Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Biological nitrogen fixation detected under Antarctic sea ice


Nitrogen fixation is the primary source of reactive nitrogen in the ocean. Most ecological models do not predict nitrogen fixation in the Antarctic Ocean because of the low availability of iron and high abundance of nitrogen. Here we extensively examined nitrogen fixation in the Antarctic Ocean, and found substantial nitrogen fixation (maximum: 44.4 nmol N l−1 d−1) near the Antarctic coast, especially around ice-covered regions. The nitrogenase gene (nifH) was detected at all coastal stations, including stations where no nitrogen fixation was found. At the stations where nitrogen fixation was detected, the nitrogen-fixing cyanobacterium UCYN-A (Candidatus ‘Atelocyanobacterium thalassa’) dominated nifH gene expression, and the nifH sequence was identical to that of the major oligotype in tropical and subtropical oceans. Our results suggest that marine nitrogen fixation is a ubiquitous process in the global ocean, and that UCYN-A is the keystone species for making it possible.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Sampling stations, maximum nitrogen fixation and diazotroph community composition in the Antarctic Ocean.
Fig. 2: Nitrogen fixation and UCYN-A abundance in the world ocean.

Data availability

The sequence datasets generated for this study can be obtained from the DNA Data Bank of Japan Sequence Read Archive (number DRA009504). Background satellite-derived data are available in the UTokyo Repository ( Source data are provided with this paper.


  1. 1.

    Gruber, N. & Galloway, J. N. An Earth-system perspective of the global nitrogen cycle. Nature 451, 293–296 (2008).

    Google Scholar 

  2. 2.

    Falkowski, P. G. Evolution of the nitrogen cycle and its influence on the biological sequestration of CO2 in the ocean. Nature 387, 272–275 (1997).

    Google Scholar 

  3. 3.

    Zehr, J. P. & Capone, D. G. Changing perspectives in marine nitrogen fixation. Science 368, eaay9514 (2020).

    Google Scholar 

  4. 4.

    Luo, Y. W. et al. Database of diazotrophs in global ocean: abundance, biomass and nitrogen fixation rates. Earth Syst. Sci. Data 4, 47–73 (2012).

    Google Scholar 

  5. 5.

    Sohm, J. A., Webb, E. A. & Capone, D. G. Emerging patterns of marine nitrogen fixation. Nat. Rev. Microbiol. 9, 499–508 (2011).

    Google Scholar 

  6. 6.

    Knapp, A. N. The sensitivity of marine N2 fixation to dissolved inorganic nitrogen. Front. Microbiol. 3, 374 (2012).

    Google Scholar 

  7. 7.

    Bentzon-Tilia, M. et al. Significant N2 fixation by heterotrophs, photoheterotrophs and heterocystous cyanobacteria in two temperate estuaries. ISME J. 9, 273–285 (2015).

    Google Scholar 

  8. 8.

    Shiozaki, T. et al. Diazotroph community structure and the role of nitrogen fixation in the nitrogen cycle in the Chukchi Sea (western Arctic Ocean). Limnol. Oceanogr. 63, 2191–2205 (2018).

    Google Scholar 

  9. 9.

    Harding, K. et al. Symbiotic unicellular cyanobacteria fix nitrogen in the Arctic Ocean. Proc. Natl Acad. Sci. USA 115, 13371–13375 (2018).

    Google Scholar 

  10. 10.

    Blais, M. et al. Nitrogen fixation and identification of potential diazotrophs in the Canadian Arctic. Glob. Biogeochem. Cycles 26, GB3022 (2012).

    Google Scholar 

  11. 11.

    Raes, E. J. et al. N2 fixation and new insights into nitrification from the ice-edge to the equator in the South Pacific Ocean. Front. Mar. Sci. 7, 389 (2020).

    Google Scholar 

  12. 12.

