Skip to main content

Thank you for visiting nature.com. 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.

The small unicellular diazotrophic symbiont, UCYN-A, is a key player in the marine nitrogen cycle

Abstract

Microbial dinitrogen (N2) fixation, the nitrogenase enzyme-catalysed reduction of N2 gas into biologically available ammonia, is the main source of new nitrogen (N) in the ocean. For more than 50 years, oceanic N2 fixation has mainly been attributed to the activity of the colonial cyanobacterium Trichodesmium1,2. Other smaller N2-fixing microorganisms (diazotrophs)—in particular the unicellular cyanobacteria group A (UCYN-A)—are, however, abundant enough to potentially contribute significantly to N2 fixation in the surface waters of the oceans36. Despite their abundance, the contribution of UCYN-A to oceanic N2 fixation has so far not been directly quantified. Here, we show that in one of the main areas of oceanic N2 fixation, the tropical North Atlantic7, the symbiotic cyanobacterium UCYN-A contributed to N2 fixation similarly to Trichodesmium. Two types of UCYN-A, UCYN-A1 and -A2, were observed to live in symbioses with specific eukaryotic algae. Single-cell analyses showed that both algae–UCYN-A symbioses actively fixed N2, contributing 20% to N2 fixation in the tropical North Atlantic, revealing their significance in this region. These symbioses had growth rates five to ten times higher than Trichodesmium, implying a rapid transfer of UCYN-A-fixed N into the food web that might significantly raise their actual contribution to N2 fixation. Our analysis of global 16S rRNA gene databases showed that UCYN-A occurs in surface waters from the Arctic to the Antarctic Circle and thus probably contributes to N2 fixation in a much larger oceanic area than previously thought. Based on their high rates of N2 fixation and cosmopolitan distribution, we hypothesize that UCYN-A plays a major, but currently overlooked role in the oceanic N cycle.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: N2 fixation rates and the relative contribution of Trichodesmium and UCYN-A to N2 fixation.
Figure 2: Single-cell imaging and cellular activities using nanoSIMS.
Figure 3: Growth rates of UCYN-A associations.
Figure 4: Distribution of UCYN-A in the world's oceans.

References

  1. Dugdale, R. C., Goering, J. J. & Ryther, J. H. High nitrogen fixation rates in the Sargasso Sea and the Arabian Sea. Limnol. Oceanogr. 9, 507–510 (1964).

    CAS  Article  Google Scholar 

  2. Capone, D. G. et al. Nitrogen fixation by Trichodesmium spp.: an important source of new nitrogen to the tropical and subtropical North Atlantic Ocean. Global Biogeochem. Cycles 19, GB2024 (2005)

    Article  Google Scholar 

  3. Zehr, J. P. et al. Unicellular cyanobacteria fix N2 in the subtropical North Pacific Ocean. Nature 412, 635–638 (2001).

    CAS  Article  Google Scholar 

  4. Montoya, J. P. et al. High rates of N2 fixation by unicellular diazotrophs in the oligotrophic Pacific Ocean. Nature 430, 1027–1032 (2004).

    CAS  Article  Google Scholar 

  5. Montoya, J. P., Voss, M. & Capone, D. G. Spatial variation in N2-fixation rate and diazotroph activity in the Tropical Atlantic. Biogeosciences 4, 369–376 (2007).

    CAS  Article  Google Scholar 

  6. Grosskopf, T. et al. Doubling of marine dinitrogen-fixation rates based on direct measurements. Nature 488, 361–364 (2012).

    CAS  Article  Google Scholar 

  7. 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).

    Article  Google Scholar 

  8. Fennel, K., Spitz, Y. H., Letelier, R. M., Abbott, M. R. & Karl, D. M. A deterministic model for N2 fixation at Stn. ALOHA in the subtropical North Pacific Ocean. Deep-Sea Res. II 49, 149–174 (2002).

