Intriguing size distribution of the uncultured and globally widespread marine non-cyanobacterial diazotroph Gamma-A


Non-cyanobacterial diazotrophs (NCDs) have recently emerged as potentially important contributors to marine nitrogen fixation. One of the most widely distributed NCDs is Gamma-A, yet information about its autecology is still scarce and solely relies on the PCR-based detection of its nitrogenase (nifH) gene in seawater, since previous metagenomic surveys targeting free-living planktonic size fractions (<3 μm) have not detected it. Here, we explore the diversity, biogeography, size-distribution, and nitrogenase gene expression of Gamma-A across four larger planktonic size-fractions (0.8–5, 5–20, 20–180, and 180–2000 μm) using metagenomes and metatranscriptomes from the Tara Oceans. We detected a single variant of a complete Gamma-A nifH gene along with other nitrogenase-related genes (nifKDT) within a metatranscriptomic-based contig of the Marine Atlas of Tara Ocean Unigenes. Gamma-A was detected in tropical and subtropical oceanic regions across all the size-fractions. However, the highest gene and transcript abundances were found in the 0.8–5 and 5–20 μm size-fractions at the surface, whereas abundances at the deep chlorophyll maximum were lower and similar across all size-fractions. The ubiquitous presence of active Gamma-A in large planktonic size-fractions suggests a filamentous or particle-attached lifestyle and places its potential to fix nitrogen in larger planktonic compartments.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Distribution of Gamma-A-MATOU in the surface ocean.
Fig. 2: Abundance and expression of the Gamma-A-MATOU nitrogenase gene cluster across size fractions and depths.


  1. 1.

    Karl D, Michaels A, Bergman B, Capone D, Carpenter E, Letelier R, et al. Dinitrogen fixation in the world’s oceans. Biogeochemistry. 2002;57/58:47–98.

    CAS  Article  Google Scholar 

  2. 2.

    Bombar D, Paerl RW, Riemann L. Marine non-cyanobacterial diazotrophs: moving beyond molecular detection. Trends Microbiol. 2016;24:916–27.

    CAS  Article  Google Scholar 

  3. 3.

    Bird C, Martinez JM, O’Donnell AG, Wyman M. Spatial distribution and transcriptional activity of an uncultured clade of planktonic diazotrophic γ-proteobacteria in the Arabian Sea. Appl Environ Microbiol. 2005;71:2079–85.

    CAS  Article  Google Scholar 

  4. 4.

    Moisander PH, Beinart RA, Voss M, Zehr JP. Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon. ISME J. 2008;2:954–67.

    CAS  Article  Google Scholar 

  5. 5.

    Moisander PH, Serros T, Paerl RW, Beinart RA, Zehr JP. Gammaproteobacterial diazotrophs and nifH gene expression in surface waters of the South Pacific Ocean. The. ISME J. 2014;8:1962–73.

    CAS  Article  Google Scholar 

  6. 6.

    Langlois R, Großkopf T, Mills M, Takeda S, LaRoche J. Widespread distribution and expression of Gamma A (UMB), an uncultured, diazotrophic, γ-proteobacterial nifH phylotype. PLoS ONE. 2015;10:e0128912.

    Article  Google Scholar 

  7. 7.

    Zehr JP, Turner PJ. Nitrogen fixation: nitrogenase genes and gene expression. Methods Microbiol. 2001;30:271–86.

    CAS  Article  Google Scholar 

  8. 8.

    Church MJ, Short CM, Jenkins BD, Karl DM, Zehr JP. Temporal patterns of nitrogenase gene (nifH) expression in the oligotrophic North Pacific Ocean. Appl Environ Microbiol. 2005;71:5362–70.

    CAS  Article  Google Scholar 

  9. 9.

    Langlois RJ, Hümmer D, LaRoche J. Abundances and distributions of the dominant nifH phylotypes in the Northern Atlantic Ocean. Appl Environ Microbiol. 2008;74:1922–31.

    CAS  Article  Google Scholar 

  10. 10.

    Bonnet S, Rodier M, Turk-Kubo KA, Germineaud C, Menkes C, Ganachaud A, et al. Contrasted geographical distribution of N2 fixation rates and nifH phylotypes in the Coral and Solomon Seas (southwestern Pacific) during austral winter conditions. Glob Biogeochem Cycles. 2015;29:1874–92.

    CAS  Article  Google Scholar 

  11. 11.

    Gradoville MR, Bombar D, Crump BC, Letelier RM, Zehr JP, White AE. Diversity and activity of nitrogen-fixing communities across ocean basins. Limnol Oceanogr. 2017;62:1895–909.

    Article  Google Scholar 

  12. 12.

    Chen TY, Chen YL, Sheu DS, Chen HY, Lin YH, Shiozaki T. Community and abundance of heterotrophic diazotrophs in the northern South China Sea: revealing the potential importance of a new alphaproteobacterium in N2 fixation. Deep Sea Res Part I. 2019;143:104–14.

