The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes
Open accessAbstract
Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and thus microbial primary productivity. Until now, cyanobacterial populations have been viewed as the main suppliers of bioavailable nitrogen in this habitat. Although PCR amplicon surveys targeting the nitrogenase reductase gene have revealed the existence of diverse non-cyanobacterial diazotrophic populations, subsequent quantitative PCR surveys suggest that they generally occur in low abundance. Here, we use state-of-the-art metagenomic assembly and binning strategies to recover nearly one thousand non-redundant microbial population genomes from the TARA Oceans metagenomes. Among these, we provide the first genomic evidence for non-cyanobacterial diazotrophs inhabiting surface waters of the open ocean, which correspond to lineages within the Proteobacteria and, most strikingly, the Planctomycetes. Members of the latter phylum are prevalent in aquatic systems, but have never been linked to nitrogen fixation previously. Moreover, using genome-wide quantitative read recruitment, we demonstrate that the discovered diazotrophs were not only widespread but also remarkably abundant (up to 0.3% of metagenomic reads for a single population) in both the Pacific Ocean and the Atlantic Ocean northwest. Our results extend decades of PCR-based gene surveys, and substantiate the importance of heterotrophic bacteria in the fixation of nitrogen in the surface 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.
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
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010) · Systematic Biology · doi:10.1093/sysbio/syq010 · Cited by 18,376
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496
Gephi: An Open Source Software for Exploring and Manipulating Networks
Bastian, M., Heymann, S., & Jacomy, M. (2009) · Proceedings of the International AAAI Conference on Web and Social Media · doi:10.1609/icwsm.v3i1.13937 · Cited by 11,675
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
Prokaryotes: The unseen majority
Whitman, W. B., Coleman, D. C., & Wiebe, W. J. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.12.6578 · Cited by 4,871
Oceanic phytoplankton, atmospheric sulphur, cloud albedo and climate
Charlson, R. J., Lovelock, J. E., Andreae, M. O., & Warren, S. G. (1987) · Nature · doi:10.1038/326655a0 · Cited by 4,305
The relative influences of nitrogen and phosphorus on oceanic primary production
Tyrrell, T. (1999) · Nature · doi:10.1038/22941 · Cited by 1,687
Cited by
A new genomic blueprint of the human gut microbiota
Almeida, A., Mitchell, A. L., Boland, M., Forster, S. C., Gloor, G. B., Tarkowska, A., Lawley, T. D., & Finn, R. D. (2019) · Nature · doi:10.1038/s41586-019-0965-1 · Cited by 1,314
The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans
Tully, B. J., Graham, E. D., & Heidelberg, J. F. (2018) · Scientific Data · doi:10.1038/sdata.2017.203 · Cited by 508
Tara Oceans: towards global ocean ecosystems biology
Sunagawa, S., Acinas, S. G., Bork, P., Bowler, C., Coordinators, T. O., Acinas, S. G., Babin, M., Bork, P., Boss, E., Bowler, C., et al. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0364-5 · Cited by 490
Changing perspectives in marine nitrogen fixation
Zehr, J. P., & Capone, D. G. (2020) · Science · doi:10.1126/science.aay9514 · Cited by 470
Accurate and complete genomes from metagenomes
Chen, L.-X., Anantharaman, K., Shaiber, A., Eren, A. M., & Banfield, J. F. (2020) · Genome Research · doi:10.1101/gr.258640.119 · Cited by 401
Self-citation
Metadata
- Authors
- Delmont, T. O., Quince, C., Shaiber, A., Esen, Ö. C., Lee, S. T., Rappé, M. S., McLellan, S. L., Lücker, S., & Eren, A. M.
- Venue
- Nature Microbiology
- Published
- 2018-06-11
- Volume
- 3
- Issue
- 7
- Pages
- 804-813
- ISSN
- 2058-5276 (ISSN-L)
- OpenAlex
- W2805238404
- Cited by
- 602
- References
- 12
- FWCI
- 47.08
- Type
- journal article
- Language
- en
- Open access
- hybrid
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. https://app.cochat.ai/papers/10.1038/s41564-018-0176-9
- The paper
- Delmont, T. O., Quince, C., Shaiber, A., Esen, Ö. C., Lee, S. T., Rappé, M. S., McLellan, S. L., Lücker, S., & Eren, A. M. (2018). Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nature Microbiology. https://doi.org/10.1038/s41564-018-0176-9
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
