Community genomics among stratified microbial assemblages in the ocean's interior

Science

Volumn 311, Issue 5760, 2006, Pages 496-503

  DeLong, Edward F ^a   Preston, Christina M ^b   Mincer, Tracy ^a   Rich, Virginia ^a   Hallam, Steven J ^a   Frigaard, Niels Ulrik ^a   Martinez, Asuncion ^a   Sullivan, Matthew B ^a   Edwards, Robert ^c   Brito, Beltran Rodriguez ^c   Chisholm, Sallie W ^a   Karl, David M ^d  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b MONTEREY BAY AQUARIUM RESEARCH INSTITUTE   (United States)

^c SAN DIEGO STATE UNIVERSITY   (United States)

^d UNIVERSITY OF HAWAII   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENERGY METABOLISM; MICROBIAL ASSEMBLAGES; MICROBIAL GENES;

CARBON; GENES; MARINE BIOLOGY; METABOLISM;

MICROBIOLOGY;

COMMUNITY COMPOSITION; GENOME; MICROBIAL ACTIVITY;

ARTICLE; COMMUNITY GENOMICS; COMPARATIVE GENOMIC HYBRIDIZATION; ENERGY METABOLISM; GENE SEQUENCE; GENOME ANALYSIS; MICROFLORA; OCEAN ENVIRONMENT; PLANKTON; PRIORITY JOURNAL; SEQUENCE ANALYSIS; TAXONOMIC RANK; VIRUS CELL INTERACTION; ZONATION;

AMINO ACID SEQUENCE; ARCHAEA; ARCHAEAL PROTEINS; BACTERIA; BACTERIAL PROTEINS; BACTERIOPHAGES; BASE SEQUENCE; CLONING, MOLECULAR; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COSMIDS; DNA, VIRAL; ECOSYSTEM; GENE LIBRARY; GENES, ARCHAEAL; GENES, BACTERIAL; GENES, RRNA; GENOMICS; MOLECULAR SEQUENCE DATA; PACIFIC OCEAN; SEAWATER; SEQUENCE ANALYSIS, DNA; WATER MICROBIOLOGY;

EID: 31544483932     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.1120250     Document Type: Article

References (51)

