Biogeographical diversity of archaeal viruses

Prokaryotic Diversity: Mechanisms and Significance: Published for the Society for General Microbiology

Volumn , Issue , 2006, Pages 131-144

  Stedman, K M ^a   Clore, A ^a   Combet Blanc, Y ^b  

^a PORTLAND STATE UNIVERSITY   (United States)

^b AIX MARSEILLE UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84927068153     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1017/CBO9780511754913.009     Document Type: Chapter

References (44)

1. Arnold, H. P., She, Q., Phan, H., Stedman, K., Prangishvili, D., Holz, I., Kristjansson, J. K., Garrett, R. A. and Zillig, W. (1999). The genetic element pSSVx of the extremely thermophilic crenarchaeon Sulfolobus is a hybrid between a plasmid and a virus. Mol Microbiol 34, 217-226.
2. Bell, T., Ager, D., Song, J. I., Newman, J. A., Thompson, I. P., Lilley, A. K. and van der Gast, C. J. (2005). Larger islands house more bacterial taxa. Science 308, 1884.
3. Breitbart, M. and Rohwer, F. (2005). Here a virus, there a virus, everywhere the same virus? Trends Microbiol 13, 278-284.
4. Breitbart, M., Salamon, P., Andresen, B., Mahaffy, J. M., Segall, A. M., Mead, D., Azam, F. and Rohwer, F. (2002). Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A 99, 14250-14255.
5. Breitbart, M., Felts, B., Kelley, S., Mahaffy, J. M., Nulton, J., Salamon, P. and Rohwer, F. (2004a). Diversity and population structure of a near-shore marine-sediment viral community. Proc Biol Sci 271, 565-574.
6. Breitbart, M., Miyake, J. H. and Rohwer, F. (2004b). Global distribution of nearly identical phage-encoded DNA sequences. FEMS Microbiol Lett 236, 249-256.
7. Finlay, B. J. (2002). Global dispersal of free-living microbial eukaryote species. Science 296, 1061-1063.
8. Gaunt, M. W., Sall, A. A., de Lamballerie, X., Falconar, A. K., Dzhivanian, T. I. and Gould, E. A. (2001). Phylogenetic relationships of flaviviruses correlate with their epidemiology, disease association and biogeography. J Gen Virol 82, 1867-1876.
9. Gould, E. A., de Lamballerie, X., Zanotto, P. M. and Holmes, E. C. (2001). Evolution, epidemiology, and dispersal of flaviviruses revealed by molecular phylogenies. Adv Virus Res 57, 71-103.
10. Häring, M., Peng, X., Brugger, K., Rachel, R., Stetter, K. O., Garrett, R. A. and Prangishvili, D. (2004). Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: a novel virus family, the Globuloviridae. Virology 323, 233-242.
11. Häring, M., Rachel, R., Peng, X., Garrett, R. A. and Prangishvili, D. (2005). Viral diversity in hot springs of Pozzuoli, Italy, and characterization of a unique archaeal virus, Acidianus bottle-shaped virus, from a new family, the Ampullaviridae. J Virol 79, 9904-9911.
12. Hendrix, R. W. (2002). Bacteriophages: evolution of the majority. Theor Popul Biol 61, 471-480.
13. Hendrix, R. W., Smith, M. C., Burns, R. N., Ford, M. E. and Hatfull, G. F. (1999). Evolutionary relationships among diverse bacteriophages and prophages: all the world’s a phage. Proc Natl Acad Sci U S A 96, 2192-2197.
14. Janekovic, D., Wunderl, S., Holz, I., Zillig, W., Gierl, A. and Neumann, H. (1983). TTV-1, TTV-2 and TTV-3: a family of viruses of the extremely thermophilic anaerobic sulfur reducing archaebacterium Thermoproteus tenax. Mol Gen Genet 192, 39-45.
15. Martin, A., Yeats, S., Janekovic, D., Reiter, W. D., Aicher, W. and Zillig, W. (1984). SAV-1, a temperate UV inducible DNA virus-like particle from the archaebacterium Sulfolobus acidocaldarius isolate B-12. EMBO J 3, 2165-2168.
16. Nelson, K. E., Clayton, R. A., Gill, S. R. and 26 other authors (1999). Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399, 323-329.
17. Pace, N. R. (1997). A molecular view of microbial diversity and the biosphere. Science 276, 734-740.
18. Palm, P., Schleper, C., Grampp, B., Yeats, S., McWilliam, P., Reiter, W. D. and Zillig, W. (1991). Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobusshibatae. Virology 185, 242-250.
19. Papke, R. T., Ramsing, N. B., Bateson, M. M. and Ward, D. M. (2003). Geographical isolation in hot spring cyanobacteria. Environ Microbiol 5, 650-659.
20. Pedulla, M. L., Ford, M. E., Houtz, J. M. and 17 other authors (2003). Origins of highly mosaic mycobacteriophage genomes. Cell 113, 171-182.
