Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre

Article metrics


Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity in the surface ocean is constrained by nutrients which are supplied, in part, by mixing with deeper water. Little is known about the time scales, frequency, or impact of mixing on microbial communities. We combined in situ sampling using the Environmental Sample Processor and a small-scale mixing experiment with lower euphotic zone water to determine how individual populations respond to mixing. Transcriptional responses were measured using the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) microarray, which targets all three domains of life and viruses. The experiment showed that mixing substantially affects photosynthetic taxa as expected, but surprisingly also showed that populations respond differently to unfiltered deep water which contains particles (organisms and detritus) compared to filtered deep water that only contains nutrients and viruses, pointing to the impact of biological interactions associated with these events. Comparison between experimental and in situ population transcription patterns indicated that manipulated populations can serve as analogs for natural populations, and that natural populations may be frequently or continuously responding to nutrients from deeper waters. Finally, this study also shows that the microarray approach, which is complementary to metatranscriptomic sequencing, is useful for determining the physiological status of in situ microbial communities.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7


  1. 1.

    DeLong EF, Karl DM. Genomic perspectives in microbial oceanography. Nature. 2005;437:336–42.

  2. 2.

    Azam F, Malfatti F. Microbial structuring of marine ecosystems. Nat Rev Microbiol. 2007;5:782–91.

  3. 3.

    Falkowski PG, Fenchel T, DeLong EF. The microbial engines that drive Earth’s biogeochemical cycles. Science. 2008;320:1034–9.

  4. 4.

    Coleman ML, Sullivan MB, Martiny AC, Steglich C, Barry K, DeLong EF, et al. Genomic islands and the ecology and evolution of Prochlorococcus. Science. 2006;311:1768–70.

  5. 5.

    Ivars-Martinez E, Martin-Cuadrado A-B, D’Auria G, Mira A, Ferriera S, Johnson J, et al. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. ISME J. 2008;2:1194–212.

  6. 6.

    Johnson ZI, Zinser ER, Coe A, McNulty NP, Woodward EMS, Chisholm SW. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science. 2006;311:1737–40.

  7. 7.

    Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 2007;5:e77.

  8. 8.

    de Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, et al. Eukaryotic plankton diversity in the sunlit ocean. Science. 2015;348:1261605.

  9. 9.

    Shilova IN, Robidart JC, DeLong EF, Zehr JP. Genetic diversity affects the daily transcriptional oscillations of marine microbial populations. PLoS ONE. 2016;11:e0146706.

  10. 10.

    Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, et al. Ocean plankton. Structure and function of the global ocean microbiome. Science. 2015;348:1261359.

  11. 11.

    Hewson I, Poretsky RS, Dyhrman ST, Zielinski B, White AE, Tripp HJ, et al. Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean. ISME J. 2009;3:1286–300.

  12. 12.

    Poretsky RS, Hewson I, Sun S, Allen AE, Zehr JP, Moran MA. Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific Subtropical Gyre. Environ Microbiol. 2009;11:1358–75.

  13. 13.

    McCarren J, Becker JW, Repeta DJ, Shi Y, Young CR, Malmstrom RR, et al. Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proc Natl Acad Sci USA. 2010;107:16420–7.

  14. 14.

    Ottesen EA, Marin R, Preston CM, Young CR, Ryan JP, Scholin CA, et al. Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. ISME J. 2011;5:1881–95.

  15. 15.

    Shilova IN, Robidart JC, Tripp HJ, Turk-Kubo K, Wawrik B, Post AF, et al. A microarray for assessing transcription from pelagic marine microbial taxa. ISME J. 2014;8:1476–91.

  16. 16.

    Karl DM, Church MJ. Ecosystem structure and dynamics in the North Pacific Subtropical Gyre: new views of an old ocean. Ecosystems. 2017;20:433–57.

  17. 17.

    Karl DM. A sea of change: biogeochemical variability in the North Pacific Subtropical Gyre. Ecosystems. 1999;2:181–214.

  18. 18.

    Ottesen EA, Young CR, Gifford SM, Eppley JM, Marin R, Schuster SC, et al. Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages. Science. 2014;345:207–12.

  19. 19.

    Johnson KS, Riser SC, Karl DM. Nitrate supply from deep to near-surface waters of the North Pacific Subtropical Gyre. Nature. 2010;465:1062–5.

  20. 20.

    Mahaffey C, Björkman KM, Karl DM. Phytoplankton response to deep seawater nutrient addition in the North Pacific Subtropical Gyre. Mar Ecol Prog Ser. 2012;460:13–34.

  21. 21.

