1887

Abstract

Comparison of both 16S rRNA coding sequences and DNA-DNA hybridization of ten strains of -subclass of currently classified as strains of has shown that they fall into two groups which are distinct from each other at the species level. Comparison with published data on the cytochrome c profiles and other 16S rRNA coding sequences in the literature has confirmed these observations and enabled several other strains also to be assigned to these two groups. Group A comprises strains ATCC 1774T (the type strain of P. ), LMD 22.2V, DSM 413, ATCC 19367, ATCC 13543, DSM 1404, DSM 1405, Pd 1222 (a genetic modification of DSM 413) and NCIMB 8944. Group B comprises ATCC 35512 (the original type strain of ), LMD 82.5, LMD 92.63, DSM 65, LMG 4218, IAM 12479, JCM 6892, DSM 11072, DSM 11073 and DSM 11104. In light of these findings, it is proposed that: (1) strains of group A are retained as P. , with ATCC 17741 as the type strain of the type species; and (2) all strains of group B are assigned to the new species combination comb, nov., with strain ATCC 35512 as the type strain. Comparative 16S rRNA sequence analysis and DNA-DNA hybridization of strains of confirm that this species is distinct from both P. and P. , but that its nearest phylogenetic neighbour is P. .

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1999-04-01
2024-05-21
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References

