Morphological and habitat evolution in the Cyanobacteria using a compartmentalization approach

Geobiology

Volumn 3, Issue 3, 2005, Pages 145-165

  Sanchez Baracaldo P ^a   Hayes, P K ^a   Blank, C E ^b  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b WASHINGTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; GENOMICS; HABITAT; MORPHOLOGY; PHYLOGENETICS; PHYLOGENY; TAXONOMY;

CYANOBACTERIA; NOSTOCALES;

EID: 33645778267     PISSN: 14724677     EISSN: 14724669     Source Type: Journal    
DOI: 10.1111/j.1472-4669.2005.00050.x     Document Type: Article

References (111)

1. Abed RMM Garcia-Pichel F Hernández-Mariné M ( 2002) Polyphasic characterization of benthic, moderately halophilic, moderately thermophilic cyanobacteria with very thin trichomes and the proposal of Halomicronema excentricum gen. nov., sp. nov. Archives of Microbiology 117, 361 370.
2. Adams DG ( 2000) Heterocyst formation in cyanobacteria. Current Opinion in Microbiology 3, 618 624.
3. Adams DG Duggan PS ( 1999) Heterocyst and akinete differentiation in cyanobacteria. New Phytologist 144, 3 33.
4. Battistuzzi FU Feijao A Hedges SB ( 2004) A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evolutionary Biology 4, 44.
5. Blank CE ( 2002) Microbial life at high temperatures and relationships through deep time. PhD Thesis, University of California, Berkeley.
6. Blank CE ( 2004) Evolutionary timing of the origins of mesophilic sulfate reduction and oxygenic photosynthesis: a phylogenomic dating approach. Geobiology 2, 1 20.
7. Boyer S Johansen JR Flechtner VR ( 2002) Phylogeny and genetic variance in terrestrial Microcoleus (Cyanophyceae) species based on sequence analysis of the 16SrRNA gene and associated 16S-23S ITS region. Journal of Phycology 38, 1222 1235.
8. Brock TD ( 1973) Lower pH limit for the existence of blue-green algae: evolutionary and ecological implications. Science 179, 480 483.
9. Brock TD ( 1978) Thermophilic Microorganisms and Life at High Temperatures. Springer-Verlag, New York.
10. Brown JR Douady CJ Italia MJ Marshall WE Stanhope MJ ( 2001) Universal trees based on large combined protein sequence data sets. Nature Genetics 28, 281 285.
11. Caspi J Amitai G Belenkiy O Pietrokovski S ( 2003) Distribution of split DnaE inteins in cyanobacteria. Molecular Microbiology 50, 1569 1577.
12. Castenholz RW ( 1973) Ecology of blue-green algae in hot springs. In : The Biology of Blue-Green Algae (eds Carr NG Whitton BA). Blackwell Scientific Publications, Oxford, UK, pp. 379 414.
13. Castenholz RW ( 1982) Motility and taxes. In : The Biology of Cyanobacteria (eds Carr NG Whitton BA). Blackwell Scientific Publications, Oxford, UK, pp. 413 439.
14. Castenholz RW ( 2001) Phylum BX. Cyanobacteria. Oxygenic photosynthetic bacteria. In : Bergey's Manual of Systematic Bacteriology. Volume 1: The Archaea and the Deeply Branching and Phototropic Bacteria, 2nd edn (eds Garrity G Boone DR Castenholz RW). Springer-Verlag, New York, pp. 474 487.
15. Castenholz R Waterbury JB ( 1989) Introduction to Cyanobacteria. In : Bergey's Manual of Systematic Bacteriolog Vol. 3 (eds Krieg NR Holt JG). Williams and Wilkens, Baltimore, MD, pp. 1710 1728.
16. Chisholm SW Olsen RJ Zettler ER Goericke R Waterbury JB Welschmeyer NA ( 1988) A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature 334, 340 343.
