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Transcriptional patterns identify resource controls on the diazotroph Trichodesmium in the Atlantic and Pacific oceans

The ISME Journalvolume 12pages14861495 (2018) | Download Citation


The N2-fixing cyanobacterium Trichodesmium is intensely studied because of the control this organism exerts over the cycling of carbon and nitrogen in the low nutrient ocean gyres. Although iron (Fe) and phosphorus (P) bioavailability are thought to be major drivers of Trichodesmium distributions and activities, identifying resource controls on Trichodesmium is challenging, as Fe and P are often organically complexed and their bioavailability to a single species in a mixed community is difficult to constrain. Further, Fe and P geochemistries are linked through the activities of metalloenzymes, such as the alkaline phosphatases (APs) PhoX and PhoA, which are used by microbes to access dissolved organic P (DOP). Here we identified significant correlations between Trichodesmium-specific transcriptional patterns in the North Atlantic (NASG) and North Pacific Subtropical Gyres (NPSG) and patterns in Fe and P biogeochemistry, with the relative enrichment of Fe stress markers in the NPSG, and P stress markers in the NASG. We also observed the differential enrichment of Fe-requiring PhoX transcripts in the NASG and Fe-insensitive PhoA transcripts in the NPSG, suggesting that metalloenzyme switching may be used to mitigate Fe limitation of DOP metabolism in Trichodesmium. This trait may underpin Trichodesmium success across disparate ecosystems.

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  1. 1.

    Marconi D, Sigman DM, Casciotti KL, Campbell EC, Alexandra Weigand M, Fawcett SE, et al. Tropical dominance of N2 fixation in the North Atlantic Ocean. Glob Biogeochem Cycles. 2017;31:1608–23.

  2. 2.

    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.

  3. 3.

    Arrigo KR. Marine microorganisms and global nutrient cycles. Nature. 2005;437:343–8.

  4. 4.

    Mulholland MR. The fate of nitrogen fixed by diazotrophs in the ocean. Biogeosciences. 2007;4:37–51.

  5. 5.

    Sohm JA, Webb EA, Capone DG. Emerging patterns of marine nitrogen fixation. Nat Rev Microbiol. 2011;9:499–508.

  6. 6.

    Tyrrell T. The relative influences of nitrogen and phosohorus on oceanic primary production. Nature. 1999;400:525–31.

  7. 7.

    Böttjer D, Dore JE, Karl DM, Letelier RM, Mahaffey C, Wilson ST, et al. Temporal variability of nitrogen fixation and particulate nitrogen export at Station ALOHA. Limnol Oceanogr. 2017;62:200–16.

  8. 8.

    Capone DG, Burns JA, Montoya JP, Subramaniam A, Mahaffey C, Gunderson T, et al. Nitrogen fixation by Trichodesmium spp.: an important source of new nitrogen to the tropical and subtropical North Atlantic Ocean. Glob Biogeochem Cycles. 2005;19:GB2024.

  9. 9.

    Karl D, Letelier R, Tupas L, Dore J, Christian J, Hebel D. The role of nitrogen fixation in biogeochemical cycling in the subtropical North Pacific Ocean. Nature. 1997;388:533–8.

  10. 10.

    Van Mooy BAS, Krupke A, Dyhrman ST, Fredricks HF, Frischkorn KR, Ossolinski JE, et al. Major role of planktonic phosphate reduction in the marine phosphorus redox cycle. Science. 2015;348:783–5.

  11. 11.

    Karl DM, Beversdorf L, Björkman KM, Church MJ, Martinez A, Delong EF. Aerobic production of methane in the sea. Nat Geosci. 2008;1:473–8.

  12. 12.

    Repeta DJ, Ferrón S, Sosa OA, Johnson CG, Repeta LD, Acker M, et al. Marine methane paradox explained by bacterial degradation of dissolved organic matter. Nat Geosci. 2016;9:884–7.

  13. 13.

    Moore JK, Doney SC, Lindsay K. Upper ocean ecosystem dynamics and iron cycling in a global three-dimensional model. Glob Biogeochem Cycles. 2004;18:1–21.

  14. 14.

    Berman-Frank I, Cullen J, Shaked Y, Sherrell R, Falkowski PG. Iron availability, cellular iron quotas, and nitrogen fixation in Trichodesmium. Limnol Oceanogr. 2001;46:1249–60.

