1887

Abstract

A Gram-staining-negative, aerobic, rod-shaped, non-spore-forming bacterial strain, Ca-34, was isolated from nodules of chickpea () in Pakistan and studied for its taxonomic affiliation. The almost full-length 16S rRNA gene sequence showed highest similarities to those of strains of the genus . Based on results of MALDI-TOF MS and 16S rRNA gene sequence similarity (98.6 %), strain Ca-34 and LMG 3301 are phylogenetic neighbours; the two strains shared DNA–DNA relatedness of 64 %. The fatty acid profile [predominantly C 7 (67.7 %) and C cyclo 8 (19.6 %)] also supported the genus affiliation. Metabolically, strain Ca-34 differed from other type strains of in many reactions and from all type strains in testing positive for gelatin hydrolysis and in testing negative for assimilation of alaninamide and -threonine. Based on phenotypic and genotypic data, we conclude that strain Ca-34 represents a novel species, for which we propose the name sp. nov. (type strain Ca-34 =DSM 22292 =CCUG 57879).

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2010-07-01
2020-01-26
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References

  1. Ali, Z., Cousin, S., Frühling, A., Brambilla, E., Schumann, P., Yang, Y. & Stackebrandt, E. ( 2009; ). Description of Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet. Int J Syst Evol Microbiol 59, 2610–2617.[CrossRef]
    [Google Scholar]
  2. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. ( 1997; ). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef]
    [Google Scholar]
  3. Bergersen, F. J. ( 1961; ). The growth of Rhizobium in synthetic media. Aust J Biol 14, 349–360.
    [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.[CrossRef]
    [Google Scholar]
  5. Cousin, S., Brambilla, E., Yang, J. & Stackebrandt, E. ( 2008; ). Culturable aerobic bacteria from the upstream region of a karst water rivulet. Int Microbiol 11, 91–100.
    [Google Scholar]
  6. De Ley, J., Cattoir, H. & Reynaerts, A. ( 1970; ). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133–142.[CrossRef]
    [Google Scholar]
  7. Doetsch, R. N. ( 1981; ). Determinative methods of light microscopy. In Manual of Methods for General Bacteriology, pp. 21–33. Edited by P. Gerhardt, R. G. E. Murray, R. N. Costilow, E. W. Nester, W. A. Wood, N. R. Krieg & G. B. Philips. Washington, DC: American Society for Microbiology.
  8. Hafeez, F. Y., Asad, S., Ahmad, T. & Malik, K. A. ( 1995; ). Host specificity and characterization of fast growing rhizobia from Macroptilium atropurpureum cv. Siratro in Pakistan. Soil Biol Biochem 27, 729–733.[CrossRef]
    [Google Scholar]
  9. Holmes, B., Popoff, M., Kiredjian, M. & Kersters, K. ( 1988; ). Ochrobactrum anthropi gen. nov., sp. nov. from human clinical specimens and previously known as Group Vd. Int J Syst Bacteriol 38, 406–416.[CrossRef]
    [Google Scholar]
  10. Huber, B., Scholz, H. C., Kämpfer, P., Falsen, E., Langer, S. & Busse, H.-J. ( 2010; ). Ochrobactrum pituitosum sp. nov., isolated from an industrial environment. Int J Syst Evol Microbiol 60, 321–326.[CrossRef]
    [Google Scholar]
  11. 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.[CrossRef]
    [Google Scholar]
  12. Kämpfer, P. & Kroppenstedt, R. M. ( 1996; ). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42, 989–1005.[CrossRef]
    [Google Scholar]