    Mills, M. M. et al. Unusual marine cyanobacteria/haptophyte symbiosis relies on N2 fixation even in N-rich environments. ISME J. 14, 2395–2406 (2020).

    Google Scholar 

  13. 13.

    Boyd, P. W., Arrigo, K. R., Strzepek, R. & van Dijken, G. L. Mapping phytoplankton iron utilization: insights into Southern Ocean supply mechanisms. J. Geophys. Res. Oceans 117, C06009 (2012).

    Google Scholar 

  14. 14.

    Kustka, A., Carpenter, E. J. & Sanudo-Wilhelmy, S. A. Iron and marine nitrogen fixation: progress and future directions. Res. Microbiol. 153, 255–262 (2002).

    Google Scholar 

  15. 15.

    Monteiro, F. M., Follows, M. J. & Dutkiewicz, S. Distribution of diverse nitrogen fixers in the global ocean. Glob. Biogeochem. Cycles 24, GB3017 (2010).

    Google Scholar 

  16. 16.

    Landolfi, A., Koeve, W., Dietze, H., Kahler, P. & Oschlies, A. A new perspective on environmental controls of marine nitrogen fixation. Geophys. Res. Lett. 42, 4482–4489 (2015).

    Google Scholar 

  17. 17.

    Wang, W. L., Moore, J. K., Martiny, A. C. & Primeau, F. W. Convergent estimates of marine nitrogen fixation. Nature 566, 205–211 (2019).

    Google Scholar 

  18. 18.

    Treguer, P. & Jacques, G. Dynamics of nutrients and phytoplankton, and fluxes of carbon, nitrogen and silicon in the Antarctic Ocean. Polar Biol. 12, 149–162 (1992).

    Google Scholar 

  19. 19.

    Redfield, A. C. The biological control of chemical factors in the environment. Am. Sci. 46, 205–221 (1958).

    Google Scholar 

  20. 20.

    Zehr, J. P., Jenkins, B. D., Short, S. M. & Steward, G. F. Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ. Microbiol. 5, 539–554 (2003).

    Google Scholar 

  21. 21.

    Thompson, A. W. et al. Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga. Science 337, 1546–1550 (2012).

    Google Scholar 

  22. 22.

    Farnelid, H., Turk-Kubo, K., Munoz-Marin, M. D. & Zehr, J. P. New insights into the ecology of the globally significant uncultured nitrogen-fixing symbiont UCYN-A. Aquat. Microb. Ecol. 77, 125–138 (2016).

    Google Scholar 

  23. 23.

    Turk-Kubo, K. A., Farnelid, H. M., Shilova, I. N., Henke, B. & Zehr, J. P. Distinct ecological niches of marine symbiotic N2-fixing cyanobacterium candidatus Atelocyanobacterium thalassa sublineages. J. Phycol. 53, 451–461 (2017).

    Google Scholar 

  24. 24.

    Sedwick, P. N. & DiTullio, G. R. Regulation of algal blooms in Antarctic shelf waters by the release of iron from melting sea ice. Geophys. Res. Lett. 24, 2515–2518 (1997).

    Google Scholar 

  25. 25.

    Duprat, L. et al. Enhanced iron flux to Antarctic sea ice via dust deposition from ice-free coastal areas. J. Geophys. Res. Oceans 124, 8538–8557 (2019).

    Google Scholar 

  26. 26.

    Shiozaki, T. et al. New estimation of N2 fixation in the western and central Pacific Ocean and its marginal seas. Glob. Biogeochem. Cycles 24, GB1015 (2010).

    Google Scholar 

  27. 27.

    Tang, W. Y. et al. Revisiting the distribution of oceanic N2 fixation and estimating diazotrophic contribution to marine production. Nat. Commun. 10, 831 (2019).

    Google Scholar 

  28. 28.

    Deutsch, C., Sarmiento, J. L., Sigman, D. M., Gruber, N. & Dunne, J. P. Spatial coupling of nitrogen inputs and losses in the ocean. Nature 445, 163–167 (2007).