17. Coddington JA ( 1988) Cladistic tests of adaptational hypotheses. Cladistics 4, 3 22.
18. Cohen Y Jørgensen BB Revsbech NP Poplawski R ( 1986) Adaptation to hydrogen sulfide of oxygenic and anoxygenic photosynthesis among cyanobacteria. Applied and Environmental Microbiology 51, 398 407.
19. Cohen Y Padan E Shilo M ( 1975) Facultative anoxygenic photosynthesis in the cyanobacterium Oscillatoria limnetica. Journal of Bacteriology 123, 855 861.
20. Crosbie ND Pöckl M Weisse T ( 2003) Dispersal and phylogenetic diversity of nonmarine picocyanobacteria, inferred from 16S rRNA gene and cpcBA-intergenic spacer sequence analyses. Applied and Environmental Microbiology 69, 5716 5721.
21. Delwiche CF Kunsel M Palmer JD ( 1995) Phylogenetic analysis of tufA sequences indicates a cyanobacterial origin of all plastids. Molecular Phylogenetics and Evolution 4, 110 128.
22. Dillon JG Castenholz RW ( 1999) Scytonemin, a cyanobacterial sheath pigment, protects against UVC radiation: Implications for early photosynthetic life. Journal of Phycology 35, 678 681.
23. van Dok W Hart BT ( 1996) Akinete diffentiation in Anabaena circinalis (Cyanophyta). Journal of Phycology 32, 557 565.
24. Doolittle WF ( 1999) Phylogenetic classification and the universal tree. Science 284, 2124 2128.
25. Douglas SE Turner S ( 1991) Molecular evidence for the origin of plastids from a cyanobacterium-like ancestor. Journal of Molecular Evolution 33, 267 273.
26. Faith DP ( 1991) Cladistic permutation tests for monophyly and nonmonophyly. Systematic Zoology 40, 366 373.
27. Faith DP Cranston PS ( 1991) Could a cladograms this short have arisen by chance alone? On permutation tests for cladistic structure. Cladistics 7, 1 28.
28. Fani R Gallo R Lio P ( 2000) Molecular evolution of nitrogen fixation: the evolutionary history of nifD, nifK, nifE, and nifN genes. Journal of Molecular Evolution 51, 1 11.
29. Farris JS Källersjö M Kluge AG Bult C ( 1994) Testing significance of incongruence. Cladistics 10, 315 319.
30. Ferris MJ Palenik B ( 1998) Niche adaptation in ocean cyanobacteria. Nature 396, 226 228.
31. Ferris MJ Ruff-Roberts AL Kopezynski ED Bateson MM Ward DM ( 1996) Enrichment culture and microscopy conceal diverse thermophilic Synechococcus population in single hot spring microbial mat habitat. Applied and Environmental Microbiology 62, 1045 1050.
32. Garcia-Pichel F ( 1998) Solar ultraviolet and the evolutionary history of Cyanobacteria. Origins of Life and Evolution of the Biosphere 28, 321 347.
33. Garcia-Pichel F Nübel U Muyzer G ( 1998) The phylogeny of unicellular, extremely halotolerant cyanobacteria. Archives of Microbiology 169, 469 482.
34. Gatesy J Arctander P ( 2000) Hidden morphological support for the phylogenetic placement of Pseudoryx nghetinhensis with bovine bovids: a combined analysis of gross anatomical evidence and DNA sequences from five genes. Systematic Biology 49, 515 538.
35. Giovannoni SJ Turner S Olsen GJ Barnes S Lane DJ Pace NR ( 1988) Evolutionary relationships among cyanobacteria and green chloroplast. Journal of Bacteriology 170, 3584 3592.
36. Gugger MF Hoffmann L ( 2004) Polyphyly of true branching cyanobacteria (Stigonematales). International Journal of Systematics and Evolutionary Microbiology 54, 349 357.
37. Gugger M Lyra C Henriksen P Couté A Humber J-F Sivonen K ( 2002) Phylogenetic comparison of the cyanobacterial genera Anabaena and Aphanizomenon. International Journal of Systematic and Evolutionary Microbiology 52, 1867 1880.