  1. Arts P. A. M., Robertson L. A., Kuenen J. G. 1995; Nitrification and denitrification by Thiosphaera pantotropha in aerobic chemostat cultures. FEMS Microbiol Lett 18:305–316
    [Google Scholar]
  2. Beijerinck M. W., Minkman D. C. J. 1910; Bildung und Verbrauch von Stickoxydul durch Bakterien. Zentbl Bakteriol Parasitenkd Infektionskr Hyg Abt II 25:30–63
    [Google Scholar]
  3. Brosius J., Palmer M. L., Kennedy J. P., Noller H. F. 1978; Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coti. Proc Natl Acad SciUSA 75:4801–4805
    [Google Scholar]
  4. Cashion P., Holder-Franklin M. A., McCully J., Franklin M. 1977; A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81:461–466
    [Google Scholar]
  5. Chandra T. S., Friedrich C. G. 1986; Tn5 induced mutations in sulfur oxidizing ability (Sox) of Thiosphaera pantotropha. J Bacteriol 166:446–452
    [Google Scholar]
  6. Davis H. D., Doudoroff M., Stanier R. Y. 1969; Proposal to reject the genus Hydrogenomonas taxonomic implications. Int J Syst Bacteriol 19:375–390
    [Google Scholar]
  7. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142
    [Google Scholar]
  8. Dobson S. J., Franzmann P. D. 1996; Unification of the genera Deleya (Baumann et al 1983), Halomonas (Vreeland et al 1980), and Halovibrio Fendrich 1988 and the species Paracoccus halodenitrificans (Robinson & Gibbons 1952) into a single genus, Halomonas and placement of the genus Zymo-bacter in the family Halomonadaceae. Int J Syst Bacteriol 46:550–558
    [Google Scholar]
  9. Escara J. F., Hutton J. R. 1980; Thermal stability and renaturation of DNA in dimethylsulphoxide solutions: acceleration of renaturation rate. Biopolymers 19:1315–1327
    [Google Scholar]
  10. Felsenstein J. 1993 phylip (phyogenetic inference package) version 3.5.1. Department of Genetics University of Washington; Seattle, WA, USA:
    [Google Scholar]
  11. Gerstenberg C., Friedrich B., Schlegel H. G. 1982; Physical evidence for plasmids in autotrophic, especially hydrogen-oxidizing bacteria. Arch Microbiol 133:90–96
    [Google Scholar]
  12. Goodhew C. F., Pettigrew G. W., Devreese B., Van Beeumen J., Van Spanning R. J. M., Baker S. C., Saunders N., Ferguson S. J., Thompson I. P. 1996; The cytochromes c-550 of Paracoccus denitrificans and Thiosphaera pantotropha a need for re-evaluation of the history of Paracoccus cultures. FEMS Microbiol Lett 137:95–101
    [Google Scholar]
  13. Harrison A. P. Jr 1983; Genomic and physiological comparisons between heterotrophic thiobacilli and Acidiphilium cryptum Thiobacillus versutus sp. nov., and Thiobacillus acido-philus nom. rev. Int J Syst Bacteriol 33:211–217
    [Google Scholar]
  14. Hiraishi A. 1992; Direct automated sequencing of 16S rDNA amplified by polymerase chain reaction from bacterial cultures without DNA purification. Lett Appl Microbiol 15:210–213
    [Google Scholar]
  15. Hiraishi A., Shin Y. K., Ueda Y., Sugiyama J. 1994; Automated sequencing of PCR-amplified 16S rDNA on ‘Hydrolink’ gels. J Microbiol Methods 19:145–154
    [Google Scholar]
  16. Hiraishi A., Kamagata Y., Nakamura K. 1995; Polymerase chain reaction amplification and restriction fragment length polymorphism analysis of 16S rRNA genes from methanogens. J Ferment Bioeng 79:523–529
    [Google Scholar]
  17. Huß V. A. R., Festl H., Schleifer K.-H. 1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192
    [Google Scholar]
  18. Jahnke K.-D. 1992; basic computer program for evaluation of spectroscopic DNA renaturation data from GILFORD SYSTEM 2600 spectrophotometer on a PC/XT/AT type personal computer. J Microbiol Methods 15:61–73
    [Google Scholar]
  19. Jordan S. L., Kraczkiewicz-Dowjat A. J., Kelly D. P., Wood A. P. 1995; Novel eubacteria able to grow on carbon disulfide. Arch Microbiol 163:131–137
    [Google Scholar]
  20. Jordan S. L., Mc Donald I. R., Kraczkiewicz-Dowjat A. J., Kelly D. P., Rainey F. A., Murrell J. C., Wood A. P. 1997; Auto-trophic growth on carbon disulfide is a property of novel strains of Paracoccus denitrificans. Arch Microbiol 163:225–236
    [Google Scholar]
  21. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism21–132 Munro N. New York: Academic Press;
    [Google Scholar]
  22. Katayama Y., Hiraishi A., Kuraishi H. 1995; Paracoccus thiocyanatus sp. nov., a new species of thiocyanate-utilizing facultative chemolithotroph, and transfer of Thiobacillus ver-sutus to the genus Paracoccus as Paracoccus versutus comb. nov. with emendation of the genus. Microbiology 141:1469–1477
    [Google Scholar]
  23. Kuenen J. G., Robertson L. A. 1989; Genus Thiosphaera Robertson and Kuenen 1984a, 91vp. In Ber gey’ s Manual of Systematic Bacteriology 31861–1862 Staley J. T., Bryant M. P., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
  24. Ludwig W., Mittenhueber G., Friedrich C. G. 1993; Transfer of Thiosphaera pantotropha to Paracoccus denitrificans. Int J Syst Bacteriol 43:363–367
    [Google Scholar]
  25. Maidak B. L., Larsen N., McCaughey M. J., Overbeek R., Olsen G. J., Fogel K., Blandy J., Woese C. R. 1994; The Ribosomal Database Project. Nucleic Acids Res 22:3485–3487
    [Google Scholar]
  26. Miller J. M., Dobson S. J., Franzmann P. D., McMeekin T. A. 1994; Reevaluating the classification of Paracoccus halo-denitrificans with sequence comparisons of 16S ribosomal DNA. Int J Syst Bacteriol 44:360–361
    [Google Scholar]
  27. Ohara M., Katayama Y., Tsuzaki M., Nakamoto S., Kuraishi H. 1990; Paracoccus kocuriisp nov., a tetramethylammonium-assimilating bacterium. Int J Syst Bacteriol 40:292–296
    [Google Scholar]
  28. Rainey F. A., Ward-Rainey N., Kroppenstadt R. M., Stacke-brandt E. 1996; The genus Nocardiopsis represents a phylo-genetically coherent taxon and a distinct actinomycete lineage : proposal of Nocardiopsiaceae fam. nov. Int J Syst Bacteriol 46:1088–1092
    [Google Scholar]
  29. Robertson L. A., Kuenen J. G. 1983; Thiosphaera pantotropha gen. nov. sp. nov., a facultatively anaerobic, facultatively autotrophic sulphur bacterium. J Gen Microbiol 129:2847–2855
    [Google Scholar]
  30. Robertson L. A., van Niel E. W. J., Torremans R. A. M., Kuenen J. G. 1988; Simultaneous nitrification and deni-trification in aerobic chemostat cultures of Thiosphaera pantotropha. Appl Environ Microbiol 54:2815–2818
    [Google Scholar]
  31. Siller H., Rainey F. A., Stackebrandt E., Winter J. 1996; Isolation and characterization of a new Gram-negative, acetone-degrading, nitrate-reducing bacterium from soil, Paracoccus solventivorans sp. nov. Int J Syst Bacteriol 46:1125–1130
    [Google Scholar]
  32. Taylor B. F., Hoare D. S. 1969; New facultative Thiobacillus and a re-evaluation of the heterotrophic potential of Thiobacillus novellus. J Bacteriol 100:487–497
    [Google Scholar]
  33. Urakami T., Tamaoka J., Suzuki K.-I., Komagata K. 1989; Paracoccus alcaliphilus sp. nov., an alkaliphilic and facultatively methylotrophic bacterium. Int J Syst Bacteriol 39:116–121
    [Google Scholar]
  34. Urakami T., Araki H., Oyanagi H., Suzuki K.-I., Komagata K. 1990; Paracoccus aminophilus sp. nov. and Paracoccus amino-vorans sp. nov., which utilize NN-dimethylformamide. Int J Syst Bacteriol 40:287–291
    [Google Scholar]
  35. Van Verseveld H. W., Stouthamer A. H. 1992; The genus Paracoccus. In The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation and Identification, 2nd.2321–2334 Balows A., Truper H. G., Dworkin M., Harder W., Schleifer K.-H. Berlin: Springer;
    [Google Scholar]
  36. Winterstein C., Ludwig B. 1998; Genes coding for respiratory complexes map on all three chromosomes of the Paracoccus denitrificans genome. Arch Microbiol 169:275–281
    [Google Scholar]
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