1887

Abstract

is a marine prosthecate -proteobacterium currently classified as a member of the order ‘’. Although this classification is supported by 16S rRNA gene sequence phylogeny, 23S rRNA gene sequence analysis, concatenated ribosomal proteins, HSP70 and EF-Tu phylogenies all support classifying as a member of the instead. The possible reasons why the 16S rRNA gene sequence gives conflicting results in this case are also discussed.

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2005-05-01
2019-12-12
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References

  1. Abraham, W. R., Strömpl, C., Meyer, H. & 8 other authors ( 1999; ). Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundimonas and Caulobacter. Int J Syst Bacteriol 49, 1053–1073.[CrossRef]
    [Google Scholar]
  2. Asai, T., Zaporojets, D., Squires, C. & Squires, C. L. ( 1999; ). An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria. Proc Natl Acad Sci U S A 96, 1820–1822.[CrossRef]
    [Google Scholar]
  3. Blattner, F. R., Plunkett, G., Bloch, C. A. & 14 other authors ( 1997; ). The complete genome sequence of Escherichia coli K-12. Science 277, 1453–1474.[CrossRef]
    [Google Scholar]
  4. Capela, D., Barloy-Hubler, F., Gouzy, J. & 25 other authors ( 2001; ). Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021. Proc Natl Acad Sci U S A 98, 9877–9882.[CrossRef]
    [Google Scholar]
  5. Cole, J. R., Chai, B., Marsh, T. L. & 8 other authors ( 2003; ). The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31, 442–443.[CrossRef]
    [Google Scholar]
  6. Delcher, A. L., Harmon, D., Kasif, S., White, O. & Salzberg, S. L. ( 1999; ). Improved microbial gene identification with glimmer. Nucleic Acids Res 27, 4636–4641.[CrossRef]
    [Google Scholar]
  7. Doolittle, W. F. ( 1999; ). Phylogenetic classification and the universal tree. Science 284, 2124–2129.[CrossRef]
    [Google Scholar]
  8. Edgar, R. C. ( 2004; ). muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792–1797.[CrossRef]
    [Google Scholar]
  9. Felsenstein, J. ( 1978; ). Cases in which parsimony and compatibility methods will be positively misleading. Syst Zool 27, 401–410.[CrossRef]
    [Google Scholar]
  10. Felsenstein, J. ( 1981; ). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.[CrossRef]
    [Google Scholar]
  11. Felsenstein, J. ( 2004; ). phylip (Phylogeny Inference Package), version 3.6b. Distributed by the author. Department of Genetics, University of Washington, Seattle, USA.
  12. Fleischmann, R. D., Adams, M. D., White, O. & 37 other authors ( 1995; ). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 279–291.
    [Google Scholar]
  13. Garrity, G. M., Bell, J. A. & Lilburn, T. ( 2005; ). Order Rhodobacterales ord. nov. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2. New York: Springer (in press).
  14. Gupta, R. S. & Golding, G. B. ( 1993; ). Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes. J Mol Evol 37, 573–582.
    [Google Scholar]
  15. Henrici, A. T. & Johnson, D. ( 1935; ). Stalked bacteria, a new order of Schizomycetes. J Bacteriol 29, 3–4.
    [Google Scholar]
  16. Hirsch, P. ( 1974; ). Budding bacteria. Annu Rev Microbiol 28, 391–444.[CrossRef]
    [Google Scholar]
  17. Howe, K., Bateman, A. & Durbin, R. ( 2002; ). quicktree: building huge neighbour-joining trees of protein sequences. Bioinformatics 18, 1546–1547.[CrossRef]
    [Google Scholar]
  18. Jones, D. T., Taylor, W. R. & Thornton, J. M. ( 1992; ). The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8, 275–282.
    [Google Scholar]
  19. Kaneko, T., Nakamura, Y., Sato, S. & 21 other authors ( 2000; ). Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res 7, 331–338.[CrossRef]
    [Google Scholar]
  20. Kaneko, T., Nakamura, Y., Sato, S. & 14 other authors ( 2002; ). Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA 110. DNA Res 9, 189–197.[CrossRef]
    [Google Scholar]
  21. Kishino, H. & Hasegawa, M. ( 1989; ). Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data and the branching order in Hominoidea. J Mol Evol 29, 170–179.[CrossRef]
    [Google Scholar]
  22. Larimer, F. W., Chain, P., Hauser, L. & 16 other authors ( 2004; ). Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat Biotechnol 22, 55–61.[CrossRef]
    [Google Scholar]
  23. Liefson, E. ( 1964; ). Hyphomicrobium neptunium sp. nov. Antonie van Leeuwenhoek 30, 249–256.[CrossRef]
    [Google Scholar]
  24. Moore, R. L., Weiner, R. M. & Gebers, R. ( 1984; ). Genus Hyphomonas Pongratz 1957 nom. rev. emend., Hyphomonas polymorpha Pongratz 1957 nom. rev. emend., and Hyphomonas neptunium ( Liefson 1964 ) comb nov. emend. (Hyphomicrobium neptunium). Int J Syst Bacteriol 34, 71–73.[CrossRef]
    [Google Scholar]
  25. Moran, M. A., Buchan, A., Gonzalez, J. M. & 32 other authors ( 2004; ). Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432, 910–913.[CrossRef]
    [Google Scholar]
  26. Nierman, W. C., Feldblyum, T. V., Laub, M. T. & 35 other authors ( 2001; ). Complete genome sequence of Caulobacter crescentus. Proc Natl Acad Sci U S A 98, 4136–4141.[CrossRef]
    [Google Scholar]
  27. Ogata, H., Audic, S., Renesto-Audiffren, P. & 8 other authors ( 2001; ). Mechanisms of evolution in Rickettsia conorii and R. prowazekii. Science 293, 2093–2098.[CrossRef]
    [Google Scholar]
  28. Parker, M. A., Lafay, B., Burdon, J. J. & van Berkum, P. ( 2002; ). Conflicting phylogeographic patterns in rRNA and nifD indicate regionally restricted gene transfer in Bradyrhizobium. Microbiology 148, 2557–2565.
    [Google Scholar]
  29. Paulsen, I. T., Seshadri, R., Nelson, K. E. & 27 other authors ( 2002; ). The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A 99, 13148–13153.[CrossRef]
    [Google Scholar]
  30. Pongratz, E. ( 1957; ). D'une bactérie pediculé isolé d'un pus de sinus. Schweiz Z Allg Pathol Bakteriol 20, 593–608 (in French).
    [Google Scholar]
  31. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  32. Schouls, L. M., Schot, C. S. & Jacobs, J. A. ( 2003; ). Horizontal transfer of segments of the 16S rRNA genes between species of the Streptococcus anginosus group. J Bacteriol 185, 7241–7246.[CrossRef]
    [Google Scholar]
  33. Sneath, P. H. A. ( 1992; ). International Code of Nomenclature of Bacteria (1990 Revision). Bacteriological Code. Washington, DC: American Society for Microbiology.
  34. Stackebrandt, E., Frederiksen, W., Garrity, G. M. & 10 other authors ( 2002; ). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043–1047.[CrossRef]
    [Google Scholar]
  35. Stahl, D. A., Key, R., Flesher, B. & Smit, J. ( 1992; ). The phylogeny of marine and freshwater caulobacters reflects their habitat. J Bacteriol 174, 2193–2198.
    [Google Scholar]
  36. Strömpl, C., Hold, G. L., Lünsdorf, H., Graham, J., Gallacher, S., Abraham, W. R., Moore, E. R. B. & Timmis, K. N. ( 2003; ). Oceanicaulis alexandrii gen. nov., sp. nov., a novel stalked bacterium isolated from a culture of the dinoflagellate Alexandrium tamarense (Lebour) Balech. Int J Syst Evol Microbiol 53, 1901–1906.[CrossRef]
    [Google Scholar]
  37. Templeton, A. R. ( 1983; ). Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37, 221–244.[CrossRef]
    [Google Scholar]
  38. Tettelin, H., Nelson, K. E., Paulsen, I. T. & 36 other authors ( 2001; ). Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293, 498–506.[CrossRef]
    [Google Scholar]
  39. Weiner, R. M., Melick, M., O'Neill, K. & Quintero, E. ( 2000; ). Hyphomonas adhaerens sp. nov., Hyphomonas johnsonii sp. nov. and Hyphomonas rosenbergii sp. nov., marine budding and prosthecate bacteria. Int J Syst Evol Microbiol 50, 459–469.[CrossRef]
    [Google Scholar]
  40. Wood, D. W., Setubal, J. C., Kaul, R. & 48 other authors ( 2001; ). The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294, 2317–2323.[CrossRef]
    [Google Scholar]
  41. Wu, M., Sun, L. V., Vamathevan, J. & 27 other authors ( 2004; ). Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol 2, E69.[CrossRef]
    [Google Scholar]
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