Synechococcus: 3 billion years of global dominance

Molecular Ecology

Volumn 23, Issue 22, 2014, Pages 5538-5551

  Dvořák, Petr ^a   Casamatta, Dale A ^b   Poulíčková, Aloisie ^a   Hašler, Petr ^a   Ondřej, Vladan ^a   Sanges, Remo ^c  

^a PALACKÝ UNIVERSITY   (Czech Republic)

^b UNIVERSITY OF NORTH FLORIDA   (United States)

^c STAZIONE ZOOLOGICA ANTON DOHRN   (Italy)

Author keywords

16S rRNA; cyanobacteria; evolution; genome; horizontal gene transfer; speciation

Indexed keywords

CYANOBACTERIA; SYNECHOCOCCUS;

BACTERIAL DNA; RNA 16S;

BACTERIAL GENOME; CLASSIFICATION; DNA SEQUENCE; EVOLUTION; GENETICS; HORIZONTAL GENE TRANSFER; MOLECULAR GENETICS; PHYLOGENY; SEQUENCE ALIGNMENT; SYNECHOCOCCUS;

BIOLOGICAL EVOLUTION; DNA, BACTERIAL; GENE TRANSFER, HORIZONTAL; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SYNECHOCOCCUS;

EID: 84928390584     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12948     Document Type: Article

References (82)

