The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific

PLoS Biology

Volumn 5, Issue 3, 2007, Pages 0398-0431

  Rusch, Douglas B ^a   Halpern, Aaron L ^a   Sutton, Granger ^a   Heidelberg, Karla B ^a,b   Williamson, Shannon ^a   Yooseph, Shibu ^a   Wu, Dongying ^a,c   Eisen, Jonathan A ^a,c   Hoffman, Jeff M ^a   Remington, Karin ^a,d   Beeson, Karen ^a   Tran, Bao ^a   Smith, Hamilton ^a   Baden Tillson, Holly ^a   Stewart, Clare ^a   Thorpe, Joyce ^a   Freeman, Jason ^a   Andrews Pfannkoch, Cynthia ^a   Venter, Joseph E ^a   Li, Kelvin ^a   Kravitz, Saul ^a   Heidelberg, John F ^a,b   Utterback, Terry ^a   Rogers, Yu Hui ^a   Falcón, Luisa I ^e   Souza, Valeria ^e   Bonilla Rosso, Germán ^e   Eguiarte, Luis E ^e   Karl, David M ^f   Sathyendranath, Shubha ^g   Platt, Trevor ^g   Bermingham, Eldredge ^h   Gallardo, Victor ⁱ   Tamayo Castillo, Giselle ^j   Ferrari, Michael R ^k   Strausberg, Robert L ^a   Nealson, Kenneth ^a,b   Friedman, Robert ^a   Frazier, Marvin ^a   Venter, J Craig ^a   more..

^a J CRAIG VENTER INSTITUTE   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d Your Genome   (United States)

^e INSTITUTO DE ECOLOGÍA   (Mexico)

^f UNIVERSITY OF HAWAII   (United States)

^g BEDFORD INSTITUTE OF OCEANOGRAPHY   (Canada)

^h SMITHSONIAN TROPICAL RESEARCH INSTITUTE   (Panama)

ⁱ UNIVERSITY OF CONCEPCIÓN   (Chile)

^j UNIVERSIDAD DE COSTA RICA   (Costa Rica)

^k RUTGERS UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE STRUCTURE; GENOMICS; MARINE SPECIES; PACIFIC OCEAN; PHYLOGENY; SEA; TROPICS; WATER SAMPLING;

EID: 33947238287     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0050077     Document Type: Article

References (104)

1. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: The unseen majority. Proc Natl Acad Sci U S A 95: 6578-6583.
2. Beja O, Koonin EV, Aravind L, Taylor LT, Seitz H, et al. (2002) Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl Environ Microbiol 68: 335-345.
3. DeLong EF, Pace NR (2001) Environmental diversity of bacteria and archaea. Systematic Biol 50: 1-9.
4. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere." Proc Natl Acad Sci U S A 103: 12115-12120.
5. Garrity GM (2001) Bergey's manual of systematic bacteriology. New York; Springer-Verlag.
6. Madigan M, Martinko JM, Parker J (2000) Brock biology of microorganisms. Upper Saddle River (NJ); Prentice Hall. 991 p.
7. Fuhrman JA, McCallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature (London) 356: 148-149.
8. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345: 60-63.
9. Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276: 734-740.
10. Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Ann Rev Microbiol 57: 369-394.
11. Stackebrandt E, Goebel BM (1994) Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44: 846-849.
12. Welch RA, Burland V, Plunkett G 3rd, Redford P, Roesch P, et al. (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci U S A 99: 17020-17024.
13. Linklater E (1972) The voyage of the Challenger. Garden City (NJ); Doubleday. 280 p.
14. Mosley HN (1879) Notes by a naturalist on the "Challenger," being an account of various observations made during the voyage of H.M.S. "Challenger" round the world, in the years 1872-1876. London: Macmillian and Company. 540 p.
15. Thompson SCW, Murray SJ, Nares GS, Thompson FT (1895) Report on the scientific results of the voyage of H.M.S. Challenger during the years 1873-76 under the command of Captain George S. Nares, R.N., F.R.S. and the late Captain Frank Tourle Thomson, R.N. Prepared under the superintendence of the late Sir C. Wyville Thomson, 1885-1895: Edinburgh: printed for H.M. Stationery off. (by order of Her Majesty's Government).
16. Fuhrman JA, Mccallum K, Davis AA (1993) Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl Environ Microbiol 59: 1294-1302.
17. Hewson I, Steele JA, Capone DG, Fuhrman JA (2006) Temporal and spatial scales of variation in bacterioplankton assemblages of oligotrophic surface waters. Mar Ecol Prog Ser 311: 67-77.
18. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families. PLoS Biol 5: e16. doi:10.1371/journal.pbio.0050016
19. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
20. DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496-503.
21. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, et al. (2000) A whole-genome assembly of Drosophila. Science 287: 2196-2204.
22. Lander ES, Waterman MS (1988) Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics 2: 231-239.
23. Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, et al. (2002) The genome sequence of the malaria mosquito Anopheles gambiae. Science 298: 129-149.
24. Kim UJ, Shizuya H, Dejong PJ, Birren B, Simon MI (1992) Stable propagation of cosmid sized human DNA inserts in an F-factor based vector. Nucleic Acids Res 20: 1083-1085.
25. Stein JL, Marsh TL, Wu KY, Shizuya H, DeLong EF (1996) Characterization of uncultivated prokaryotes: Isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 178: 591-599.
26. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
27. Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, et al. (2000) PipMaker: A Web server for aligning two genomic DNA sequences. Genome Res 10: 577-586.
28. Coleman ML, Sullivan MB, Martiny AC, Steglich C, Barry K, et al. (2006) Genomic islands and the ecology and evolution of Prochlorococcus. Science 311: 1768-1770.
29. Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, et al. (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309: 1242-1245.
30. Hagstrom A, Pommier T, Rohwer F, Simu K, Stolte W, et al. (2002) Use of 16S ribosomal DNA for delineation of marine bacterioplankton species. Appl Environ Microbiol 68: 3628-3633.
31. Giovannoni S, Rappe M (2002) Evolution, diversity and molecular ecology of marine Prokaryotes. In: Kirchman DL, editor. Microbial ecology of the oceans. New York: Wiley-Liss. pp. 47-84.
32. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, et al. (2005) Comparative metagenomics of microbial communities. Science 308: 554-557.
33. Haft DH, Selengut JD, White O (2003) The TIGRFAMs database of protein families. Nucleic Acids Res 31: 371-373.
34. Conkright M, Levitus S, Boyer T. (1994) World ocean atlas 1994. Volume 1: Nutrients. Washington, D.C. U.S. Department of Commerce.
35. Levitus S, Burgett R, Boyer T (1994) World ocean atlas 1994. Volume 3: Nutrients. Washington, D.C.: U.S. Department of Commerce.
36. Parekh P, Follows MJ, Boyle E (2004) Modeling the global ocean iron cycle. Global Biogeochem Cycles 18: GB1002.
37. Scanlan DJ, Wilson WH (1999) Application of molecular techniques to addressing the role of P as a key effector in marine ecosystems. Hydrobiologia 401: 149-175.
