1887

Abstract

Three mesophilic bacteria (strains AMX 26B, UR374_02 and 12-3) isolated respectively from an anaerobic digester, human urine and urban riverside soil were characterized. Cells were Gram-negative, motile, non-sporulating, straight to curved rods with one polar flagellum and had a strictly respiratory metabolism with O as the preferential terminal electron acceptor. Phylogenetic analysis based on 16S rRNA gene sequences revealed that all strains clustered within the branch of the . Isolates AMX 26B and UR374_02 exhibited 100 % 16S rRNA gene sequence similarity and both were related to strain 12-3 (99·6 % similarity). The closest relative of all the isolates was DSM 12573 (similarity 97·1–97·5 %), and they were equidistantly related to species (95·4–96·6 %), species (95·3–96·1 %) and ATCC BAA-4040 (95·3–95·4 %). Chemotaxonomic and biochemical data (branched-chain cellular fatty acid pattern without C iso 3-OH, ubiquinone with eight isoprenoid units, limited range of substrates used, ability to reduce nitrite but not nitrate with the production of NO) supported their affiliation to the genus . The results of DNA–DNA hybridization and/or phenotypic analysis allowed them to be differentiated from the two species with validly published names and showed that strain 12-3 was genomically and phenotypically distinct from the other two isolates. On the basis of these results, two novel species of the genus are proposed: sp. nov., consisting of strains AMX 26B (=ATCC 700993=CIP 106674=JCM 11524) (type strain) and UR374_02 (=DSM 15133), and sp. nov., consisting of strain 12-3 (=CCUG 48231=CIP 107388=JCM 11525). The report of these two novel species leads to the emendation of the description of the genus and the re-evaluation of the phenotype of DSM 12573 necessitates the emendation of its description.

