Learning to Read the Oceans. Genomics of Marine Phytoplankton

Advances in Marine Biology

Volumn 60, Issue , 2011, Pages 1-39

  Rynearson, Tatiana A ^a   Palenik, Brian ^b  

^a UNIVERSITY OF RHODE ISLAND   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOGEOCHEMICAL CYCLE; CYANOBACTERIUM; DECADAL VARIATION; ENVIRONMENTAL STRESS; EVOLUTIONARY BIOLOGY; FUTURE PROSPECT; GENOME; GENOMICS; LEARNING; MARINE ECOSYSTEM; NANOTECHNOLOGY; NET PRIMARY PRODUCTION; PHYLOGENETICS; PHYTOPLANKTON; SCAVENGING (FEEDING);

CYANOBACTERIA; EUKARYOTA; PROKARYOTA;

EID: 80053323000     PISSN: 00652881     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385529-9.00001-9     Document Type: Chapter

References (134)

1. Ahlgren N.A., Rocap G. Culture isolation and culture-independent clone libraries reveal new marine Synechococcus ecotypes with distinctive light and N physiologies. Applied and Environmental Microbiology 2006, 72:7193-7204.
2. Allen A.E., LaRoche J., Maheswari U., Lommer M., Schauer N., Lopez P.J., Finazzi G., Fernie A.R., Bowler C. Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation. Proceedings of the National Academy of Sciences of the United States of America 2008, 105:10438-10443.
3. Andersen R.A. Biology and systematics of heterokont and haptophyte algae. American Journal of Botany 2004, 91:1508-1522.
4. Armbrust E.V., Berges J.A., Bowler C., Green B.R., Martinez D., Putnam N.H., Zhou S.G., 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., Kroger N., Lau W.W.Y., 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. The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science 2004, 306:79-86.
5. Armbrust E.V., Rynearson T.A., Jenkins B.D. Genomic insights into diatom evolution and metabolism. Genome Evolution of Eukaryotic Microbes 2006, 201-213. Oxford University Press, Oxford. L.A. Katz, D. Bhattacharya (Eds.).
6. Bidle K.D., Azam F. Accelerated dissolution of diatom silica by marine bacterial assemblages. Nature 1999, 397:508-512.
7. 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., Huysman M.J.J., Jenkins B.D., Jiroutova K., Jorgensen R.E., Joubert Y., Kaplan A., Kroger N., Kroth P.G., La Roche J., Lindquist E., Lommer M., Martin-Jezequel V., Lopez P.J., Lucas S., Mangogna M., McGinnis K., Medlin L.K., Montsant A., Secq M.-P.O.-L., Napoli C., Obornik M., Parker M.S., Petit J.-L., Porcel B.M., Poulsen N., Robison M., Rychlewski L., Rynearson T.A., Schmutz J., Shapiro H., Siaut M., Stanley M., Sussman M.R., Taylor A.R., 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. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 2008, 456:239-244.
8. Butterfield N.J. Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology 2000, 26:386-404.
9. Capone D.G., Zehr J.P., Paerl H.W., Bergman B., Carpenter E.J. Trichodesmium, a globally significant marine cyanobacterium. Science 1997, 276:1221-1229.
10. Carpenter E., Janson S. Intracellular cyanobacterial symbionts in the marine diatom Climacodium frauenfeldianum (Bacillariophyceae). Journal of Phycology 2000, 36:540-544.
11. Casteleyn G., Leliaert F., Backeljau T., Debeer A.-E., Kotaki Y., Rhodes L., Lundholm N., Sabbe K., Vyverman W. Limits to gene flow in a cosmopolitan marine planktonic diatom. Proceedings of the National Academy of Sciences 2010, 107:12952-12957.
12. Chappell P.D., Webb E.A. A molecular assessment of the iron stress response in the two phylogenetic clades of Trichodesmium. Environmental Microbiology 2010, 12:13-27.
13. Chisholm S.W., Olson R.J., Zettler E.R., Goericke R., Waterbury J.B., Welschmeyer N.A. A novel free-living Prochlorophyte abundant in the oceanic euphotic zone. Nature 1988, 334:340-343.
