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.

  • Review Article
  • Published:

Genomic perspectives in microbial oceanography

A Corrigendum to this article was published on 23 February 2006

Abstract

The global ocean is an integrated living system where energy and matter transformations are governed by interdependent physical, chemical and biotic processes. Although the fundamentals of ocean physics and chemistry are well established, comprehensive approaches to describing and interpreting oceanic microbial diversity and processes are only now emerging. In particular, the application of genomics to problems in microbial oceanography is significantly expanding our understanding of marine microbial evolution, metabolism and ecology. Integration of these new genome-enabled insights into the broader framework of ocean science represents one of the great contemporary challenges for microbial oceanographers.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Marine microbial interactions in the upper ocean.
Figure 2: Selected milestones in marine microbial oceanography.
Figure 3: Microbial systems analysis in oceanography.

Similar content being viewed by others

References

  1. Fuhrman, J. A. & Azam, F. Thymidine incorporation as a measure of heterotrophic bacterioplankton production in marine surface waters. Mar. Biol. 66, 109–120 (1982).

    Article  Google Scholar 

  2. Rappé, M. S., Connon, S. A., Vergin, K. L. & Giovannoni, S. J. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418, 630–633 (2002).

    Article  ADS  PubMed  Google Scholar 

  3. Olsen, G. J., Lane, D. J., Giovannoni, S. J., Pace, N. R. & Stahl, D. A. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40, 337–365 (1986).

    Article  CAS  PubMed  Google Scholar 

  4. DeLong, E. F., Wickham, G. S. & Pace, N. R. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243, 1360–1363 (1989).

    Article  ADS  CAS  PubMed  Google Scholar 

  5. Stein, J. L., Marsh, T. L., Wu, K. Y., Shizuya, H. & DeLong, E. F. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J. Bacteriol. 178, 591–599 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Handelsman, J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68, 669–685 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Karl, D. M. Cellular nucleotide measurements and applications in microbial ecology. Microbiol. Rev. 44, 739–796 (1980).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Hobbie, J. E., Daley, R. J. & Jasper, S. Use of Nuclepore filters for counting bacteria by fluorescence microscopy. Appl. Environ. Microbiol. 33, 1225–1228 (1977).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Karl, D. M. Measurement of microbial activity and growth in the ocean by rates of stable ribonucleic acid synthesis. Appl. Environ. Microbiol. 38, 850–860 (1979).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Azam, F. et al. The ecological role of water-column microbes in the sea. Mar. Ecol. Prog. Ser. 10, 257–263 (1983).

    Article  ADS  Google Scholar 

  11. Pomeroy, L. R. The ocean's food web, a changing paradigm. BioScience 24, 499–504 (1974).

    Article  Google Scholar 

  12. Waterbury, J. B., Watson, S. W., Guillard, R. R. L. & Brand, L. E. Widespread ocurrence of a unicellular marine, planktonic, cyanobacterium. Nature 277, 293–294 (1979).

    Article  ADS  Google Scholar 

  13. Johnson, P. W. & Sieburth, J. M. Chroococcoid cyanobacteria in the sea: a ubiquitous and diverse phototrophic biomass. Limnol. Oceanogr. 24, 928–935 (1979).

    Article  ADS  Google Scholar 

  14. Chisholm, S. W. et al. A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature 334, 340–343 (1988).

    Article  ADS  Google Scholar 

  15. Corliss, J. B. et al. Submarine thermal springs on the Galapagos Rift. Science 203, 1073–1083 (1979).

    Article  ADS  CAS  PubMed  Google Scholar 

  16. Yayanos, A. A., Dietz, A. S. & Van Boxtel, R. Obligately barophilic bacterium from the Mariana Trench. Proc. Natl Acad. Sci. USA 78, 5212–5215 (1981).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  17. Stahl, D. A., Lane, D. J., Olsen, G. J. & Pace, N. R. Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science 224, 409–411 (1984).

    Article  ADS  CAS  PubMed  Google Scholar 

  18. Giovannoni, S. J., Britschgi, T. B., Moyer, C. L. & Field, K. G. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60–63 (1990).

    Article  ADS  CAS  PubMed  Google Scholar 

  19. DeLong, E. F. Archaea in coastal marine environments. Proc. Natl Acad. Sci. USA 89, 5685–5689 (1992).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  20. Karner, M. B., DeLong, E. F. & Karl, D. M. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409, 507–510 (2001).

    Article  ADS  CAS  PubMed  Google Scholar 

  21. Fuhrman, J. A., McCallum, K. & Davis, A. A. Novel major archaebacterial group from marine plankton. Nature 356, 148–149 (1992).

    Article  ADS  CAS  PubMed  Google Scholar 

  22. Moon-van der Staay, S. Y., De Wachter, R. & Vaulot, D. Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409, 607–610 (2001).

    Article  ADS  CAS  PubMed  Google Scholar 

  23. Kolber, Z. S., Van Dover, C. L., Niederman, R. A. & Falkowski, P. G. Bacterial photosynthesis in surface waters of the open ocean. Nature 407, 177–179 (2000).

    Article  ADS  CAS  PubMed  Google Scholar 

  24. Béjà, O. et al. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289, 1902–1906 (2000).

    Article  ADS  PubMed  Google Scholar 

  25. Bergh, O., Borsheim, K. Y., Bratbak, G. & Heldal, M. High abundance of viruses found in aquatic environments. Nature 340, 467–468 (1989).