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2004-11-01
2020-08-10
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References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990; Basic local alignment search tool. J Mol Biol 215:403–410 [CrossRef]
    [Google Scholar]
  2. Assih E. A., Ouattara A. S., Thierry S., Cayol J.-L., Labat M., Macarie H. 2002; Stenotrophomonas acidaminiphila sp. nov., a strictly aerobic bacterium isolated from an upflow anaerobic sludge blanket (UASB) reactor. Int J Syst Evol Microbiol 52:559–568
    [Google Scholar]
  3. Bauer A. W., Kirby W. M. M., Sherris J. C., Turk M. 1966; Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45:493–496
    [Google Scholar]
  4. Benson D. A., Boguski M. S., Lipman D. J., Ostell J., Ouellette B. F., Rapp B. A., Wheeler D. L. 1999; GenBank. Nucleic Acids Res 27:12–17 [CrossRef]
    [Google Scholar]
  5. CASFM 2002; Communiqué 2002 . Special number SFM. pp  1–47 Paris: Comité de l'antibiogramme de la Société Française de Microbiologie (in French) http://www.sfm.asso.fr
  6. Chen M.-Y., Tsay S.-S., Chen K.-Y., Shi Y.-C., Lin Y.-T., Lin G.-H. 2002; Pseudoxanthomonas taiwanensis sp. nov., a novel thermophilic, N2O-producing species isolated from hot springs. Int J Syst Evol Microbiol 52:2155–2161 [CrossRef]
    [Google Scholar]
  7. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
    [Google Scholar]
  8. Finkmann W., Altendorf K., Stackebrandt E., Lipski A. 2000; Characterization of N2O-producing Xanthomonas -like isolates from biofilters as Stenotrophomonas nitritireducens sp.nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov.. Int J Syst Evol Microbiol 50:273–282 [CrossRef]
    [Google Scholar]
  9. Hall T. A. 1999; BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 48:95–98
    [Google Scholar]
  10. Hiraishi A., Hoshino Y., Kitamura H. 1984; Isoprenoid quinone composition in the classification of Rhodospirillaceae . J Gen Appl Microbiol 30:197–210 [CrossRef]
    [Google Scholar]
  11. Iizuka T., Yamanaka S., Nishiyama T., Hiraishi A. 1998; Isolation and phylogenetic analysis of aerobic copiotrophic ultramicrobacteria from urban soil. J Gen Appl Microbiol 44:75–84 [CrossRef]
    [Google Scholar]
  12. Jørgensen K. S., Tiedje J. M. 1993; Survival of denitrifiers in nitrate-free, anaerobic environments. Appl Environ Microbiol 59:3297–3305
    [Google Scholar]
  13. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism vol 3 pp  21–132 Edited by Munro H. N. New York: Academic Press;
    [Google Scholar]
  14. Kodaka H., Armfield A. Y., Lombard G. L., Dowell V. R. 1982; Practical procedure for demonstrating bacterial flagella. J Clin Microbiol 16:948–952
    [Google Scholar]
  15. Lipski A., Klatte S., Bendinger B., Altendorf K. 1992; Differentiation of Gram-negative, non fermentative bacteria isolated from biofilters on the basis of fatty acid composition, quinone system, and physiological reaction profile. Appl Environ Microbiol 58:2053–2065
    [Google Scholar]
  16. Maidak B. L., Cole J. R., Lilburn T. G. 7 other authors 2001; The RDP-II (Ribosomal database project). Nucleic Acids Res 29:173–174 [CrossRef]
    [Google Scholar]
  17. Marchal N., Bourdon J. L., Richard C. 1987 Culture Medium for the Isolation and Biochemical Identification of Bacteria , 3rd edn. Paris: Doin Editeurs (in French
    [Google Scholar]
  18. Mayfield C. I., Inniss W. E. 1977; A rapid, simple method for staining bacterial flagella. Can J Microbiol 23:1311–1313 [CrossRef]
    [Google Scholar]
  19. Murray R. G. E., Doetsch R. N., Robinow C. F. 1994; Determinative and cytological light microscopy. In Methods for General and Molecular Bacteriology pp  21–41 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  20. Relman D. A., Lepp P. W., Sadler K. N., Schmidt T. M. 1992; Phylogenetic relationships among the agent of bacillary angiomatosis, Bartonella bacilliformis , and other alpha-proteobacteria. Mol Microbiol 6:1801–1807 [CrossRef]
    [Google Scholar]
  21. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  22. Sasser M. 1990; Identification of bacteria through fatty acid analysis. In Methods in Phytobacteriology pp  119–204 Edited by Klement Z., Rudolph K., Sands D. C. Budapest: Akademiai Kiado;
    [Google Scholar]
  23. Schlötelburg C. 2001; Microbial diversity and dynamic in a 1,2-dichloropropane dechlorinating mixed culture . PhD thesis Humboldt-University; Berlin, Germany: (in German) http://dochost.rz.hu-berlin.de/abstract.php3/dissertationen/schloetelburg
  24. Smibert R. M., Krieg W. R. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology pp  607–654 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  25. Stackebrandt E., Goebel B. M. 1994; Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849 [CrossRef]
    [Google Scholar]
  26. 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]
  27. Tiedje J. M. 1988; Ecology of denitrification and dissimilatory nitrate reduction to ammonium. In Biology of Anaerobic Microorganisms pp  179–244 Edited by Zenhder A. J. M. Chichester: Wiley;
    [Google Scholar]
  28. Van de Peer Y., De Wachter R. 1994; treecon for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10:569–570
    [Google Scholar]
  29. Wayne L. G., Brenner D. J., Colwell R. R. 9 other authors 1987; International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [CrossRef]
    [Google Scholar]
  30. Yang P., Vauterin L., Vancanneyt M., Swings J., Kersters K. 1993; Application of fatty acid methylesters for the taxonomic analysis of the genus Xanthomonas . Syst Appl Microbiol 16:47–71
    [Google Scholar]
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