14. Chretiennot-Dinet M.-J., Courties C., Vaquer A., Neveux J., Claustre H., Lautier J., Machado M.C. A new marine picoeucaryote: Ostreococcus tauri gen. et sp. nov. (Chlorophyta, Prasinophyceae). Phycologia 1995, 34:285-292.
15. Cuvelier M.L., Allen A.E., Monier A., McCrow J.P., Messie M., Tringe S.G., Woyke T., Welsh R.M., Ishoey T., Lee J.-H., Binder B.J., DuPont C.L., Latasa M., Guigand C.D., Buck K.R., Hilton J., Thiagarajan M., Caler E., Read B., Lasken R.S., Chavez F.P., Worden A.Z. Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proceedings of the National Academy of Sciences of the United States of America 2010, 107:14679-14684.
16. Damste J.S.S., Muyzer G., Abbas B., Rampen S.W., Masse G., Allard W.G., Belt S.T., Robert J.-M., Rowland S.J., Moldowan J.M., Barbanti S.M., Fago F.J., Denisevich P., Dahl J., Trindade L.A.F., Schouten S. The rise of the rhizosolenid diatoms. Science 2004, 304:584-587.
17. Derelle E., Ferraz C., Rombauts S., Rouze P., Worden A.Z., Robbens S., Partensky F., Degroeve S., Echeynie S., Cooke R., Saeys Y., Wuyts J., Jabbari K., Bowler C., Panaud O., Piegu 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. 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 2006, 103:11647-11652.
18. Donia M.S., Hathaway B.J., Sudek S., Haygood M.G., Rosovitz M.J., Ravel J., Schmidt E.W. Natural combinatorial peptide libraries in cyanobacterial symbionts of marine ascidians. Nature Chemical Biology 2006, 2:729-735.
19. Dufresne A., Ostrowski M., Scanlan D.J., Garczarek L., Mazard S., Palenik B.P., Paulsen I.T., de Marsac N.T., Wincker P., Dossat C., Ferriera S., Johnson J., Post A.F., Hess W.R., Partensky F. Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biology 2008, 9:R90.
20. Dupont C.L., Buck K.N., Palenik B., Barbeau K. Nickel utilization in phytoplankton assemblages from contrasting oceanic regimes. Deep Sea Research Part I: Oceanographic Research Papers 2010, 57:553-566.
21. Falkowski P., Barber R., Smetacek V. Biogeochemical controls and feedbacks on ocean primary production. Science 1998, 281:200-206.
22. Falkowski P.G., Katz M.E., Knoll A.H., Quigg A., Raven J.A., Schofield O., Taylor F.J.R. The evolution of modern eukaryotic phytoplankton. Science 2004, 305:354-360.
23. Ferris M.J., Palenik B. Niche adaptation in ocean cyanobacteria. Nature 1998, 396:226-228.
24. Field C.B., Behrenfeld M.J., Randerson J.T., Falkowski P. Primary production of the biosphere: Integrating terrestrial and oceanic components. Science 1998, 281:237-240.
25. Frigeri L.G., Radabaugh T.R., Haynes P.A., Hildebrand M. Identification of Proteins from a Cell Wall Fraction of the Diatom Thalassiosira pseudonana. Molecular & Cellular Proteomics 2006, 5:182-193.
26. Fuller N.J., Marie D., Partensky F., Vaulot D., Post A.F., Scanlan D.J. Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea. Applied and Environmental Microbiology 2003, 69:2430-2443.
27. Gobler C.J., Lonsdale D.J., Boyer G.L. A synthesis and review of causes and impact of harmful brown tide blooms caused by the alga, Aureococcus anophagefferens. Estuaries 2005, 28:726-749.