38. Guglielmi G Cohem-Bazire G Bryant D ( 1981) The structure of Gloeobacter violaceus and its phycobilisomes. Archives of Microbiology 129, 181 189.
39. Hansmann S Martin W ( 2000) Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis. International Journal of Systematic and Evolutionary Microbiology 50, 1655 1663.
40. Henson BJ Hesselbrock SM Watson LE Barnum SR ( 2004) Molecular phylogeny of the heterocystous cyanobacteria (subsections IV and V) based on nifD. International Journal of Systematics and Evolutionary Microbiology 54, 493 497.
41. Hoiczyk E ( 1998) Structural and biochemical analysis of the sheath of Phormidium uncinatum. Journal of Bacteriology 180, 3923 3932.
42. Hoiczyk E ( 2000) Gliding motility in cyanobacteria: observations and possible explanations. Archives of Microbiology 174, 11 17.
43. Honda D Yokota A Sugiyama J ( 1999) Detection of seven major evolutionary lineages in cyanobacteria based on the 16S rRNA gene sequence analysis with new sequences of five marine Synechococcus strain. Journal of Molecular Evolution 48, 723 739.
44. House CH Fitz-Gibbon ST ( 2002) Using homolog groups to create a whole-genomic tree of free-living organisms: an update. Journal of Molecular Evolution 54, 539 547.
45. Huelsenbeck JP Ronquist F ( 2001) mrbayes: Bayesian inference of phylogeny. Bioinformatics 17, 754 755.
46. Ishida T Watanabe MM Sugiyama J Yokota A ( 2001) Evidence for polyphyletic origin of the members of the orders of Oscillatoriales and Pleurocapsales as determined by 16S rDNA analysis. FEMS Microbiology Letters 201, 79 82.
47. Ishida T Yokota A Sugiyama J ( 1997) Phylogenetic relationships of filamentous cyanobacterial taxa inferred from 16S rRNA sequence divergence. Journal of General and Applied Microbiology 43, 237 241.
48. Iteman I Rippka R de Marsac NT Herdman M ( 2002) rDNA analyses of planktonic heterocystous cyanobacteria, including members of the genera Anabaenopsis and Cyanospira. Microbiology 148, 481 496.
49. Jain R Rivera MC Lake JA ( 1999) Horizontal gene transfer among genomes: The complexity hypothesis. Proceedings of the National Academy of Sciences, USA 96, 3801 3806.
50. Kishino H Hasegawa M ( 1998) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. Journal of Molecular Evolution 29, 170 179.
51. Kress WJ Price LM Hahn WJ Zimmer EA ( 2001) Unraveling the evolutionary radiation of the families of the Zingiberales using morphological and molecular evidence. Systematic Biology 50, 926 944.
52. Lanchance MA ( 1981) Genetic relatedness of heterocystous cyanobacteria by deoxyribonucleic acid-deoxyribonucleic acid reassociation. International Journal of Systematic Bacteriology 31, 139 147.
53. Litvaitis MK ( 2002) A molecular test of cyanobacterial phylogeny: inferences from constraint analyses. Hydrobiologia 468, 135 145.
54. Maddison D Maddison W ( 2000) macclade, version 4.05, http://macclade.org.
55. Meeks JC Campbell EL Summers ML Wong FC ( 2002) Cellular differentiation in the cyanobacterium Nostoc punctiforme. Archives of Microbiology 178, 395 403.
56. Miller SR Bebout BM ( 2004) Variation in sulfide tolerance of photosystem II in phylogenetically diverse cyanobacteria from sulfidic habitats. Applied and Environmental Microbiology 70, 736 744.
57. Miller SR Castenholz RW ( 2000) Evolution of thermotolerance in hot springs cyanobacteria of the genus Synechococcus. Applied and Environmental Microbiology 66, 4222 4229.
58. Mishler B ( 1994) Cladistic analysis of molecular and morphological data. American Journal of Physical Anthropology 94, 143 156.
59. Mishler BD ( 2005) The logic of the data matrix in phylogenetic analysis. In : Parsimony, Phylogeny, and Genomics (ed. Albert VA). Oxford University Press, Oxford, UK, pp. 57 70.
60. Morden CW Golden SS ( 1989) psbA genes indicate common ancestry of prochlorophytes and chloroplasts. Nature 337, 382 385. Corrigendum 339:400.
61. Neilan BA Burns BP Relman DA Lowe DR ( 2002) Molecular identification of cyanobacteria associated with stromatolites from distinct geographical locations. Astrobiology 2, 271 280.
62. Neilan BA Jacobs D Del Dot T Blackall LL Hawkins PR Cox PT Goodman AE ( 1997) rRNA sequences and evolutionary relationships among toxic and non-toxic cyanobacteria of the genus Microcystis. International Journal of Systematic Bacteriology 47, 693 697.
63. Nelissen B De Baere R Wilmotte A De Watcher R ( 1996) Phylogenetic relationships of nonaxenic filamentous cyanobacterial strains based on 16S rRNA sequence analysis. Journal of Molecular Evolution 42, 194 200.
64. Nelissen B Van de Peer Y Wilmotte A De Wachter R ( 1995) An early origin of plastids within the cyanobacterial divergence is suggested by evolutionary trees based on complete 16S rRNA sequences. Molecular Biology and Evolution 12, 1166 1173.
65. Nicolaus B Panico A Lama L Romano I Cristina M De Giulio A Gambacorta A ( 1999) Chemical composition and production of exopolysaccharides from representative members of heterocystous and non-heterocystous cyanobacteria. Phytochemistry 52, 639 647.
66. Nübel U Garcia-Pichel F Muyzer G ( 2000) The halotolerance and phylogeny of cyanobacteria with tightly coiled trichomes (Spirulina Turpin) and the description of Halospirulina tapeticola gen. nov., sp. nov. International Journal of Systematics and Evolutionary Microbiology 50, 1265 1277.
67. Oren A Padan E Malkin S ( 1979) Sulfide inhibition of photosystem II in cyanobacteria (blue-green algae) and tobacco chloroplasts. Biochimica et Biophysica Acta 546, 270 279.
68. Otsuka S Suda S Shibata S Oyaizu H Matsumoto S Watanabe MM ( 2001) A proposal for the unification of five species of cyanobacterial genus Microcystis Kützing ex Lemmermann 1907 under the Rules of the Bacteriological Code. International Journal of Systematics and Evolutionary Microbiology 51, 873 879.
69. Pate JL ( 1988) Gliding motility in prokaryotic cells. Canadian Journal of Microbiology 34, 459 465.
70. Posada D Crandall KA ( 1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817 818.
71. Potts M ( 1994) Desiccation tolerance of prokaryotes. Microbiological Reviews 58, 755 805.
72. de Queiroz K ( 1996) Including the characters of interest during tree reconstruction and the problems of circularity and bias in studies of character evolution. American Naturalist 148, 700 708.
73. Rambaut A ( 1996) Sequence Alignment Editor se-al version 2.0a9, Andrew Rambaut, Department of Zoology, University of Oxford, Oxford, UK. http://evolve.zoo.ox.ac.uk.
74. Ramsing NB Ferris MJ Ward DM ( 1997) Light-induced motility of thermophilic Synechococcus isolates from Octopus Spring, Yellowstone National Park. Applied Environmental Microbiology 63, 2347 2354.
75. Raymond J Siefert JL Staples CR Blankenship RE ( 2004) The natural history of nitrogen fixation. Molecular Biology and Evolution 21, 541 554.
76. Reid RP Visscher PT Decho AQ Stolz JF Bebout BM Dupraz C Macintyre LG Paerl HQ Pickney JL Prufer-Bebout L Steppe FT DesMarais DJ ( 2000) The role of microbes in accretion, lamination and early lithification of modern marine stromatolites. Nature 406, 989 992.