  15. 15.

    Rouco M, Haley ST, Alexander H, Wilson ST, Karl DM, Dyhrman ST. Variable depth distribution of Trichodesmium clades in the North Pacific Ocean. Environ Microbiol Rep. 2016a;8:1058–66.

  16. 16.

    Rouco M, Joy-Warren H, McGillicuddy DJ, Waterbury JB, Dyhrman ST. Trichodesmium sp. clade distributions in the western North Atlantic Ocean. Limnol Oceanogr. 2014;59:1899–909.

  17. 17.

    Fitzsimmons JN, Hayes CT, Al-Subiai SN, Zhang R, Morton P, Weisend R, 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. 2015;171:303–24.

  18. 18.

    Saito MA, Goepfert TJ, Ritt JT. Some thoughts on the concept of colimitation: three definitions and the importance of bioavailability. Limnol Oceanogr. 2008;53:276–90.

  19. 19.

    Landolfi A, Koeve W, Dietze H, Kähler P, Oschlies A. A new perspective on environmental controls of marine nitrogen fixation. Geophys Res Lett. 2015;42:4482–9.

  20. 20.

    Snow JT, Schlosser C, Woodward EMS, Mills MM, Achterberg EP, Mahaffey C, et al. Environmental controls on the biogeography of diazotrophy and Trichodesmium in the Atlantic Ocean. Glob Biogeochem Cycles. 2015;29:865–84.

  21. 21.

    Ward BA, Dutkiewicz S, Mark Moore C, Follows MJ. Iron, phosphorus, and nitrogen supply ratios define the biogeography of nitrogen fixation. Limnol Oceanogr. 2013;58:2059–75.

  22. 22.

    Van Mooy BAS, Fredricks HF, Pedler BE, Dyhrman ST, Karl DM, Koblízek M, et al. Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity. Nature. 2009;458:69–72.

  23. 23.

    Morrissey J, Bowler C. Iron utilization in marine cyanobacteria and eukaryotic algae. Front Microbiol. 2012;3:1–13.

  24. 24.

    Roe KL, Barbeau K. Uptake mechanisms for inorganic iron and ferric citrate in Trichodesmium erythraeum IMS101. Metallomics. 2014;6:2042–51.

  25. 25.

    Polyviou D, Hitchcock A, Baylay AJ, Moore CM, Bibby TS. Phosphite utilization by the globally important marine diazotroph Trichodesmium. Environ Microbiol Rep. 2015;7:824–30.

  26. 26.

    Dyhrman ST, Chappell PD, Haley ST, Moffett JW, Orchard ED, Waterbury JB, et al. Phosphonate utilization by the globally important marine diazotroph Trichodesmium. Nature. 2006;439:68–71.

  27. 27.

    Dyhrman ST, Webb EA, Anderson DM, Moffett JW, Waterbury JB. Cell-specific detection of phosphorus stress in Trichodesmium from the Western North Atlantic. Limnol Oceanogr. 2002;47:1832–6.

  28. 28.

    Orchard ED, Ammerman JW, Lomas MW, Dyhrman ST. Dissolved inorganic and organic phosphorus uptake in Trichodesmium and the microbial community: the importance of phosphorus ester in the Sargasso Sea. Limnol Oceanogr. 2010;55:1390–9.

  29. 29.

    Orchard ED, Webb EA, Dyhrman ST. Molecular analysis of the phosphorus starvation response in Trichodesmium spp. Environ Microbiol. 2009;11:2400–11.

  30. 30.

    Sebastian M, Ammerman JW. The alkaline phosphatase PhoX is more widely distributed in marine bacteria than the classical PhoA. ISME J. 2009;3:563–72.

  31. 31.

    Wu J-R, Shien J-H, Shieh HK, Hu C-C, Gong S-R, Chen L-Y, et al. Cloning of the gene and characterization of the enzymatic properties of the monomeric alkaline phosphatase (PhoX) from Pasteurella multocida strain X-73. FEMS Microbiol Lett. 2007;267:113–20.

  32. 32.

    Yong SC, Roversi P, Lillington J, Rodriguez F, Krehenbrink M, Zeldin OB, et al. A complex iron-calcium cofactor catalyzing phosphotransfer chemistry. Science. 2014;345:1170–3.