28. Gobler C.J., Berry D.L., Dyhrman S.T., Wilhelm S.W., Salamov A., Lobanov A.V., Zhang Y., Collier J.L., Wurch L.L., Kustka A.B., Dill B.D., Shah M., VerBerkmoes N.C., Kuo A., Terry A., Pangilinan J., Lindquist E.A., Lucas S., Paulsen I.T., Hattenrath-Lehmann T.K., Talmage S.C., Walker E.A., Koch F., Burson A.M., Marcoval M.A., Tang Y.-Z., LeCleir G.R., Coyne K.J., Berg G.M., Bertrand E.M., Saito M.A., Gladyshev V.N., Grigoriev I.V. Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. Proceedings of the National Academy of Sciences of the United States of America 2011, 108:4352-4357.
29. Green B., Durnford D. The chlorophyll-carotenoid proteins of oxygenic photosynthesis. Annual Reviews of Plant Physiology and Plant Molecular Biology 1996, 47:685-714.
30. Grossman A.R., Karpowicz S.J., Heinnickel M., Dewez D., Hamel B., Dent R., Niyogi K.K., Johnson X., Alric J., Wollman F.A., Li H.Y., Merchant S.S. Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation. Photosynthesis Research 2010, 106:3-17.
31. 2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean. ISME Journal 2010, 4:1180-1192.
32. Johnson P.W., Sieburth J.M. Chroococcoid cyanobacteria in the sea - Ubiquitous and diverse phototrophic biomasss. Limnology and Oceanography 1979, 24:928-935.
33. Jones A.C., Monroe E.A., Eisman E.B., Gerwick L., Sherman D.H., Gerwick W.H. The unique mechanistic transformations involved in the biosynthesis of modular natural products from marine cyanobacteria. Natural Product Reports 2010, 27:1048-1065.
34. Kalaitzis J.A., Lauro F.M., Neilan B.A. Mining cyanobacterial genomes for genes encoding complex biosynthetic pathways. Natural Product Reports 2009, 26:1447-1465.
35. Keeling P.J., Archibald J.M., Fast N.M., Palmer J.D. "Comment on "The Evolution of Modern Eukaryotic Phytoplankton".". Science 2004, 306:2191.
36. 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. Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLOS Genetics 2007, 3:2515-2528.
37. Kim E., Harrison J.W., Sudek S., Jones M.D.M., Wilcox H.M., Richards T.A., Worden A.Z., Archibald J.M. Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life. Proceedings of the National Academy of Sciences of the United States of America 2011, 108:1496-1500.
38. Koester J.A., Swalwell J.E., von Dassow P., Armbrust E.V. Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii (Bacillariophyta). BMC Evolutionary Biology 2010, 10:1.
39. Kooistra W.H.C.F., Medlin L.K. Evolution of the diatoms (Bacillariophyta) IV. A reconstruction of their age from small subunit rRNA coding regions and the fossil record. Molecular Phylogenetics and Evolution 1996, 3:391-407.
40. Kroeger N., Bergsdorf C., Sumper M. A new calcium binding glycoprotein family constitutes a major diatom cell wall component. EMBO Journal 1994, 13:4676-4683.
41. Kroeger N., Deutzmann R., Bergsdorf C., Sumper M. Species-specific polyamines from diatoms control silica morphology. Proceedings of the National Academy of Sciences of the United States of America 2000, 97:14133-14138.
42. Kroeger N., Lorenz S., Brunner E., Sumper M. Self-Assembly of highly phosphorylated silaffins and their function in biosilica morphogenesis. Science 2002, 298:584-586.
43. Lea P., Miflin B. Transport and metabolism of asparagine and other nitrogen compounds within the plant. The Biochemistry of Plants 1980, 569-607. Academic Press, New York. P. Stumpt, E. Conn (Eds.).
44. Levitan O., Sudhaus S., LaRoche J., Berman-Frank I. The influence of pCO(2) and temperature on gene expression of carbon and nitrogen pathways in Trichodesmium IMS101. PLOS One 2010, 5:e15104.
45. Lewin R.A., Cheng L. Prochloron: A microbial enigma 1989, Chapman and Hall, New York.
46. Lewis L.A., McCourt R.M. Green algae and the origin of land plants. American Journal of Botany 2004, 91:1535-1556.
47. Lin S.J., Zhang H.A., Zhuang Y.Y., Tran B., Gill J. Spliced leader-based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates. Proceedings of the National Academy of Sciences of the United States of America 2010, 107:20033-20038.
