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
2019-10-23
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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 H. N. Munro. New York: Academic Press.
  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).
  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 P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
  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 Z. Klement, K. Rudolph & D. C. Sands. Budapest: Akademiai Kiado.
  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 P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
  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 A. J. M. Zenhder. Chichester: Wiley.
  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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Transmission electron micrographs of negatively stained cells of strains AMX 26B (a) and 12-3 (b), showing the presence of a single polar flagellum. Bar, 1 µm.

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[PDF file of Figs B and C](88 KB)

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