Microbial community genomics in the ocean

Nature Reviews Microbiology

Volumn 3, Issue 6, 2005, Pages 459-469

  DeLong, Edward F ^a  

^a USA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMMUNITY DYNAMICS; COMMUNITY STRUCTURE; ECOLOGY; EVOLUTION; GENETIC VARIABILITY; GENOMICS; MARINE ENVIRONMENT; MICROFLORA; NONHUMAN; PRIORITY JOURNAL; REVIEW; SEA;

BACTERIA; BASE SEQUENCE; CLONING, MOLECULAR; DNA, BACTERIAL; ECOSYSTEM; GENOMICS; NUCLEIC ACID CONFORMATION; SEAWATER;

EID: 19144362371     PISSN: 17401526     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrmicro1158     Document Type: Review

References (113)

1. Woese, C. R. Bacterial evolution. Microbial. Rev. 51, 221-271 (1987).
2. 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).
3. Pace, N. R. A molecular view of microbial diversity and the biosphere. Science 276, 734-740 (1997).
4. Rappe, M. S. & Giovannoni, S. J. The uncultured microbial majority. Annu. Rev. Microbiol. 57, 369-394 (2003).
5. Hugenholtz, P, Goebel, B. M. & Pace, N. R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180, 4765-4774 (1998).
6. DeLong, E. F. Microbial seascapes revisited. Curr. Opin. Microbiol. 4, 290-295 (2001).
7. Wright, T D., Vergin, K. L., Boyd, P. W. & Giovannoni, S. J. A novel δ-subdivision proteobacterial lineage from the lower ocean surface layer. Appl. Environ. Microbiol. 63, 1441-1448 (1997).
8. DeLong, E. F. Archaea in coastal marine environments. Proc. Natl Acad. Sci. USA 89, 5685-5689 (1992).
9. Bult, C. J. et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273, 1058-1073 (1996).
10. 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).
11. Rocap, G. et al. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424, 1042-1047 (2003).
12. Palenik, B. et al. The genome of a motile marine Synechococcus. Nature 424, 1037-1042 (2003).
13. Hou, S. et al. Genome sequence of the deep-sea γ-proteobacterium Idiomarina Ioihiensis reveals amino acid fermentation as a source of carbon and energy. Proc. Natl Acad. Sci. USA 101, 18036-18041 (2004).
14. Moran, M. A. et al. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432, 910-913 (2004).
15. Chen, C. Y. et al. Comparative genome analysis of Vibrio vulnificus, a marine pathogen. Genome Res. 13, 2577-2587 (2003).
16. Makino K. et al. Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae. Lancet 361, 743-749 (2003).
17. Nelson, K. E. et al. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399, 323-329 (1999).
18. Rabus, R. et al. The genome of Desufotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments. Environ. Microbiol. 6, 887-902 (2004).
19. 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).
20. Takami, H., Takaki, Y. & Uchiyama, I. Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments. Nucleic Acids Res. 30, 3927-3935 (2002).
21. Vezzi, A. et al. Life at depth: Photobacterium profundum genome sequence and expression analysis. Science 307, 1459-1461 (2005).
22. 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).
23. Chinen, A., Uchiyama, I. & Kobayashi, I. Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms. Gene 259, 109-121 (2000).
24. Galagan, J. E. et al. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12, 532-542 (2002).
25. Hendrickson, E. L. et al. Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis. J. Bacteriol. 186, 6956-6969 (2004).
26. Kawarabayasi, Y. et al. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 5, 55-76 (1998).
27. Kawarabayasi, Y. et al. Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res. 6, 83-101, 145-152 (1999).
28. Klenk, H. P. et al. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390, 364-370 (1997).
29. Robb, F. T et al. Genomic sequence of hyperthermophile, Pyrococcus furiosus: implications for physiology and enzymology. Methods Enzymol. 330, 134-157 (2001).
30. Slesarev, A. I. et al. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archael methanogens. Proc. Natl Acad. Sci. USA 99, 4644-4649 (2002).