48. Lindell D., Jaffe J.D., Coleman M.L., Futschik M.E., Axmann I.M., Rector T., Kettler G., Sullivan M.B., Steen R., Hess W.R., Church G.M., Chisholm S.W. Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature 2007, 449:83-86.
49. Liu H., Probert I., Uitz J., Claustre H., Aris-Brosou S.P., Frada M., Not F., de Vargas C. Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:12803-12808.
50. Liu H., Aris-Brosou S.P., Probert I., de Vargas C. A time line of the environmental genetics of the Haptophytes. Molecular Biology and Evolution 2010, 27:161-176.
51. Lomas M.W., Gilbert P.M. Comparisons of nitrate uptake, storage, and reduction in marine diatoms and flagellates. Journal of Phycology 2000, 36:903-913.
52. Mann D.G., Droop S.J.M. Biodiversity, biogeography and conservation of diatoms. Hydrobiologia 1996, 336:19-32.
53. Marchetti A., Parker M.S., Moccia L.P., Lin E.O., Arrieta A.L., Ribalet F., Murphy M.E.P., Maldonado M.T., Armbrust E.V. Ferritin is used for iron storage in bloom-forming marine pennate diatoms. Nature 2009, 457:467-470.
54. Martiny A.C., Coleman M.L., Chisholm S.W. Phosphate acquisition genes in Prochlorococcus ecotypes: Evidence for genome-wide adaptation. Proceedings of the National Academy of Sciences of the United States of America 2006, 103:12552-12557.
55. Martiny A.C., Tai A.P.K., Veneziano D., Primeau F., Chisholm S.W. Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus. Environmental Microbiology 2009, 11:823-832.
56. Maumus F., Allen A.E., Mhiri C., Hanhua H., Jabbari K., Vardi A., Grandbastien M.-A., Bowler C. Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. BMC Genomics 2009, 10:624-642.
57. McCarren J., Brahamsha B. Transposon mutagenesis in a marine Synechococcus strain: Isolation of swimming motility mutants. Journal of Bacteriology 2005, 187:4457-4462.
58. Medlin L.K., Kaczmarska I. Evolution of the diatoms: V. Morphological and cytological support for the major clades and a taxonomic revision. Phycologia 2004, 43:245-270.
59. Medlin L.K., Sáez A.G., Young J.R. A molecular clock for coccolithophores and implications for selectivity of phytoplankton extinctions across the K/T boundary. Marine Micropaleontology 2008, 67:69-86.
60. Merchant S.S., Prochnik S.E., Vallon O., Harris E.H., Karpowicz S.J., Witman G.B., Terry A., Salamov A., Fritz-Laylin L.K., Marechal-Drouard L., Marshall W.F., Qu L.H., Nelson D.R., Sanderfoot A.A., Spalding M.H., Kapitonov V.V., Ren Q.H., Ferris P., Lindquist E., Shapiro H., Lucas S.M., Grimwood J., Schmutz J., Cardol P., Cerutti H., Chanfreau G., Chen C.L., Cognat V., Croft M.T., Dent R., Dutcher S., Fernandez E., Fukuzawa H., Gonzalez-Ballester D., Gonzalez-Halphen D., Hallmann A., Hanikenne M., Hippler M., Inwood W., Jabbari K., Kalanon M., Kuras R., Lefebvre P.A., Lemaire S.D., Lobanov A.V., Lohr M., Manuell A., Meir I., Mets L., Mittag M., Mittelmeier T., Moroney J.V., Moseley J., Napoli C., Nedelcu A.M., Niyogi K., Novoselov S.V., Paulsen I.T., Pazour G., Purton S., Ral J.P., Riano-Pachon D.M., Riekhof W., Rymarquis L., Schroda M., Stern D., Umen J., Willows R., Wilson N., Zimmer S.L., Allmer J., Balk J., Bisova K., Chen C.J., Elias M., Gendler K., Hauser C., Lamb M.R., Ledford H., Long J.C., Minagawa J., Page M.D., Pan J.M., Pootakham W., Roje S., Rose A., Stahlberg E., Terauchi A.M., Yang P.F., Ball S., Bowler C., Dieckmann C.L., Gladyshev V.N., Green P., Jorgensen R., Mayfield S., Mueller-Roeber B., Rajamani S., Sayre R.T., Brokstein P., Dubchak I., Goodstein D., Hornick L., Huang Y.W., Jhaveri J., Luo Y.G., Martinez D., Ngau W.C.A., Otillar B., Poliakov A., Porter A., Szajkowski L., Werner G., Zhou K.M., Grigoriev I.V., Rokhsar D.S., Grossman A.R., Chlamydomonas A., Team J.G.I.A. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 2007, 318:245-251.