  13. Kämpfer, P., Buczolits, S., Albrecht, A., Busse, H.-J. & Stackebrandt, E. ( 2003; ). Towards a standardized format for the description of a novel species (of an established genus): Ochrobactrum gallinifaecis sp. nov. Int J Syst Evol Microbiol 53, 893–896.[CrossRef]
    [Google Scholar]
  14. Kämpfer, P., Scholz, H. C., Huber, B., Falsen, E. & Busse, H.-J. ( 2007; ). Ochrobactrum haematophilum sp. nov. and Ochrobactrum pseudogrignonense sp. nov., isolated from human clinical specimens. Int J Syst Evol Microbiol 57, 2513–2518.[CrossRef]
    [Google Scholar]
  15. Kämpfer, P., Sessitsch, A., Schloter, M., Huber, B., Busse, H. J. & Scholz, H. C. ( 2008; ). Ochrobactrum rhizosphaerae sp. nov. and Ochrobactrum thiophenivorans sp. nov., isolated from the environment. Int J Syst Evol Microbiol 58, 1426–1431.[CrossRef]
    [Google Scholar]
  16. Kimura, M. ( 1980; ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.[CrossRef]
    [Google Scholar]
  17. Labrenz, M., Collins, M. D., Lawson, P. A., Tindall, B. J., Braker, G. & Hirsch, P. ( 1998; ). Antarctobacter heliothermus gen. nov., sp. nov., a budding bacterium from hypersaline and heliothermal Ekho Lake. Int J Syst Bacteriol 48, 1363–1372.[CrossRef]
    [Google Scholar]
  18. Lebuhn, M., Achouak, W., Schloter, M., Berge, O., Meier, H., Barakat, M., Hartmann, A. & Heulin, T. ( 2000; ). Taxonomic characterization of Ochrobactrum sp. isolates from soil samples and wheat roots, and description of Ochrobactrum tritici sp. nov. and Ochrobactrum grignonense sp. nov. Int J Syst Evol Microbiol 50, 2207–2223.[CrossRef]
    [Google Scholar]
  19. Mesbah, M., Premachandran, U. & Whitman, W. B. ( 1989; ). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159–167.[CrossRef]
    [Google Scholar]
  20. Ngom, A., Nakagawa, Y., Sawada, H., Tsukahara, J., Wakabayashi, S., Uchiumi, T., Nuntagij, A., Kotepong, S., Suzuki, A. & other authors ( 2004; ). A novel symbiotic nitrogen-fixing member of the Ochrobactrum clade isolated from root nodules of Acacia mangium. J Gen Appl Microbiol 50, 17–27.[CrossRef]
    [Google Scholar]
  21. Rivas, R., Velázquez, E., Palomo, J. L., Mateos, P., García-Benavides, P. & Martínez-Molina, E. ( 2002; ). Rapid identification of Clavibacter michiganensis subspecies sepedonicus using two primers random amplified polymorphic DNA (TP-RAPD) fingerprints. Eur J Plant Pathol 108, 179–184.[CrossRef]
    [Google Scholar]
  22. Rivas, R., Willems, A., Palomo, J. L., García-Benavides, P., Mateos, F. P., Martínez-Molina, E., Gillis, M. & Velázquez, E. ( 2004; ). Bradyrhizobium betae sp. nov., isolated from roots of Beta vulgaris affected by tumour-like deformations. Int J Syst Evol Microbiol 54, 1271–1275.[CrossRef]
    [Google Scholar]
  23. Romero, C., Gamazo, C., Pardo, M. & Lopez-Goni, I. ( 1995; ). Specific detection of Brucella DNA by PCR. J Clin Microbiol 33, 615–618.
    [Google Scholar]
  24. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  25. Sasser, M. ( 1990; ). Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark, DE: MIDI Inc.
  26. Scholz, H. C., Tomaso, H., Dahouk, S. A., Witte, A., Schloter, M. & Kämpfer, P. ( 2006; ). Genotyping of Ochrobactrum anthropi by recA-based comparative sequence, PCR-RFLP, and 16S rRNA gene analysis. FEMS Microbiol Lett 257, 7–16.[CrossRef]
    [Google Scholar]
  27. Scholz, H. C., Al Dahouk, S., Tomaso, H., Neubauer, H., Witte, A., Schloter, M., Kämpfer, P., Falsen, E., Pfeffer, M. & Engel, M. ( 2008; ). Genetic diversity and phylogenetic relationships of bacteria belonging to the Ochrobactrum-Brucella group by recA and 16S rRNA gene-based comparative sequence analysis. Syst Appl Microbiol 31, 1–16.[CrossRef]
