Phylogenetic relationships within the order Halobacteriales inferred from 16S rRNA gene sequences

International Journal of Systematic and Evolutionary Microbiology

Volumn 56, Issue 6, 2006, Pages 1223-1227

  Wright, André Denis Girard ^a  

^a CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ANIMAL CELL; ARTICLE; CLADISTICS; CONTROLLED STUDY; GENUS; HALOARCULA; HALOBACTERIALES; HALOBACTERIUM; HALOCOCCUS; HALOFERAX; HALOPHILIC BACTERIUM; HALORUBRUM; MACROMOLECULE; MONOPHYLY; NATRONOBACTERIUM; NATRONOCOCCUS; NEIGHBOR JOINING METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PARAPHYLY; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; REGRESSION ANALYSIS; RNA SEQUENCE; STRAIN DIFFERENCE; TAXONOMY; UNINDEXED SEQUENCE;

BASE SEQUENCE; HALOBACTERIALES; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S;

HALOARCULA; HALOBACTERIALES; HALOBACTERIUM; HALOBACULUM; HALOBIFORMA; HALOCOCCUS; HALOFERAX; HALOGEOMETRICUM; HALOMICROBIUM; HALORHABDUS; HALORUBRUM; HALOSIMPLEX; HALOTERRIGENA; NATRIALBA; NATRINEMA; NATRONOBACTERIUM; NATRONOCOCCUS; NATRONOMONAS; NATRONORUBRUM;

EID: 33745289445     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.63776-0     Document Type: Article

References (37)