61. 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. 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 2008, 105:1579-1584.
62. 2 fixation domain. Science 2010, 327:1512-1514.
63. Moore L.R., Rocap G., Chisholm S.W. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 1998, 393:464-467.
64. Moshkovitz S., Ehrlich A., Soudry D. Siliceous microfossils of the Upper Cretaceous Mishash formation, Central Negev, Israel. Cretaceous Research 1983, 4:73-194.
65. Moustafa A., Beszteri B., Maier U.G., Bowler C., Valentin K., Bhattacharya D. Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science 2009, 324:1724-1726.
66. Nielsen E.S. Production of organic matter in the sea. Nature 1952, 169:956-957.
67. Nunnery J.K., Mevers E., Gerwick W.H. Biologically active secondary metabolites from marine cyanobacteria. Current Opinion in Biotechnology 2010, 21:787-793.
68. Olson R.J., Chisholm S.W., Zettler E.R., Altabet M.A., Dusenberry J.A. Spatial and temporal distributions of prochlorophyte picoplankton in the North-Atlantic ocean. Deep Sea Research Part A. Oceanographic Research Papers 1990, 37:1033-1051.
69. Olson R.J., Chisholm S.W., Zettler E.R., Armbrust E.V. Pigments, size, and distribution of Synechococcus in the North-Atlantic and Pacific oceans. Limnology and Oceanography 1990, 35:45-58.
70. Orchard E.D., Webb E.A., Dyhrman S.T. Molecular analysis of the phosphorus starvation response in Trichodesmium spp. Environmental Microbiology 2009, 11:2400-2411.
71. Palenik B. Cyanobacterial community structure as seen from RNA-polymerase gene sequence analysis. Applied and Environmental Microbiology 1994, 60:3212-3219.
72. Palenik B. Recent functional genomics studies in marine Synechococcus. Functional Genomics and Evolution of Photosynthetic Systems 2011, 103-118. Springer, Amsterdam. R. Burnap, W. Vermaas (Eds.).
73. Palenik B., Brahamsha B., Larimer F.W., Land M., Hauser L., Chain P., Lamerdin J., Regala W., Allen E.E., McCarren J., Paulsen I., Dufresne A., Partensky F., Webb E.A., Waterbury J. The genome of a motile marine Synechococcus. Nature 2003, 424:1037-1042.
74. Palenik B., Ren Q.H., 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. 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 2006, 103:13555-13559.
75. Palenik B., Grimwood J., Aerts A., Rouze 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.V., 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. 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 2007, 104:7705-7710.
76. Palenik B., Ren Q., Tai V., Paulsen I.T. Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity. Environmental Microbiology 2009, 11:349-359.
77. Partensky F., Garczarek L. Prochlorococcus: Advantages and limits of minimalism. Annual Review of Marine Science 2010, 2:305-331.
78. Pierson L., Gaffney T., Lam S, Gong F. Molecular analysis of genes encoding phenazine biosynthesis in the biological control bacterium, Pseudomonas aureofaciens 30-84. FEMS Microbiology Letters 1995, 134:299-307.
79. Poulsen N., Kroeger N. Silica morphogenesis by alternative processing of silaffins in the diatom Thalassiosira pseudonana. Journal of Biological Chemistry 2004, 279:42993-42999.
80. Quinn P., Bowers R.M., Zhang X., Wahlund T.M., Fanelli M.A., Olszova D., Read B.A. cDNA microarrays as a tool for identification of biomineralization proteins in the coccolithophorid Emiliania huxleyi (Haptophyta). Applied and Environmental Microbiology 2006, 72:5512-5526.
