What can we learn from genomics approaches in marine ecology? From sequences to eco-systems biology!

Marine Ecology

Volumn 33, Issue 2, 2012, Pages 131-148

  Mock, Thomas ^a   Kirkham, Amy ^a  

^a UNIVERSITY OF EAST ANGLIA   (United Kingdom)

Author keywords

Adaptation; Algae; Bacteria; Biogeochemistry; Biological oceanography; Evolution; Genomics; Marine ecology; Metagenomics; Microbes; Phytoplankton

Indexed keywords

ADAPTATION; ALGA; BACTERIUM; BIOGEOCHEMISTRY; ECOSYSTEM RESPONSE; ENVIRONMENTAL STRESS; EVOLUTION; GENETIC ANALYSIS; GENOMICS; MARINE ECOSYSTEM; PHYTOPLANKTON; SPECIATION (BIOLOGY);

ALGAE; BACTERIA (MICROORGANISMS);

EID: 84860143072     PISSN: 01739565     EISSN: 14390485     Source Type: Journal    
DOI: 10.1111/j.1439-0485.2011.00479.x     Document Type: Review

References (92)

1. Aminov R.I., Mackie R.I. (2007) Evolution and ecology of antibiotic resistance genes. FEMS Microbiology Letters, 271, 147-161.
2. Angly F.E., Felts B., Breitbart M., Salamon P., Edwards R.A., Carlson C., Chan A.M., Haynes M., Kelley S., Liu H., Mahaffy J.M., Mueller J.E., Nulton J., Olson R., Parsons R., Rayhawk S., Suttle C.A., Rohwer F. (2006) The marine viromes of four oceanic regions. PLoS Biology, 4, e368.
3. Armbrust E.V., Berges J.A., Bowler C., Green B.R., Martinez D., Putnam N.H., Zhou S., Allen A.E., Apt K.E., Bechner M., Brzezinski M.A., Chaal B.K., Chiovitti A., Davis A.K., Demarest M.S., Detter J.C., Glavina T., Goodstein D., Hadi M.Z., Hellsten U., Hildebrand M., Jenkins B.D., Jurka J., Kapitonov V.V., Kröger N., Lau W.W., Lane T.W., Larimer F.W., Lippmeier J.C., Lucas S., Medina M., Montsant A., Obornik M., Parker M.S., Palenik B., Pazour G.J., Richardson P.M., Rynearson T.A., Saito M.A., Schwartz D.C., Thamatrakoln K., Valentin K., Vardi A., Wilkerson F.P., Rokhsar D.S. (2004) The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science, 306, 79-86.
4. Bossdorf O., Richards C.L., Pigliucci M. (2008) Epigenetics for ecologists. Ecological Letters, 11, 106-115.
5. Bowler C., Allen A.E., Badger J.H., Grimwood J., Jabbari K., Kuo A., Maheswari U., Martens C., Maumus F., Otillar R.P., Rayko E., Salamov A., Vandepoele K., Beszteri B., Gruber A., Heijde M., Katinka M., Mock T., Valentin K., Verret F., Berges J.A., Brownlee C., Cadoret J.-P., Chiovitti A., Choi C.J., Coesel S., De Martino A., Detter J.C., Durkin C., Falciatore A., Fournet J., Haruta M., Huysmann M., Jenkins B.D., Jiroutova K., Jorgensen R.E., Joubert Y., Kaplan A., Kroeger N., Kroth P., La Roche J., Lindquist E., Lommer M., Martin-Jezequel V., Lopez P.J., Lucas S., Mangogna M., McGinnis K., Medlin L.K., Montsant A., Oudot-Le Secq M.-P., Napoli C., Obornik M., Petit J.-L., Porcel B.M., Poulsen N., Robison M., Rychlewski L., Rynearson T.A., Schmutz J., Schnitzler Parker M., Shapiro H., Siaut M., Stanley M., Sussman M.J., Taylor A., Vardi A., von Dassow P., Vyverman W., Willis A., Wyrwicz L.S., Rokhsar D.S., Weissenbach J., Armbrust E.V., Green B.R., Van de Peer Y., Grigoriev I.V. (2008) The Phaeodactylum genome reveals the dynamic nature and multi-lineage evolutionary history of diatom genomes. Nature, 456, 239-244.
