Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera

  • Nature Microbiology 2, Article number: 17118 (2017)
  • doi:10.1038/nmicrobiol.2017.118
  • Download Citation
Published online:


The temporal dynamics of phytoplankton growth and activity have large impacts on fluxes of matter and energy, yet obtaining in situ metabolic measurements of sufficient resolution for even dominant microorganisms remains a considerable challenge. We performed Lagrangian diel sampling with synoptic measurements of population abundances, dinitrogen (N2) fixation, mortality, productivity, export and transcription in a bloom of Crocosphaera over eight days in the North Pacific Subtropical Gyre (NPSG). Quantitative transcriptomic analyses revealed clear diel oscillations in transcript abundances for 34% of Crocosphaera genes identified, reflecting a systematic progression of gene expression in diverse metabolic pathways. Significant time-lagged correspondence was evident between nifH transcript abundance and maximal N2 fixation, as well as sepF transcript abundance and cell division, demonstrating the utility of transcriptomics to predict the occurrence and timing of physiological and biogeochemical processes in natural populations. Indirect estimates of carbon fixation by Crocosphaera were equivalent to 11% of net community production, suggesting that under bloom conditions this diazotroph has a considerable impact on the wider carbon cycle. Our cross-scale synthesis of molecular, population and community-wide data underscores the tightly coordinated in situ metabolism of the keystone N2-fixing cyanobacterium Crocosphaera, as well as the broader ecosystem-wide implications of its activities.

  • Subscribe to Nature Microbiology for full access:



Additional access options:

Already a subscriber?  Log in  now or  Register  for online access.


  1. 1.

    , , & Prochlorococcus: the structure and function of collective diversity. Nat. Rev. Microbiol. 13, 13–27 (2015).

  2. 2.

    & in Methods in Enzymology Vol. 167 (eds Packer, L. & Glazer, A. N) 100–105 (Academic, 1988).

  3. 3.

    et al. Whole genome comparison of six Crocosphaera watsonii strains with differing phenotypes. J. Phycol. 49, 786–801 (2013).

  4. 4.

    , , , & Low genomic diversity in tropical oceanic N2-fixing cyanobacteria. Proc. Natl Acad. Sci. USA 104, 17807–17812 (2007).

  5. 5.

    , & Diel variation of molybdenum and iron in marine diazotrophic cyanobacteria. Limnol. Oceanogr. 49, 978–990 (2004).

  6. 6.

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

  7. 7.

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

  8. 8.

    et al. Distribution of nano-sized Cyanobacteria in the western and central Pacific Ocean. Aquat. Microbial Ecol. 59, 273–282 (2010).

  9. 9.

    et al. Ecogenomic sensor reveals controls on N2-fixing microorganisms in the North Pacific Ocean. ISME J. 8, 1175–1185 (2014).

  10. 10.

    et al. Phenotypic and genotypic characterization of multiple strains of the diazotrophic cyanobacterium, Crocosphaera watsonii, isolated from the open ocean. Environ. Microbiol. 11, 338–348 (2009).

  11. 11.

    , & Diel rhythm of nitrogen and carbon metabolism in the unicellular, diazotrophic cyanobacterium Crocosphaera watsonii WH8501. Environ. Microbiol. 12, 412–421 (2010).

  12. 12.

    et al. Iron conservation by reduction of metalloenzyme inventories in the marine diazotroph Crocosphaera watsonii. Proc. Natl Acad. Sci. USA 108, 2184–2189 (2011).

  13. 13.

    et al. Physical forcing of nitrogen fixation and diazotroph community structure in the North Pacific subtropical gyre. Global Biogeochem. Cycles 23, GB2020 (2009).

  14. 14.

    , , & Two subpopulations of Crocosphaera watsonii have distinct distributions in the North and South Pacific. Environ. Microbiol. 18, 514–524 (2016).

  15. 15.

    , , & Two strains of Crocosphaera watsonii with highly conserved genomes are distinguished by strain-specific features. Front. Microbiol. 2, 261 (2011).