81. Rocap G., Distel D.L., Waterbury J.B., Chisholm S.W. Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Applied and Environmental Microbiology 2002, 68:1180-1191.
82. 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. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 2003, 424:1042-1047.
83. Rosado C.J. A common fold mediates vertebrate defense and bacterial attack. Science 2007, 317:1548-1551.
84. Rothpletz A. ber die Flysch-Fucoiden und einige andere fossile Algen, sowie über liasische, Diatomeen führende Horenschwämme. Zeitschrift der Deutschen Geologischen Gesellschaft 1896, 48:854-914.
85. Round F.E., Crawford R.M., Mann D.G. The Diatoms 1990, Cambridge University Press, Cambridge.
86. Rusch D.B., Martiny A.C., Dupont C.L., Halpern A.L., Venter J.C. Characterization of Prochlorococcus clades from iron-depleted oceanic regions. Proceedings of the National Academy of Sciences of the United States of America 2010, 107:16184-16189.
87. Rynearson T.A., Armbrust E.V. Genetic differentiation among populations of the planktonic marine diatom Ditylum brightwellii (Bacillariophyceae). Journal of Phycology 2004, 40:34-43.
88. Rynearson T.A., Armbrust E.V. Maintenance of clonal diversity during a spring bloom of the centric diatom Ditylum brightwellii. Molecular Ecology 2005, 14:1631-1640.
89. Rynearson T.A., Lin E.O., Armbrust E.V. Metapopulation structure in the planktonic diatom Ditylum brightwellii (Bacillariophyceae). Protist 2009, 60:11-121.
90. Saez A.G., Probert I., Geisen M., Quinn P., Young J.R., Medlin L.K. Pseudo-cryptic speciation in coccolithophores. Proceedings of the National Academy of Sciences of the United States of America 2003, 1-6.
91. Sandh G., Ran L.A., Xu L.H., Sundqvist G., Bulone V., Bergman B. Comparative proteomic profiles of the marine cyanobacterium Trichodesmium erythraeum IMS101 under different nitrogen regimes. Proteomics 2011, 11:406-419.
92. Scanlan D.J., Ostrowski M., Mazard S., Dufresne A., Garczarek L., Hess W.R., Post A.F., Hagemann M., Paulsen I., Partensky F. Ecological genomics of marine picocyanobacteria. Microbiology and Molecular Biology Reviews 2009, 73:249-299.
93. Scheffel A., Poulsen N., Shian S., Kroeger N. Nanopatterned protein microrings from a diatom that direct silica morphogenesis. Proceedings of the National Academy of Sciences of the United States of America 2011, 108:3175-3180.
94. Schmid A.M.M. 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 2003, 39:122-138.
95. Schmidt E.W., Nelson J.T., Rasko D.A., Sudek S., Eisen J.A., Haygood M.G., Ravel J. Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:7315-7320.
96. Soria-Dengg S., Hortsman U. Ferrioxamines B and E as iron sources for the marine diatom Phaeodactylum tricornutum. Marine Ecology Progress Series 1995, 127:269-277.
97. Steglich C., Futschik M., Rector T., Steen R., Chisholm S.W. Genome-wide analysis of light sensing in Prochlorococcus. Journal of Bacteriology 2006, 188:7796-7806.
98. Steinberg D.K., Carlson C.A., Bates N.R., Johnson R.J., Michaels A.F., Knap A.H. Overview of the US JGOFS Bermuda Atlantic Time-series Study (BATS): A decade-scale look at ocean biology and biogeochemistry. Deep Sea Research Part II: Topical Studies in Oceanography 2001, 48:1405-1447.
99. Strickland J.D. Phytoplankton and marine primary production. Annual Review of Microbiology 1965, 19:127-162.
100. Stuart R.K., Dupont C.L., Johnson D.A., Paulsen I.T., Palenik B. Coastal strains of marine Synechococcus species exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to those of open-ocean strains. Applied and Environmental Microbiology 2009, 75:5047-5057.
101. Su Z.C., Mao F.L., Dam P., Wu H.W., Olman V., Paulsen I.T., Palenik B., Xu Y. Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102. Nucleic Acids Research 2006, 34:1050-1065.
102. Sudek S., Haygood M.G., Youssef D.T.A., Schmidt E.W. Structure of trichamide, a cyclic peptide from the bloom-forming cyanobacterium Trichodesmium erythraeum, predicted from the genome sequence. Applied and Environmental Microbiology 2006, 72:4382-4387.
103. Sutak R., Slapeta J., San Roman M., Camadro J.-M., Lesuisse E. Nonreductive iron uptake mechanism in the marine alveolate Chromera velia. Plant Physiology 2010, 154:991-1000.
104. Swingley W.D., Chen M., Cheung P.C., Conrad A.L., Dejesa L.C., Hao J., Honchak B.M., Karbach L.E., Kurdoglu A., Lahiri S., Mastrian S.D., Miyashita H., Page L., Ramakrishna P., Satoh S., Sattley W.M., Shimada Y., Taylor H.L., Tomo T., Tsuchiya T., Wang Z.T., Raymond J., Mimuro M., Blankenship R.E., Touchman J.W. Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acarylochloris marina. Proceedings of the National Academy of Sciences of the United States of America 2008, 105:2005-2010.
105. Tai V., Palenik B. Temporal variation of Synechococcus clades at a coastal Pacific ocean monitoring site. ISME Journal 2009, 3:903-915.
106. Tai V., Paulsen I.T., Phillippy K., Johnson D.A., Palenik B. Whole-genome microarray analyses of Synechococcus-Vibrio interactions. Environmental Microbiology 2009, 11:2698-2709.
107. Tetu S.G., Brahamsha B., Johnson D.A., Tai V., Phillippy K., Palenik B., Paulsen I.T. Microarray analysis of phosphate regulation in the marine cyanobacterium Synechococcus sp. WH 8102. ISME Journal 2009, 3:835-849.
108. Thamatrakoln K., Hildebrand M. Analysis of Thalassiosira pseudonana silicon transporters indicates distinct regulatory levels and transport activity through the cell cycle. Eukaryotic Cell 2007, 6:271-279.
109. Thierstein H.R., Geitzenauer K.R., Molfino B. Global synchroneity of late quaternary coccolith datum levels - validation by oxygen isotopes. Geology 1977, 5:400-404.
110. Thomas, E.V., Phillippy, K.H., Brahamsha, B., Haaland, D.M., Timlin, J.A., Elbourne, L.D.H., Palenik, B. and Paulsen, I.T. (2009). Statistical analysis of microarray data with replicated spots: A case study with Synechococcus WH8102. Comparative and Functional Genomics 2009, 11 pp.
111. Toledo G., Palenik B. Synechococcus diversity in the California current as seen by RNA polymerase (RpoC1) gene sequences of isolated strains. Applied and Environmental Microbiology 1997, 63:4298-4303.
112. Toledo G., Palenik B. A Synechococcus serotype is found preferentially in surface marine waters. Limnology and Oceanography 2003, 48:1744-1755.
113. Tolonen A.C., Aach J., Lindell D., Johnson Z.I., Rector T., Steen R., Church G.M., Chisholm S.W. Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability. Molecular Systems Biology 2006, 2:1-15.
114. Toulza E., Shin M.S., Blanc G., Audic S., Laabir M., Collos Y., Claverie J.M., Grzebyk D. Gene expression in proliferating cells of the dinoflagellate Alexandrium catenella (Dinophyceae). Applied and Environmental Microbiology 2010, 76:4521-4529.
115. Tripp H.J., Bench S.R., Turk K.A., Foster R.A., Desany B.A., Niazi F., Affourtit J.P., Zehr J.P. Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium. Nature 2010, 464:90-94.
116. Villareal T.A., Pilskaln C., Brzezinski M., Lipschultz F., Dennett M., Gardner G.B. Upward transport of oceanic nitrate by migrating diatom mats. Nature 1999, 397:423-425.
117. Volcani B.E. Silicon and Siliceous Structures in Biological Systems 1981, 157-200. Springer, Berlin. T.L. Simpson, B.E. Volcani (Eds.).
118. von Dassow P., Petersen T.W., Chepurnov V.A., Armbrust E.V. Inter- and intraspecific relationships between nuclear DNA content and cell size in selected members of the centric diatom genus Thalassiosira (Bacillariophyceae). Journal of Phycology 2008, 44:335-349.
119. von Dassow P., Ogata H., Probert I., Wincker P., Da Silva C., Audic S., Claverie J.-M., de Vargas C. Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell. Genome Biology 2009, 10:R114.
120. Waterbury J., Watson S., Valois F., Franks D. Biological and ecological characterization of the marine unicellular cyanobacterium Synechococcus. Canadian Bulletin of Fisheries and Aquatic Sciences 1986, 214:71-120.
121. Waterbury J.B., Watson S.W., Guillard R.R.L., Brand L.E. Widespread occurrence of a unicellular, marine, planktonic, cyanobacterium. Nature 1979, 277:293-294.
122. Welsh E.A., Liberton M., Stoeckel J., Loh T., Elvitigala T., Wang C., Wollam A., Fulton R.S., Clifton S.W., Jacobs J.M., Aurora R., Ghosh B.K., Sherman L.A., Smith R.D., Wilson R.K., Pakrasi H.B. The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle. Proceedings of the National Academy of Sciences of the United States of America 2008, 105:15094-15099.
123. Wenzl S., Hett R., Richthammer P., Sumper M. Silacidins: Highly acidic phosphopeptides from diatom shells assist in silica precipitation in vitro. Angewandte Chemie International Edition 2008, 47:1729-1732.
124. West N.J., Schonhuber W.A., Fuller N.J., Amann R.I., Rippka R., Post A.F., Scanlan D.J. Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotides. Microbiology 2001, 147:1731-1744.
125. Wisecaver J.H., Hackett J.D. Transcriptome analysis reveals nuclear-encoded proteins for the maintenance of temporary plastids in the dinoflagellate Dinophysis acuminata. BMC Genomics 2010, 11:366.
126. Worden A.Z., Lee J.-H., Mock T., Rouze 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.X., 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. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 2009, 324:268-272.
127. Yang I., John U., Beszteri S., Glockner G., Krock B., Goesmann A., Cembella A. Comparative gene expression in toxic versus non-toxic strains of the marine dinoflagellate Alexandrium minutum. BMC Genomics 2010, 11:248.
128. Yang I., Selander E., Pavia H., John U. Grazer-induced toxin formation in dinoflagellates: A transcriptomic model study. European Journal of Phycology 2011, 46:66-73.
129. Yoon H.S., Hackett J.D., Ciniglia C., Pinto G., Bhattacharya D. A molecular timeline for the origin of photosynthetic eukaryotes. Molecular Biology and Evolution 2004, 21:809-818.
130. Zehr J.P., Carpenter E., Villareal T.A. New perspectives on nitrogen-fixing microorganisms in tropical and subtropical oceans. Trends in Microbiology 2000, 8:68-73.
131. Zhaxybayeva O., Doolittle W.F., Papke R.T., Gogarten J.P. Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus. Genome Biology and Evolution 2009, 2009:325-339.
132. Zinser E.R., Coe A., Johnson Z.I., Martiny A.C., Fuller N.J., Scanlan D.J., Chisholm S.W. Prochlorococcus ecotype abundances in the North Atlantic Ocean as revealed by an improved quantitative PCR method. Applied and Environmental Microbiology 2006, 72:723-732.
133. Zinser E.R., Lindell D., Johnson Z.I., Futschik M.E., Steglich C., Coleman M.L., Wright M.A., Rector T., Steen R., McNulty N., Thompson L.R., Chisholm S.W. Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph Prochlorococcus. PLOS One 2009, 4.
134. Zwirglmaier K., Jardillier L., Ostrowski M., Mazard S., Garczarek L., Vaulot D., Not F., Massana R., Ulloa O., Scanlan D.J. Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes. Environmental Microbiology 2008, 10:147-161.