6. Brookfield J.F.Y. (2010) Experimental evolution: the rate of adaptive evolution. Current Biology, 20, R23-R25.
7. Canchaya C., Fournous G., Chibani-Chennoufi S., Dillmann M.L., Bruessow H. (2003) Phage as agents of lateral gene transfer. Current Opinion in Microbiology, 6, 417-424.
8. Cavalier-Smith T. (1999) Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. Journal of Eukaryotic Microbiology, 46, 347-366.
9. Chapin F.S., Matson P.A., Mooney H.A. (2002) Principles of Terrestrial Ecosystem Ecology. Springer, New York: 443.
10. Clark A.G., Kao T.H. (1991) Excess nonsynonymous substitution at shared polymorphic sites among self-incompatibility alleles of Solanaceae. Proceedings of the National Academy of Sciences of the United States of America, 88, 9823-9827.
11. Cock J.M., Sterck L., Rouzé P., Scornet D., Allen A.E., Amoutzias G., Anthouard V., Artiguenave F., Aury J.M., Badger J.H., Beszteri B., Billiau K., Bonnet E., Bothwell J.H., Bowler C., Boyen C., Brownlee C., Carrano C.J., Charrier B., Cho G.Y., Coelho S.M., Collén J., Corre E., Da Silva C., Delage L., Delaroque N., Dittami S.M., Doulbeau S., Elias M., Farnham G., Gachon C.M., Gschloessl B., Heesch S., Jabbari K., Jubin C., Kawai H., Kimura K., Kloareg B., Küpper F.C., Lang D., Le Bail A., Leblanc C., Lerouge P., Lohr M., Lopez P.J., Martens C., Maumus F., Michel G., Miranda-Saavedra D., Morales J., Moreau H., Motomura T., Nagasato C., Napoli C.A., Nelson D.R., Nyvall-Collén P., Peters A.F., Pommier C., Potin P., Poulain J., Quesneville H., Read B., Rensing S.A., Ritter A., Rousvoal S., Samanta M., Samson G., Schroeder D.C., Ségurens B., Strittmatter M., Tonon T., Tregear J.W., Valentin K., von Dassow P., Yamagishi T., Van de Peer Y., Wincker P. (2010) The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature, 465, 617-621.
12. 2. Nature, 9, 129-135.
13. Crombach A., Hogeweg P. (2009) Evolution of resource cycling in ecosystems and individuals. BMC Evolutionary Biology, 9, 122.
14. von Dassow P., Ogata H., Probert I., Wincker P., Da Silva C., Audic S., Claverie J.M., de Vargas C. (2009) Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell. Genome Biology, 10, R114.
15. Davidson K., Sayegh F., Montagnes D.J.S. (2010) Oxyrrhis marina-based models as a tool to interpret protozoan population dynamics. Journal of Plankton Research, 33, 651-663.
16. DeLong E.F. (2009) The microbial ocean from genomes to biomes. Nature, 459, 200-206.
17. Derelle E., Ferraz C., Rombauts S., Rouzé P., Worden A.Z., Robbens S., Partensky F., Degroeve S., Echeynié S., Cooke R., Saeys Y., Wuyts J., Jabbari K., Bowler C., Panaud O., Piégu B., Ball S.G., Ral J.P., Bouget F.Y., Piganeau G., De Baets B., Picard A., Delseny M., Demaille J., Van de Peer Y., Moreau H. (2006) Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proceedings of the National Academy of Sciences of the United States of America, 103, 11647-11652.
18. Derelle E., Ferraz C., Escande M.L., Eychenié S., Cooke R., Piganeau G., Desdevises Y., Bellec L., Moreau H., Grimsley N. (2008) Life-cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga Ostreococcus tauri. PLoS ONE, 28, e2250.