77. Reinartz M Tschape J Bruser T Truper HG Dahl C ( 1998) Sulfide oxidation in the phototrophic sulfur bacterium Chromatium vinosum. Archives of Microbiology 170, 59 68.
78. Rippka R Deruelles J Waterbury JB Herdman M Stanier RY ( 1979) Generic assignments, strain histories and properties of pure cultures of cyanobacteria. Journal of General Microbiology 111, 1 61.
79. Robertson BR Tezuka N Watanabe MM ( 2001) Phylogenetic analyses of Synechococcus strains (cyanobacteria) using sequences of 16S rDNA and part of the phycocyanin operon reveal multiple evolutionary lines and reflect phycobilin content. International Journal of Systematic and Evolutionary Microbiology 51, 861 871.
80. Rocap G Distel L Waterbury JB Chisholm SW ( 2002) Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Applied Environmental Microbiology 68, 1180 1191.
81. Rokas A Williams BL King N Carroll SB ( 2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425, 798 804.
82. Selstam E Campbell D ( 1996) Membrane lipid composition of the unusual cyanobacterium Gloeobacter violaceus sp. PCC 7421, which lacks sulfoquinovosyl diacylglycerol. Archives of Microbiology 63, 132 135.
83. Seo PS Yokota A ( 2003) The phylogenetic relationships of cyanobacteria inferred from 16S rRNA, gyrB, rpoC1 and rpoD1 gene sequences. Journal of General and Applied Microbiology 49, 191 203.
84. Shimodaira H Hasegawa M ( 1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16, 1114 1116.
85. Stal LC ( 1995) Physiological ecology of cyanobacteria in microbial mats and other communities. New Phytologist 131, 1 32.
86. Stam WT ( 1980) Relationships between a number of filamentous blue-green algal strains (Cyanophyceae) revealed by DNA-DNA hybridization. Archiv für Hydrobiologie 25, 351 374.
87. Suda S Watanabe MM Otsuka S Mahakahant A Yongmanitchai W Nopartnaraporn N Liu Y Day JG ( 2002) Taxonomic revision of water-bloom-forming species of oscillatorioid cyanobacteria. International Journal of Systematic and Evolutionary Microbiology 52, 1577 1595.
88. Swofford D ( 2001) paup*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Versions 4.0b5 and 4.0b8a. Sinauer Associates, Sunderland, Massachusetts.
89. Tandeau de Marsac NT ( 1994) Differentiation of hormogonia and relationships with other biological processes. In : The Molecular Biology of Cyanobacteria (ed. Bryant DA). Kluwer, Boston, MA, pp. 825 842.
90. Templeton AR ( 1983) Convergent evolution and non-parametric inferences from restriction fragment and DNA sequence data. In : Statistical Analysis of DNA Sequence Data (ed. Weir BS). Dekker, New York, pp. 151 179.
91. Turner S Burger-Wiersma T Giovannoni SJ Mur LR Pace NR ( 1989) The relationship of a prochlorophyte, Prochlorothix hollandica, to green chloroplast. Nature 337, 380 382.
92. Turner S Huang TC Chaw SM ( 2001) Molecular phylogeny of nitrogen-fixing unicellular cyanobacteria. Botanical Bulletin of Academia Sinica 42, 181 186.
93. Turner S Pryer KM Miao VPW Palmer JD ( 1999) Investigating deep phylogenetic relationships among cyanobacteria and plastids by small submit rRNA sequence analysis. Journal of Eukaryotic Microbiology 46, 327 338.
94. Urbach E Robertson DL Chisholm SW ( 1992) Multiple evolutionary origins of prochlorophytes within the cyanobacterial radiation. Nature 355, 267 270.