  33. 33.

    Browning TJ, Achterberg EP, Yong JC, Rapp I, Utermann C, Engel A, et al. Iron limitation of microbial phosphorus acquisition in the tropical North Atlantic. Nat Commun. 2017;8:15465.

  34. 34.

    Frischkorn KR, Rouco M, Van Mooy BAS, Dyhrman ST. Epibionts dominate metabolic functional potential of Trichodesmium colonies from the oligotrophic ocean. ISME J. 2017;11:2090–101.

  35. 35.

    Hmelo LR, Van Mooy BAS, Mincer T. Characterization of bacterial epibionts on the cyanobacterium Trichodesmium. Aquat Microb Ecol. 2012;67:1–14.

  36. 36.

    Rouco M, Haley ST, Dyhrman ST. Microbial diversity within the Trichodesmium holobiont. Environ Microbiol. 2016b;18:5151–60.

  37. 37.

    Van Mooy BA, Hmelo LR, Sofen LE, Campagna SR, May AL, Dyhrman ST, et al. Quorum sensing control of phosphorus acquisition in Trichodesmium consortia. ISME J. 2012;6:422–9.

  38. 38.

    Chappell PD, Webb EA. A molecular assessment of the iron stress response in the two phylogenetic clades of Trichodesmium. Environ Microbiol. 2010;12:13–27.

  39. 39.

    Martínez A, Osburne MS, Sharma AK, DeLong EF, Chisholm SW. Phosphite utilization by the marine picocyanobacterium Prochlorococcus MIT9301. Environ Microbiol. 2012;14:1363–77.

  40. 40.

    Webb E, Moffett J, Waterbury J. Iron stress in open-ocean cyanobacteria (Synechococcus, Trichodesmium, and Crocosphaera spp.): identification of the IdiA protein. Appl Environ Microbiol. 2001;67:5444–52.

  41. 41.

    Saito MA, McIlvin MR, Moran DM, Goepfert TJ, DiTullio GR, Post AF, et al. Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers. Science. 2014;345:1173–7.

  42. 42.

    El-Shehawy R, Lugomela C, Ernst A, Bergman B. Diurnal expression of hetR and diazocyte development in the filamentous non-heterocystous cyanobacterium Trichodesmium erythraeum. Microbiology. 2003;149:1139–46.

  43. 43.

    Rimmelin P, Moutin T. Re-examination of the MAGIC method to determine low orthophosphate concentration in seawater. Anal Chim Acta. 2005;548:174–82.

  44. 44.

    Chappell PD, Moffett JW, Hynes AM, Webb EA. Molecular evidence of iron limitation and availability in the global diazotroph Trichodesmium. ISME J. 2012;6:1728–39.

  45. 45.

    Bruland KW, Orians KJ, Cowen JP. Reactive trace metals in the stratified central North Pacific. Geochim Cosmochim Acta. 1994;58:3171–82.

  46. 46.

    Diaz JM, Björkman KM, Haley ST, Ingall ED, Karl DM, Longo AF, et al. Polyphosphate dynamics at Station ALOHA, North Pacific subtropical gyre. Limnol Oceanogr. 2016;61:227–39.

  47. 47.

    Jakuba RW, Moffett JW, Dyhrman ST. Evidence for the linked biogeochemical cycling of zinc, cobalt, and phosphorus in the western North Atltic Ocean. Glob Biogeochem Cycles. 2008;22:GB4012.

  48. 48.

    Reinthaler T, Sintes E, Herndl GJ. Dissolved organic matter and bacterial production and respiration in the sea-surface microlayer of the open Atlantic and the western Mediterranean Sea. Limnol Oceanogr. 2008;53:122–36.

  49. 49.

    Bergquist BA, Boyle EA. Dissolved iron in the tropical and subtropical Atlantic Ocean. Glob Biogeochem Cycles. 2006;20:GB1015.

  50. 50.

    Rue EL, Bruland KW. Complexation of iron(III) by natural organic ligands in the Central North Pacific as determined by a new competitive ligand equilibration/adsorptive cathodic stripping voltammetric method. Mar Chem. 1995;50:117–38.

  51. 51.