38. Moore L, Ostrowski M, Scanlan D, Feren K, Sweetsir T (2005) Ecotypic variation in phosphorus acquisition mechanisms within marine picocyanobacteria. Aquat Microb Ecol 39: 257-269.
39. Kelemen BR, Du M, Jensen RB (2003) Proteorhodopsin in living color: Diversity of spectral properties within living bacterial cells. Biochim Biophys Acta 1618: 25-32.
40. Man D, Wang W, Sabehi G, Aravind L, Post AF, et al. (2003) Diversification and spectral tuning in marine proteorhodopsins. EMBO J 22: 1725-1731.
41. Man-Aharonovich D, Sabehi G, Sineshchekov OA, Spudich EN, Spudich JL, et al. (2004) Characterization of RS29, a blue-green proteorhodopsin variant from the Red Sea. Photochem Photobiol Sci 3: 459-462.
42. Bielawski JP, Dunn KA, Sabehi G, Beja O (2004) Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment. Proc Natl Acad Sci U S A 101: 14824-14829.
43. Johnsen S, Sosik H. (2005) Shedding light on light in the ocean. Oceanus Mag 43: 24-28.
44. Braun C, Smirnov S (1993) Why is water blue. J Chem Educ 70: 612-615.
45. Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd A, et al. (2000) Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. Science 289: 1902-1906.
46. de la Torre JR, Christianson LM, Beja O, Suzuki MT, Karl DM, et al. (2003) Proteorhodopsin genes are distributed among divergent marine bacterial taxa. Proc Natl Acad Sci U S A 100: 12830-12835.
47. Sabehi G, Beja O, Suzuki MT, Preston CM, DeLong EF (2004) Different SAR86 subgroups harbour divergent proteorhodopsins. Environ Microbiol 6: 903-910.
48. Frigaard NU, Martinez A, Mincer TJ, DeLong EF (2006) Proteorhodopsin lateral gene transfer between marine planktonic bacteria and archaea. Nature 439: 847-850.
49. Yokoyama S (2000) Phylogenetic analysis and experimental approaches to study color vision in vertebrates. Methods Enzymol 315: 312-325.
50. Read TD, Salzberg SL, Pop M, Shumway M, Umayam L, et al. (2002) Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296: 2028-2033.
51. Brown MV, Fuhrman JA (2005) Marine bacterial microdiversity as revealed by internal transcribed spacer analysis. Aquat Microb Ecol 41: 15-23.
52. Rocap G, Distel DL, Waterbury JB, Chisholm SW (2002) Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Appl Environ Microbiol 68: 1180-1191.
53. Schleper C, DeLong EF, Preston CM, Feldman RA, Wu KY, et al. (1998) Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J Bacteriol 180: 5003-5009.
54. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9: 552-569.
55. Rappe MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418: 630-633.
56. Johnson ZI, Zinser ER, Coe A, McNulty NP, Woodward EM, et al. (2006) Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311: 1737-1740.
57. Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63: 4516-4522.
58. Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65: 4630-4636.
59. Hess WR, Rocap G, Ting CS, Larimer F, Stilwagen S, et al. (2001) The photosynthetic apparatus of Prochlorococcus: Insights through comparative genomics. Photosynth Res 70: 53-71.
60. Martiny AC, Coleman ML, Chisholm SW (2006) Phosphate acquisition genes in Prochlorococcus ecotypes: Evidence for genome-wide adaptation. Proc Natl Acad Sci U S A 103: 12552-12557.
61. Moore LR, Chisholm SW (1999) Photophysiology of the marine cyanobacterium Prochlorococcus: Ecotypic differences among cultured isolates. Limnol Oceanogr 44: 628-638.
62. Moore LR, Rocap G, Chisholm SW (1998) Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393: 464-467.
63. Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, et al. (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 1042-1047.
64. Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW (2005) Three Prochlorococcus cyanophage genomes: Signature features and ecological interpretations. PLoS Biol 3: e144.
65. Ting CS, Rocap G, King J, Chisholm SW (2002) Cyanobacterial photosynthesis in the oceans: The origins and significance of divergent light-harvesting strategies. Trends Microbiol 10: 134-142.
66. Zinser ER, Coe A, Johnson ZI, Martiny AC, Fuller NJ, et al. (2006) Prochlorococcus ecotype abundances in the North Atlantic Ocean as revealed by an improved quantitative PCR method. Appl Environ Microbiol 72: 723-732.
67. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, et al. (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37: 463-464.
68. Thompson JR, Pacocha S, Pharino C, Klepac-Ceraj V, Hunt DE, et al. (2005) Genotypic diversity within a natural coastal bacterioplankton population. Science 307: 1311-1313.
69. Acinas SG, Klepac-Ceraj V, Hunt DE, Pharino C, Ceraj I, et al. (2004) Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430: 551-554.
70. Lawrence JG, Ochman H (1998) Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A 95: 9413-9417.
71. Scheffer M, Rinaldi S, Huisman J, Weissing FJ (2003) Why plankton communities have no equilibrium: Solutions to the paradox. Hydrobiologia 491: 9-18.