    Article  ADS  CAS  PubMed  Google Scholar 

  26. Paul, J. H., Sullivan, M. B., Segall, A. M. & Rohwer, F. Marine phage genomics. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 133, 463–476 (2002).

    Article  PubMed  Google Scholar 

  27. Falkowski, P. G. et al. The evolution of modern eukaryotic phytoplankton. Science 305, 354–360 (2004).

    Article  ADS  CAS  PubMed  Google Scholar 

  28. Lerat, E., Daubin, V., Ochman, H. & Moran, N. A. Evolutionary origins of genomic repertoires in bacteria. PLoS Biol. 3, e130 (2005).

    Article  PubMed  PubMed Central  Google Scholar 

  29. DeLong, E. F. Microbial community genomics in the ocean. Nature Rev. Microbiol. 3, 459–469 (2005).

    Article  CAS  Google Scholar 

  30. Thompson, J. R. et al. Genotypic diversity within a natural coastal bacterioplankton population. Science 307, 1311–1313 (2005).

    Article  ADS  CAS  PubMed  Google Scholar 

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

    Article  ADS  CAS  PubMed  Google Scholar 

  32. Moran, M. A. et al. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432, 910–913 (2004).

    Article  ADS  CAS  PubMed  Google Scholar 

  33. Rocap, G. et al. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424, 1042–1047 (2003).

    Article  ADS  CAS  PubMed  Google Scholar 

  34. Dufresne, A. et al. Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc. Natl Acad. Sci. USA 100, 10020–10025 (2003).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  35. Palenik, B. et al. The genome of a motile marine Synechococcus. Nature 424, 1037–1042 (2003).

    Article  ADS  CAS  PubMed  Google Scholar 

  36. Glockner, F. O. et al. Complete genome sequence of the marine planctomycete Pirellula sp. strain 1. Proc. Natl Acad. Sci. USA 100, 8298–8303 (2003).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  37. Hou, S. et al. Genome sequence of the deep-sea gammaproteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc. Natl Acad. Sci. USA 101, 18036–18041 (2004).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  38. Rabus, R. et al. The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments. Environ. Microbiol. 6, 887–902 (2004).

    Article  CAS  PubMed  Google Scholar 

  39. Ruby, E. G. et al. Complete genome sequence of Vibrio fischeri: a symbiotic bacterium with pathogenic congeners. Proc. Natl Acad. Sci. USA 102, 3004–3009 (2005).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  40. Vezzi, A. et al. Life at depth: Photobacterium profundum genome sequence and expression analysis. Science 307, 1459–1461 (2005).

    Article  ADS  CAS  PubMed  Google Scholar 

  41. Giovanonni, S. J. et al. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309, 1242–1245 (2005).

    Article  ADS  Google Scholar 

  42. Schmidt, T. M., DeLong, E. F. & Pace, N. R. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173, 4371–4378 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Béjà, O., Spudich, E. N., Spudich, J. L., Leclerc, M. & DeLong, E. F. Proteorhodopsin phototrophy in the ocean. Nature 411, 786–789 (2001).

    Article  ADS  PubMed  Google Scholar 

  44. Venter, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74 (2004).

    Article  ADS  CAS  PubMed  Google Scholar 

  45. Tringe, S. G. et al. Comparative metagenomics of microbial communities. Science 308, 554–557 (2005).

    Article  ADS  CAS  PubMed  Google Scholar 

  46. Suzuki, M. T., Preston, C. M., Chavez, F. & DeLong, E. F. Quantitative mapping of bacterioplankton populations in seawater: field tests across an upwelling plume in the Monterey Bay. Aquat. Microb. Ecol. 24, 117–127 (2001).

    Article  Google Scholar 

  47. Doney, S. C., Abbott, M. R., Cullen, J. J., Karl, D. M. & Rothstein, L. From genes to ecosystems: the ocean's new frontier. Front. Ecol. Environ. 2, 457–466 (2004).

    Article  Google Scholar 

  48. Stahl, D. A. & Tiedje, J. M. Microbial Ecology and Genomics: A Crossroads of Opportunity (American Society for Microbiology, Washington D.C., 2002).

    Google Scholar 

  49. Karl, D. M., Bidigare, R. R. & Letelier, R. M. Long-term changes in plankton community structure and productivity in the North Pacific Subtropical Gyre: The domain shift hypothesis. Deep-Sea Res. II 48, 1449–1470 (2001).

    Article  ADS  Google Scholar 

  50. Hallam, S. J. et al. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305, 1457–1462 (2004).

    Article  ADS  CAS  PubMed  Google Scholar 

  51. Karl, D. M. Accurate estimation of microbial loop processes and rates. Microbiol. Ecol 28, 147–150 (1994).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors' work is supported by the NSF, the Gordon and Betty Moore Foundation, and the Department of Energy. We thank our colleagues, students and CMORE collaborators for their ideas, inspiration and enthusiasm.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Edward F. DeLong.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Additional information

Author Information Reprints and permissions information is available at npg.nature.com/reprintsandpermissions.

Rights and permissions

Reprints and permissions

About this article

Cite this article

DeLong, E., Karl, D. Genomic perspectives in microbial oceanography. Nature 437, 336–342 (2005). https://doi.org/10.1038/nature04157

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature04157

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

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