  16. 16.

    , , & Constitutive extracellular polysaccharide (EPS) production by specific isolates of Crocosphaera watsonii. Front. Microbiol. 2, 229 (2011).

  17. 17.

    & WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9, 559 (2008).

  18. 18.

    et al. Microbial community transcriptional networks are conserved in three domains at ocean basin scales. Proc. Natl Acad. Sci. USA 112, 5443–5448 (2015).

  19. 19.

    , , & Genome-wide analysis of diel gene expression in the unicellular N2-fixing cyanobacterium Crocosphaera watsonii WH8501. ISME J. 4, 621–632 (2010).

  20. 20.

    et al. Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages. Science 345, 207–212 (2014).

  21. 21.

    et al. Pattern and synchrony of gene expression among sympatric marine microbial populations. Proc. Natl Acad. Sci. USA 110, E488–E497 (2013).

  22. 22.

    et al. Global transcriptomic analysis of Cyanothece 51142 reveals robust diurnal oscillation of central metabolic processes. Proc. Natl Acad. Sci. USA 105, 6156–6161 (2008).

  23. 23.

    et al. Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light–dark cycle. BMC Genomics 15, 1185 (2014).

  24. 24.

    , & SeaFlow: a novel underway flow-cytometer for continuous observations of phytoplankton in the ocean. Limnol. Oceanogr. Methods 9, 466–477 (2011).

  25. 25.

    et al. Structural and genetic analyses reveal the protein SepF as a new membrane anchor for the Z ring. Proc. Natl Acad. Sci. USA 110, E4601–E4610 (2013).

  26. 26.

    et al. Growth and carbon content of three different-sized diazotrophic cyanobacteria observed in the subtropical North Pacific. J. Phycol. 44, 1212–1220 (2008).

  27. 27.

    Size-dependent growth rates in eukaryotic and prokaryotic algae exemplified by green algae and cyanobacteria: comparisons between unicells and colonial growth forms. J. Plankton Res. 28, 489–498 (2006).

  28. 28.

    , , , & Temporal patterns of nitrogenase gene (nifH) expression in the oligotrophic North Pacific Ocean. Appl. Environ. Microbiol. 71, 5362–5370 (2005).

  29. 29.

    , & Dinitrogen fixation and release of ammonium and dissolved organic nitrogen by Trichodesmium IMS101. Aquat. Microbial Ecol. 37, 85–94 (2004).

  30. 30.

    et al. Hydrogen cycling by the unicellular marine diazotroph Crocosphaera watsonii strain WH8501. Appl. Environ. Microbiol. 20, 6797–6803 (2010).

  31. 31.

    , & A quantitative analysis of the direct and indirect costs of nitrogen fixation: a model based on Azotobacter vinelandii. ISME J. 11, 166–175 (2016).

  32. 32.

    et al. Temporal variability in dinitrogen fixation and particulate nitrogen export at Station ALOHA. Limnol. Oceanogr. 62, 200–216 (2017).

  33. 33.

    & In vitro and in situ gross primary production and net community production in the North Pacific Subtropical Gyre using labeled and natural abundance isotopes of dissolved O2. Global Biogeochem. Cycles 19, GB3009 (2005).

  34. 34.

    et al. Biological production in the NE Pacific and its influence on air–sea CO2 flux: evidence from dissolved oxygen isotopes and O2/Ar. J. Geophys. Res. 117, C05022 (2012).

  35. 35.

    & Photosynthetic picoplankton community structure in the subtropical North Pacific Ocean near Hawaii (Station ALOHA). Deep-Sea Res. I 40, 2043–2060 (1993).

  36. 36.

    , & Temporal and vertical variability in picophytoplankton primary productivity in the North Pacific Subtropical Gyre. Mar. Ecol. Prog. Ser. 562, 1–18 (2016).

  37. 37.

    Annual net community production and the biological carbon flux in the ocean. Global Biogeochem. Cycles 28, 14–28 (2014).