19. Dinsdale E.A., Edwards R.A., Hall D., Angly F., Breitbart M., Bruic J.M., Furlan M., Desnaes C., Haynes M., Li L., McDaniel L., Moran M.A., Nelson K.E., Nilsson C., Olson R., Paul J., Brito B., Ruan Y., Swan B.K., Stevens R., Valentine D.L., Vega Thurber R., Wegley L., White B.A., Rohwe F. (2008) Functional metagenomic profiling of nine biomes. Nature, 452, 629-632.
20. Douglas S., Zauner S., Fraunholz M., Beaton M., Penny S., Deng L.T., Wu X., Reith M., Cavalier-Smith T., Maier U.G. (2001) The highly reduced genome of an enslaved algal nucleus. Nature, 410, 1091-1096.
21. Dufresne A., Salanoubat M., Partensky F., Artiguenave F., Axmann I.M., Barbe V., Duprat S., Galperin M.Y., Koonin E.V., Le Gall F., Makarova K.S., Ostrowski M., Oztas S., Robert C., Rogozin I.B., Scanlan D.J., Tandeau de Marsac N., Weissenbach J., Wincker P., Wolf Y.I., Hess W.R. (2003) Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proceedings of the National Academy of Sciences of the United States of America, 100, 10020-10025.
22. Falkowski P.G., Katz M.E., Knoll A.H., Quigg A., Raven J.A., Schofield O., Taylor F.J.R. (2004) The evolution of modern eukaryotic phytoplankton. Science, 305, 354-360.
23. Field C.B., Behrenfeld M.J., Randerson J.T., Falkowski P. (1998) Primary production of the biosphere: integrating terrestrial and oceanic components. Science, 281, 237-240.
24. Fleischmann R., Adams M., White O., Clayton R., Kirkness E., Kerlavage A., Bult C., Tomb J., Dougherty B., Merrick J. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269, 496-512.
25. Follows M.J., Dutkiewicz S., Grant S., Chisholm S.W. (2007) Emergent biogeography of microbial communities in a model ocean. Science, 315, 1843-1848.
26. Francis C.A., Beman J.M., Kuypers M.M.M. (2007) New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME Journal, 1, 19-27.
27. Fraser C.M., Goeayne J.D., White O., Adams M.D., Clayton R.A., Fleithmann R.D., Bult C.J., Kerlavage A.R., Sutton G., Kelley J.M., Fitchmann R.D., Weidmann J.F., Small K.V., Sandvsky M., Fuhrmann J., Nguyen D., Utterback T.R., Savdek D.M., Phillips C.A., Merrick J.M., Tomb J.F., Doughtery B.A., Bott K.F., Hu P.C., Lucier T.S., Peterson S.N., Smith H.O., Hutchison C.A. III, Venter J.C. (1995) The minimal gene complement of Mycoplasma genitalium. Science, 270, 397-404.
28. Frias-Lopez J., Shi Y., Tyson G.W., Coleman M.L., Schuster S.C., Chisholm S.W., DeLong E.F. (2008) Microbial community gene expression in ocean surface waters. Proceedings of the National Academy of Sciences of the United States of America, 105, 3805-3810.
29. Frommolt R., Werner S., Paulsen H., Goss R., Wilhelm C., Zauner S., Maier U.G., Grossman A.R., Bhattacharya D., Lohr M. (2008) Ancient recruitment by chromists of green algal genes encoding enzymes for carotenoid biosynthesis. Molecular Biology and Evolution, 25, 2653-2667.
30. Gifford S.M., Sharma S., Rinta-Kanto J.M., Moran M.A. (2011) Quantitative analysis of a deeply sequenced marine metatranscriptome. ISME Journal, 5, 461-472.
31. Gilbert J., Field D., Huang Y., Edwards R., Li W., Gilna P., Joint I. (2008) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE, 8, e3042.