72. Hutchinson GE (1961) The paradox of the plankton. Am Nat 95: 137-145.
73. Cohan F (2002) Concepts of bacterial biodiversity for the age of genomics. In: Fraser CM, Read TD, Nelson KE, editors. Microbial genomes. Totowa (New Jersey): Humana Press. pp. 175-194.
74. Hacker J, Blum-Oehler G, Hochhut B, Dobrindt U (2003) The molecular basis of infectious diseases: Pathogenicity islands and other mobile genetic elements. A review. Acta Microbiol Immunol Hung 50: 321-330.
75. McCann KS (2000) The diversity-stability debate. Nature 405: 228-233.
76. Fuller NJ, West NJ, Marie D, Yallop M, Rivlin T, et al. (2005) Dynamics of community structure and phosphate status of picocyanobacterial populations in the Gulf of Aqaba, Red Sea. Limnol Oceanogr 50: 363-375.
77. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-1359.
78. Brown MV, Schwalbach MS, Hewson I, Fuhrman JA (2005) Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: Development and application to a time series. Environ Microbiol 7: 1466-1479.
79. Garcia-Martinez J, Rodriguez-Valera F (2000) Microdiversity of uncultured marine prokaryotes: The SAR11 cluster and the marine Archaea of Group I. Mol Ecol 9: 935-948.
80. Jenkins BD, Steward GF, Short SM, Ward BB, Zehr JP (2004) Fingerprinting Diazotroph communities in the Chesapeake Bay by using a DNA macroarray. Appl Environ Microbiol 70: 1767-1776.
81. Legeckis R (1988) Upwelling off the Gulfs of Panama and Papagayo in the tropical Pacific during March 1985. J Geophys Res 93: 15485-15489.
82. McCreary JP, Lee HS, Enfield DB (1989) The response of the coastal ocean to strong offshore winds: With application to circulation in the gulfs of Tehuantepec and Papagayo. J Mar Res 47: 81-109.
83. Palacios DM (2003) Oceanographic conditions around the Galápagos Archipelago and their influence on Cetacean community structure. [PhD diss]. Corvallis: Oregon State University. 178 p.
84. Christian JR, Lewis MR, Karl DM (1997) Vertical fluxes of carbon, nitrogen, and phosphorus in the North Pacific Subtropical Gyre near Hawaii. J Geophys Res 102: 15667-15677.
85. Doney SC, Abbott MR, Cullen JJ, Karl DM, Rothstein L (2004) From genes to ecosystems: The ocean's new frontier. Front Ecol Environ 2: 457-466.
86. McGillicuddy DJ, Anderson LA, Doney SC, Maltrud ME (2003) Eddy-driven sources and sinks of nutrients in the upper ocean: Results from a 0.1° resolution model of the North Atlantic. Global Biogeochem Cycles 17: 1035.
87. van der Staay SYM, van der Staay GWM, Guillou L, Vaulot D, Claustre H, et al. (2000) Abundance and diversity of prymnesiophytes in the picoplankton community from the equatorial Pacific Ocean inferred from 18S rDNA sequences. Limnol Oceanogr 45: 98-109.
88. Blanchot J, Charpy L, Borgne RL (1989) Size composition of particulate organic matter in the lagoon of Tikehau Atoll (Tuiamotu Archipelago). Mar Biol 102: 329-339.
89. Torréton JP, Dufour P (1996) Bacterioplankton production determined by DNA synthesis, protein synthesis and frequency of dividing cells in Tuamotu atoll lagoons and surrounding ocean. Microb Ecol 32: 185-202.
90. Torréton JP, Dufour P (1996) Temporal and spatial stability of bacterioplankton biomass and productivity in an atoll lagoon. Aquat Microb Ecol 11: 251-261.
91. Rutala WA, Weber DJ (1997) Uses of inorganic hypochlorite (bleach) in health-care facilities. Clin Microbiol Rev 10: 597-610.
92. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning. A laboratory manual. Cold Spring Harbor (NY): Cold Spring Laboratory Press.
93. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74: 5463-5467.
94. Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
95. Felsenstein J (1989) PHYLIP: Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
96. Bingham J, Sudarsanam S (2000) Visualizing large hierarchical clusters in hyperbolic space. Bioinformatics 16: 660-661.
97. Bray JR, Curtis JT. (1957) An ordination of upland forest communities of southern Wisconsin. Ecol Monogr 27: 325-349.
98. Myers G (1999) A fast bit-vector algorithm for approximate string matching based on dynamic programming. J ACM 46: 395-415.
99. Penn K, Wu D, Eisen JA, Ward N (2006) Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska Seamounts. Appl Environ Microbiol 72: 1680-1683.
100. Ludwig W, Strunk O, Westram R, Richter L, Meier H, et al. (2004) ARB: A software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
101. Hugenholtz P (2002) Exploring prokaryotic diversity in the genomic era. Genome Biol 3: REVIEWS0003.
102. Angly F, Rodriguez-Brito B, Bangor D, McNairnie P, Breitbart M, et al. (2005) PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics 6: 41.
103. R Development Core Team (2004) R: A language and environment for statistical computing [computer program]. Vienna, Austria: R Foundation for Statistical Computing. http://www.R-project.org.
104. Gomez-Consarnau L, Gonzalez JM, Coll-Llado M, Gourdon P, Pascher T, et al. (2007) Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature 445: 210-213.