  38. 38.

    et al. Marine phytoplankton temperature versus growth responses from polar to tropical waters—outcome of a scientific community-wide study. PLoS ONE 8, e63091 (2013).

  39. 39.

    et al. Differing responses of marine N2 fixers to warming and consequences for future diazotroph community structure. Aquat. Microb. Ecol. 72, 33–46 (2014).

  40. 40.

    , , , & Nitrogen fixation in the western equatorial Pacific: rates, diazotrophic cyanobacterial size class distribution, and biogeochemical significance. Global Biogeochem. Cycles 23, GB3012 (2009).

  41. 41.

    et al. In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii. ISME J. 3, 618–631 (2009).

  42. 42.

    et al. Daily to decadal variability of size-fractionated iron and iron-binding ligands at the Hawaii Ocean Time-series Station ALOHA. Geochim. Cosmochim. Acta 171, 303–324 (2015).

  43. 43.

    et al. Short-term variability in euphotic zone biogeochemistry and primary productivity at Station ALOHA: a case study of summer 2012. Global Biogeochem. Cycles 29, 1145–1164 (2015).

  44. 44.

    , , & Transcriptome and proteome dynamics of a light–dark synchronized bacterial cell cycle. PLoS ONE 7, e43432 (2012).

  45. 45.

    , , & Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon. ISME J. 2, 954–967 (2008).

  46. 46.

    et al. Abundance and distribution of major groups of diazotrophic cyanobacteria and their potential contribution to N2 fixation in the tropical Atlantic Ocean. Environ. Microbiol. 12, 3272–3289 (2010).

  47. 47.

    , , & Comparative assessment of nitrogen fixation methodologies conducted in the oligotrophic North Pacific Ocean. Appl. Environ. Microbiol. 78, 6491–6498 (2012).

  48. 48.

    , , , & Metabolic balance in the mixed layer of the oligotrophic North Pacific Ocean from diel changes in O2/Ar saturation ratios. Geophys. Res. Lett. 42, 3421–3430 (2015).

  49. 49.

    , & A refined dilution technique for measuring the community grazing impact of microzooplankton, with experimental tests in the central equatorial Pacific. Mar. Ecol. Prog. Ser. 120, 53–63 (1995).

  50. 50.

    , , , & Quantitative transcriptomics reveals the growth- and nutrient-dependent response of a streamlined marine methylotroph to methanol and naturally occurring dissolved organic matter. mBio 7, e01279–16 (2016).

  51. 51.

    , , , & Adaptive seeds tame genomic sequence comparison. Genome Res. 21, 487–493 (2011).

  52. 52.

    & Detecting rhythms in time series with RAIN. J. Biol. Rhythms 29, 391–400 (2014).

  53. 53.

    & Carbon to volume relationships for dinoflagellates, diatoms, and other protist plankton. Limnol. Oceanogr. 45, 569–579 (2000).

  54. 54.

    Photosynthetic quotients, new production and net community production in the open ocean. Deep-Sea Res. 38, 143–167 (1991).

  55. 55.

    & Eigengene networks for studying the relationships between co-expression modules. BMC Syst. Biol. 1, 54 (2007).

Download references


The dataset presented here resulted from the efforts of many scientists who contributed to the success of the 2015 expedition. The authors thank T. Clemente for cruise leadership of KOK1507, J. Collins, J. Ossolinski and B. Van Mooy for net trap samples used for δ15N isotope analysis and E. Boyle for support of the dissolved iron measurements. For assistance with field and laboratory work, the authors thank the operational staff of the Simons Collaboration on Ocean Processes and Ecology (SCOPE), D. Böttjer, P. Den Uyl, L. Jensen, N. Lanning, M. Linney and A. Nelson. This work was supported by grants from the Simons Foundation (no. 329108 to D.M.K. and E.F.D.), the Gordon and Betty Moore Foundation (no. 3777 to E.F.D., no. 3794 to D.M.K., no. 3776 to E.V.A.) and the Balzan Prize for Oceanography (to D.M.K.). In addition, the authors acknowledge the National Science Foundation for support of the HOT programme (OCE1260164 to M.J.C. and D.M.K.) and the Center for Microbial Oceanography: Research and Education (C-MORE; EF0424599 to D.M.K. and E.F.D.). This work is a contribution of SCOPE and C-MORE.

