Phylogenetic relationships between Bacillus species and related genera inferred from 16S rDNA sequences;Relações filogenéticas entre espécies de Bacillus e gêneros relacionados baseadas em sequencias 16S rDNA

Brazilian Journal of Microbiology

Volumn 40, Issue 3, 2009, Pages 505-521

  Wang, Wei ^a   Sun, Mi ^a  

^a YELLOW SEA FISHERIES RESEARCH INSTITUTE   (China)

Author keywords

16S rDNA; Bacillus phylogeny; Bayesian inference; Evolutionary trees

Indexed keywords

BACILLACEAE; BACILLI (CLASS); BACILLUS (BACTERIUM); BACILLUS EDAPHICUS; BACILLUS MUCILAGINOSUS; BACILLUS SALARIUS; BACILLUS SCHLEGELII; BACILLUS SUBTILIS; BACILLUS TUSCIAE; CARYOPHANACEAE; PLANOCOCCACEAE;

EID: 70349479165     PISSN: 15178382     EISSN: 16784405     Source Type: Journal    
DOI: 10.1590/s1517-83822009000300013     Document Type: Article

References (37)

1. Ash, C.; Farrow, J.A.E.; Wallbanks, S.; Collins, M.D. (1991). Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett. Appl. Microbiol., 13(4), 202-206.
2. Bonjour, F.; Aragno, M. (1984). Bacillus tusciae, a new species of thermoacidophilic, facultatively chemolithoautotrophic hydrogen oxidizing sporeformer from a geothermal area. Arch. Microbiol., 139(4), 397-401.
3. Boone, D.R.; Liu, Y.; Zhao, Z.J.; Balkwill, D.L.; Drake, G.R.; Stevens, T.O.; Aldrich, H.C. (1995). Bacillus infernus sp. nov., an Fe(III)- and Mn(IV)-reducing anaerobe from the deep terrestrial subsurface. Int. J. Syst. Bacteriol., 45(3), 441-448.
4. Chun, J.; Lee, J.H.; Jung, Y.; Kim, M.; Kim, S.; Kim, B.K.; Lim, Y.W. (2007). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol., 57(10), 2259-2261.
5. Combet-Blanc, Y.; Ollivier, B.; Streicher, C.; Patel, B.K.; Dwivedi, P.P.; Pot, B.; Prensier, G.; Garcia, J.L. (1995). Bacillus thermoamylovorans sp. nov., a moderately thermophilic and amylolytic bacterium. Int. J. Syst. Bacteriol., 45(1), 9-16.
6. Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. Int J Syst Bacteriol, 47(2), 590-592.
7. Garrity, G.M.; Lilburn, T.G.; Cole, J.R.; Harrison, S.H.; Euzeby, J.; Tindall, B.J. (2007). Taxonomic Outline of the Bacteria and Archaea (Release 7.7 ed.): Michigan State University Board of Trustees.
8. Ghosh, A.; Bhardwaj, M.; Satyanarayana, T.; Khurana, M.; Mayilraj, S.; Jain, R.K. (2007). Bacillus lehensis sp. nov., an alkalitolerant bacterium isolated from soil. Int. J. Syst. Evol. Microbiol., 57(2), 238-242.
9. Goto, K.; Omura, T.; Hara, Y.; Sadaie, Y. (2000). Application of the partial 16S rDNA sequence as an index for rapid identification of species in the genus Bacillus. J. Gen. Appl. Microbiol., 46(1), 1-8.
10. Hall, T.A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser., 41, 95-98.
11. Holder, M.; Lewis, P.O. (2003). Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet., 4(4), 275-284.
12. Kitahara, K.; Suzuki, J. (1963). Sporolactobacillus nov. subgen. J. Gen. Appl. Microbiol., 9(1), 59-71.
13. La Duc, M.T.; Satomi, M.; Venkateswaran, K. (2004). Bacillus odysseyi sp. nov., a round-spore-forming bacillus isolated from the Mars Odyssey spacecraft. Int. J. Syst. Evol. Microbiol., 54(1), 195-201.
14. Lim, J.M.; Jeon, C.O.; Kim, C.J. (2006). Bacillus taeanensis sp. nov., a halophilic Gram-positive bacterium from a solar saltern in Korea. Int. J. Syst. Evol. Microbiol., 56(12), 2903-2908.
15. Lim, J.M.; Jeon, C.O.; Lee, S.M.; Lee, J.C.; Xu, L.H.; Jiang, C.L.; Kim, C.J. (2006). Bacillus salarius sp. nov., a halophilic, spore-forming bacterium isolated from a salt lake in China. Int. J. Syst. Evol. Microbiol., 56(2), 373-377.
16. Moreira, D.; von der Heyden, S.; Bass, D.; Lopez-Garcia, P.; Chao, E.; Cavalier-Smith, T. (2007). Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata. Mol. Phylogenet. Evol., 44(1), 255-266.
17. Nazina, T.N.; Tourova, T.P.; Poltaraus, A.B.; Novikova, E.V.; Grigoryan, A.A.; Ivanova, A.E.; Lysenko, A.M.; Petrunyaka, V.V.; Osipov, G.A.; Belyaev, S.S.; Ivanov, M.V. (2001). Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. thermocatenulatus, G. thermoleovorans, G. kaustophilus, G. thermoglucosidasius and G. thermodenitrificans. Int. J. Syst. Evol. Microbiol., 51(2), 433-446.
