Assembling the marine metagenome, one cell at a time

PLoS ONE

Volumn 4, Issue 4, 2009, Pages

  Woyke, Tanja ^a   Xie, Gary ^b   Copeland, Alex ^a   González, José M ^c   Han, Cliff ^b   Kiss, Hajnalka ^b   Saw, Jimmy H ^b,f   Senin, Pavel ^b,g   Yang, Chi ^b,h   Chatterji, Sourav ^d   Cheng, Jan Fang ^a   Eisen, Jonathan A ^a,d   Sieracki, Michael E ^e   Stepanauskas, Ramunas ^e  

^a DOE JOINT GENOME INSTITUTE   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c UNIVERSIDAD DE LA LAGUNA   (Spain)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e BIGELOW LABORATORY FOR OCEAN SCIENCES   (United States)

^f UNIVERSITY OF HAWAII   (United States)

^g University of Hawai'i at Manoa   (United States)

^h NATIONAL YANG MING UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; PROTEORHODOPSIN; RHODOPSIN; RNA 16S;

ARTICLE; BACTERIAL GENOME; BACTERIUM CULTURE; BIOGEOGRAPHY; CONTROLLED STUDY; DNA SEQUENCE; ECOLOGICAL NICHE; EVOLUTIONARY ADAPTATION; FLAVOBACTERIUM; FLUORESCENCE ACTIVATED CELL SORTING; GENOME SIZE; GEOGRAPHIC DISTRIBUTION; METAGENOMICS; MOLECULAR PHYLOGENY; NONHUMAN; SEQUENCE ANALYSIS; UNITED STATES; ANIMAL; BACTERIAL GENE; BIODIVERSITY; BIOLOGY; GENETICS; GENOMICS; METABOLISM; METHODOLOGY; PHYLOGENY; PLANKTON;

FLAVOBACTERIA;

ANIMALS; BIODIVERSITY; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMICS; MARINE BIOLOGY; PHYLOGENY; PLANKTON; RHODOPSIN; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 65449134335     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0005299     Document Type: Article

References (55)

