Reclassification of ‘Thiobacillus prosperus’ Huber and Stetter 1989 as Acidihalobacter prosperus gen. nov., sp. nov., a member of the family Ectothiorhodospiraceae

References

1. Davis-Belmar C.S., Nicolle J.L.C., Norris P.R. ( 2008;). Ferrous iron oxidation and leaching of copper ore with halotolerant bacteria in ore columns. Hydrometallurgy 94 144–147 [View Article].
   [Google Scholar]
2. Delsuc F., Brinkmann H., Philippe H. ( 2005;). Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6 361–375 [View Article] [PubMed].
   [Google Scholar]
3. Goris J., Konstantinidis K.T., Klappenbach J.A., Coenye T., Vandamme P., Tiedje J.M. ( 2007;). DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57 81–91 [View Article] [PubMed].
   [Google Scholar]
4. Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. ( 2010;). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59 307–321 [View Article] [PubMed].
   [Google Scholar]
5. Hallberg K.B., Hedrich S., Johnson D.B. ( 2011;). Acidiferrobacter thiooxydans, gen. nov. sp. nov., an acidophilic, thermo-tolerant, facultatively anaerobic iron- and sulfur-oxidizer of the family Ectothiorhodospiraceae. Extremophiles 15 271–279 [View Article] [PubMed].
   [Google Scholar]
6. Huber H., Stetter K.O. ( 1989;). Thiobacillus prosperus sp. nov., represents a new group of halotolerant metal-mobilizing bacteria isolated from a marine geothermal field. Arch Microbiol 151 479–485 [View Article].
   [Google Scholar]
7. Imhoff J.M. ( 2005;). Family II. Ectothiorhodospiraceae Imhoff 1984b, 339^VP . . In Bergey's Manual of Systematic Bacteriology The Proteobacteria, Part B: The Gammaproteobacteria, Vol. 2 , 2nd edn.., pp. 41–57. Edited by Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. New York: Springer;.
   [Google Scholar]
8. Katoh K., Standley D.M. ( 2014;). mafft: iterative refinement and additional methods. Methods Mol Biol 1079 131–146 [View Article] [PubMed].
   [Google Scholar]
9. Keane T.M., Creevey C.J., Pentony M.M., Naughton T.J., Mclnerney J.O. ( 2006;). Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol 6 29 [View Article] [PubMed].
   [Google Scholar]
10. Kelly D.P., Wood A.P. ( 2000;). Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov. Int J Syst Evol Microbiol 50 511–516 [View Article] [PubMed].
    [Google Scholar]
11. Kelly D.P., Wood A.P., Stackebrandt E. ( 2005;). Genus II. Thiobacillus Beijerinck 1904. . In Bergey's Manual of Systematic Bacteriology Vol. 2 , 2nd edn.., pp. 764–769. Edited by Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. The Proteobacteria, Part C, The Alpha-, Beta-, Delta-, and Epsilonproteobacteria New York: [View Article] Springer;.
    [Google Scholar]
12. Kim M., Oh H.-S., Park S.-C., Chun J. ( 2014;). Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64 346–351 [View Article] [PubMed].
    [Google Scholar]
13. Konstantinidis K.T., Tiedje J.M. ( 2005;). Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187 6258–6264 [View Article] [PubMed].
    [Google Scholar]
14. Ossandon F.J., Cárdenas J.P., Corbett M., Quatrini R., Holmes D.S., Watkin E. ( 2014;). Draft genome sequence of the iron-oxidizing, acidophilic, and halotolerant “Thiobacillus prosperus” type strain DSM 5130. Genome Announc 2 e01042–e01014 [View Article] [PubMed].
    [Google Scholar]
15. Richter M., Rosselló-Móra R. ( 2009;). Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106 19126–19131 [View Article] [PubMed].
    [Google Scholar]
16. Simmons S., Norris R. ( 2002;). Acidophiles of saline water at thermal vents of Vulcano. Italy. Extremophiles 6 201–207 [View Article] [PubMed].
    [Google Scholar]
17. Tatusov R.L., Fedorova N.D., Jackson J.D., Jacobs A.R., Kiryutin B., Koonin V., Krylov D.M., Mazumder R., Mekhedov S.L., other authors. ( 2003;). The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4 41. [CrossRef]
    [Google Scholar]
18. Williams K.P., Kelly D.P. ( 2013;). Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria. Int J Syst Evol Microbiol 63 2901–2906 [View Article] [PubMed].
    [Google Scholar]
19. Yutin N., Puigbò P., Koonin E.V., Wolf Y.I. ( 2012;). Phylogenomics of prokaryotic ribosomal proteins. PLoS One 7 e36972 [View Article] [PubMed].
    [Google Scholar]