Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Microbial oceanography in a sea of opportunity

Abstract

Plankton use solar energy to drive the nutrient cycles that make the planet habitable for larger organisms. We can now explore the diversity and functions of plankton using genomics, revealing the gene repertoires associated with survival in the oceans. Such studies will help us to appreciate the sensitivity of ocean systems and of the ocean's response to climate change, improving the predictive power of climate models.

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Methods of visualizing plankton.
Figure 2: Proposed framework for assessing oceanic microbial diversity in a functional context.
Figure 3: Miniaturized ecogenomic sensors to measure microbial activity.

References

  1. 1

    Curtin, T. B. & Belcher, E. O. Innovation in oceanographic instrumentation. Oceanography 21, 44–53 (2008).

    Article  Google Scholar 

  2. 2

    Dawson, M. N., Sen Gupta, A. & England, M. H. Coupled biophysical global ocean model and molecular genetic analyses identify multiple introductions of cryptogenic species. Proc. Natl Acad. Sci. USA 102, 11968–11973 (2005).

    CAS  Article  ADS  Google Scholar 

  3. 3

    Follows, M. J., Dutkiewicz, S., Grant, S. & Chisholm, S. W. Emergent biogeography of microbial communities in a model ocean. Science 315, 1843–1846 (2007).

    CAS  Article  ADS  Google Scholar 

  4. 4

    Falkowski, P. G., Fenchel, T. & Delong, E .F. The microbial engines that drive Earth's biogeochemical cycles. Science 320, 1034–1039 (2008).

    CAS  Article  ADS  Google Scholar 

  5. 5

    Field, C. B., Behrenfeld, M. J., Randerson, J. T. & Falkowski, P. Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281, 237–240 (1998).

    CAS  Article  ADS  Google Scholar 

  6. 6

    Kolber, Z. Energy cycle in the ocean: powering the microbial world. Oceanography 20, 79–87 (2007).

    Article  Google Scholar 

  7. 7

    Longhurst, A. R. Ecological Geography of the Sea (Academic, 1998).

    Google Scholar 

  8. 8

    Rusch, D. B. et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 5, e77 (2007).

    Article  Google Scholar 

  9. 9

    Huber, J. A. et al. Microbial population structures in the deep marine biosphere. Science 318, 97–100 (2007).

    CAS  Article  ADS  Google Scholar 

  10. 10

    Frias-Lopez, J. et al. Microbial community gene expression in ocean surface waters. Proc. Natl Acad. Sci. USA 105, 3805–3810 (2008).

    CAS  Article  ADS  Google Scholar 

  11. 11

    Armbrust, E. V. et al. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306, 79–86 (2004).

    CAS  Article  ADS  Google Scholar 

  12. 12

    Bowler, C. et al. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456, 239–244 (2008).

    CAS  Article  ADS  Google Scholar 

  13. 13

    Allen, A. E. et al. Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation. Proc. Natl Acad. Sci. USA 105, 10438–10443 (2008).

    CAS  Article  ADS  Google Scholar 

  14. 14

    Mock, T. et al. Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses. Proc. Natl Acad. Sci. USA 105, 1579–1584 (2008).

    CAS  Article  ADS  Google Scholar 

  15. 15

    Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133–138 (2009).

    CAS  Article  ADS  Google Scholar 

  16. 16

    Brandt, A. et al. First insights into the biodiversity and biogeography of the Southern Ocean deep sea. Nature 447, 307–311 (2007).

    CAS  Article  ADS  Google Scholar 

  17. 17

    Olson, R. J. & Sosik, H. M. A submersible imaging-in-flow instrument to analyze nano- and microplankton: Imaging FlowCytobot. Limnol. Oceanogr. Methods 5, 195–203 (2007).

    Article  Google Scholar 

  18. 18

    Stemmann, L. et al. Global zoogeography of fragile macrozooplankton in the upper 100–1000 m inferred from the underwater video profiler. ICES J. Mar. Sci. 65, 433–442 (2008).

    Article  Google Scholar 

  19. 19

    Polovina, J. J., Howell, E. A. & Abecassis, M. Ocean's least productive waters are expanding. Geophys. Res. Lett. 35, L03618 (2008).

    Article  ADS  Google Scholar 

  20. 20

    Hutchins, D. A. et al. CO2 control of Trichodesmium N2 fixation, photosynthesis, growth rates, and elemental ratios: implications for past, present, and future ocean biogeochemistry. Limnol. Oceanogr. 52, 1293–1304 (2007).

    CAS  Article  ADS  Google Scholar 

  21. 21

    Beaugrand, G., Reid, P. C., Ibañez, F., Lindley, J. A. & Edwards, M. Reorganization of North Atlantic marine copepod biodiversity and climate. Science 296, 1692–1694 (2002).

    CAS  Article  ADS  Google Scholar 

  22. 22

    John, D. E. et al. Phytoplankton carbon fixation gene (RuBisCO) transcripts and air–sea CO2 flux in the Mississippi River plume. ISME J. 1, 517–531 (2007).