1. Abascal F, Zardoya R, Posada D, (2005) prottest: selection of best-fit models of protein evolution. Bioinformatics, 21, 2104-2105.
2. Achtman M, Wagner M, (2008) Microbial diversity and the genetic nature of microbial species. Nature Review Microbiology, 6, 431-440.
3. Allewalt JP, Bateson MM, Revsbech NP, Slack K, Ward DM, (2006) Effect of temperature and light on growth of and photosynthesis by Synechococcus isolates typical of those predominating in the Octopus spring microbial mat community of Yellowstone National Park. Applied and Environmental Microbiology, 72, 544-550.
4. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. Journal of Molecular Biology, 215, 403-410.
5. Amard B, Bertrand-Sarfati J, (1997) Microfossils in 2000 ma old cherty stromatolites of the Franceville group, Gabon. Precambrian Research, 81, 197-221.
6. Aziz RK, Bartels D, Best AA, et al,. (2008) The rast Server: rapid annotations using subsystems technology. BMC Genomics, 9, 75.
7. Bahl J, Lau MCY, Smith GJD, et al,. (2011) Ancient origins determine global biogeography of hot and cold desert cyanobacteria. Nature Communications, 2, 163.
8. 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, 8, 44.
9. Bekker A, Holland HD, Wang P-L, et al,. (2004) Dating the rise of atmospheric oxygen. Nature, 427, 117-120.
10. Blank CE, Sanchez-Baracaldo P, (2010) Timing of morphological and ecological innovations in the cyanobacteria-a key to understanding the rise in atmospheric oxygen. Geobiology, 8, 1-23.
11. Brocks JJ, Logan GA, Buick R, Summons RE, (1999) Archaean molecular fossils and the early rise of eukaryotes. Science, 285, 1033-1036.
12. Callieri C, Coci M, Corno G, et al,. (2013) Phylogenetic diversity of nonmarine picocyanobacteria. FEMS Microbiology Ecology, 85, 293-301.
13. Castresana J, (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17, 540-552.
14. Chan PP, Lowe TM, (2009) gtrnadb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Research, 37, D93-D97.
15. Chevreux B, Wetter T, Suhai S, (1999) Genome sequence assembly using trace signals and additional sequence information. Computer Science and Biology, Proceedings of the German Conference on Bioinformatics, 99, 45-56.
16. Dagan T, Roettger M, Stucken K, et al,. (2012) Genomes of stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis form prokaryotes to plastids. Genome Evolution and Biology, 5, 31-44.
17. David LA, Alm EJ, (2010) Rapid evolutionary innovation during an Archaean genetic expansion. Nature, 469, 93-96.
18. van Dongen S, (2000) Graph Clustering by Flow Simulation. University of Utrecht, Utrecht.
19. Dvořák P, Hašler P, Poulíčková A, (2012) Phylogeography of the Microcoleus vaginatus (cyanobacteria) from three continents-a spatial and temporal characterization. PLoS ONE, 7, e40153.
20. Dvořák P, Hindák F, Hašler P, Hindáková A, Poulíčková A, (2014) Morphological and molecular studies of Neosynechococcus sphagnicola, gen. et sp. nov. (Cyanobacteria, Synechococcales). Phytotaxa, 170, 24-34.
21. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792-1797.
22. Erwin PM, Thacker W, (2008) Cryptic diversity of the symbiotic cyanobacterium Synechococcus spongiarum among sponge hosts. Molecular Ecology, 17, 2937-2947.
23. Falcon LI, Magallon S, Castillo A, (2010) Dating the cyanobacteria ancestor of the chloroplast. ISME Journal, 4, 777-783.
24. Flombaum P, Gallegos JL, Gordillo RA, et al,. (2013) Present and future global distributions of the marine cyanobacteria Prochlorococcus and Synechococcus. Proceedings of the National Academy of Sciences, 110, 9824-9829.
25. Fraser C, Hanage WP, Spratt BG, (2007) Recombination and the nature of bacterial speciation. Science, 315, 476-480.
26. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696-704.
27. Hammer Ø, Harper DAT, Ryan PD, (2001) past: paleontological statistics software package for education and data analysis. Palaeontologia Electronica, 4, 9.
28. Hanage WP, Fraser C, Spratt BG, (2005) Fuzzy species among recombinogenic bacteria. BMC Biology, 3, 6.
29. Haverkamp THA, Schouten D, Doeleman M, Wollenzien U, Huisman J, Stal JL, (2009) Colorful microdiversity of Synechococcus strains (picocyanobacteria) isolated for the Baltic Sea. ISME Journal, 3, 397-408.
30. Havig JR, (2009) Geochemistry of hydrothermal biofilms: composition of biofilms in a siliceous sinter-deposition hot spring. PhD Thesis, Arizona State University, Phoenix.
31. Hedges SB, Hsiong C, Kumar S, Wang DYC, Thompson AS, Watanabe H, (2001) A genomic timescale for the origin of eukaryotes. BMC Evolutionary Biology, 1, 4.
32. Holt JG, Krieg NR, Sneath PHA, Staley JT, Williamsn ST, (1994) Group 11. Oxygenic phototrophic bacteria. In: Bergey's Manual of Determinative Bacteriology, 9th edn (ed., Holt JG,), pp. 377-425. Williams & Wilkins, Baltimore.
33. 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 strains. Journal of Molecular Evolution, 48, 723-739.
34. Johansen JR, Casamatta DA, (2005) Recognizing cyanobacterial diversity through adoption of a new species paradigm. Algological Studies, 117, 71-93.
35. Kasting JF, Howard MT, (2006) Atmospheric composition and climate on the early Earth. Philosophical Transactions of the Royal Society B, 361, 1733-1742.
36. Kirschvink JL, Gaidos EJ, Bertani LE, et al,. (2000) Paleoproterozoic snowball Earth: extreme climatic and geochemical global change and its biological consequences. Proceedings of the National Academy of Sciences, 97, 1400-1405.
37. Komárek J, Kopecký J, Cepák V, (1999) Generic characters of the simplest cyanoprokaryotes Cyanobium, Cyanobacterium and Synechococcus. Cryptogamie Algologie, 20, 209-222.
38. Konstantinidis KT, Tiedje JM, (2004) Trends between gene content and genome size in prokaryotic species with larger genomes. Proceedings of the National Academy of Sciences, 101, 3160-3165.
39. Kopp RE, Kirschvink JL, Hilburn IA, Nash CZ, (2005) The Paleoproterozoic snowball Earth: a climate disaster triggered by the evolution of oxygenic photosynthesis. Proceedings of the National Academy of Sciences, 102, 11131-11136.
40. 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.
41. Lynch M, (2007) Streamlining and simplification of microbial genome architecture. Annual Review of Microbiology, 60, 327-349.
42. Maddison WP, Maddison DR, (2011) Mesquite: A Modular System for Evolutionary Analysis. Version 2.75, http://mesquiteproject.org.