    Robidart JC, Church MJ, Ryan JP, Ascani F, Wilson ST, Bombar D, et al. Ecogenomic sensor reveals controls on N2-fixing microorganisms in the North Pacific Ocean. ISME J. 2014;8:1175–85.

  22. 22.

    McAndrew PM, Björkman KM, Church MJ, Morris PJ, Jachowski N, Williams PJlB, et al. Metabolic response of oligotrophic plankton communities to deep water nutrient enrichment. Mar Ecol Prog Ser. 2007;332:63–75.

  23. 23.

    Shi Y, McCarren J, DeLong EF. Transcriptional responses of surface water marine microbial assemblages to deep-sea water amendment. Environ Microbiol. 2012;14:191–206.

  24. 24.

    Alexander H, Rouco M, Haley ST, Wilson ST, Karl DM, Dyhrman ST. Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean. Proc Natl Acad Sci USA. 2015;112:E5972–9.

  25. 25.

    Karl DM, Tien G. MAGIC: a sensitive and precise method for measuring dissolved phosphorus in aquatic environments. Limnol Oceanogr. 1992;37:105–16.

  26. 26.

    Dore JE, Karl DM. Nitrification in the euphotic zone as a source for nitrite, nitrate, and nitrous oxide at Station ALOHA. Limnol Oceanogr. 1996;41:1619–28.

  27. 27.

    Wilson ST, Böttjer D, Church MJ, Karl DM. Comparative assessment of nitrogen fixation methodologies, conducted in the oligotrophic North Pacific Ocean. Appl Environ Microbiol. 2012;78:6516–23.

  28. 28.

    Turk-Kubo KA, Achilles KM, Serros TR, Ochiai M, Montoya JP, Zehr JP. Nitrogenase (nifH) gene expression in diazotrophic cyanobacteria in the Tropical North Atlantic in response to nutrient amendments. Front Microbiol. 2012;3:73–103.

  29. 29.

    Green SJ, Venkatramanan R, Naqib A. Deconstructing the polymerase chain reaction: understanding and correcting bias associated with primer degeneracies and primer-template mismatches. PLoS ONE. 2015;10:e0128122.

  30. 30.

    McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217.

  31. 31.

    The R Core Team. R: a Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, 2017).

  32. 32.

    Shilova IN, Mills MM, Robidart JC, Turk-Kubo KA, Björkman KM, Kolber Z, et al. Differential effects of nitrate, ammonium, and urea as N sources for microbial communities in the North Pacific Ocean. Limnol Oceanogr. 2017;62:2550–74.

  33. 33.

    Bolstad BM, Irizarry RA, Åstrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003;19:185–93.

  34. 34.

    Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4:249–64.

  35. 35.

    Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47.

  36. 36.

    Dore JE, Letelier RM, Church MJ, Lukas R, Karl DM. Summer phytoplankton blooms in the oligotrophic North Pacific Subtropical Gyre: historical perspective and recent observations. Prog Oceanogr. 2008;76:2–38.

  37. 37.

    Pichard SL, Campbell L, Kang JB, Tabita FR, Paul JH. Regulation of ribulose bisphosphate carboxylase gene expression in natural phytoplankton communities. I. Diel Rhythms. Mar Ecol Prog Ser. 1996;139:257–65.

  38. 38.

    John DE, Wang ZA, Liu X, Byrne RH, Corredor JE, López JM, et al. Phytoplankton carbon fixation gene (RuBisCO) transcripts and air-sea CO2 flux in the Mississippi River plume. ISME J. 2007;1:517–31.

  39. 39.

    Zinser ER, Lindell D, Johnson ZI, Futschik ME, Steglich C, Coleman ML, et al. Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, Prochlorococcus. PLoS ONE. 2009;4:e5135.

  40. 40.

    Liu H, Nolla HA, Campbell L. Prochlorococcus growth rate and contribution to primary production in the equatorial and subtropical North Pacific Ocean. Aquat Microb Ecol. 1997;12:39–47.

  41. 41.

    Thompson LR, Zeng Q, Chisholm SW. Gene expression patterns during light and dark infection of Prochlorococcus by cyanophage. PLoS ONE. 2016;11:e0165375.

  42. 42.

    Puxty RJ, Evans DJ, Millard AD, Scanlan DJ. Energy limitation of cyanophage development: implications for marine carbon cycling. ISME J. 2018;12:1273–86.

  43. 43.

    Tolonen AC, Aach J, Lindell D, Johnson ZI, Rector T, Steen R, et al. Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability. Mol Syst Biol. 2006;2:53.

  44. 44.