31. Armbrust, E. V. et al. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306, 79-86 (2004).
32. 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).
33. 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).
34. Béjà, O. et al. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289, 1902-1906 (2000).
35. Béjà, O. et al. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415, 630-633 (2002).
36. Breitbart, M. et al. Genomic analysis of uncultured marine viral communities. Proc. Natl Acad. Sci. USA 99, 14250-14255 (2002).
37. Breitbart, M. et al. Diversity and population structure of a near-shore marine-sediment viral community. Proc. Biol. Sci. 271, 565-574 (2004).
38. de la Torre, J. R. et al. Proteorhodopsin genes are distributed among divergent marine bacterial taxa. Proc. Natl Acad. Sci. USA 100, 12830-12835 (2003).
39. Sabehi, G., Beia, O., Suzuki, M. T., Preston, C. M. & DeLong, E. F. Different SAR86 subgroups harbour divergent proteorhodopsins. Environ. Microbiol. 6, 903-910 (2004).
40. Schleper, C. et al. Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J. Bacteriol. 180, 5003-5009 (1998).
41. Vergin, K. L. et al. Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales. Appl. Environ. Microbiol. 64, 3075-3078 (1998).
42. Rondon, M. R. et al. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66, 2541-2547 (2000).
43. Lopez-Garcia, P., Brochier, C., Moreira, D. & Rodriguez-Valera, F. Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers. Environ. Microbiol. 6, 19-34 (2004).
44. Treusch, A. H. et al. Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea. Environ. Microbiol. 6, 970-980 (2004).
45. Moreira, D., Rodriguez-Valera, F. & Lopez-Garcia, P. Analysis of a genome fragment of a deep-sea uncultivated group II euryarchaeote containing 16S rDNA, a spectinomycin-like operon and several energy metabolism genes. Environ. Microbiol. 6, 959-969 (2004).
46. Quaiser, A. et al. Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol. Microbiol. 50, 563-575 (2003).
47. Quaiser, A. et al. First insight into the genome of an uncultivated crenarchaeote from soil. Environ. Microbiol. 4, 603-611 (2002).
48. Schleper, C., Swanson, R. V., Mathur, E. J. & DeLong, E. F. Characterization of a DNA polymerase from the uncultivated psychrophilic archaeon Cenarchaeum symbiosum. J. Bacteriol. 179, 7803-7811 (1997).
49. Preston, C. M., Wu, K. Y., Molinski, T. F. & DeLong, E. F. A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov. Proc. Natl Acad. Sci. USA 93, 6241-6246 (1996).
50. Handelsman, J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68, 669-685 (2004).
51. Riesenfeld, C. S., Schloss, P. D. & Handelsman, J. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38, 525-552 (2004).
52. Stein, J. L., Haygood, M. & Fellback, H. Nucleotide sequence and expression of a deep-sea ribulose-1,5-bisphosphate carboxylase gene cloned from a chemoautotrophic bacterial endosymbiont. Proc. Natl Acad. Sci. USA 87, 8850-8854 (1990).
53. Cottrell, M. T., Moore, J. A. & Kirchman, D. L. Chitinases from uncultured marine microorganisms. Appl. Environ. Microbiol. 65, 2553-2557 (1999).
54. Hallam, S. J. et al. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305, 1457-1462 (2004).
55. Tringe, S. G. et al. Comparative metagenomics of microbial communities. Science 308, 554-557 (2005).
56. DeLong, E. F. in Microbial Genomics (eds Fraser, C. M., Nelson., K. E. & Read, T. D.) 419-442 (Human Press Inc., Totowa, New Jersey, 2004).
57. DeLong, E. F. Microbial population genomics and ecology. Curr. Opin. Microbiol. 5, 520-524 (2002).
58. DeLong, E. F. Towards microbial systems science: integrating microbial perspective, from genomes to biomes. Environ. Microbiol. 4, 9-10 (2002).
59. Rodriguez-Valera, F. Approaches to prokaryotic biodiversity: a population genetics perspective. Environ. Microbiol. 4, 628-633 (2002).