    Sañudo-Wilhelmy SA, Kustka AB, Gobler CJ, Hutchins DA, Yang M, Lwiza K, et al. Phosphorus limitation of nitrogen fixation by Trichodesmium in the central Atlantic Ocean. Nature. 2001;411:66–9.

  52. 52.

    Sohm J, Capone D. Phosphorus dynamics of the tropical and subtropical north Atlantic: Trichodesmium spp. versus bulk plankton. Mar Ecol Prog Ser. 2006;317:21–8.

  53. 53.

    Wilson ST, Barone B, Ascani F, Bidigare RR, Church MJ, Del Valle DA, et al. Short-term variability in euphotic zone biogeochemistry and primary productivity at Station ALOHA: a case study of summer 2012. Glob Biogeochem Cycles. 2015;29:1145–64.

  54. 54.

    Wu J, Boyle E. Iron in the Sargasso Sea: implications for the processes controlling dissolved Fe distribution in the ocean. Glob Biogeochem Cycles. 2002;16:1–8.

  55. 55.

    Wu J, Sunda W, Boyle EA, Karl DM. Phosphate depletion in the western North Atlantic. Ocean Sci. 2000;289:759–62.

  56. 56.

    Brown MT, Landing WM, Measures CI. Dissolved and particulate Fe in the western and central North Pacific: results from the 2002 IOC cruise. Geochem, Geophys Geosystems. 2005;6:Q10001.

  57. 57.

    Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinforma. 2011;12:323.

  58. 58.

    Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Meth. 2012;9:357–9.

  59. 59.

    Hilton JA, Satinsky BM, Doherty M, Zielinski B, Zehr JP. Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume. ISME J. 2015;9:1557–69.

  60. 60.

    Spungin D, Pfreundt U, Berthelot H, Bonnet S, AlRoumi D, Natale F, et al. Mechanisms of Trichodesmium bloom demise within the New Caledonia Lagoon during the VAHINE mesocosm experiment. Biogeosci Discuss. 2016;13:1–44.

  61. 61.

    Wu YW, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2015;32:605–7.

  62. 62.

    Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 2010;11:119.

  63. 63.

    Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.

  64. 64.

    Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinforma. 2004;5:1–19.

  65. 65.

    Oksanen J. Multivariate analysis of ecological communities in R: vegan tutorial. 2015. URL:

  66. 66.

    Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57:289–300.

  67. 67.

    Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001;26:32–46.

  68. 68.

    Zapala MA, Schork NJ. Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables. Proc Natl Acad Sci USA. 2006;103:19430–5.

  69. 69.

    Robinson M, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11:R25.

  70. 70.

    Robinson MD, Smyth GK. Moderated statistical tests for assessing differences in tag abundance. Bioinformatics. 2007;23:2881–7.

  71. 71.

    Krishnamurthy A, Moore JK, Mahowald N, Luo C, Zender CS. Impacts of atmospheric nutrient inputs on marine biogeochemistry. J Geophys Res. 2010;115:1–13.

  72. 72.

    Chen YB, Chen YB, Dominic B, Dominic B, Mellon MT, Mellon MT, et al. Circadian rhythm of nitrogenase gene expression in the diazotrophic filamentous nonheterocystous cyanobacterium Trichodesmium sp strain IMS101. J Bacteriol. 1998;180:3598–605.

  73. 73.

    Wyman M, Zehr JP, Capone DG. Temporal variability in nitrogenase gene expression in natural populations of the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol. 1996;62:1073–5.

  74. 74.

    Shi T, Sun Y, Falkowski PG. Effects of iron limitation on the expression of metabolic genes in the marine cyanobacterium Trichodesmium erythraeum IMS101. Environ Microbiol. 2007;9:2945–56.

  75. 75.

    Webb E, Jakuba R, Moffett J, Dyhrman S. Molecular assessment of phosphorus and iron physiology in Trichodesmium populations from the western Central and western South Atlantic. Limnol Oceanogr. 2007;52:2221–32.

  76. 76.

    Karl DM. Microbially mediated transformations of phosphorus in the sea: new views of an old cycle. Ann Rev Mar Sci. 2014;6:279–337.

  77. 77.

    Vershinina O, Znamenskaya L. The Pho regulons of bacteria. Microbiology. 2002;71:581–95.

  78. 78.