32. Gilson P.R., Su V., Slamovits C.H., Reith M.E., Keeling P.J., McFadden G.I. (2006) Complete nucleotide sequence of the chlorarachniophyte nucleomorph: nature's smallest nucleus. Proceedings of the National Academy of Sciences of the United States of America, 103, 9566-9571.
33. Giovannoni S.J., Tripp H.J., Givan S., Podar M., Vergin K.L., Baptista D., Bibbs L., Eads J., Richardson T.H., Noordewier M., Rappé M.S., Short J.M., Carrington J.C., Mathur E.J. (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science, 309, 1242-1245.
34. Gloeckner F.O., Kube M., Bauer M., Teeling H., Lombardot T., Ludwig W., Gade D., Beck A., Borzym K., Heitmann K., Rabus R., Schlesner H., Amann R., Reinhardt R. (2003) Complete genome sequence of the marine planctomycete Pirellula sp. strain 1. Proceedings of the National Academy of Sciences of the United States of America, 100, 8298-8303.
35. Gómez-Consarnau L., Akram N., Lindell K., Pedersen A., Neutze R., Milton D.L., González J.M., Pinhassi J. (2010) Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation. PLoS Biology, 8, e1000358.
36. Gresham D., Desai M.M., Tucker C.M., Jenq H.T., Pai D.A., Ward A., DeSevo C.G., Botstein D., Dunham M.J. (2008) The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genetics, 4, e1000303.
37. Grzymski J.J., Murry A.E., Campbell B.J., Kaplarevic M., Gao G.R., Lee C., Daniel R., Ghadriri A., Feldman R.A., Cary S.C. (2008) Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility. Proceedings of the National Academy of Sciences of the United States of America, 105, 17516-17521.
38. Herring C.D., Raghunathan A., Honisch C., Patel T., Applebee M.K., Joyce A.R., Albert T.J., Blattner F.R., van den Boom D., Cantor C.R., Palsson B.Ø. (2006) Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nature Genetics, 38, 1406-1412.
39. Hessen D.O., Jeyasingh P.D., Neiman M., Weider L.J. (2009) Genome streamlining and the elemental costs of growth. Trends in Ecology and Evolution, 25, 75-80.
40. 2-fixing taxon Crocosphaera watsonii. ISME Journal, 5, 618-631.
41. Hulot F.D., Huisman J. (2004) Allelopathic interactions between phytoplankton species; the roles of heterotrophic bacteria and mixing intensity. Limnology and Oceanography, 49, 1424-1434.
42. Iyer L.M., Koonin E.V., Aravind L. (2004) Evolution of bacterial RNA polymerase: implications for large-scale bacteria phylogeny, domain accretion, and horizontal gene transfer. Gene, 335, 73-88.
43. Jonsson P.R., Pavia H., Toth G. (2009) Formation of harmful algal blooms cannot be explained by allelopathic interactions. Proceedings of the National Academy of Sciences of the United States of America, 106, 11177-11182.
44. Kettler G.C., Martiny A.C., Huang K., Zucker J., Coleman M.L., Rodrigue S., Chen F., Lapidus A., Ferriera S., Johnson J., Steglich C., Church G.M., Richardson P., Chisholm S.W. (2007) Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PloS Genetics, 3, e231.
45. Kooistra H.C.F., Medlin L.K. (1996) Evolution of the diatoms IV. A reconstruction of their age from small subunit rRNA coding regions and the fossil record. Molecular Phylogenetics and Evolution, 6, 391-407.
46. Koonin E.V., Wolf Y.I. (2008) Genomics of Bacteria and Archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Research, 36, 6688-6719.
47. LeQuéré C., Harrison S.P., Prentice I.C., Buitenhuis E.T., Aumont O., Bopp L., Claustre H., DaCunha L.C., Geider R., Giraud X., Klaas C., Kohfeld K.E., Legendre L., Manizza M., Platt T., Rivkin R., Sathyendranath S., Uitz J., Watson A.J., Wolf-Gladrow D. (2005) Ecosystem dynamics based on plankton functional types of global biogeochemistry models. Global Change Biology, 11, 2016-2040.