    CAS  Article  Google Scholar 

  23. 23

    Prasil, O., Suggett, D. J., Cullen, J. J., Babin, M. & Govindjee. Aquafluo 2007: chlorophyll fluorescence in aquatic sciences, an international conference held in Nové Hrady. Photosynth. Res. 95, 111–115 (2008).

    CAS  Article  Google Scholar 

  24. 24

    Short, S. M. & Zehr, J. P. Nitrogenase gene expression in the Chesapeake Bay Estuary. Environ. Microbiol. 9, 1591–1596 (2007).

    CAS  Article  Google Scholar 

  25. 25

    Karl, D. M. Microbial oceanography: paradigms, processes and promise. Nature Rev. Microbiol. 5, 759–769 (2007).

    CAS  Article  Google Scholar 

  26. 26

    Delong, E. F. et al. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311, 496–503 (2006).

    CAS  Article  ADS  Google Scholar 

  27. 27

    Feely, R. A., Sabine, C. L., Hernandez-Ayon, J. M., Ianson, D. & Hales, B. Evidence for upwelling of corrosive 'acidified' water onto the continental shelf. Science 320, 1490–1492 (2008).

    CAS  Article  ADS  Google Scholar 

  28. 28

    Stramma, L., Johnson, G. C., Sprintfall, J. & Mohrholz, V. Expanding oxygen-minimum zones in the tropical oceans. Science 320, 655–658 (2008).

    CAS  Article  ADS  Google Scholar 

  29. 29

    Murray, A. E. & Grzymski, J. J. Diversity and genomics of Antarctic marine micro-organisms. Phil. Trans. R. Soc. Lond. B 362, 2259–2271 (2007).

    CAS  Article  Google Scholar 

  30. 30

    Seshadri, R., Kravitz, S. A., Smarr, L., Gilna, P. & Frazier, M. CAMERA: a community resource for metagenomics. PLoS Biol. 5, e75 (2007).

    Article  Google Scholar 

  31. 31

    Colwell, R. R. et al. Climate change and human health. Science 279, 968–969 (1998).

    CAS  Article  ADS  Google Scholar 

  32. 32

    Diaz, R. J. & Rosenberg, R. Spreading dead zones and consequences for marine ecosystems. Science 321, 926–929 (2008).

    CAS  Article  ADS  Google Scholar 

  33. 33

    Thompson, R. C. et al. Lost at sea: where is all the plastic? Science 304, 838 (2004).

    CAS  Article  Google Scholar 

  34. 34

    Constantin de Magny, G. et al. Environmental signatures associated with cholera epidemics. Proc. Natl Acad. Sci. USA 105, 17676–17681 (2008).

    CAS  Article  ADS  Google Scholar 

  35. 35

    Alam, M. et al. Viable but nonculturable Vibrio cholerae O1 in biofilms in the aquatic environment and their role in cholera transmission. Proc. Natl Acad. Sci. USA 104, 17801–17806 (2007).

    CAS  Article  ADS  Google Scholar 

  36. 36

    Nakagawa, S. et al. Deep-sea vent ɛ-proteobacterial genomes provide insights into emergence of pathogens. Proc. Natl Acad. Sci. USA 104, 12146–12150 (2007).

    CAS  Article  ADS  Google Scholar 

  37. 37

    Desclés, J. et al. New tools for labeling silica in living diatoms. New Phytol. 177, 822–829 (2008).

    Article  Google Scholar 

  38. 38

    Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: the unseen majority. Proc. Natl Acad. Sci. USA 95, 6578–6583 (1998).

    CAS  Article  ADS  Google Scholar 

  39. 39

    Richardson, A. J. & Polooczanska, E. S. Under-resourced, under threat. Science 320, 1294–1295 (2008).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

Many of the themes discussed here were inspired by a workshop entitled 'Implications and Opportunities of the Marine Genomics Revolution' held in Bermuda in October 2007 and sponsored by the Marine Genomics Europe Network of Excellence (GOCE-CT-2004-505403), the Centre National de la Recherche Scientifique (CNRS), the Gordon and Betty Moore Foundation (GBMF), the US National Science Foundation (NSF), the US Office of Naval Research Global, the Bermuda Institute of Ocean Sciences, and the Japanese Science and Technology Agency. We thank the participants of this meeting as well as the anonymous reviewers for helpful comments on the manuscript. We apologize to colleagues whose work we could not cite because of space restrictions. Work in our laboratories is supported by the European Union, the Agence Nationale de la Recherche and CNRS (C.B.), the NSF (grant number EF-04245599), GBMF and Agouron Institute (D.M.K.), and the NSF (grant number 0813066), the National Institutes of Health (grant number 1RO1A139129-01) and the National Oceanic and Atmospheric Administration (grant number S0660009) (R.R.C.).

Author information

Affiliations

Authors

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Additional information

Reprints and permissions information is available at http://www.nature.com/reprints.

Correspondence should be addressed to C.B. (cbowler@biologie.ens.fr).

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Bowler, C., Karl, D. & Colwell, R. Microbial oceanography in a sea of opportunity. Nature 459, 180–184 (2009). https://doi.org/10.1038/nature08056

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing