1887

Abstract

Analysis of phylogenomic metrics of a recently released draft genome sequence of the halotolerant, acidophile ‘’ DSM 5130 indicates that it is not a member of the genus within the class as originally proposed. Based on data from 16S rRNA gene phylogeny, and analyses of multiprotein phylogeny and average nucleotide identity (ANI), we show that it belongs to a new genus within the family , for which we propose the name gen. nov. In accordance, it is proposed that ‘’ DSM 5130 be named gen. nov., sp. nov. DSM 5130 ( = JCM 30709) and that it becomes the type strain of the type species of this genus.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000468
2015-10-01
2019-10-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/10/3641.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000468&mimeType=html&fmt=ahah

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 [CrossRef].
    [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 [CrossRef] [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 [CrossRef] [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 [CrossRef] [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 [CrossRef] [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 [CrossRef].
    [Google Scholar]
  7. Imhoff J.M. . ( 2005;). Family II. Ectothiorhodospiraceae Imhoff 1984b, 339VP . . 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 [CrossRef] [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 [CrossRef] [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 [CrossRef] [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: [CrossRef] 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 [CrossRef] [PubMed].
    [Google Scholar]
  13. Konstantinidis K.T. , Tiedje J.M. . ( 2005;). Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187: 6258–6264 [CrossRef] [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 [CrossRef] [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 [CrossRef] [PubMed].
    [Google Scholar]
  16. Simmons S. , Norris R. . ( 2002;). Acidophiles of saline water at thermal vents of Vulcano. Italy. Extremophiles 6: 201–207 [CrossRef] [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 [CrossRef] [PubMed].
    [Google Scholar]
  19. Yutin N. , Puigbò P. , Koonin E.V. , Wolf Y.I. . ( 2012;). Phylogenomics of prokaryotic ribosomal proteins. PLoS One 7: e36972 [CrossRef] [PubMed].
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000468
Loading
/content/journal/ijsem/10.1099/ijsem.0.000468
Loading

Data & Media loading...

Supplements

Supplementary Data



PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error