95. Urbach E Scanlan DJ Distel DL Waterbury JB Chisholm SW ( 1998) Rapid diversification of marine picophytoplankton with dissimilar light-harvesting structures inferred from sequences of Prochlorococcus and Synechococcus (cyanobacteria). Journal of Molecular Evolution 48, 723 739.
96. Vincent WF Bowman JP Rankin LM McMeekin TA ( 2000) Phylogenetic diversity of picocyanobacteria in Arctic and Antarctic ecosystems. In : Microbial Biosystems: New Frontiers (eds Bell CR Brylinsky M Johnson-Green P). Proceedings of the 8th International Symposium on Microbial Ecology. Atlantic Canada Society for Microbial Ecology, Halifax, pp. 317 322.
97. Visser JM deJong GAH Robertson LA Kuenen JG ( 1997) A novel membrane-bound flavocytochrome c sulfide dehydrogenase from the colourless sulfur bacterium Thiobacillus sp. W5. Archives of Microbiology 167, 295 301.
98. Walsby AE ( 1985) The permeability of heterocysts to the gases nitrogen and oxygen. Proceedings of the Royal Society of London. Series B, Biological Sciences 226, 345 366.
99. Waterbury JB Watson SW Guillard RRL Brand LE ( 1979) Widespread occurrence of a unicellular, marine, planktonic cyanobacterium. Nature 277, 293 294.
100. Waterbury JB Willey JM Franks DG Valois FW Watson SW ( 1985) A cyanobacterium capable of swimming motility. Science 230, 74 76.
101. Watson GMF Tabita FR ( 1997) Microbial ribulose 1,5-bisphosphate carboxylase/oxigenase: a molecule for phylogenetic and enzymological investigation. FEMS Microbiology Letters 146, 13 22.
102. Whitton BA Potts M ( 2000) Introduction to the Cyanobacteria. In : The Ecology of Cyanobacteria (eds Whitton BA Potts M). Kluwer Academic Publishers Netherlands, pp. 1 11.
103. Wilmotte A ( 1994) Molecular evolution and taxonomy of the Cyanobacteria. In : The Molecular Biology of Cyanobacteria (ed. Bryant DA). Kluwer Academic, Dordrecht, the Netherlands, pp. 1 25.
104. Wilmotte A Golubic S ( 1991) Morphological and genetic criteria in the taxonomy of Cyanophyta/Cyanobacteria. Archiv für Hydrobiologie 64, 1 24 (Suppl. 92).
105. Wilmotte A Herdman M ( 2001) Phylogenetic relationships among the Cyanobacteria based on 16S rRNA sequences. In : Bergey's Manual of Systematic Bacteriology. Volume 1: The Archaea and the Deeply Branching and Phototropic Bacteria (eds Garrity G Boone DR Castenholz RW), 2nd edn. Springer-Verlag, New York, pp. 487 493.
106. Wilmotte A Van der Auwera G De Wachter R ( 1993) Structure of the 16S ribosomal RNA of the thermophilic cyanobacterium Chlorogloeopsis HTF ('Mastigobladus laminosus HTF') strain PCC7518, and phylogenetic analysis. FEBS Letters 317, 96 100.
107. Woese C ( 1998) The universal ancestor. Proceedings of the National Academy of Sciences, USA 95, 6854 6859.
108. Wolk CP ( 2000) Heterocyst formation in Anabaena. In : Prokaryotic Development (eds Brun YV Shimkets LJ). American Society of Microbiology, Washington DC, pp. 83 104.
109. Wolk CP Ernst A Elhai J ( 1994) Heterocyst metabolism and development. In : The Molecular Biology of Cyanobacteria (ed. Bryant DA). Kluwer, Boston, pp. 769 823.
110. Zehr J Jenkins BD Short SM Steward GF ( 2003) Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environmental Microbiology 5, 539 554.
111. Zeidner G Preseton CM Delong EF Massana R Post AF Scanlan SJ Béjà O ( 2003) Molecular diversity among marine picophytoplankton as revealed by psbA analyses. Environmental Microbiology 5, 212 216.