell biology and molecular basis of denitrification
Zumft, W. G. (1997) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.61.4.533-616.1997 · Cited by 3,560
Isolation of an autotrophic ammonia-oxidizing marine archaeon
Könneke, M., Bernhard, A. E., de la Torre, J. R., Walker, C. B., Waterbury, J. B., & Stahl, D. A. (2005) · Nature · doi:10.1038/nature03911 · Cited by 2,864
Archaea in coastal marine environments.
DeLong, E. F. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.12.5685 · Cited by 2,758
Rusch, D. B., Halpern, A. L., Sutton, G. G., Heidelberg, K. B., Williamson, S. J., Yooseph, S., Wu, D., Eisen, J. A., Hoffman, J., Remington, K., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050077 · Cited by 2,044
Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria
Martens‐Habbena, W., Berube, P. M., Urakawa, H., de la Torre, J. R., & Stahl, D. A. (2009) · Nature · doi:10.1038/nature08465 · Cited by 1,707
Archaeal dominance in the mesopelagic zone of the Pacific Ocean
Karner, M. B., DeLong, E. F., & Karl, D. M. (2001) · Nature · doi:10.1038/35054051 · Cited by 1,630
Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota
Brochier‐Armanet, C., Boussau, B., Gribaldo, S., & Forterre, P. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1852 · Cited by 1,249
The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss
Morris, J., Lenski, R. E., & Zinser, E. R. (2012) · mBio · doi:10.1128/mbio.00036-12 · Cited by 1,231
Genome Streamlining in a Cosmopolitan Oceanic Bacterium
Giovannoni, S. J., Tripp, H. J., Givan, S. A., Podar, M., Vergin, K. L., Baptista, D., Bibbs, L., Eads, J. R., Richardson, T. H., Noordewier, M. O., et al. (2005) · Science · doi:10.1126/science.1114057 · Cited by 1,224
Nitrososphaera viennensis , an ammonia oxidizing archaeon from soil
Tourna, M., Stieglmeier, M., Spang, A., Könneke, M., Schintlmeister, A., Urich, T., Engel, M., Schloter, M., Wagner, M., Richter, A. A., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1013488108 · Cited by 962
Cited by
Sorted by citations
SAR11 Bacteria: The Most Abundant Plankton in the Oceans
Giovannoni, S. J. (2016) · Annual Review of Marine Science · doi:10.1146/annurev-marine-010814-015934 · Cited by 554
Marine methane paradox explained by bacterial degradation of dissolved organic matter
Repeta, D. J., Ferrón, S., Sosa, O. A., Johnson, C. G., Repeta, L. D., Acker, M., DeLong, E. F., & Karl, D. M. (2016) · Nature Geoscience · doi:10.1038/ngeo2837 · Cited by 362
Alves, R. E., Minh, B. Q., Urich, T., von Haeseler, A., & Schleper, C. (2018) · Nature Communications · doi:10.1038/s41467-018-03861-1 · Cited by 359
Ahlgren, N. A., Ren, J., Lu, Y. Y., Fuhrman, J. A., & Sun, F. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1002 · Cited by 313
Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters
Bristow, L. A., Dalsgaard, T., Tiano, L., Mills, D. B., Bertagnolli, A. D., Wright, J. J., Hallam, S., Ulloa, O., Canfield, D. E., Revsbech, N. P., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1600359113 · Cited by 298
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