    Young CL, Ingall ED. Marine dissolved organic phosphorus composition: insights from samples recovered using combined electrodialysis/reverse osmosis. Aquat Geochem. 2010;16:563–74.

  79. 79.

    Hynes AM, Chappell PD, Dyhrman ST, Doney SC, Webb EA. Cross-basin comparison of phosphorus stress and nitrogen fixation in Trichodesmium. Limnol Oceanogr. 2009;54:1438–48.

  80. 80.

    Mahaffey C, Reynolds S, Davis CE, Lohan MC, Lomas MW. Alkaline phosphatase activity in the subtropical ocean: insights from nutrient, dust and trace metal addition experiments. Front Mar Sci. 2014;1:1–13.

  81. 81.

    Sohm JA, Mahaffey C, Capone DG. Assessment of relative phosphorus limitation of Trichodesmium spp. in the North Pacific, North Atlantic, and the north coast of Australia. Limnol Oceanogr. 2008;53:2495–502.

  82. 82.

    Kim EE, Wyckoff HW. Reaction mechanism of alkaline phosphatase based on crystal structures. J Mol Biol. 1991;218:449–64.

  83. 83.

    Sowadski JM, Handschumacher MD, Krishna Murthy HM, Foster BA, Wyckoff HW. Refined structure of alkaline phosphatase from Escherichia coli at 2.8 A resolution. J Mol Biol. 1985;186:417–33.

  84. 84.

    Barnett JP, Millard A, Ksibe AZ, Scanlan DJ, Schmid R, Blindauer CA. Mining genomes of marine cyanobacteria for elements of zinc homeostasis. Front Microbiol. 2012;3:1–21.

  85. 85.

    Bruland KW. Oceanographic distributions of cadmium, zinc, nickel, and copper in the North Pacific. Earth Planet Sci Lett. 1980;47:176–198.

  86. 86.

    Kim T, Obata H, Kondo Y, Ogawa H, Gamo T. Distribution and speciation of dissolved zinc in the western North Pacific and its adjacent seas. Mar Chem. 2015;173:330–41.

  87. 87.

    Lohan MC, Statham PJ, Crawford DW. Total dissolved zinc in the upper water column of the subarctic North East Pacific. Deep Res Part II Top Stud Oceanogr. 2002;49:5793–808.

  88. 88.

    Hutchins DA, Fu F-X, Zhang Y, Warner ME, Feng Y, Portune K, et al. CO2 control of Trichodesmium N2 fixation, photosynthesis, growth rates, and elemental ratios: implications for past, present, and future ocean biogeochemistry. Limnol Oceanogr. 2007;52:1293–304.

  89. 89.

    Hutchins DA, Walworth NG, Webb EA, Saito MA, Moran D, McIlvin MR, et al. Irreversibly increased nitrogen fixation in Trichodesmium experimentally adapted to elevated carbon dioxide. Nat Commun. 2015;6:8155.

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We thank D McGillicuddy, J Waterbury, C Davis, S Wilson, A Heithoff, L Wurch, and E Olson for participating in the sample collection, and the captain and crew of the R/V Oceanus and R/V Kilo Moana for their help at sea. We thank H Joy-Warren for her help with nutrient analyses. We additionally thank the National Center for Genome Analysis Support (NCGAS) for access to computational time on Indiana University resources and data storage. This research was supported by the National Science Foundation Biological Oceanography Program (Ocean Sciences-0925284) and the Center for Microbial Oceanography: Research and Education, C-MORE (National Science Foundation award DBI04-24599). This work was also supported in part by the Simons Foundation (SCOPE award ID 329108 to STD), and is a contribution of the Simons Collaboration on Ocean Processes and Ecology (SCOPE).

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  1. Biology and Paleo Environment Division, Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, 10964, USA

    • Mónica Rouco
    • , Kyle R. Frischkorn
    • , Sheean T. Haley
    •  & Sonya T. Dyhrman
  2. Department of Earth and Environmental Sciences, Columbia University, New York, NY, 10027, USA

    • Mónica Rouco
    • , Kyle R. Frischkorn
    •  & Sonya T. Dyhrman
  3. Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA

    • Harriet Alexander


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The authors declare that they have no conflict of interest.

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Correspondence to Sonya T. Dyhrman.

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