    Google Scholar 

  29. 29.

    Rogers, A. D. Evolution and biodiversity of Antarctic organisms: a molecular perspective. Philos. Trans. R. Soc. B 362, 2191–2214 (2007).

    Google Scholar 

  30. 30.

    Patarnello, T., Bargelloni, L., Varotto, V. & Battaglia, B. Krill evolution and the Antarctic ocean currents: evidence of vicariant speciation as inferred by molecular data. Mar. Biol. 126, 603–608 (1996).

    Google Scholar 

  31. 31.

    Mock, T. et al. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature 541, 536–540 (2017).

    Google Scholar 

  32. 32.

    Cornejo-Castillo, F. M. et al. Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton. Nat. Commun. 7, 11071 (2016).

    Google Scholar 

  33. 33.

    Orsi, A. H., Whitworth, T. & Nowlin, W. D. On the meridional extent and fronts of the Antarctic Circumpolar Current. Deep Sea Res. Part I 42, 641–673 (1995).

    Google Scholar 

  34. 34.

    World Ocean Atlas 2018 (NOAA, 2019);

  35. 35.

    Capone, D. G., Zehr, J. P., Paerl, H. W., Bergman, B. & Carpenter, E. J. Trichodesmium, a globally significant marine cyanobacterium. Science 276, 1221–1229 (1997).

    Google Scholar 

  36. 36.

    Mohr, W., Grosskopf, T., Wallace, D. W. R. & LaRoche, J. Methodological underestimation of oceanic nitrogen fixation rates. PLoS ONE 5, e12583 (2010).

    Google Scholar 

  37. 37.

    Dabundo, R. et al. The contamination of commercial 15N2 gas stocks with 15N-labeled nitrate and ammonium and consequences for nitrogen fixation measurements. PLoS ONE 9, e110335 (2014).

    Google Scholar 

  38. 38.

    Shiozaki, T. et al. Why is Trichodesmium abundant in the Kuroshio? Biogeosciences 12, 6931–6943 (2015).

    Google Scholar 

  39. 39.

    Shiozaki, T., Furuya, K., Kodama, T. & Takeda, S. Contribution of N2 fixation to new production in the western North Pacific Ocean along 155°E. Mar. Ecol. Prog. Ser. 377, 19–32 (2009).

    Google Scholar 

  40. 40.

    Montoya, J. P., Voss, M., Kahler, P. & Capone, D. G. A simple, high-precision, high-sensitivity tracer assay for N2 fixation. Appl. Environ. Microbiol. 62, 986–993 (1996).

    Google Scholar 

  41. 41.

    Gradoville, M. R. et al. Diversity and activity of nitrogen-fixing communities across ocean basins. Limnol. Oceanogr. 62, 1895–1909 (2017).

    Google Scholar 

  42. 42.

    Shiozaki, T. et al. Basin scale variability of active diazotrophs and nitrogen fixation in the North Pacific, from the tropics to the subarctic Bering Sea. Glob. Biogeochem. Cycles 31, 996–1009 (2017).

    Google Scholar 

  43. 43.

    Turk, K. A. et al. Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North Atlantic. ISME J. 5, 1201–1212 (2011).

    Google Scholar 

  44. 44.

    Zehr, J. P. & Turner, P. J. Nitrogen fixation: nitrogenase genes and gene expression. Methods Microbiol. 30, 272–286 (2001).

    Google Scholar 

  45. 45.

    Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).

    Google Scholar 

  46. 46.

    Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12 (2011).

    Google Scholar 

  47. 47.

    Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).

    Google Scholar 

  48. 48.

    Shiozaki, T. et al. Seasonal variations of unicellular diazotroph groups A and B, and Trichodesmium in the northern South China Sea and neighboring upstream Kuroshio Current. Cont. Shelf Res. 80, 20–31 (2014).