    CAS  Article  Google Scholar 

  9. Hood, R. R., Coles, V. J. & Capone, D. G. Modeling the distribution of Trichodesmium and nitrogen fixation in the Atlantic Ocean. J. Geophys. Res. 109, C06006 (2004).

    Article  Google Scholar 

  10. Moore, J. K., Doney, S. C. & Lindsay, K. Upper ocean ecosystem dynamics and iron cycling in a global three-dimensional model. Global Biogeochem. Cycles 18, GB4028 (2004).

    Article  Google Scholar 

  11. 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).

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  13. Zehr, J. P. et al. Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II. Science 322, 1110–1112 (2008).

    CAS  Article  Google Scholar 

  14. Krupke, A. et al. The effect of nutrients on carbon and nitrogen fixation by the UCYN-A-haptophyte symbiosis. ISME J. 9, 1635–1647 (2015).

    CAS  Article  Google Scholar 

  15. Krupke, A. et al. In situ identification and N2 and C fixation rates of uncultivated cyanobacteria populations. System. Appl. Microbiol. 36, 259–271 (2013).

    CAS  Article  Google Scholar 

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

    Article  Google Scholar 

  17. Zehr, J. P. How single cells work together. Science 349, 1163–1164 (2015).

    CAS  Article  Google Scholar 

  18. Thompson, A. et al. Genetic diversity of the unicellular nitrogen-fixing cyanobacteria UCYN-A and its prymnesiophyte host. Environ. Microbiol. 16, 3238–3249 (2014).

    CAS  Article  Google Scholar 

  19. 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).

    CAS  Article  Google Scholar 

  20. LaRoche, J. & Breitbarth, E. Importance of the diazotrophs as a source of new nitrogen in the ocean. J. Sea Res. 53, 67–91 (2005).

    CAS  Article  Google Scholar 

  21. Goebel, N. L., Edwards, C. A., Carter, B. J., Achilles, K. M. & Zehr, J. P. Growth and carbon content of three different-sized diazotrophic cyanobacteria observed in the subtropical North Pacific. J. Phycol. 44, 1212–1220 (2008).

    Article  Google Scholar 

  22. Krupke, A. et al. Distribution of a consortium between unicellular algae and the N2 fixing cyanobacterium UCYN-A in the North Atlantic Ocean. Environ. Microbiol. 16, 3153–3167 (2014).

    CAS  Article  Google Scholar 

  23. Scavotto, R. E., Dziallas, C., Bentzon-Tilia, M., Riemann, L. & Moisander, P. H. Nitrogen-fixing bacteria associated with copepods in coastal waters of the North Atlantic Ocean. Environ. Microbiol. 17, 3754–3765 (2015).

    CAS  Article  Google Scholar 

  24. Wilhelm, S. W. & Suttle, C. A. Viruses and nutrient cycles in the sea—viruses play critical roles in the structure and function of aquatic food webs. Bioscience 49, 781–788 (1999).

    Article  Google Scholar 

  25. Eberl, R. & Carpenter, E. J. Association of the copepod Macrosetella gracilis with the cyanobacterium Trichodesmium spp. in the North Pacific Gyre. Marine Ecol. Progress Series 333, 205–212 (2007).

    Article  Google Scholar 

  26. Moisander, P. H. et al. Unicellular cyanobacterial distributions broaden the oceanic N2 fixation domain. Science 327, 1512–1514 (2010).

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  28. Messer, L. F., Doubell, M., Jeffries, T. C., Brown, M. V. & Seymour, J. R. Prokaryotic and diazotrophic population dynamics within a large oligotrophic inverse estuary. Aquat. Microbial Ecol. 74, 1–15 (2015).

    Article  Google Scholar 

  29. Breitbarth, E., Oschlies, A. & LaRoche, J. Physiological constraints on the global distribution of Trichodesmium-effect of temperature on diazotrophy. Biogeosciences 4, 53–61 (2007).