    CAS  Article  Google Scholar 

  13. 13.

    Moisander PH, Benavides M, Bonnet S, Berman-Frank I, White AE, Riemann L. Chasing after non-cyanobacterial nitrogen fixation in marine pelagic environments. Front Microbiol. 2017;8:1736.

    Article  Google Scholar 

  14. 14.

    Farnelid H, Turk-Kubo K, Ploug H, Ossolinski JE, Collins JR, Van Mooy BA, et al. Diverse diazotrophs are present on sinking particles in the North Pacific Subtropical Gyre. ISME J. 2019;13:170–82.

    Article  Google Scholar 

  15. 15.

    Cornejo-Castillo FM. Diversity, ecology and evolution of marine diazotrophic microorganisms. Barcelona: Universitat Politècnica de Catalunya; 2017.

  16. 16.

    Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, et al. Nitrogen-fixing populations of planctomycetes and proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol. 2018;3:804–13.

    CAS  Article  Google Scholar 

  17. 17.

    Benavides M, Moisander PH, Daley MC, Bode A, Aristegui J. Longitudinal variability of diazotroph abundances in the subtropical North Atlantic Ocean. J Plankton Res. 2016;38:662–72.

    CAS  Article  Google Scholar 

  18. 18.

    Gradoville MR, Farnelid H, White AE, Turk-Kubo KA, Stewart B, Ribalet F, et al. Latitudinal constraints on the abundance and activity of the cyanobacterium UCYN-A and other marine diazotrophs in the North Pacific. Limnol Oceanogr. 2020.

  19. 19.

    Scavotto RE, Dziallas C, Bentzon-Tilia M, Riemann L, Moisander PH. Nitrogen-fixing bacteria associated with copepods in coastal waters of the North Atlantic Ocean. Environ Microbiol. 2015;17:3754–65.

    CAS  Article  Google Scholar 

  20. 20.

    Carradec Q, Pelletier E, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, et al. A global ocean atlas of eukaryotic genes. Nat Commun. 2018;9:1–3.

    CAS  Article  Google Scholar 

  21. 21.

    Karl DM, Church MJ, Dore JE, Letelier RM, Mahaffey C. Predictable and efficient carbon sequestration in the North Pacific Ocean supported by symbiotic nitrogen fixation. Proc Natl Acad Sci. 2012;109:1842–9.

    CAS  Article  Google Scholar 

  22. 22.

    Pedersen JN, Bombar D, Paerl RW, Riemann L. Diazotrophs and N2-fixation associated with particles in coastal estuarine waters. Front Microbiol. 2018;9:2759.

    Article  Google Scholar 

  23. 23.

    Ploug H, Kühl M, Buchholz-Cleven B, Jørgensen BB. Anoxic aggregates-an ephemeral phenomenon in the pelagic environment? Aquat Microb Ecol. 1997;13:285–94.

    Article  Google Scholar 

  24. 24.

    Ploug H. Small-scale oxygen fluxes and remineralization in sinking aggregates. Limnol Oceanogr. 2001;46:1624–31.

    CAS  Article  Google Scholar 

  25. 25.

    Bentzon-Tilia M, Severin I, Hansen LH, Riemann L. Genomics and ecophysiology of heterotrophic nitrogen-fixing bacteria isolated from estuarine surface water. MBio. 2015;6:e00929–15.

    CAS  Article  Google Scholar 

  26. 26.

    Bergman B, Sandh G, Lin S, Larsson J, Carpenter EJ. Trichodesmium—a widespread marine cyanobacterium with unusual nitrogen fixation properties. FEMS Microbiol Rev. 2013;37:286–302.

    CAS  Article  Google Scholar 

  27. 27.

    Moraru C, Lam P, Fuchs BM, Kuypers MM, Amann R. GeneFISH—an in situ technique for linking gene presence and cell identity in environmental microorganisms. Environ Microbiol. 2010;12:3057–73.

    CAS  Article  Google Scholar 

  28. 28.

    Batani G, Bayer K, Böge J, Hentschel U, Thomas T. Fluorescence in situ hybridization (FISH) and cell sorting of living bacteria. Sci Rep. 2019;9:1–3.

    Article  Google Scholar 

Download references


We specially thank Ana M. Cabello, Rosie Gradoville, Katie Harding, Marine Landa, Kendra Turk-Kubo and Clara Ruiz-Gonzalez for their helpful comments and suggestions on the manuscript. JPZ was supported by Simons Collaboration on Ocean Processes and Ecology (SCOPE, grant 329108). FMC-C was supported by a Marie Curie Individual Global Fellowship—Horizon 2020 European Framework Programme (UCYN2PLAST, grant 749380).

Author information



Corresponding authors

Correspondence to Francisco M. Cornejo-Castillo or Jonathan P. Zehr.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

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

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Cornejo-Castillo, F.M., Zehr, J.P. Intriguing size distribution of the uncultured and globally widespread marine non-cyanobacterial diazotroph Gamma-A. ISME J (2020).

Download citation