48. Ludwig W., Schleifer K.H. (1994) Bacterial phylogeny based on 16S and 23S rRNA analysis. FEMS Microbiology Review, 15, 155-173.
49. Lynch M. (2007) The frailty of adaptive hypotheses of the origins of organismal complexity. Proceedings of the National Academy of Sciences of the United States of America, 104, 8597-8604.
50. Lynch M., Conery J.S. (2003) The origins of genome complexity. Science, 302, 1401-1404.
51. Markert S., Arndt C., Felbeck H., Becher D., Sievert S.M., Huegler M., Albrecht D., Robidart J., Bench S., Feldman R.A., Hecker M., Schweder T. (2007) Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila. Science, 315, 247-250.
52. Martin W., Stoebe B., Goremykin V., Hansmann S., Hasegawa M., Kowallik K.V. (1998) Gene transfer to the nucleus and the evolution of chloroplasts. Nature, 393, 162-165.
53. Martin W., Baross J., Kelley D., Russell M.J. (2008) Hydrothermal vents and the origin of life. Nature Review Microbiology, 6, 805-814.
54. Mattick J.S., Makunin I.V. (2006) Non-coding RNA. Human Molecular Genetics, 15, R17-R19.
55. Maumus F., Allen A.E., Mhiri C., Hu H., Jabbari K., Vardi A., Grandbastien M.-A., Bowler C. (2009) Potential impact of stress activated retrotransposons ongenome evolution in a marine diatom. BMC Genomics, 10, 624.
56. McClintock B. (1948) Mutable loci in Maize. Carnegie Institution of Washington Yearbook, 47, 155-169.
57. Mock T., Samanta M.P., Iverson V., Berthiaume C., Robison M., Holtermann K., Durkin C., Bondurant S.S., Richmond K., Rodesch M., Kallas T., Huttlin E.L., Cerrina F., Sussman M.R., Armbrust E.V. (2008) Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses. Proceedings of the National Academy of Sciences of the United States of America, 105, 1579-1584.
58. Monier A., Pagarete A., de Vargas C., Allen M.J., Read B., Claverie J.M., Ogata H. (2009) Horizontal gene transfer of an entire metabolic pathway between an eukaryotic alga and its DNA virus. Genome Research, 19, 1441-1449.
59. Moran M.A. (2009) Metatranscriptomics: eavesdropping on complex microbial communities. Microbe, 4, 329-335.
60. Moustafa A., Beszteri B., Maier U.G., Bowler C., Valentin K., Bhattacharya D. (2009) Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science, 324, 1724-1726.
61. Ochman H., Lawrence J.G., Goisman E.A. (2000) Lateral gene transfer and the nature of bacterial innovation. Nature, 405, 299-303.
62. Odum E.P. (1977) The emergence of ecology as a new integrative discipline. Science, 195, 1289-1293.
63. Odum H.T. (1983) Systems Ecology: An Introduction. Wiley, London: 644.
64. Palenik B., Ren Q., Dupont C.L., Myers G.S., Heidelberg J.F., Badger J.H., Madupu R., Nelson W.C., Brinkac L.M., Dodson R.J., Durkin A.S., Daugherty S.C., Sullivan S.A., Khouri H., Mohamoud Y., Halpin R., Paulsen I.T. (2006) Genome sequence of Synechococcus CC9311: insights into adaptation to a coastal environment. Proceedings of the National Academy of Sciences of the United States of America, 103, 13555-13559.
65. Palenik B., Grimwood J., Aerts A., Rouzé P., Salamov A., Putnam N., Dupont C., Jorgensen R., Derelle E., Rombauts S., Zhou K., Otillar R., Merchant S.S., Podell S., Gaasterland T., Napoli C., Gendler K., Manuell A., Tai V., Vallon O., Piganeau G., Jancek S., Heijde M., Jabbari K., Bowler C., Lohr M., Robbens S., Werner G., Dubchak I., Pazour G.J., Ren Q., Paulsen I., Delwiche C., Schmutz J., Rokhsar D., Van de Peer Y., Moreau H., Grigoriev I.V. (2007) The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proceedings of the National Academy of Sciences of the United States of America, 104, 7705-7710.
