Microbial oceanography: Paradigms, processes and promise

Nature Reviews Microbiology

Volumn 5, Issue 10, 2007, Pages 759-769

  Karl, David M ^a  

^a UNIVERSITY OF HAWAII   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOGENESIS; BIOME; BIOSPHERE; CLIMATE CHANGE; ENVIRONMENTAL CHANGE; EVOLUTION; METABOLISM; MICROBIAL GENETICS; MICROORGANISM; MOLECULAR ECOLOGY; NONHUMAN; OCEANOGRAPHY; PRIORITY JOURNAL; PROTEIN FAMILY; REMOTE SENSING; REVIEW; SEA; SOCIETY; TECHNOLOGY;

BACTERIA; BIODIVERSITY; MARINE BIOLOGY; OCEANS AND SEAS; SEAWATER; WATER MICROBIOLOGY;

EID: 34548716455     PISSN: 17401526     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrmicro1749     Document Type: Review

References (84)

1. Karl, D. M. & Proctor, L. Foundations of microbial oceanography. Oceanography 20, 14-25 (2007).
2. Duarte, C. M., Gasol, J. M. & Vaque, D. Role of experimental approaches in marine microbial ecology. Aquat. Microb. Ecol. 13, 101-111 (1997).
3. Doney, S. C., Abbott, M. R., Cullen, J. J., Karl, D. M. & Rothstein, L. From genes to ecosystems: The ocean's new frontier. Frontiers Ecol. Environ. 2, 457-466 (2004).
4. Rothstein, L. M. et al. Modeling ocean ecosystems: The PARADIGM program. Oceanography 19, 17-45 (2006).
5. van Leeuwenhoek, A. Concerning little animals by him observed in rain-, well-, sea- and snow-water; as also in water wherein pepper had lain infused. Phil. Trans. Royal Soc. London 12, 821-831 (1677).
6. Karl, D. M. & Dore, J. E. in Methods in Microbiology Vol. 30 (ed. Paul, J. H.). 13-39 (Academic Press, San Diego, 2001).
7. Rusch, D. B. et al. The Sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol. 5, 0398-0431 (2007).
8. Whitman, W.B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: The unseen majority. Proc. Natl Acad. Sci. USA 95, 6578-6583 (1998).
9. Hunter-Cevera, J., Karl, D. & Buckley, M. Marine Microbial Diversity: The Key to Earth's Habitability (American Academy of Microbiology Washington, DC, 2005).
10. Pace, N. R. A molecular view of microbial diversity and the biosphere. Science 276, 734-740 (1997).
11. Sogin, M. L. et al. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc. Natl Acad. Sci. USA 103 12115-12120 (2006).
12. Tringe, S. G. & Rubin, E. M. Metagenomics: DNA sequencing of environmental samples. Nature Rev. Genetics 6, 805-814 (2005).
13. Venter, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74 (2004).
14. Yooseph, S. et al. The Sorcerer II global ocean sampling expedition: Expanding the universe of protein families. PLoS Biol. 5, 0432-0466 (2007).
15. Ryther, J. H. Potential productivity of the sea. Science 130 602-608 (1959).
16. Kolber, Z. Energy cycle in the ocean: Powering the microbial world. Oceanography 20, 82-91 (2007).
17. Cullen, J. J., Franks, P. J. S., Karl, D. M. & Longhurst, A. in The Sea Vol. 12 (eds Robinson, A. R., McCarthy, J. J. & Rothschild, B. J.) 297-336 (John Wiley & Sons, Inc., New York, 2002).
18. Béjà, O. et al. Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. Science 289, 1902-1906 (2000).
19. Martinez, A., Bradley, A. S., Waldbauer, J. R., Summons, R. E. & DeLong, E. F. Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proc. Natl Acad. Sci. USA 104, 5590-5595 (2007).
20. Karl, D. M. Hidden in a sea of microbes. Nature 415, 590-591 (2002).
21. Giovannoni, S. J. et al. Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438, 82-85 (2005).
22. Gómez-Consarnau, L. et al. Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature 445, 210-213 (2007).
23. del Giorgio, P. A., Cole, J. J. & Cimbleris, A. Respiration rates in bacteria exceed phytoplankton production in unproductive aquatic systems. Nature 385, 148-151 (1997).
24. 2 balance of unproductive aquatic ecosystems. Science 281, 234-236 (1998).
25. Williams, P. J. le B. Morris, P. J. & Karl, D. M. Net community production and metabolic balance at the oligotrophic ocean site, Station ALOHA. Deep-Sea Res. I 51, 1563-1578 (2004).