60. Rodriguez-Valera, F. Environmental genomics, the big picture? FEMS Microbiol. Lett. 231, 153-158 (2004).
61. Beja, O. To BAC or not to BAC: marine ecogenomics. Curr. Opin. Biotechnol. 15, 187-190 (2004).
62. Doney, S. C., Abbott, M. R., Cullen, J. J., Karl, D. M. & Rothstein, L. From genes to ecosystems: the ocean's new frontier. Frontiers in Ecology and the Environment 2, 457-466 (2004).
63. Kim, U.-J., Shizuya, H., Dejong, P., Birren, B. & Simon, M. Stable propagation of cosmid sized human DNA inserts in an F-factor based vector. Nucleic Acids Res. 20, 1083-1185 (1992).
64. Shizuya, H. et al. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Natl Acad. Sci. USA 89, 8794-8797 (1992).
65. Béjà, O. et al. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2, 516-529 (2000).
66. Fleischmann, R. D. et al. Whole-genome random sequencing and assembly of Haemiophilus influenzae Rd. Science 269, 496-512 (1995).
67. Tamas, I. et al. 50 million years of genomic stasis in endosymbiotic bacteria. Science 296, 2376-2379 (2002).
68. Shigenobu, S., Watanabe, H., Hattori, M., Sakaki, Y. & Ishikawa, H. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407, 81-86 (2000).
69. Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37-43 (2004).
70. Waterston, R. H., Lander, E. S. & Sulston, J. E. On the sequencing of the human genome. Proc. Natl Acad. Sci. USA 99, 3712-3716 (2002).
71. Waterston, R. H., Lander, E. S. & Sulston, J. E. More on the sequencing of the human genome. Proc. Natl Acad. Sci. USA 100, 3022-3024; author reply 3025-3026 (2003).
72. Oz. A., Sabehi, G., Koblizek, M., Massana, R. & Beja, O. Roseobacter-like bacteria in Red and Mediterranean Sea aerobic anoxygenic photosynthetic populations. Appl. Environ. Microbiol. 71, 344-353 (2005).
73. Sabehi, G. et al. Novel proteorhodopsin variants from the Mediterranean and Red Seas. Environ. Microbiol. 5, 842-849 (2003).
74. Man, D. et al. Diversification and spectral tuning in marine proteorhodopsins. EMBO J. 22, 1725-1731 (2003).
75. Béjà, O., Spudich, E. N., Spudich, J. L., Leclerc, M. & DeLong, E. F. Proteorhodopsin phototrophy in the ocean. Nature 411, 786-789 (2001).
76. Falkowski, P. G. & de Vargas, C. Shotgun sequencing in the sea: a blast from the past? Science 304, 58-60 (2004).
77. Venter, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74 (2004).
78. Kruger, M. et al. A conspicuous nickel protein in microbial mats that oxidize methane anaerobically. Nature 426, 878-881 (2003).
79. Teeling, H., Meyerdierks, A., Bauer, M., Amann, R. & Glockner, F. O. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ. Microbiol. 6, 938-947 (2004).
80. Bielawski, J. P., Dunn, K. A., Sabehi, G. & Beja, O. Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment. Proc. Natl Acad. Sci. USA 101, 14824-14829 (2004).
81. Krebs, R. A., Alexiev, U., Partha, R., DeVita, A. M. & Braiman, M. S. Detection of fast light-activated H+ release and M intermediate formation from proteorhodopsin. BMC Physiol. 2, 5 (2002).
82. Friedrich, T. et al. Proteorhodopsin is a light-driven proton pump with variable vectoriality. J. Mol. Biol. 321, 821-838 (2002).
83. Varo, G., Brown, L. S., Lakatos, M. & Lanyi, J. K. Characterization of the photochemical reaction cycle of proteorhodopsin. Biophys. J. 84, 1202-1207 (2003).
84. Lakatos, M., Lanyi, J. K., Szakacs, J. & Varo, G. The photochemical reaction cycle of proteorhodopsin at low pH. Biophys. J. 84, 3252-3256 (2003).
85. Dioumaev, A. K. et al. Proton transfers in the photochemical reaction cycle of proteorhodopsin. Biochemistry 41, 5348-5358 (2002).
86. Wang, W. W., Sineshchekov, O. A., Spudich, E. N. & Spudich, J. L. Spectroscopic and photochemical characterization of a deep ocean proteorhodopsin. J. Biol. Chem. 278, 33985-33991 (2003).
87. Lakatos, M. & Varo, G. The influence of water on the photochemical reaction cycle of proteorhodopsin at low and high pH. J. Photochem. Photobiol. B 73, 177-182 (2004).
88. Man-Aharonovich, D. et al. Characterization of RS29, a blue-green proteorhodopsin variant from the Red Sea. Photochem. Photobiol. Sci. 3, 459-462 (2004).
89. Bergo, V., Amsden, J. J., Spudich, E. N., Spudich, J. L. & Rothschild, K. J. Structural changes in the photoactive site of proteorhodopsin during the primary photoreaction. Biochemistry 43, 9075-9083 (2004).
90. Imasheva, E. S., Balashov, S. P., Wang, J. M., Dioumaev, A. K. & Lanyi, J. K. Selectivity of retinal photoisomerization in proteorhodopsin is controlled by aspartic acid 227. Biochemistry 43, 1648-1655 (2004).
91. Dioumaev, A. K., Wang, J. M., Balint, Z., Varo, G. & Lanyi, J. K. Proton transport by proteorhodopsin requires that the retinal Schiff base counterion Asp-97 be anionic. Biochemistry 42, 6582-6587 (2003).
92. Kelemen, B. R., Du, M. & Jensen, R. B. Proteorhodopsin in living color: diversity of spectral properties within living bacterial cells. Biochim. Biophys. Acta 1618, 25-32 (2003).
93. 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).
94. Kolber, Z. S. et al. Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean. Science 292, 2492-2495 (2001).
95. Pradella, S. et al. Genome organization and localization of the pufLM genes of the photosynthesis reaction center in phylogenetically diverse marine α-proteobacteria. Appl. Environ. Microbiol. 70, 3360-3369 (2004).
96. Allgaier, M., Uphoff, H., Felske, A. & Wagner-Dobler, I. Aerobic anoxygenic photosynthesis in Roseobacter clade bacteria from diverse marine habitats. Appl. Environ. Microbiol. 69, 5051-5059 (2003).
97. Giovannoni, S. J., Britschgi, T. B., Moyer, C. L. & Field, K. G. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60-63 (1990).
98. Acinas, S. G. et al. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430, 551-554 (2004).
99. Moore, L. R., Rocap, G. & Chisholm, S. W. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393, 464-467 (1998).
100. Field, K. G. et al. Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl. Environ. Microbiol. 63, 63-70 (1997).
101. Béjà, O. et al. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl. Environ. Microbiol. 68, 335-345 (2002).
102. Garcia-Martinez, J. & Rodriguez-Valera, F. Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I. Mol. Ecol. 9, 935-948 (2000).
103. Klepac-Ceraj, V. et al. High overall diversity and dominance of microdiverse relationships in salt marsh sulphate-reducing bacteria. Environ. Microbiol. 6, 686-698 (2004).
104. Thompson, J. R. et al. Genotypic diversity within a natural coastal bacterioplankton population. Science 307, 1311-1313 (2005).
105. Acinas, S. G., Marcelino, L. A., Klepac-Ceraj, V. & Polz, M. F. Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J. Bacteriol. 186, 2629-2635 (2004).
106. Hinrichs, K. U., Hayes, J. M., Sylva, S. P., Brewer, P. G. & DeLong, E. F. Methane-consuming archaebacteria in marine sediments. Nature 398, 802-805 (1999).
107. Orphan, V J., House, C. H., Hinrichs, K. U., McKeegan, K. D. & DeLong, E. F. Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc. Natl Acad. Sci. USA 99, 7663-7668 (2002).
108. Orphan, V. J., House, C. H., Hinrichs, K. U., McKeegan, K. D. & DeLong, E. F. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293, 484-487 (2001).
109. Hallam, S. J., Girguis, P. R., Preston, C. M., Richardson, P. M. & DeLong, E. F. Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Appl. Environ. Microbiol. 69, 5483-5491 (2003).
110. Detter, J. C. et al. Isothermal strand-displacement amplification applications for high-throughput genomics. Genomics 80, 691-698 (2002).
111. Suzuki, M. T. et al. Phylogenetic screening of ribosomal RNA gene-containing clones in bacterial artificial chromosome (BAC) libraries from different depths in Monterey Bay. Microb. Ecol. 48, 473-488 (2004).
112. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
113. Fitz-Gibbon, S. T. et al. Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc. Natl Acad. Sci. USA 99, 984-989 (2002).