66. Parker M.S., Mock T., Armbrust E.V. (2008) Genomic insights into marine microalgae. Annual Reviews of Genetics, 42, 619-645.
67. Patel P.V., Gianoulis T.A., Bjornson R.D., Yip K.Y., Engelman D.M., Gerstein M.B. (2010) Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families. Genome Research, 20, 960-971.
68. Peers G., Price N.M. (2006) Copper-containing plastocyanin used for electron transport by an ocean diatom. Nature, 441, 341-344.
69. Putman R.J., Wratten S.D. (1984) Principles of Ecology. University of California Press, Berkeley and Los Angeles, California: 384.
70. Raes J., Bork P. (2008) Molecular eco-systems biology: towards an understanding of community function. Nature Review Microbiology, 6, 693-699.
71. Rocap G., Larimer F.W., Lamerdin J., Malfatti S., Chain P., Ahlgren N.A., Arellano A., Coleman M., Hauser L., Hess W.R., Johnson Z.I., Land M., Lindell D., Post A.F., Regala W., Shah M., Shaw S.L., Steglich C., Sullivan M.B., Ting C.S., Tolonen A., Webb E.A., Zinser E.R., Chisholm S.W. (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature, 424, 1042-1047.
72. Rusch D.B., Halpern A.L., Sutton G., Heidelberg K.B., Williamson S., Yooseph S., Wu D., Eisen J.A., Hoffman J.M., Remington K., Beeson K., Tran B., Smith H., Baden-Tillson H., Stewart C., Thorpe J., Freeman J., Andrews-Pfannkoch C., Venter J.E., Li K., Kravitz S., Heidelberg J.F., Utterback T., Rogers Y.H., Falcón L.I., Souza V., Bonilla-Rosso G., Eguiarte L.E., Karl D.M., Sathyendranath S., Platt T., Bermingham E., Gallardo V., Tamayo-Castillo G., Ferrari M.R., Strausberg R.L., Nealson K., Friedman R., Frazier M., Venter J.C. (2007) The Sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern tropical Pacific. PLoS Biology, 5, e77.
73. Schmid A.-M.M. (2003) Endobacteria in the diatom Pinnularia (Bacillariophyceae). I. Scattered CT-nucleoids explained: DAPI-DNA complexes stem from exoplastidial bacteria boring into the chloroplasts. Journal of Phycology, 39, 122-138.
74. Schneiker S., Perlova O., Kaiser O., Gerth K., Alici A., Altmeyer M.O., Bartels D., Bekel T., Beyer S., Bode E., Bode H.B., Bolten C.J., Choudhuri J.V., Doss S., Elnakady Y.A., Frank B., Gaigalat L., Goesmann A., Groeger C., Gross F., Jelsbak L., Jelsbak L., Kalinowski J., Kegler C., Knauber T., Konietzny S., Kopp M., Krause L., Krug D., Linke B., Mahmud T., Martinez-Arias R., McHardy A.C., Merai M., Meyer F., Mormann S., Muñoz-Dorado J., Perez J., Pradella S., Rachid S., Raddatz G., Rosenau F., Rückert C., Sasse F., Scharfe M., Schuster S.C., Suen G., Treuner-Lange A., Velicer G.J., Vorhölter F.J., Weissman K.J., Welch R.D., Wenzel S.C., Whitworth D.E., Wilhelm S., Wittmann C., Blöcker H., Pühler A., Müller R. (2007) Complete genome sequence of the myxobacterium Sorangium cellulosum. Nature Biotechnology, 25, 1281-1289.