26. Karl, D. M., Laws, E. A., Morris, P., Williams, P. J. leB. & Emerson, S. Metabolic balance of the open sea. Nature 426 32 (2003).
27. Platt, T et al. Biological production of the oceans: The case for a consensus. Mar. Ecol. Prog. Ser. 52, 77-88 (1989).
28. McGowan, J. A. & Hayward, T. L. Mixing and oceanic productivity. Deep-Sea Res 25, 771-793 (1978).
29. McGillicuddy, Jr D. J. et al. Influence of mesoscale eddies on new production in the Sargasso Sea. Nature 394, 263-266 (1998).
30. Uz, B. M., Yoder, J. A. & Osychny, V. Pumping of nutrients to ocean surface waters by the action of propagating planetary waves. Nature 409, 597-600 (2001).
31. McAndrew, P. M. et al. Metabolic response of oligotrophic plankton communities to deep water nutrient enrichment. Mar. Ecol. Prog. Ser. 332, 63-75 (2007).
32. Dachs, J. et al. High atmosphere-ocean exchange of organic carbon in the NE subtropical Atlantic. Geophys. Res. Lett. 32, L21807 (2005).
33. DeLong, E. F. Archaea in coastal marine environments. Proc. Natl Acad. Sci. USA 89, 5685-5689 (1992).
34. Fuhrman. J. A., McCallum, K. & Davis, A. A. Novel major archaebacterial group from marine plankton. Nature 356, 148-149 (1992).
35. DeLong, E. F., Wu, K. Y. Prezelin, B. B. & Jovine, R. V. High abundance of Archaea in Antarctic marine picoplankton. Nature 371, 695-697 (1994).
36. Massana, R., Murray, A. E., Preston, C. M. & DeLong, E. F. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara channel. Appl. Environ. Microbiol. 63, 50-56 (1997).
37. Karner, M. B., DeLong, E. F. & Karl, D. M. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409, 507-510 (2001).
38. DeLong, E. F. Microbial domains in the ocean: A lesson from the Archaea. Oceanography 20, 124-129 (2007).
39. Karl, D. M., Knauer, G., Martin, J. & Ward, B. Bacterial chemolithotrophy in the ocean is associated with sinking particles, Nature 309, 54-56 (1984).
40. 14C analysis. Geochim. Cosmochim. Acta 65, 3123-3137 (2001).
41. Wuchter, C., Schouten, S., Boschker, H. T. & Sinninghe Darnste, J. S. Bicarbonate uptake by marine Crenarchaeota. FEMS Microbiol. Lett. 219, 203-207 (2003).
42. Könneke, M. et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437, 543-546 (2005).
43. Ingalls, A. E. et al. Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. Proc. Natl Acad. Sci. USA 103, 6442-6447 (2006).
44. Nicol, G. W. & Schleper, C. Ammonia-oxidising Crenarchaeota: Important players in the nitrogen cycle? Trends Microbiol. 14, 207-212 (2006).
45. Wuchter, C. et al. Archaeal nitrification in the ocean. Proc. Natl Acad. Sci. USA 103, 12317-12322 (2006).
46. Schleper C., Jurgens, G. & Jonuscheit, M. Genomic studies of uncultivated archaea. Nature Rev. Microbiol. 3, 479-488 (2005).
47. Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E. & Oakley, B. B. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc. Natl Acad. Sci. USA 102, 14683-14688 (2005).
48. Mincer, T. J. et al. Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ. Microbiol. 1162-1175 (2007).
49. Costa, E., Perez, J. & Kreft, J.-U. Why is metabolic labour divided in nitrification? Trends Microbiol. 14, 213-219 (2006).
50. Ouverney, C. C. & Fuhrman, J. A. Marine planktonic Archaea take up amino acids. Appl. Environ. Microbiol. 66, 4829-4833 (2000).
51. Herndl, G. J. et al. Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean. Appl. Environ. Microbiol. 71, 2303-2309 (2005).
52. Teira, E., van Aken, H., Veth, C. & Herndl, G. J. Archaeal uptake of enantiomeric amino acids in the meso- and bathypelagic waters of the North Atlantic. Limnol. Oceonogr. 51, 60-69 (2006).
53. Hallam, S. J. et al. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol. 4, 0520-0536 (2006).
54. Karl, D. M. A sea of change: Biogeochemical variability in the North Pacific Subtropical Gyre. Ecosystems 2, 181-214 (1999).
55. Michaels, A. F., Karl, D. M. & Capone, D. G. Element stoichiometry, new production and nitrogen fixation. Oceanography 14, 68-77 (2001).
56. Karl, D. M. et al. in Nitrogen in the Marine Environment (eds Bronk, D., Mulholland, M., Capone, D. & Carpenter, E.) in press (Academic Press).