1. Arahal, D. R., Dewhirst, F. E., Paster, B. J., Volcani, B. E. & Ventosa, A. (1996). Phylogenetic analyses of some extremely halophilic archaea isolated from Dead Sea water, determined on the basis of their 16S rRNA sequences. Appl Environ Microbiol 62, 3779-3786.
2. Baliga, N. S., Bonneau, R., Facciotti, M. T. & 12 other authors (2004). Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res 14, 2221-2234.
3. Boucher, Y., Douady, C. J., Sharma, A. K., Kamekura, M. & Doolittle, W. F. (2004). Intragenomic heterogeneity and intragenomic recombination among haloarchaeal rRNA genes. J Bacteriol 186, 3980-3990.
4. de Rijk, P. & de Wachter, R. (1993). DCSE, an interactive tool for sequence alignment and secondary structure research. Comput Appl Biosci 9, 735-740.
5. Elazari-Volcani, B. (1957). Genus XII. Halobacterium. In Bergey's Manual of Determinative Bacteriology, 7th edn, pp. 207-212. Edited by R. S. Breed, E. G. D. Murray & N. R. Smith. Baltimore: Williams & Wilkins
6. Felsenstein, J. (2004). PHYLIP - Phylogeny Inference Package documentation files, version 3.62c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
7. Fitch, W. K. & Margoliash, E. (1967). Construction of phylogenetic trees. Science 155, 279-284.
8. Galinski, E. A. & Tindall, B. J. (1992). Biotechnological prospects for halophiles and halotolerant microorganisms. In Molecular Biology and Biotechnology of Extremophiles, pp. 76-114. Edited by R. A. Herbert & R. J. Sharp. Glasgow: Mackie.
9. Goo, Y. A., Roach, J., Glusman, G., Baliga, N. S., Deutsch, K., Pan, M., Kennedy, S., DasSarma, S., Ng, W. V. & Hood, L. (2004). Low-pass sequencing for microbial comparative genomics. BMC Genomics 3, 1-19.
10. Grant, W. D. & Larsen, H. (1989). Extremely halophilic archaeobacteria. Order Halobacteriales ord. nov. In Bergey's Manual of Systematic Bacteriology, vol. 3, pp. 2216-2218. Edited by J. T. Staley, M. P. Bryant, N. Pfennig & J. G. Holt. Baltimore: Williams & Wilkins.
11. Grant, W. D., Kamekura, M., McGenity, T. J. & Ventosa, A. (2001). Class III. Halobacteria class. nov. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, p. 294. Edited by D. R. Boone, R. W. Castenholz & G. M. Garrity. New York: Springer.
12. Hezayen, F. F., Tindall, B. J., Steinbuchel, A. & Rehm, B. H. A. (2002). Characterization of a novel halophilic archaeon, Halobiforma haloterrestris gen. nov., sp. nov., and transfer of Natronobacterium nitratireducens to Halobiforma nitratireducens comb. nov. Int J Syst Evol Microbiol 52, 2271-2280.
13. Kamekura, M. & Dyall-Smith, M. L. (1995). Taxonomy of the family Halobacteriaceae and the description of two new genera Halorubrobacterium and Natrialba. J Gen Appl Microbiol 41, 333-350.
14. Kamekura, M., Dyall-Smith, M. L., Upasani, V., Ventosa, A. & Kates, M. (1997). Diversity of alkaliphilic halobacteria: proposals for transfer of Natronobacterium vacuolatum, Natronobacterium magadii, and Natronobacterium pharaonis to Halorubrum, Natrialba, and Natronomonas gen. nov., respectively, as Halorubrum vacuolatum comb. nov., Natrialba magadii comb. nov., and Natronomonas pharaonis comb. nov., respectively. Int J Syst Bacteriol 47, 853-857.
15. Kimura, M. (1980). A simple method of estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111-120.
16. McGenity, T. J. & Grant, W. D. (1995). Transfer of Halobacterium saccharovorum, Halobacterium sodomense, Halobacterium trapanicum NRC 34041 and Halobacterium lacusprofundi to the genus Halorubrum gen. nov., as Halorubrum saccharovorum comb. nov., Halorubrum sodomense comb. nov., Halorubrum trapanicum comb. nov., and Halorubrum lacusprofundi comb. nov. Syst Appl Microbiol 18, 237-243.
17. McGenity, T. J., Gemmell, R. T. & Grant, W. D. (1998). Proposal of a new halobacterial genus Natrinema gen. nov., with two species Natrinema pellirubrum nom. nov. and Natrinema pallidum nom. nov. Int J Syst Bacteriol 48, 1187-1196.
18. Montalvo-Rodriguez, R., Vreeland, R. H., Oren, A., Kessel, M., Betancourt, C. & Lopez-Garriga, J. (1998). Halogeometricum borinquense gen. nov., sp. nov., a novel halophilic archaeon from Puerto Rico. Int J Syst Bacteriol 48, 1305-1312.
19. Mylvaganam, S. & Dennis, P. P. (1992). Sequence heterogeneity between the two genes encoding 165 rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics 130, 399-410.
20. Oren, A. (1994). The ecology of extremely halophilic archaea. FEMS Microbiol Rev 13, 415-440.
21. Oren, A. (1999). Bioenergetic aspects of halophilism. Microbiol Mol Biol Rev 63, 334-348.
22. Oren, A. (2000). Life at high salt concentrations. In The Prokaryotes. An Evolving Electronic Resource for the Microbiological Community, release 3.1. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K. H. Schleifer & E. Stackebrandt. New York: Springer-Verlag. http://141.150.157.117:8080/prokPUB/index.htm
23. Oren, A. (2002). Diversity of halophilic microorganisms: environments, phylogeny, physiology, and applications. J Ind Microbiol Biotechnol 28, 56-63.
24. Oren, A., Gurevich, P., Gemmell, R. T. & Teske, A. (1995). Halobaculum gomorrense gen. nov., sp. nov., a novel extremely halophilic archaeon from the Dead Sea. Int J Syst Bacteriol 45, 747-754.
25. Oren, A., Elevi, R., Watanabe, S., Ihara, K. & Corcelli, A. (2002). Halomicrobium mukohataei gen. nov., comb. nov., and emended description of Halomicrobium mukohataei. Int J Syst Evol Microbiol 52, 1831-1835.
26. Rodriguez-Valera, F. (1992). Biotechnological potential of halobacteria. In The Archaebacteria: Biochemistry and Biotechnology, pp. 135-147. Edited by M. J. Danson, D. W. Hough & G. G. Lunt. London: Biochemical Society.
27. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
28. Schoop, G. (1935). Halococcus litoralis, ein obligat halphiler Farbstoffbildner. Dtsch Tierarztl Wochenschr 43, 817-820 (in German).
29. Tindall, B. J. (2003). Taxonomic problems arising in the genera Haloterrigena and Natrinema. Int J Syst Evol Microbiol 53, 1697-169.
30. Tindall, B. J., Ross, H. N. M. & Grant, W. D. (1984). Natronobacterium gen. nov. and Natronococcus gen. nov., two new genera of haloalkaliphilic archaebacteria. Syst Appl Microbiol 5, 41-57.
31. Torreblanca, M., Rodriguez-Valera, F., Juez, G., Ventosa, A., Kamekura, M. & Kates, M. (1986). Classification of non-alkaliphilic halobacteria based on numerical taxonomy and polar lipid composition, and description of Haloarcula gen. nov. and Haloferax gen. nov. Syst Appl Microbiol 8, 89-99.
32. Ventosa, A. & Nieto, J. J. (1995). Biotechnological applications and potentialities of halophilic microorganisms. World J Microbiol Biotechnol 11, 85-94.
33. Ventosa, A., Gutierrez, M. C., Kamekura, M. & Dyall-Smith, M. L. (1999). Proposal to transfer Halococcus turkmenicus, Halobacterium trapanicum JCM 9743 and strain GSL-11 to Haloterrigena turkmenica gen. nov., comb. nov. Int J Syst Bacteriol 49, 131-136.
34. Vreeland, R. H., Straight, S., Krammes, J., Dougherty, K., Rosenzweig, W. D. & Kamekura, M. (2002). Halosimplex carlsbadense gen. nov., sp. nov., a unique halophilic archaeon, with three 165 rRNA genes, that grows only in defined medium with glycerol and acetate or pyruvate. Extremophiles 6, 445-452.
35. Wainø, M., Tindall, B. J. & Ingvorsen, K. (2000). Halorhabdus utahensis gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea from Great Salt Lake, Utah. Int J Syst Evol Microbiol 50, 183-190.
36. Watrous, L. E. & Wheeler, Q. D. (1981). The out-group comparison method of character analysis. Syst Zool 30, 1-11.
37. Xu, Y., Zhou, P. & Tian, X. (1999). Characterization of two novel haloalkaliphilic archaea, Natronorubrum bangense gen. nov., sp. nov. and Natronorubrum tibetense gen. nov., sp. nov. Int J Syst Bacteriol 49, 261-266.