43. Marshall WA, Chalmers MO, (1997) Airborne dispersal of Antarctic terrestrial algae and cyanobacteria. Ecography, 20, 585-594.
44. Mazard S, Ostrowski M, Partensky F, Scalan DJ, (2011) Multi-locus sequence analysis, taxonomic resolution and biogeography of marine Synechococcus. Environmental Microbiology, 14, 372-386.
45. Merhej V, Royer-Carenzi M, Pontarotii P, Raoult D, (2009) Massive comparative genomics analysis reveals convergent evolution of specialized bacteria. Biology Direct, 4, 13.
46. Miller MA, Pfeiffer W, Schwartz T, (2010) Creating the CIPRES science gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (eds, Pierce M, Thomas M, Wilkins-Diehr N,), pp. 1-8. IEEE, New Orleans.
47. Miyagishima S, Wolk CP, Osteryoung KW, (2005) Identification of cyanobacterial cell division genes by comparative and mutational analyses. Molecular Microbiology, 56, 126-143.
48. Moore LR, Goericke R, Chrisholm SW, (1995) Comparative physiology of Synechococcus and Prochlorococcus: influence of light and temperature of growth, pigments, fluorescence and absorptive properties. Marine Ecology Progress Series, 116, 259-275.
49. Morel A, Ahn Y-H, Partensky F, Vaulot D, Claustre H, (1993) Prochlorococcus and Synechococcus: a comparative study of their optical properties in relation to their size and pigmentation. Journal of Marine Research, 51, 617-649.
50. Nabout JC, da Silva Rocha B, Carneiro FM, Sant'Anna CL, (2013) How many species of Cyanobacteria are there? Using a discovery curve to predict the species number. Biodiversity and Conservation, 22, 2907-2918.
51. Nisbet EG, Sleep NH, (2001) The habitat and nature of early life. Nature, 409, 1083-1091.
52. Ohmoto H, Watanabe Y, Ikemi H, Poulson SR, Taylor BE, (2006) Sulphur isotope evidence for an oxic Archean atmosphere. Nature, 442, 908-911.
53. Palenik B, Ren Q, Tai V, Paulsen IT, (2008) Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity. Environmental Microbiology, 11, 349-359.
54. Papke RT, Ramsin NB, Bateson MM, Ward DM, (2003) Geographical isolation in hot spring cyanobacteria. Environmental Microbiology, 5, 650-659.
55. Polz MF, Alm EJ, Hanage WP, (2013) Horizontal gene transfer and the evolution of bacterial and archeal population structure. Trends in Genetics, 39, 170-175.
56. Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T, (2011) Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Research, 21, 599-609.
57. Posada D, (2008) jmodeltest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256.
58. Robbertse B, Yoder RJ, Boyd A, Reeves J, Spatafora JW, (2011) Hal: and automated pipeline for phylogenetic analyses of genomic data. PLoS Currents, 3, RRN1213.
59. Robertson BR, Tezuka N, Watanabe M, (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.
60. Rocap G, Distel DL, Waterbury JB, Chisholm SW, (2002) Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Applied and Environmental Microbiology, 68, 1180-1192.
61. Ronquist F, Huelsenbeck JP, (2003) mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
62. Rost B, Liu J, Nair R, Wrzeszcynski KO, Ofran Y, (2003) Automatic prediction of protein function. Cellular and Molecular Life Sciences, 60, 1637-2650.
63. Sanderson MJ, (2002) Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution, 19, 101-109.
64. Sanderson MJ, (2012) r8s version 1.8. Analysis of Rates ('r8s') of Evolution. Section of Evolution and Ecology. University of California, Davis. http://loco.biosci.arizona.edu/r8s/.
65. Schopf JW, (1994) Disparate rates, differing fates: tempo and mode of evolution changed from the precambrian to the phanerozoic. Proceedings of the National Academy of Sciences, 91, 6735-6742.
66. Schopf JW, (2001) The fossil record: tracing the roots of the cyanobacterial lineage. In: The Ecology of Cyanobacteria: Their Diversity in Time and Space (eds, Whitton BA, Potts M,), pp. 13-35. Springer, Berlin.
67. Shapiro BJ, Friedman J, Cordero OX, et al,. (2012) Population genomics of early events in the ecological differentiation of bacteria. Science, 336, 48-51.
68. Shi T, Falkowski PG, (2008) Genome evolution in cyanobacteria: the stable core and the variable shell. Proceedings of the National Academy of Sciences, 105, 2510-2515.
69. Shih PM, Wu D, Latifi A, et al,. (2013) Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proceedings of the National Academy of Sciences, 110, 1053-1058.
70. Shirrmeister BE, Vos JM, Antonelli A, Bagheri HC, (2013) Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event. Proceedings of the National Academy of Sciences, 110, 1791-1796.
71. Sleep NH, (2010) The Hadean-Archean environment. Cold Spring Harbor Perspectives in Biology, 2, a002527.
72. Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ, (2011) Ecology drives a global network of gene exchange connecting the human microbiome. Nature, 480, 241-244.
73. Smit AFA, Hubley R, Green P, (2013) repeatmasker open -4.0. http://www.repeatmasker.org.
74. Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688-2690.
75. Staub R, (1961) Research on physiology of nutrients of the planktonic cyanobacterium Oscillatoria rubescens. Schweizerische Zeitschrift fur Hydrologie, 23, 83-198.
76. Szollosi GJ, Boussau B, Abby SS, Tannier E, Daubin V, (2012) Phylogenetic modelling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proceedings of the National Academy of Sciences, 43, 17513-17518.
77. Usher KM, Fromont J, Sutton DC, Toze S, (2004) The biogeography and phylogeny o unicellular cyanobacterial symbionts in sponges form Australia and the Mediterranean. Microbial Ecology, 48, 167-177.
78. Warren SG, Brandt RE, Grenfell TC, McKay CP, (2002) Snowball Earth: ice thickness on the tropical ocean. Journal of Geophysical Research: Oceans, 107, 31-1-31-18.
79. Waterbury JB, Rippka R, (1989) Subsection I. Order Chroococcales Wettstein 1924, emend. Rippka et al. (1979). In: Bergey's Manual of Systematic Bacteriology (eds, Staley JT, Bryandt MP, Pfenning N, Holt JG,), pp. 1728-1746. Williams & Wilkins, Baltimore.
80. Whitton BA, Potts M, (2000) The Ecology of Cyanobacteria. Their Diversity in Time and Space. Springer, Berlin.
81. Young KD, (2007) Bacterial morphology: why have different shapes? Current Opinion in Microbiology, 10, 596-600.
82. Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle F, Papke RT, (2006) Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Research, 16, 1099-1108.