    Dekaezemacker J, Bonnet S. Sensitivity of N2 fixation to combined nitrogen forms (NO3 - and NH4 +) in two strains of the marine diazotroph Crocosphaera watsonii (Cyanobacteria). Mar Ecol Prog Ser. 2011;438:33–46.

  45. 45.

    Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR, Stahl DA. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature. 2009;461:976–9.

  46. 46.

    Li B, Karl DM, Letelier RM, Bidigare RR, Church MJ. Variability of chromophytic phytoplankton in the North Pacific Subtropical Gyre. Deep Sea Res II. 2013;93:84–95.

  47. 47.

    Decho A. Microbial exopolymer secretions in ocean environments: their role(s) in food webs and marine processes. Oceanogr Mar Biol Annu Rev. 1990;28:73–153.

  48. 48.

    Hassler CS, Norman L, Mancuso Nichols CA, Clementson LA, Robinson C, Schoemann V, et al. Iron associated with exopolymeric substances is highly bioavailable to oceanic phytoplankton. Mar Chem. 2015;173:136–47.

  49. 49.

    Amin SA, Hmelo LR, van Tol HM, Durham BP, Carlson LT, Heal KR, et al. Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria. Nature. 2015;522:98–101.

  50. 50.

    Landa M, Burns AS, Roth SJ, Moran MA. Bacterial transcriptome remodeling during sequential co-culture with a marine dinoflagellate and diatom. ISME J. 2017;11:2677–90.

  51. 51.

    Ouverney CC, Fuhrman JA. Marine planktonic Archaea take up amino acids. Appl Environ Microbiol. 2000;66:4829–33.

  52. 52.

    Shi Y, Tyson GW, Eppley JM, DeLong EF. Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J. 2011;5:999–1013.

  53. 53.

    Aylward FO, Eppley JM, Smith JM, Chavez FP, Scholin CA, DeLong EF. Microbial community transcriptional networks are conserved in three domains at ocean basin scales. Proc Natl Acad Sci USA. 2015;112:5443–8.

  54. 54.

    Sohm JA, Ahlgren NA, Thomson ZJ, Williams C, Moffett JW, Saito MA, et al. Co-occurring Synechococcus ecotypes occupy four major oceanic regimes defined by temperature, macronutrients and iron. ISME J. 2016;10:333–45.

  55. 55.

    Farrant GK, Dore H, Cornejo-Castillo FM, Partensky F, Ratin M, Ostrowski M, et al. Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria. Proc Natl Acad Sci USA. 2016;113:E3365–74.

  56. 56.

    Amin SA, Parker MS, Armbrust EV. Interactions between diatoms and bacteria. Microbiol Mol Biol Rev. 2012;76:667–84.

  57. 57.

    Krupke A, Hmelo LR, Ossolinski JE, Mincer TJ, Van Mooy BA. Quorum sensing plays a complex role in regulating the enzyme hydrolysis activity of microbes associated with sinking particles in the ocean. Front Mar Sci. 2016;3:55.

  58. 58.

    Thompson AW, Foster RA, Krupke A, Carter BJ, Musat N, Vaulot D, et al. Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga. Science. 2012;337:1546–50.

  59. 59.

    Thompson AW, Zehr JP. Cellular interactions: lessons from the nitrogen‐fixing cyanobacteria. J Phycol. 2013;49:1024–35.

  60. 60.

    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.

Download references


The authors would like to thank the Center for Microbial Oceanography, Research and Education (C-MORE grant number EF0424599, J.Z. and D.M.K.), the Simons Collaboration on Ocean Processes and Ecology (a grant from the Simons Foundation – SCOPE Award ID 329108, J.Z. and D.M.K.), the David and Lucile Packard Foundation, the Gordon and Betty Moore Foundation MEGAMER Facilities Grant (number 1761 to J.Z.) and Investigator Award (number 3794 to D.M.K.) and National Science Foundation Dimensions of Biodiversity Program (grant number 1241221, J.Z.) for funding and resources. The expertise of the international MicroTOOLs Team was crucial in the development of a successful environmental microarray. The MicroTOOLs array hybridization was performed at the Roy J. Carver Center for Genomics, The University of Iowa, USA. Steve Poulos and Lance Fujieki kindly provided Seaglider density data and images. We also thank Ariel Rabines, Roman Marin III, John Ryan, Gene Massion, Blake Watkins, Mariona Segura-Noguera, Susan Curless and the captain and crew of the R/V Kilo Moana.

Author information

Correspondence to J. P. Zehr.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Robidart, J.C., Magasin, J.D., Shilova, I.N. et al. Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre. ISME J 13, 374–387 (2019) doi:10.1038/s41396-018-0280-0

Download citation