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 oceans3–6. 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
Subscribe to Journal
Get full journal access for 1 year
only $9.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Get time limited or full article access on ReadCube.
All prices are NET prices.
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).
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)
Zehr, J. P. et al. Unicellular cyanobacteria fix N2 in the subtropical North Pacific Ocean. Nature 412, 635–638 (2001).
Montoya, J. P. et al. High rates of N2 fixation by unicellular diazotrophs in the oligotrophic Pacific Ocean. Nature 430, 1027–1032 (2004).
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).
Grosskopf, T. et al. Doubling of marine dinitrogen-fixation rates based on direct measurements. Nature 488, 361–364 (2012).
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).
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).
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).
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).
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).
Thompson, A. W. et al. Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga. Science 337, 1546–1550 (2012).
Zehr, J. P. et al. Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II. Science 322, 1110–1112 (2008).
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).
Krupke, A. et al. In situ identification and N2 and C fixation rates of uncultivated cyanobacteria populations. System. Appl. Microbiol. 36, 259–271 (2013).
Mohr, W., Großkopf, T., Wallace, D. W. & LaRoche, J. Methodological underestimation of oceanic nitrogen fixation rates. PLoS ONE 5, e12583 (2010).
Zehr, J. P. How single cells work together. Science 349, 1163–1164 (2015).
Thompson, A. et al. Genetic diversity of the unicellular nitrogen-fixing cyanobacteria UCYN-A and its prymnesiophyte host. Environ. Microbiol. 16, 3238–3249 (2014).
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).
LaRoche, J. & Breitbarth, E. Importance of the diazotrophs as a source of new nitrogen in the ocean. J. Sea Res. 53, 67–91 (2005).
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).
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).
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).
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).
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).
Moisander, P. H. et al. Unicellular cyanobacterial distributions broaden the oceanic N2 fixation domain. Science 327, 1512–1514 (2010).
Bentzon-Tilia, M. et al. Significant N2 fixation by heterotrophs, photoheterotrophs and heterocystous cyanobacteria in two temperate estuaries. ISME J. 9, 273–285 (2015).
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).
Breitbarth, E., Oschlies, A. & LaRoche, J. Physiological constraints on the global distribution of Trichodesmium-effect of temperature on diazotrophy. Biogeosciences 4, 53–61 (2007).
Cabello, A. M. et al. Global distribution and vertical patterns of a prymnesiophyte–cyanobacteria obligate symbiosis. ISME J. 10, 693–706 (2015).
Hansen, H. P. & Koroleff, F. in Methods of Seawater Analysis 3rd edn (eds Grasshoff, K., Kremling, K. & Ehrhardt, M. ) 159–228 (Wiley–VCH, 2007).
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).
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).
Warembourg, F. Nitrogen Isotopes Techniques (eds Knowles, K. & Blackburn, T. H. ) 127–156 (Academic, 1993).
Löscher, C. R. et al. Facets of diazotrophy in the oxygen minimum zone waters off Peru. ISME J. 8, 2180–2192 (2014).
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).
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).
Zehr, J. P. & Turner, P. J. in Methods in Microbiology Vol. 30 (ed. Paul, J. ) 271–286 (Academic, 2001).
Camacho, C. et al. BLAST plus: architecture and applications. BMC Bioinformatics 10, 421 (2009).
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).
Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European molecular biology open software suite. Trends Genet. 16, 276–277 (2000).
Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222–D230 (2014).
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).
Le, S. Q. & Gascuel, O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25, 1307–1320 (2008).
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).
Ludwig, W. et al. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363–1371 (2004).
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).
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).
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).
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).
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).
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).
Musat, N. et al. A single-cell view on the ecophysiology of anaerobic phototrophic bacteria. Proc. Natl Acad. Sci. USA 105, 17861–17866 (2008).
Polerecky, L. et al. Look@NanoSIMS—a tool for the analysis of nanoSIMS data in environmental microbiology. Environ. Microbiol. 14, 1009–1023 (2012).
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).
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).
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).
Amaral-Zettler, L. et al. in Life in the World's Oceans (ed. McIntyre, A. ) 221–245 (Wiley-Blackwell, 2010).
Kopf, A. et al. The ocean sampling day consortium. GigaScience 4, 27 (2015).
Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015).
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).
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.
The authors declare no competing financial interests.
Supplementary Figure 1–7, legends for Supplementary Tables 1 and 2, Supplementary Table 3, Supplementary References (PDF 13443 kb)
Diazotroph abundances, CO2 and N2 fixation rates and nutrient concentrations during the M96 cruise. (XLSX 26 kb)
Metadata of ICoMM, OSD, and TARA Oceans samples analysed in this study and the descriptive statistics from the SILVAngs pipeline. (XLS 189 kb)
About this article
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
Nature Reviews Microbiology (2022)
Niche partitioning by photosynthetic plankton as a driver of CO2-fixation across the oligotrophic South Pacific Subtropical Ocean
The ISME Journal (2022)
Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean
The ISME Journal (2022)
ISME Communications (2022)
The ISME Journal (2022)