Author information

Author notes

    • Samuel T. Wilson
    •  & Frank O. Aylward

    These authors contributed equally to this work

    • Frank O. Aylward
    •  & Matthew J. Church

    Present addresses: Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA (F.O.A.); Flathead Lake Biological Station, University of Montana, Polson, Montana 59860, USA (M.J.C.).


  1. Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawaii, Honolulu, Hawaii 96822, USA

    • Samuel T. Wilson
    • , Frank O. Aylward
    • , Benedetto Barone
    • , John R. Casey
    • , John M. Eppley
    • , Sara Ferrón
    • , Anna E. Romano
    • , Alice Vislova
    • , Matthew J. Church
    • , David M. Karl
    •  & Edward F. DeLong
  2. School of Oceanography, University of Washington, Seattle, Washington 98195, USA

    • Francois Ribalet
    •  & E. Virginia Armbrust
  3. Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA

    • Paige E. Connell
    •  & David A. Caron
  4. Department of Oceanography, Texas A&M University, College Station, Texas 77843, USA

    • Jessica N. Fitzsimmons
  5. School of Ocean Science and Technology, University of Southern Mississippi, Stennis Space Center, Mississippi 39529, USA

    • Christopher T. Hayes
  6. Ocean Sciences Department, University of California, Santa Cruz, California 95064, USA

    • Kendra A. Turk-Kubo
    •  & Jonathan P. Zehr


  1. Search for Samuel T. Wilson in:

  2. Search for Frank O. Aylward in:

  3. Search for Francois Ribalet in:

  4. Search for Benedetto Barone in:

  5. Search for John R. Casey in:

  6. Search for Paige E. Connell in:

  7. Search for John M. Eppley in:

  8. Search for Sara Ferrón in:

  9. Search for Jessica N. Fitzsimmons in:

  10. Search for Christopher T. Hayes in:

  11. Search for Anna E. Romano in:

  12. Search for Kendra A. Turk-Kubo in:

  13. Search for Alice Vislova in:

  14. Search for E. Virginia Armbrust in:

  15. Search for David A. Caron in:

  16. Search for Matthew J. Church in:

  17. Search for Jonathan P. Zehr in:

  18. Search for David M. Karl in:

  19. Search for Edward F. DeLong in:


All authors contributed to the design of the study. S.T.W. and D.M.K. measured nitrogen fixation and provided the water-column hydrography and biogeochemical data. F.O.A., A.E.R., A.V., J.M.E. and E.F.D. sampled, prepared and analysed the metatranscriptomic and metagenomic data. F.R. and E.V.A. conducted the underway enumeration of Crocosphaera abundances. B.B. and F.R. quantified the abundances of larger size Crocosphaera. D.A.C. and P.E.C. performed the microscopy analyses and dilution grazing experiments. S.F. and J.R.C. conducted the productivity measurements. M.J.C. provided the time-series nifH abundances and measured particle export. J.R.C. and B.B. collected and analysed the isotopic composition of sinking particles. K.A.T.-K. and J.P.Z. analysed the nifH abundances. C.T.H. and J.N.F. measured dissolved iron concentrations. S.T.W., F.O.A., D.M.K. and E.F.D. wrote the manuscript with contributions from all coauthors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Edward F. DeLong.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    Supplementary Methods, Table and Figures.

Excel files

  1. 1.

    Supplementary Dataset 1

    Sequencing statistics.

  2. 2.

    Supplementary Dataset 2

    Annotation information and statistical test results for the genes analysed in this study.

  3. 3.

    Supplementary Dataset 3

    Normalization coefficients.

Text files

  1. 1.

    Supplementary Dataset 4

    Sequence data.