57. Karl, D. et al. The role of nitrogen fixation in biogeochemical cycling in the subtropical North Pacific Ocean. Nature 388, 533-538 (1997).
58. Dore, J. E., Brum, J. R., Tupas, L. M. & Karl, D. M. Seasonal and interannual variability in sources of nitrogen supporting export in the oligotrophic subtropical North Pacific Ocean. Limnol. Oceonogr. 47, 1595-1607 (2002).
59. Bertilsson, S., Berglund, O., Karl, D. M. & Chisholm, S. W. Elemental composition of marine Prochlorococcus and Synechococcus: implications for the ecological stoichiometry of the sea. Limnol. Oceanogr. 48, 1721-1731 (2003).
60. White, A., Spitz, Y., Karl, D. M. & Letelier, R. M. Flexible elemental stoichiometry in Trichodesmium spp. and its ecological implications. Limnol. Oceanogr. 51, 1777-1790 (2006).
61. Sterner, R. W. & Elser, J. J. Ecological Stoichiometry: The Biology offlements ftom Molecules to the Biosphere (Princeton University Press, Princeton, 2002).
62. Karl, D. M. in Manual of Environmental Microbiology, Third Edition (eds Hurst, C. J. et al.) (American Society of Microbiology Press, Washington D. C., 2007).
63. Karl; D. M. Nutrient dynamics in the deep blue sea. Trends Microbiol. 10, 410-418 (2002).
64. Schindler, D. W. Replication versus realism: The need for ecosystem-scale experiments. Ecosystems 1, 323-334 (1998).
65. de Baar, H. J. W. et al. Synthesis of iron fertilization experiments: From the Iron Age to the Age of Enlightenment. J. Geophys. Res. 110. C09S16 (2005).
66. Boyd, P. W. et al. Mesoscale iron enrichment experiments 1993-2005: Synthesis and future directions, Science 315 612-617 (2007).
67. Thingstad, T. F. et al. Nature of phosphorus limitation in the ultraoligotrophic Eastern Mediterranean. Science 309, 1068-1071 (2005).
68. Berman, T., Walline, P. D., Schneller, A., Rothenberg, J & Townsend, D. W. Secchi disk depth record: A claim for the Eastern Mediterranean. Limnol. Oceanogr. 30, 447-448 (1985).
69. Krom, M. D., Kress, N., Brenner, S. & Gordon, L. I. Phosphorus limitation of primary productivity in the Eastern Mediterranean Sea. Limnol. Oceanogr. 36, 424-432 (1991).
70. Rees, A. P., Law, C. S. & Woodward, E. M. S. High rates of nitrogen fixation during an in-situ phosphate release experiment in the Eastern Mediterranean Sea. Geophys. Res. Lett. 33, L10607 (2006).
71. Krom, M. D. Preface: CYCLOPS dedicated volume. Deep-Sea Res. II 52, 2877-2878 (2005).
72. Chisholm, S. W., Falkowski, P. G. & Cullen, J. J. Discrediting ocean fertilization. Science 294, 309-310 (2001).
73. Doney, S. C. The dangers of ocean acidification. Sci. Amer. 294 58-65 (2006).
74. ZoBell, C. E. Marine Microbiology: A Monograph on Hydrobacteriology (Chronica Botanica Company, Waltham, 1946).
75. Wood, E. J. F. Marine Microbial Ecology (Reinhold Publishing Corp., New York, 1965).
76. Sieburth, J. McN., Smetacek, V. & Lenz, J. Pelagic ecosystem structure: heterotrophic compartments of plankton and their relationship to plankton size fractions. Limnol. Oceanogr. 23, 1256-1263 (1978).
77. Waterbury, J. B., Watson, S. W., Guillard. R. R. L. & Brand, L. E. Widespread occurrence of a unicellular, marine, planktonic, cyanobacterium. Nature, 277, 293-294 (1979).
78. Chisholm, S. W., Olson, R. J., Zettler, E. R., Goericke, R., Waterbury J. B. & Welschmeyer, N. A. A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature 334, 340-343 (1988).
79. Pace, N. R. Time for a change. Nature 441, 289 (2006).
80. Longhurst, A. Ecological Geography of the Sea (Academic Press, San Diego, 1998).
81. DeLong, E. F. et al. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311, 496-503 (2006).
82. Karl, D. M. & Lukas, R. The Hawaii ocean time-series (HOT) program: background, rationale and field implementation. Deep-Sea Res. II 43, 129-156 (1996).
83. 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).
84. Corno, G. et al. Impact of climate forcing on ecosystem processes in the North Pacific Subtropical Gyre. J. Geophys. Res. 112, C04021 (2007).