18. Nicolaus, B.; Lama, L.; Esposito, E.; Manca, M.C.; di Prisco, G.; Gambacorta, A. (1996). "Bacillus thermoantarcticus" sp. nov., from Mount Melbourne, Antarctica: a novel thermophilic species. Polar Biol., 16(2), 101-104.
19. Nielsen, P.; Rainey, F.A.; Outtrup, H.; Priest, F.G.; Fritze, D. (1994). Comparative 16S rDNA sequence analysis of some alkaliphilic bacilli and the establishment of a sixth rRNA group within the genus Bacillus. FEMS Microbiol. Lett., 117(1), 61-65.
20. Nogi, Y.; Takami, H.; Horikoshi, K. (2005). Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel species. Int. J. Syst. Evol. Microbiol., 55(6), 2309-2315.
21. Nowlan, B.; Dodia, M.S.; Singh, S.P.; Patel, B.K. (2006). Bacillus okhensis sp. nov., a halotolerant and alkalitolerant bacterium from an Indian saltpan. Int. J. Syst. Evol. Microbiol., 56(5), 1073-1077.
22. Posada, D.; Crandall, K.A. (1998). MODELTEST: testing the model of DNA substitution. Bioinformatics, 14(9), 817-818.
23. Priest, F.G.; Goodfellow, M.; Todd, C. (1988). A numerical classification of the genus Bacillus. J. Gen. Microbiol., 134(7), 1847-1882.
24. Rheims, H.; Fruhling, A.; Schumann, P.; Rohde, M.; Stackebrandt, E. (1999). Bacillus silvestris sp. nov., a new member of the genus Bacillus that contains lysine in its cell wall. Int. J. Syst. Bacteriol., 49(2), 795-802.
25. Ronquist, F.; Huelsenbeck, J.P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19(12), 1572-1574.
26. Santini, J.M.; Streimann, I.C.; vanden Hoven, R.N. (2004). Bacillus macyae sp. nov., an arsenate-respiring bacterium isolated from an Australian gold mine. Int. J. Syst. Evol. Microbiol., 54(6), 2241-2244.
27. Stackebrandt, E.; Swiderski, J. (2002). From phylogeny to systematics: the dissection of the genus Bacillus. In Berkeley R, Heyndrickx M, Logan N & De Vos P (Eds.), Applications and systematics of Bacillus and relatives (pp. 8-22). Malden: Blackwell.
28. Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22(21), 2688-2690.
29. Tamura, K.; Dudley, J.; Nei, M.; Kumar, S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol., 24(8), 1596-1599.
30. Tamura, K.; Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol., 10(3), 512-526.
31. Tavaré, S. (1986). Some probabilistic and statistical problems on the analysis of DNA sequences. Lect. Math. Life Sc., 17, 262-272.
32. Thompson, J.D.; Gibson, T.J.; Plewniak, F.; Jeanmougin, F.; Higgins, D.G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25(24), 4876-4882.
33. Wang, Q.F.; Li, W.; Liu, Y.L.; Cao, H.H.; Li, Z.; Guo, G.Q. (2007). Bacillus qingdaonensis sp. nov., a moderately haloalkaliphilic bacterium isolated from a crude sea-salt sample collected near Qingdao in eastern China. Int. J. Syst. Evol. Microbiol., 57(5), 1143-1147.
34. Xu, D.; Cote, J.C. (2003). Phylogenetic relationships between Bacillus species and related genera inferred from comparison of 3' end 16S rDNA and 5' end 16S-23S ITS nucleotide sequences. Int. J. Syst. Evol.Microbiol., 53(3), 695-704.
35. Yoon, J.H.; Kang, S.S.; Lee, K.C.; Lee, E.S.; Kho, Y.H.; Kang, K.H.; Park, Y.H. (2001). Planomicrobium koreense gen. nov., sp. nov., a bacterium isolated from the Korean traditional fermented seafood jeotgal, and transfer of Planococcus okeanokoites (Nakagawa et al. 1996) and Planococcus mcmeekinii (Junge et al. 1998) to the genus Planomicrobium. Int. J. Syst. Evol. Microbiol., 51(4), 1511-1520.
36. Yoon, J.H.; Kim, I.G.; Kang, K.H.; Oh, T.K.; Park, Y.H. (2004). Bacillus hwajinpoensis sp. nov. and an unnamed Bacillus genomospecies, novel members of Bacillus rRNA group 6 isolated from sea water of the East Sea and the Yellow Sea in Korea. Int. J. Syst. Evol. Microbiol., 54(3), 803-808.
37. Zhang, L.; Xu, Z.; Patel, B.K. (2007). Bacillus decisifrondis sp. nov., isolated from soil underlying decaying leaf foliage. Int. J. Syst. Evol. Microbiol., 57(5), 974-978.