    CAS  Article  Google Scholar 

  30. Cabello, A. M. et al. Global distribution and vertical patterns of a prymnesiophyte–cyanobacteria obligate symbiosis. ISME J. 10, 693–706 (2015).

    Article  Google Scholar 

  31. Hansen, H. P. & Koroleff, F. in Methods of Seawater Analysis 3rd edn (eds Grasshoff, K., Kremling, K. & Ehrhardt, M. ) 159–228 (Wiley–VCH, 2007).

    Google Scholar 

  32. Holmes, R. M., Aminot, A., Kérouel, R., Hooker, B. A. & Peterson, B. J. A simple and precise method for measuring ammonium in marine and freshwater ecosystems. Can. J. Fisheries Aquat. Sci. 56, 1801–1808 (1999).

    CAS  Article  Google Scholar 

  33. Murphy, J. & Riley, J. P. A single-solution method for the determination of soluble phosphate in sea water. J. Mar. Biol.Assoc. UK 37, 9–14 (1958).

    CAS  Article  Google Scholar 

  34. Warembourg, F. Nitrogen Isotopes Techniques (eds Knowles, K. & Blackburn, T. H. ) 127–156 (Academic, 1993).

    Book  Google Scholar 

  35. Löscher, C. R. et al. Facets of diazotrophy in the oxygen minimum zone waters off Peru. ISME J. 8, 2180–2192 (2014).

    Article  Google Scholar 

  36. Langlois, R. J., Hümmer, D. & LaRoche, J. Abundances and distributions of the dominant nifH phylotypes in the Northern Atlantic Ocean. Appl. Environ. Microbiol. 74, 1922–1931 (2008).

    CAS  Article  Google Scholar 

  37. Church, M. J., Short, C. M., Jenkins, B. D., Karl, D. M. & Zehr, J. P. Temporal patterns of nitrogenase gene (nifH) expression in the oligotrophic North Pacific Ocean. Appl. Environ. Microbiol. 71, 5362–5370 (2005).

    CAS  Article  Google Scholar 

  38. Zehr, J. P. & Turner, P. J. in Methods in Microbiology Vol. 30 (ed. Paul, J. ) 271–286 (Academic, 2001).

  39. Camacho, C. et al. BLAST plus: architecture and applications. BMC Bioinformatics 10, 421 (2009).

    Article  Google Scholar 

  40. Gaby, J. C. & Buckley, D. H. A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria. Database 2014, bau001 (2014).

    Article  Google Scholar 

  41. Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European molecular biology open software suite. Trends Genet. 16, 276–277 (2000).

    CAS  Article  Google Scholar 

  42. Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222–D230 (2014).

    CAS  Article  Google Scholar 

  43. Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26, 1641–1650 (2009).

    CAS  Article  Google Scholar 

  44. Le, S. Q. & Gascuel, O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25, 1307–1320 (2008).

    CAS  Article  Google Scholar 

  45. Abascal, F., Zardoya, R. & Telford, M. J. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res. 38, W7–13 (2010).

    CAS  Article  Google Scholar 

  46. Ludwig, W. et al. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363–1371 (2004).

    CAS  Article  Google Scholar 

  47. Pernthaler, A., Pernthaler, J. & Amann, R. I. in Molecular Microbial Ecology Manual Vols 1 and 2 (eds Kowalchuk, G. A. et al.) 711–725 (Springer, 2004).

    Google Scholar 

  48. Simon, N. et al. Oligonucleotide probes for the identification of three algal groups by dot blot and fluorescent whole-cell hybridization. J. Eukaryot. Microbiol. 47, 76–84 (2000).

    CAS  Article  Google Scholar 

  49. Amann, R. I. et al. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56, 1919–1925 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Daims, H., Brühl, A., Amann, R., Schleifer, K.-H. & Wagner, M. The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst. Appl. Microbiol. 22, 434–444 (1999).