21. Peng, X., Blum, H., She, Q., Mallok, S., Brugger, K., Garrett, R. A., Zillig, W. and Prangishvili, D. (2001). Sequences and replication of genomes of the archaeal rudiviruses SIRV1 and SIRV2: relationships to the archaeal lipothrixvirus SIFV and some eukaryal viruses. Virology 291, 226-234.
22. Peng, X., Kessler, A., Phan, H., Garrett, R. A. and Prangishvili, D. (2004). Multiple variants of the archaeal DNA rudivirus SIRV1 in a single host and a novel mechanism of genomic variation. Mol Microbiol 54, 366-375.
23. Prangishvili, D. and Garrett, R. A. (2005). Viruses of hyperthermophilic crenarchaea. Trends Microbiol 13, 535-542.
24. Prangishvili, D., Arnold, H. P., Gotz, D., Ziese, U., Holz, I., Kristjansson, J. K. and Zillig, W. (1999). A novel virus family, the Rudiviridae: structure, virus-host interactions and genome variability of the Sulfolobus viruses SIRV1 and SIRV2. Genetics 152, 1387-1396.
25. Rabenstein, F., Seifers, D. L., Schubert, J., French, R. and Stenger, D. C. (2002). Phylogenetic relationships, strain diversity and biogeography of tritimoviruses. J Gen Virol 83, 895-906.
26. Rambaut, A., Posada, D., Crandall, K. A. and Holmes, E. C. (2004). The causes and consequences of HIV evolution. Nat Rev Genet 5, 52-61.
27. Reiter, W. D., Palm, P., Henschen, A., Lottspeich, F., Zillig, W. and Grampp, B. (1987). Identification and characterization of the genes encoding three structural proteins of the Sulfolobus virus-like particle SSV1. Mol Gen Genet 206, 144-153.
28. Rice, G., Stedman, K., Snyder, J., Wiedenheft, B., Willits, D., Brumfield, S., McDermott, T. and Young, M. J. (2001). Viruses from extreme thermal environments. Proc Natl Acad Sci U S A 98, 13341-13345.
29. Rice, G., Tang, L., Stedman, K., Roberto, F., Spuhler, J., Gillitzer, E., Johnson, J. E., Douglas, T. and Young, M. (2004). The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life. Proc Natl Acad Sci U S A 101, 7716-7720.
30. Roberts, M. S. and Cohan, F. M. (1995). Recombination and migration rates in natural populations of Bacillus subtilis and Bacillus mojavensis. Evolution 49, 1081-1094.
31. Rohwer, F. (2003). Global phage diversity. Cell 113, 141.
32. Rohwer, F. and Edwards, R. (2002). The phage proteomic tree: a genome-based taxonomy for phage. J Bacteriol 184, 4529-4535.
33. Schleper, C., Kubo, K. and Zillig, W. (1992). The particle SSV1 from the extremely thermophilic archaeon Sulfolobus is a virus: demonstration of infectivity and of transfection with viral DNA. Proc Natl Acad Sci U S A 89, 7645-7649.
34. She, Q., Singh, R. K., Confalonieri, F. and 28 other authors (2001). The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A 98, 7835-7840.
35. Short, C. M. and Suttle, C. A. (2005). Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl Environ Microbiol 71, 480-486.
36. Smith, J. M., Dowson, C. G. and Spratt, B. G. (1991). Localized sex in bacteria. Nature 349, 29-31.
37. Snyder, J. (2005). Virus dynamics, archaeal populations, and water chemistry of three acidic hot springs in Yellowstone National Park. PhD thesis, Montana State University, Bozeman, MT, USA.
38. Snyder, J. C., Spuhler, J., Wiedenheft, B., Roberto, F. F., Douglas, T. and Young, M. J. Effects of culturing on the population structure of a hyperthermophilic virus. Microb Ecol 48, 561-566.
39. Stedman, K. M., She, Q., Phan, H., Arnold, H. P., Holz, I., Garrett, R. A. and Zillig, W. (2003). Relationships between fuselloviruses infecting the extremely thermophilic archaeon Sulfolobus: SSV1 and SSV2. Res Microbiol 154, 295-302.
40. Vestergaard, G., Haring, M., Peng, X., Rachel, R., Garrett, R. A. and Prangishvili, D. A novel rudivirus, ARV1, of the hyperthermophilic archaeal genus Acidianus. Virology 336, 83-92.
41. Whitaker, R. J., Grogan, D. W. and Taylor, J. W. (2003). Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301, 976-978.
42. Wiedenheft, B., Stedman, K., Roberto, F., Willits, D., Gleske, A. K., Zoeller, L., Snyder, J., Douglas, T. and Young, M. (2004). Comparative genomic analysis of hyperthermophilic archaeal Fuselloviridae viruses. J Virol 78, 1954-1961.
43. Yeats, S., McWilliam, P. and Zillig, W. (1982). A plasmid in the archaebacterium Sulfolobus solfataricus. EMBO J 1, 1035-1038.
44. Zillig, W., Arnold, H. P., Holz, I. and 7 other authors (1998). Genetic elements in the extremely thermophilic archaeon Sulfolobus. Extremophiles 2, 131-140