    [Google Scholar]
  28. Stackebrandt, E. & Ebers, J. ( 2006; ). Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33, 152–155.
    [Google Scholar]
  29. Tan, Z.-Y., Xu, X.-D., Wang, E.-T., Gao, J.-L., Martínez-Romero, E. & Chen, W.-X. ( 1997; ). Phylogenetic and genetic relationships of Mesorhizobium tianshanense and related rhizobia. Int J Syst Bacteriol 47, 874–879.[CrossRef]
    [Google Scholar]
  30. Teyssier, C., Marchandin, H., Siméon de Buochberg, M., Ramuz, R. & Jumas-Bilak, E. ( 2003; ). Atypical 16S rRNA gene copies in Ochrobactrum intermedium strains reveal a large genomic rearrangement by recombination between rrn copies. J Bacteriol 185, 2901–2909.[CrossRef]
    [Google Scholar]
  31. Teyssier, C., Marchandin, H., Jean-Pierre, H., Darbas, H., Siméon de Buochberg, M., Diego, I., Gouby, A. & Jumas-Bilak, E. ( 2005; ). Molecular and phenotypic features for identification of the opportunistic pathogens Ochrobactrum spp. J Med Microbiol 54, 945–953.[CrossRef]
    [Google Scholar]
  32. Teyssier, C., Marchandin, H., Jean-Pierre, H., Masnou, A., Dusart, G. & Bilak, E. J. ( 2007; ). Ochrobactrum pseudintermedium sp. nov., a novel member of the family Brucellaceae, isolated from human clinical samples. Int J Syst Evol Microbiol 57, 1007–1013.[CrossRef]
    [Google Scholar]
  33. Tien, T. M., Gaskins, M. H. & Hubbel, D. H. ( 1979; ). Plant growth substances produced by Azospirillum brasilense and their effect on the growth of pearl millet (Pennisetum americanum L.). Appl Environ Microbiol 37, 1016–1024.
    [Google Scholar]
  34. Tripathi, A. K., Verma, S. C., Chowdhury, S. P., Lebuhn, M., Gattinger, A. & Schloter, M. ( 2006; ). Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India. Int J Syst Evol Microbiol 56, 1677–1680.[CrossRef]
    [Google Scholar]
  35. Trujillo, M. E., Willems, A., Abril, A., Planchuelo, A. M., Rivas, R., Ludena, D., Mateos, P. F., Martinez-Molina, E. & Velazquez, E. ( 2005; ). Nodulation of Lupinus albus by strains of Ochrobactrum lupini sp. nov. Appl Environ Microbiol 71, 1318–1327.[CrossRef]
    [Google Scholar]
  36. Valverde, A. M., Benito, M. & Lorenzo, M. ( 2005; ). The brown adipose cell: a model for understanding the molecular mechanisms of insulin resistance. Acta Physiol Scand 183, 59–73.[CrossRef]
    [Google Scholar]
  37. Velasco, J., Romero, C., López-Goñi, I., Leiva, J., Díaz, R. & Moriyón, I. ( 1998; ). Evaluation of the relatedness of Brucella spp. and Ochrobactrum anthropi and description of Ochrobactrum intermedium sp. nov., a new species with a closer relationship to Brucella spp. Int J Syst Bacteriol 48, 759–768.[CrossRef]
    [Google Scholar]
  38. Vincent, J. M. ( 1970; ). A Manual for the Practical Study of the Root Nodule Bacteria. IBP Handbook no. 15. Oxford: Blackwell Scientific.
  39. Zurdo-Piñeiro, J. L., Rivas, R., Trujillo, M. E., Vizcaíno, N., Carrasco, J. A., Chamber, M., Palomares, M., Mateos, P. F., Martínez-Molina, E. & Velázquez, E. ( 2007; ). Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain. Int J Syst Evol Microbiol 57, 784–788.[CrossRef]
    [Google Scholar]
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Representative ARDRA profiles of Ca-34 (lane 2) and type strains of some species digested with restriction enzyme RI ( III).

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