1. Falkowski PG, Fenchel T, DeLong EF (2008) The Microbial Engines that Drive Earth's Biogeochemical Cycles. Science 320: 1034-1039.
2. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, et al. (2007) The Human Microbiome Project. Nature 449: 804-810.
3. Haefner B (2003) Drugs from the deep: Marine natural products as drug candidates. Drug Discovery Today 8: 536-544.
4. Pace NR, Stahl DA, Lane DJ, Olsen GJ (1986) The Analysis of Natural Microbial-Populations by Ribosomal-RNA Sequences. Advances in Microbial Ecology 9: 1-55.
5. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, et al. (2005) Comparative metagenomics of microbial communities. Science 308: 554-557.
6. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biology 5: e77.
7. Hallam SJ, Konstantinidis KT, Putnam N, Schleper C, Watanabe YI, et al. (2006) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proceedings of the National Academy of Sciences of the United States of America 103: 18296-18301.
8. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43.
9. Woyke T, Teeling H, Ivanova NN, Huntemann M, Richter M, et al. (2006) Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443: 950-955.
10. Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, et al. (2002) Cultivating the uncultured. Proceedings of the National Academy of Sciences of the United States of America 99: 15681-15686.
11. Rappe MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418: 630-633.
12. Stingl U, Tripp HJ, Giovannoni SJ (2007) Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site. ISME Journal 1: 361-371.
13. Beja O, Spudich EN, Spudich JL, Leclerc M, DeLong EF (2001) Proteorhodopsin phototrophy in the ocean. Nature 411: 786-789.
14. 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.
15. Stepanauskas R, Sieracki ME (2007) Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proceedings of the National Academy of Sciences of the United States of America 104: 9052-9057.
16. Lasken RS, Stockwell TB (2007) Mechanism of chimera formation during the Multiple Displacement Amplification reaction. BMC Biotechnology 7.
17. Marcy Y, Ishoey T, Lasken RS, Stockwell TB, Walenz BP, et al. (2007) Nanoliter reactors improve multiple displacement amplification of genomes from single cells. PLoS Genetics 3: 1702-1708.
18. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, et al. (2006) Sequencing genomes from single cells by polymerase cloning. Nature Biotechnology 24: 680-686.
19. Marcy Y, Ouverney C, Bik EM, Losekann T, Ivanova N, et al. (2007) Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proceedings of the National Academy of Sciences of the United States of America 104: 11889-11894.
20. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, et al. (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. International Journal of Systematic and Evolutionary Microbiology 57: 81-91.
21. Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, et al. (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309: 1242-1245.
22. Vila M, Simo R, Kiene RP, Pinhassi J, Gonzalez JM, et al. (2004) Use of microautoradiography combined with fluorescence in situ hybridization to determine dimethylsulfoniopropionate incorporation by marine bacterioplankton taxa. Applied and Environmental Microbiology 70: 4648-4657.
23. Gomez-Consarnau L, Gonzalez JM, Coll-Llado M, Gourdon P, Pacher T, et al. (2007) Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature 445: 210-213.
24. Atama-Ismael N, Sabehi G, Sharon I, Witzel KP, Labrenz M, et al. (2008) Widespread distribution of proteorhodopsins in freshwater and brackish ecosystems. The ISME Journal 2: 656-662.
25. Moran MA, Miller WL (2007) Resourceful heterotrophs make the most of light in the coastal ocean. Nature Reviews Microbiology 5: 792-800.
26. Stingl U, Desiderio RA, Cho JC, Vergin KL, Giovannoni SJ (2007) The SAR92 clade: an abundant coastal clade of culturable marine bacteria possessing proteorhodopsin. Applied and Environmental Microbiology 73: 2290-2296.
27. Punshon S, Moore RM (2008) Photochemical production of molecular hydrogen in lake water and coastal seawater. Marine Chemistry 108: 215-220.
28. Melis A, Zhang L, Forestier M, Ghirardi ML, Seibert M (2000) Sustained photobiological hydrogen gas production upon reversible inactivation of oxygen evolution in the green alga Chlamydomonas reinhardtii. Plant Physiology 122: 127-135.
29. Braun ST, Proctor LM, Zani S, Mellon MT, Zehr JP (1999) Molecular evidence for zooplankton-associated nitrogen-fixing anaerobes based on amplification of the nifH gene. FEMS Microbiology Ecology 28: 273-279.
30. Gonzalez JM, Fernandez-Gomez B, Fernandez-Guerra A, Gomez-Consarnau L, Sanchez O, et al. (2008) Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria). Proceedings of the National Academy of Sciences of the United States of America 105: 8724-8729.
31. Kirchman DL (2002) The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiology Ecology 39: 91-100.
32. Petersohn A, Brigulla M, Haas S, Hoheisel JD, Volker U, et al. (2001) Global analysis of the general stress response of Bacillus subtilis. Journal of Bacteriology 183: 5617-5631.
33. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M, eds. Nucleic acid techniques in bacterial systematics. Chichester, UK: John Wiley.
34. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
35. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
36. Chatterji S, Yamazaki I, Bai Z, Eisen JA (2008) CompostBin: A DNA composition-based algorithm for binning environmental shotgun reads. In: Vingron M, Wong L, eds. Research in computational molecular biology. Berlin/Heidelberg: Springer. pp 17-28.
37. Jolliffe IT (2002) Principal component analysis. New York, NY.
38. Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Research 17: 377-386.
39. Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Research 8: 186-194.
40. Gordon D, Abajian C, Green P (1998) Consed: A graphical tool for sequence finishing. Genome Research 8: 195-202.
41. Han CS, Xie G, Challacombe JF, Altherr MR, Bhotika SS, et al. (2006) Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis. Journal of Bacteriology 188: 3382-3390.
42. Rogers YC, Munk AC, Meincke LJ, Han CS (2005) Closing bacterial genomic sequence gaps with adaptor-PCR. Biotechniques 39: 31-34.
43. Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G, et al. (2006) The integrated microbial genomes (IMG) system. Nucleic Acids Research 34: D344-348.
44. Badger JH, Olsen GJ (1999) CRITICA: Coding region identification tool invoking comparative analysis. Molecular Biology and Evolution 16: 512-524.
45. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Research 27: 4636-4641.
46. Lowe TM, Eddy SR (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25: 955-964.
47. Eddy SR (2002) A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics 3: 18.
48. Bendtsen JD, Nielsen H, Von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. Journal of Molecular Biology 340: 783-795.
49. Krogh A, Larsson B, Von Heijne G, Sonnhammer ELL (2001) Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. Journal of Molecular Biology 305: 567-580.
50. Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, et al. (2005) PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 21: 617-623.
51. Bendtsen JD, Nielsen H, Widdick D, Palmer T, Brunak S (2005) Prediction of twin-arginine signal peptides. BMC Bioinformatics 6: 167.
52. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Research 34: D32-36.
53. Caspi R, Foerster H, Fulcher CA, Hopkinson R, Ingraham J, et al. (2006) MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Research 34: D511-516.
54. Delcher AL, Phillippy A, Carlton J, Salzberg SL (2002) Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Research 30: 2478-2483.
55. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biology 5: R12.