1. E. Forbes, in Physical Atlas of Natural Phenomena, A. K. Johnston, Ed. (William Blackwood & Sons, London and Edinburgh, 1856).
2. P. W. Hochachka, G. N. Somero, Biochemical Adaptation (Princeton Univ. Press, Princeton, NJ, 1984), pp. 450-495.
3. G. Rocap et al., Nature 424, 1042 (2003).
4. Z. I. Johnson et al., manuscript submitted.
5. N. J. West et al., Microbiology 147, 1731 (2001).
6. A. A. Yayanos, Annu. Rev. Microbiol. 49, 777 (1995).
7. N. R. Pace, Science 276, 734 (1997).
8. M. S. Rappé, S. J. Giovannoni, Annu. Rev. Microbiol. 57, 369 (2003).
9. M. T. Suzuki et al., Microb Ecol (2005).
10. O. Béjá et al., Inviron. Microbiol. 2, 516 (2000).
11. R. M. Morris, M. S. Rappé, E. Urbach, S. A. Connon, S. J. Giovannoni, Appl. Environ. Microbiol. 70, 2836 (2004).
12. S. Y. Moon-van der Staay et al., Nature 409, 607 (2001).
13. J. A. Fuhrman, K. McCallum, A. A. Davis, Nature 356, 148 (1992).
14. E. F. DeLong, Prac. Natl. Acad. Sci. U.S.A. 89, 5685 (1992).
15. M. B. Karner et al., Nature 409, 507 (2001).
16. J. Handelsman, Microbiol. Mol. Biol. Rev. 68, 669 (2004).
17. E. F. Delong, Nat Rev Microbiol (2005).
18. G. W. Tyson et al., Nature 428, 37 (2004).
19. J. C. Venter et al., Science 304, 66 (2004).
20. S. G. Tringe et al., Science 308, 554 (2005).
21. S. J. Hallam et al., Science 305, 1457 (2004).
22. D. M. Karl, K. Lukas, Deep-Sea Res. II 43, 129 (1996).
23. D. M. Karl et al., Deep-Sea Res. II 48, 1449 (2001).
24. R. M. Letelier et al., Limnol. Oceanogr. 49, 508 (2004).
25. E. F. DeLong et al., Appl. Environ. Microbiol. 65, 5554 (1999).
26. A. Pernthaler et al., Appl. Environ. Microbiol. 68, 661 (2002).
27. N. U. Frigaard et al., Nature, in press.
28. S. M. Barns, C. F. Delwiche, J. D. Palmer, N. R. Pace, Proc. Natl. Acad. Sci. U.S.A. 93, 9188 (1996).
29. M. Kanehisa et al., Nucleic Acids Res. 32, D277 (2004).
30. R. L. Tatusov et al., BMC Bioinformatics 4, 41 (2003).
31. R. Overbeek et al., Nucleic Acids Res. 33, 5691 (2005).
32. S. F. Altschul et al., J. Mol. Biol. 215, 403 (1990).
33. M. J. L. de Hoon et al., Bioinformatics 12, 1453 (2004).
34. M. B. Eisen, P. T. Spellman, P. O. Brown, Proc. Natl. Acad. Sci. U.S.A. 94, 14863 (1998).
35. Materials and methods are available as supporting material on Science Online.
36. K. D. Pruitt, T. Tatusova, D. R. Maglott, Nucleic Acids Res. 33, D501 (2005).
37. M. G. Weinbauer, FEMS Microbiol. Rev. 28, 127 (2004).
38. J. Waterbury, F. Valois, Appl. Environ. Microbiol. 59, 3393 (1993).
39. M. B. Sullivan et al., Nature 424, 1047 (2003).
40. R. A. Edwards, F. Rohwer, Nat. Rev. Microbiol. 3, 504 (2005).
41. J. Filee, F. Tetart, C. A. Suttle, H. M. Krisch, Proc. Natl. Acad. Sci. U.S.A. 102, 12471 (2005).
42. M. Breitbart, J. H. Miyake, F. Rohwer, FEMS Microbiol. Lett. 236, 249 (2004).
43. M. B. Sullivan et al., PLoS Biol. 3, e144 (2005).
44. D. Lindell et al., Proc. Natl. Acad. Sci. U.S.A. 101, 11013 (2004).
45. M. G. Weinbauer, I. Brettar, M. G. Hofle, Limnol. Oceanogr. 48, 1457 (2003).
46. F. Azam, Science 280, 694 (1998).
47. C. R. Woese, Microbiol. Mol. Biol. Rev. 68, 173 (2004).
48. E. F. DeLong, D. M. Karl, Nature 437, 336 (2005).
49. (http://hahana.soest.hawaii.edu/hot/parameters.html).
50. (http://hahana.soest.hawaii.edu/hot/hot-dogs).
51. This work was supported by a grant from the Gordon and Betty Moore Foundation, NSF grants MCB-0084211, MCB-0348001, and MCB-0509923 to E.F.D., and OCE-0326616 to D.M.K., and sequencing support from the U.S. Department of Energy Microbial Genomics Program. We thank Dennis Ryan for help with scripting and sequence analyses, the officers and crew of the R/V Ka'imikai-O-Kanaloa and the HOT team for assistance at sea, and L. Fujieki for help with oceanographic data display. J. Chapman, A. Salamov, and P. Richardson of the DOE Joint Genome Institute provided advice and assistance in DNA sequencing and analyses. Sequences have been deposited in GenBank with accession numbers DU731018-DU796676 and DU8008S0-DU800864 corresponding to fosmid end sequences, and accession numbers DQ300508-DQ300926 corresponding to SSU rRNA gene sequences.