    Google Scholar 

  49. 49.

    Shiozaki, T. et al. Linkage between dinitrogen fixation and primary production in the oligotrophic south pacific ocean. Glob. Biogeochem. Cycles 32, 1028–1044 (2018).

    Google Scholar 

  50. 50.

    Tang, W. Y. & Cassar, N. Data-driven modeling of the distribution of diazotrophs in the global ocean. Geophys. Res. Lett. 46, 12258–12269 (2019).

    Google Scholar 

Download references


We thank the captain, crew and participants of the 60th Japanese Antarctic Research Expedition (JARE-60) for their cooperation at sea and on land. We also thank H. Endo and C. Deutsch for helpful discussions, N. Takeda for help with the nutrient analyses and K. Turk-Kubo for providing the sequence data for UCYN-A. This research was supported financially by JSPS KAKENHI grant numbers JP19H04263 (T.S.), 20H04985 (T.S.), 17H01852 (F.H.) and JP15H05712 (N.H.) and the Simons Foundation (Simons Postdoctoral Fellowship in Marine Microbial Ecology) under award number 544338 (K.I.).

Author information




T.S. and N.H. designed the research and collected the samples. T.S. conducted the measurements of the nitrogen fixation rate. A.F. conducted the satellite data analyses and visualized the data. T.S. and Y.H. supervised the molecular analyses. F.H. oversaw the nutrient analyses. T.S. and K.I. wrote the manuscript, with contributions from all co-authors.

Corresponding author

Correspondence to Takuhei Shiozaki.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Primary Handling Editor: Clare Davis.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Spatial distribution of environmental variables and UCYN-A1 abundance in the Antarctic Ocean.

(a) surface nitrate. (b) the surface total inorganic nitrogen/phosphate ratio in the surface water. (c) the maximum abundance of UCYN-A1. The details regarding the background contours and lines are described in Fig. 1.

Source data

Extended Data Fig. 2 Nonmetric multidimensional scaling (nMDS) plot derived from a Bray–Curtis distance matrix of the diazotroph community at each sampling station.

Beach (Sta. N and T), fast-ice (Sta. A–C), ice-edge (Sta. D, E, and EL), and ice-free (Sta. BP, CD0, and CD1) areas are shown in yellow, red, green, and blue, respectively.

Source data

Extended Data Fig. 3 Maximum-likelihood tree of diazotrophs constructed from nifH gene sequences.

The major phylotypes in the Southern Ocean (≥10% of total reads for each sample) are shown in red. The nifH sequences from isolated culture are shown in bold. Bootstrap values (> 50%) determined from 1,000 iterations are shown as purple circles, with the area proportional to the value.

Source data

Extended Data Fig. 4 Global map of the maximum abundance of UCYN-A.

Details of the dataset used in this study are written in Methods. Black circles indicate that UCYN-A was not detectable. Background contour lines indicate surface nitrate concentrations, obtained from the World Ocean Atlas 201834.

Source data

Source data

Source Data Fig. 1

Sampling locations, nitrogen fixation, diazotroph community composition and satellite data in the Antarctic Ocean. Background satellite-derived data are available in the UTokyo Repository (

Source Data Fig. 2

The depth-integrated rate of nitrogen fixation and maximum abundance of UCYN-A in the world ocean.

Source Data Extended Data Fig. 1

Nitrate, total inorganic nitrogen/phosphate ratio and UCYN-A in the Antarctic Ocean.

Source Data Extended Data Fig. 2

Sequence variant table used for the nMDS analysis.

Source Data Extended Data Fig. 3

Sequence data used to construct the phylogenetic tree.

Source Data Extended Data Fig. 4

Maximum abundance of UCYN-A in the world ocean.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Shiozaki, T., Fujiwara, A., Inomura, K. et al. Biological nitrogen fixation detected under Antarctic sea ice. Nat. Geosci. 13, 729–732 (2020).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing