Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific Subtropical Gyre

Applied and Environmental Microbiology

Volumn 75, Issue 16, 2009, Pages 5345-5355

  Konstantinidis, Konstantinos T ^a,c   Braff, Jennifer ^a   Karl, David M ^b   DeLong, Edward F ^a  

^a Massachusetts Institute of Technology Cambridge   (United States)

^b UNIVERSITY OF HAWAII   (United States)

^c Georgia Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMMUNITY IS; DEEP SEA; DEEP WATER; GENE CONTENT; GENE EXPRESSION LEVELS; GENETIC ELEMENTS; GENOME SIZES; METABOLIC VERSATILITY; METAGENOMIC ANALYSIS; MICROBIAL COMMUNITIES; NORTH PACIFIC; PACIFIC OCEAN; PLANKTONIC MICROBES; PROPHAGES; PROTEIN SEQUENCES; SEQUENCE DATA; SUBTROPICAL GYRE; WATER DEPTH; WHOLE-GENOME SHOTGUN;

AMINES; AMINO ACIDS; ENERGY RESOURCES; GENE EXPRESSION; OCEANOGRAPHY; ORGANIC ACIDS;

SEAWATER;

TRANSPOSASE;

ADAPTATION; AMINO ACID; COMMUNITY STRUCTURE; COMPARATIVE STUDY; DEEP SEA; GENE EXPRESSION; GENETIC ANALYSIS; GENOMICS; MICROBIAL COMMUNITY; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOME; CONTROLLED STUDY; CRENARCHAEOTA; DEEP SEA SPECIES; ENERGY RESOURCE; EVOLUTIONARY ADAPTATION; GENE EXPRESSION; GENE LIBRARY; HYDROPHOBICITY; METAGENOMICS; MICROBIAL COMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PACIFIC OCEAN; PLANKTON; PROPHAGE; SEA SURFACE WATERS; SPECIES COMPOSITION; TAXONOMIC IDENTIFICATION;

ARCHAEA; ARCHAEAL PROTEINS; BACTERIA; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; ECOSYSTEM; GENOMIC LIBRARY; GENOMICS; HAWAII; METABOLIC NETWORKS AND PATHWAYS; MOLECULAR SEQUENCE DATA; PACIFIC OCEAN; PLANKTON; SEAWATER; SEQUENCE ANALYSIS, DNA;

EID: 68549085316     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00473-09     Document Type: Article

References (46)

1. Agogue, H., M. Brink, J. Dinasquet, and G. J. Herndl. 2008. Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic. Nature 456:788-791.
2. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
3. Beja, O., E. N. Spudich, J. L. Spudich, M. Leclerc, and E. F. DeLong. 2001. Proteorhodopsin phototrophy in the ocean. Nature 411:786-789.
4. Benson, D. A., I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler. 2007. GenBank. Nucleic Acids Res. 35:D21-D25.
5. Berezovsky, I. N., K. B. Zeldovich, and E. I. Shakhnovich. 2007. Positive and negative design in stability and thermal adaptation of natural proteins. PLoS Comput. Biol. 3:e52.
6. Brindley, A. A., R. W. Pickersgill, J. C. Partridge, D. J. Dunstan, D. M. Hunt, and M. J. Warren. 2008. Enzyme sequence and its relationship to hyperbaric stability of artificial and natural fish lactate dehydrogenases. PLoS ONE 3:e2042.
7. Cavicchioli, R. 2006. Cold-adapted archaea. Nat. Rev. Microbiol. 4:331-343.
8. De Corte, D., T. Yokokawa, M. M. Varela, H. Agogue, and G. J. Herndl. 2009. Spatial distribution of Bacteria and Archaea and amoA gene copy numbers throughout the water column of the Eastern Mediterranean Sea. ISME J. 3:147-158.
9. Delong, E. F., D. G. Franks, and A. A. Yayanos. 1997. Evolutionary relationships of cultivated psychrophilic and barophilic deep-sea bacteria. Appl. Environ. Microbiol. 63:2105-2108.
10. DeLong, E. F., C. M. Preston, T. Mincer, V. Rich, S. J. Hallam, N. U. Frigaard, A. Martinez, M. B. Sullivan, R. Edwards, B. R. Brito, S. W. Chisholm, and D. M. Karl. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311:496-503.
11. Eloe, E. A., F. M. Lauro, R. F. Vogel, and D. H. Bartlett. 2008. The deep-sea bacterium Photobacterium profundum SS9 utilizes separate flagellar systems for swimming and swarming under high-pressure conditions. Appl. Environ. Microbiol. 74:6298-6305.
12. Finn, R. D., J. Mistry, B. Schuster-Bockler, S. Griffiths-Jones, V. Hollich, T. Lassmann, S. Moxon, M. Marshall, A. Khanna, R. Durbin, S. R. Eddy, E. L. Sonnhammer, and A. Bateman. 2006. Pfam: clans, web tools and services. Nucleic Acids Res. 34:D247-D251.
13. Frias-Lopez, J., Y. Shi, G. W. Tyson, M. L. Coleman, S. C. Schuster, S. W. Chisholm, and E. F. Delong. 2008. Microbial community gene expression in ocean surface waters. Proc. Natl. Acad. Sci. USA 105:3805-3810.
14. Georlette, D., V. Blaise, T. Collins, S. D'Amico, E. Gratia, A. Hoyoux, J. C. Marx, G. Sonan, G. Feller, and C. Gerday. 2004. Some like it cold: biocatalysis at low temperatures. FEMS Microbiol. Rev. 28:25-42.
15. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63.
16. Grzymski, J. J., B. J. Carter, E. F. DeLong, R. A. Feldman, A. Ghadiri, and A. E. Murray. 2006. Comparative genomics of DNA fragments from six Antarctic marine planktonic bacteria. Appl. Environ. Microbiol. 72:1532-1541.
17. Hallam, S. J., K. T. Konstantinidis, N. Putnam, C. Schleper, Y. Watanabe, J. Sugahara, C. Preston, J. de la Torre, P. M. Richardson, and E. F. DeLong. 2006. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc. Natl. Acad. Sci. USA 103:18296-18301.
18. Hallam, S. J., T. J. Mincer, C. Schleper, C. M. Preston, K. Roberts, P. M. Richardson, and E. F. DeLong. 2006. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol. 4:e95.
19. Haney, P. J., J. H. Badger, G. L. Buldak, C. I. Reich, C. R. Woese, and G. J. Olsen. 1999. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc. Natl. Acad. Sci. USA 96:3578-3583.
20. Karner, M. B., E. F. DeLong, and D. M. Karl. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507-510.
21. Konstantinidis, K. T., and E. F. DeLong. 2008. Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. ISME J. 2:1052-1065.
22. Konstantinidis, K. T., and J. M. Tiedje. 2004. Trends between gene content and genome size in prokaryotic species with larger genomes. Proc. Natl. Acad. Sci. USA 101:3160-3165.
23. Lauro, F. M., and D. H. Bartlett. 2008. Prokaryotic lifestyles in deep sea habitats. Extremophiles 12:15-25.
24. Lawrence, J. 2003. When ELFs are ORFs, but don't act like them. Trends Genet. 19:131-132.
25. Martin-Cuadrado, A. B., P. Lopez-Garcia, J. C. Alba, D. Moreira, L. Monticelli, A. Strittmatter, G. Gottschalk, and F. Rodriguez-Valera. 2007. Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS ONE 2:e914.
26. Methe, B. A., K. E. Nelson, J. W. Deming, B. Momen, E. Melamud, X. Zhang, J. Moult, R. Madupu, W. C. Nelson, R. J. Dodson, L. M. Brinkac, S. C. Daugherty, A. S. Durkin, R. T. DeBoy, J. F. Kolonay, S. A. Sullivan, L. Zhou, T. M. Davidsen, M. Wu, A. L. Huston, M. Lewis, B. Weaver, J. F. Weidman, H. Khouri, T. R. Utterback, T. V. Feldblyum, and C. M. Fraser. 2005. The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses. Proc. Natl. Acad. Sci. USA 102:10913-10918.
27. Ochman, H. 2002. Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes. Trends Genet. 18:335-337.
28. Raes, J., J. O. Korbel, M. J. Lercher, C. von Mering, and P. Bork. 2007. Prediction of effective genome size in metagenomic samples. Genome Biol. 8:R10.
29. Rocha, E. P., J. M. Smith, L. D. Hurst, M. T. Holden, J. E. Cooper, N. H. Smith, and E. J. Feil. 2006. Comparisons of dN/dS are time dependent for closely related bacterial genomes. J. Theor. Biol. 239:226-235.
30. Rost, B. 1999. Twilight zone of protein sequence alignments. Protein Eng. 12:85-94.
31. Rusch, D. B., A. L. Halpern, G. Sutton, K. B. Heidelberg, S. Williamson, S. Yooseph, D. Wu, J. A. Eisen, J. M. Hoffman, K. Remington, K. Beeson, B. Tran, H. Smith, H. Baden-Tillson, C. Stewart, J. Thorpe, J. Freeman, C. Andrews-Pfannkoch, J. E. Venter, K. Li, S. Kravitz, J. F. Heidelberg, T. Utterback, Y. H. Rogers, L. I. Falcon, V. Souza, G. Bonilla-Rosso, L. E. Eguiarte, D. M. Karl, S. Sathyendranath, T. Platt, E. Bermingham, V. Gallardo, G. Tamayo-Castillo, M. R. Ferrari, R. L. Strausberg, K. Nealson, R. Friedman, M. Frazier, and J. C. Venter. 2007. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 5:e77.
32. Sander, C., and R. Schneider. 1991. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9:56-68.
33. Somero, G. N. 1992. Adaptations to high hydrostatic pressure. Annu. Rev. Physiol. 54:557-577.
34. Suyama, M., D. Torrents, and P. Bork. 2006. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34:W609-W612.
35. Tatusov, R., N. Fedorova, J. Jackson, A. Jacobs, B. Kiryutin, E. Koonin, D. Krylov, R. Mazumder, S. Mekhedov, A. Nikolskaya, B. S. Rao, S. Smirnov, A. Sverdlov, S. Vasudevan, Y. Wolf, J. Yin, and D. Natale. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41.
36. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
37. van Nimwegen, E. 2003. Scaling laws in the functional content of genomes. Trends Genet. 19:479-484.
38. Venter, J. C., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, J. A. Eisen, D. Wu, I. Paulsen, K. E. Nelson, W. Nelson, D. E. Fouts, S. Levy, A. H. Knap, M. W. Lomas, K. Nealson, O. White, J. Peterson, J. Hoffman, R. Parsons, H. Baden-Tillson, C. Pfannkoch, Y. H. Rogers, and H. O. Smith. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74.
39. Vezzi, A., S. Campanaro, M. D'Angelo, F. Simonato, N. Vitulo, F. M. Lauro, A. Cestaro, G. Malacrida, B. Simionati, N. Cannata, C. Romualdi, D. H. Bartlett, and G. Valle. 2005. Life at depth: Photobacterium profundum genome sequence and expression analysis. Science 307:1459-1461.
40. von Mering, C., L. J. Jensen, M. Kuhn, S. Chaffron, T. Doerks, B. Kruger, B. Snel, and P. Bork. 2007. STRING 7 - recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 35:D358-D362.
41. Wang, F., J. Wang, H. Jian, B. Zhang, S. Li, X. Zeng, L. Gao, D. H. Bartlett, J. Yu, S. Hu, and X. Xiao. 2008. Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3. PLoS ONE 3:e1937.
42. Whitman, W. B., D. C. Coleman, and W. J. Wiebe. 1998. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA 95:6578-6583.
43. Xu, K., and B. G. Ma. 2007. Comparative analysis of predicted gene expression among deep-sea genomes. Gene 397:136-142.
44. Yang, Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24:1586-1591.
45. Yayanos, A. A. 1995. Microbiology to 10,500 meters in the deep sea. Annu. Rev. Microbiol. 49:777-805.
46. Zeldovich, K. B., I. N. Berezovsky, and E. I. Shakhnovich. 2007. Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput. Biol. 3:e5.