    CAS  Article  Google Scholar 

  51. Wallner, G., Amann, R. I. & Beisker, W. Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14, 136–143 (1993).

    CAS  Article  Google Scholar 

  52. Bombar, D., Heller, P., Sanchez-Baracaldo, P., Carter, B. J. & Zehr, J. P. Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria. ISME J. 8, 2530–2542 (2014).

    CAS  Article  Google Scholar 

  53. Musat, N. et al. A single-cell view on the ecophysiology of anaerobic phototrophic bacteria. Proc. Natl Acad. Sci. USA 105, 17861–17866 (2008).

    CAS  Article  Google Scholar 

  54. Polerecky, L. et al. Look@NanoSIMS—a tool for the analysis of nanoSIMS data in environmental microbiology. Environ. Microbiol. 14, 1009–1023 (2012).

    CAS  Article  Google Scholar 

  55. Verity, P. G. et al. Relationships between cell volume and the carbon and nitrogen content of marine photosynthetic nanoplankton. Limnol. Oceanogr. 37, 1434–1446 (1992).

    CAS  Article  Google Scholar 

  56. Musat, N. et al. The effect of FISH and CARD-FISH on the isotopic composition of 13C- and 15N-labeled Pseudomonas putida cells measured by nanoSIMS. Syst. Appl. Microbiol. 37, 267–276 (2014).

    CAS  Article  Google Scholar 

  57. Woebken, D. et al. Revisiting N2 fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach. ISME J. 9, 485–496 (2015).

    CAS  Article  Google Scholar 

  58. Amaral-Zettler, L. et al. in Life in the World's Oceans (ed. McIntyre, A. ) 221–245 (Wiley-Blackwell, 2010).

    Book  Google Scholar 

  59. Kopf, A. et al. The ocean sampling day consortium. GigaScience 4, 27 (2015).

    Article  Google Scholar 

  60. Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015).

    Article  Google Scholar 

  61. Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–6 (2012).

    Article  Google Scholar 

Download references

Acknowledgements

The authors thank the captain and crew of R/V Meteor M96 cruise, and G. Klockgether, A. Ellrott, C. Hoffmann, M. Philippi and L. Piepgras for cruise and technical support. The authors thank T. Ferdelman, J. Milucka and H. Marchant for discussions. This research was funded by the Max Planck Society, the Collaborative Research Center 754 (SFB754), the Fundació ‘La Caixa’, the German Academic Exchange Service (DAAD) and a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme.

Author information

Authors and Affiliations

Authors

Contributions

M.M.M.K., together with R.A.S., C.M.-P. and J.D., designed the study. C.M.-P., W.M. and J.D. performed the experiments. C.M.-P., W.M., C.R.L., J.D., G.L. and S.L. analysed samples and data. P.Y. analysed and mapped the nifH and next-generation sequencing databases. N.L., B.M.F. and J.L.R. analysed the nifH amplicon sequences and generated the phylogenetic trees. B.M.F. contributed to the CARD–FISH identification of the two different UCYN-A–haptophyte symbioses. J.L.R. contributed unpublished nifH qPCR data. C.M.-P., W.M. and M.M.M.K. wrote the manuscript with the contributions of all co-authors.

Corresponding author

Correspondence to Wiebke Mohr.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary information

Supplementary Figure 1–7, legends for Supplementary Tables 1 and 2, Supplementary Table 3, Supplementary References (PDF 13443 kb)

Supplementary Table 1

Diazotroph abundances, CO2 and N2 fixation rates and nutrient concentrations during the M96 cruise. (XLSX 26 kb)

Supplementary Table 2

Metadata of ICoMM, OSD, and TARA Oceans samples analysed in this study and the descriptive statistics from the SILVAngs pipeline. (XLS 189 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Martínez-Pérez, C., Mohr, W., Löscher, C. et al. The small unicellular diazotrophic symbiont, UCYN-A, is a key player in the marine nitrogen cycle. Nat Microbiol 1, 16163 (2016). https://doi.org/10.1038/nmicrobiol.2016.163

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1038/nmicrobiol.2016.163

Further reading

Search

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