75. Schuster S.C. (2008) Next-generation sequencing transforms today's biology. Nature Methods, 5, 16-18.
76. Shi Y., Tyson G.W., DeLong E.F. (2009) Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature, 456, 266-269.
77. Sims P.A., Mann D.G., Medlin L.K. (2006) Evolution of diatoms: insights from fossil, biological and molecular data. Phycologia, 45, 361-402.
78. Slapeta J., Lopez-Garcia P., Moreira D. (2006) Global dispersal and ancient cryptic species in the smallest marine eukaryotes. Molecular Biology and Evolution, 23, 23-29.
79. Smith M.W., Feng D.F., Doolittle R.F. (1992) Evolution by acquisition: the case for horizontal gene transfers. Trends in Biochemical Science, 17, 489-493.
80. Steglich C., Futschik M.E., Lindell D., Voss D., Chisholm S.W., Hess W.R. (2008) The challenge of regulation in a minimal photoautotroph: non-coding RNAs in Prochlorococcus. PLoS Genetics, 4, e1000173.
81. Syvanen M. (1994) Horizontal gene transfer: evidence and possible consequences. Annual Review of Genetics, 28, 237-261.
82. Tripp H.J., Bench S.R., Turk K.A., Foster R.A., Desany B.A., Niazi F., Affourtit J.P., Zehr J.P. (2010) Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium. Nature, 464, 90-94.
83. Tunnicliffe V., Flower C.M.R. (1996) Influence of sea-floor spreading on the global hydrothermal vent fauna. Nature, 379, 531-533.
84. Van Dover C.L. (1990) Biogeography of hydrothermal vent communities along seafloor spreading centers. Trends in Ecology and Evolution, 5, 242-246.
85. Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., Wu D., Paulsen I., Nelson K.E., Nelson W., Fouts D.E., Levy S., Knap A.H., Lomas M.W., Nealson K., White O., Peterson J., Hoffman J., Parsons R., Baden-Tillson H., Pfannkoch C., Rogers Y.H., Smith H.O. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304, 66-74.
86. Vieira-Silva S., Rocha E.P.C. (2010) The systemic imprint of growth and its uses in ecological (meta)genomics. PLoS Genetics, 6, e1000808.
87. Waddington C.H. (1953) Genetic assimilation of an acquired character. Evolution, 7, 118-126.
88. Wecker P., Klockow C., Ellrott A., Quast C., Langhammer P., Harder J., Glöckner F.O. (2009) Transcriptional response of the model planctomycete Rhodopirellula baltica SHI to changing environmental conditions. BMC Genomics, 10, 410.
89. Weinberg Z., Perreault J., Meyer M.M., Breaker R.R. (2009) Exceptional structured noncoding RNAs revealed by bacteria metagenome analysis. Nature, 462, 656-659.
90. Woese C.R. (1987) Bacterial evolution. Microbiological Reviews, 51, 221-271.
91. Worden A.Z., Lee J.H., Mock T., Rouzé P., Simmons M.P., Aerts A.L., Allen A.E., Cuvelier M.L., Derelle E., Everett M.V., Foulon E., Grimwood J., Gundlach H., Henrissat B., Napoli C., McDonald S.M., Parker M.S., Rombauts S., Salamov A., Von Dassow P., Badger J.H., Coutinho P.M., Demir E., Dubchak I., Gentemann C., Eikrem W., Gready J.E., John U., Lanier W., Lindquist E.A., Lucas S., Mayer K.F., Moreau H., Not F., Otillar R., Panaud O., Pangilinan J., Paulsen I., Piegu B., Poliakov A., Robbens S., Schmutz J., Toulza E., Wyss T., Zelensky A., Zhou K., Armbrust E.V., Bhattacharya D., Goodenough U.W., Van de Peer Y., Grigoriev I.V. (2009) Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science, 324, 268-272.
92. Woyke T., Xie G., Copeland A., González J.M., Han C., Kiss H., Saw J.H., Senin P., Yang C., Chatterji S., Cheng J.F., Eisen J.A., Sieracki M.E., Stepanauskas R. (2009) Assembling the marine metagenome, one cell at a time. PLoS ONE, 4, e5299.