1887

International Journal of Systematic and Evolutionary Microbiology

Volume 58, Issue 8

sp. nov., a chitinolytic bacterium isolated from cattle-farm compost Free

Abstract

A bacterial strain, designated X.bu-b, with chitin-, xylan-, cellulose- and starch-degrading activities, was isolated from compost at a cattle farm near Daejeon, Republic of Korea. The strain comprised Gram-positive, aerobic or facultatively anaerobic, non-motile, rod-shaped bacteria. On the basis of an analysis of 16S rRNA gene sequences, the phylogenetic position of X.bu-b was within the genus , and the strain exhibited relatively high sequence similarities with respect to DSM 20112 (98.1 %), DSM 20118 (98.1 %), DSM 20113 (98.0 %), DB5 (97.9 %), ATCC 25174 (97.7 %), XIL11 (97.5 %), DSM 20107 (97.4 %), DSM 20111 (97.3 %), O (97.3 %) and DSM 20109 (97.0 %). The phylogenetic distance from other species with validly published names was greater than 3 % (i.e. less than 97.0 % sequence similarity). Chemotaxonomic data also supported the classification of strain X.bu-b within the genus : -ornithine was the cell-wall diamino acid, anteiso-C and anteiso-C were the major fatty acids, rhamnose, galactose, xylose and ribose were the cell-wall sugars, MK-9(H) was the predominant menaquinone and diphosphatidylglycerol and phosphatidylglycerol were present in the polar lipids. The G+C content of the genomic DNA was 73.6 mol%. DNA–DNA hybridization experiments showed that the values for DNA–DNA relatedness between strain X.bu-b and the phylogenetically closest neighbours were below 23 %. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain X.bu-b represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is X.bu-b (=KCTC 19133 =DSM 17922).

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2008-08-01
2020-08-13
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References

  1. An, D.-S., Im, W.-T., Yang, H.-C., Kang, M. S., Kim, K. K., Jin, L., Kim, M. K. & Lee, S.-T. ( 2005; ). Cellulomonas terrae sp. nov., a cellulolytic and xylanolytic bacterium isolated from soil. Int J Syst Evol Microbiol 55, 1705–1709.[CrossRef]
    [Google Scholar]
  2. Atlas, R. M. ( 1993; ). Handbook of Microbiological Media. Edited by L. C. Parks. Boca Raton, FL: CRC Press.
  3. Bagnara, C., Toci, R., Gaudin, C. & Belaich, J. P. ( 1985; ). Isolation and characterization of a cellulolytic microorganism, Cellulomonas fermentans sp. nov. Int J Syst Bacteriol 35, 502–507.[CrossRef]
    [Google Scholar]
  4. Bhat, M. K. ( 2000; ). Cellulases and related enzymes in biotechnology. Biotechnol Adv 18, 355–383.[CrossRef]
    [Google Scholar]
  5. Brown, J. M., Frazier, R. P., Morey, R. E., Steigerwalt, A. G., Pellegrini, G. J., Daneshvar, M. I., Hollis, D. G. & McNeil, M. M. ( 2005; ). Phenotypic and genetic characterization of clinical isolates of CDC coryneform group A-3: proposal of a new species of Cellulomonas, Cellulomonas denverensis sp. nov. J Clin Microbiol 43, 1732–1737.[CrossRef]
    [Google Scholar]
  6. Buck, J. D. ( 1982; ). Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44, 992–993.
     [Google Scholar]
  7. Cappuccino, J. G. & Sherman, N. ( 2002; ). Microbiology: a Laboratory Manual, 6th edn. Menlo Park, CA: Benjamin/Cummings.
  8. Collins, M. D. & Pascual, C. ( 2000; ). Reclassification of Actinomyces humiferus (Gledhill and Casida) as Cellulomonas humilata nom. corrig., comb. nov. Int J Syst Evol Microbiol 50, 661–663.[CrossRef]
    [Google Scholar]
  9. Elberson, M. A., Malekzadeh, F., Yazdi, M. T., Kameranpour, N., Noori-Daloii, M. R., Matte, M. H., Shahamat, M., Colwell, R. R. & Sowers, K. R. ( 2000; ). Cellulomonas persica sp. nov. and Cellulomonas iranensis sp. nov., mesophilic cellulose-degrading bacteria isolated from forest soils. Int J Syst Evol Microbiol 50, 993–996.[CrossRef]
    [Google Scholar]
  10. Ezaki, T., Hashimoto, Y. & Yabuuchi, E. ( 1989; ). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39, 224–229.[CrossRef]
    [Google Scholar]
  11. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  12. Fitch, W. M. ( 1971; ). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406–416.[CrossRef]
    [Google Scholar]
  13. Funke, G., Ramos, C. P. & Collins, M. D. ( 1995; ). Identification of some clinical strains of CDC coryneform group A-3 and A-4 bacteria as Cellulomonas species and proposal of Cellulomonas hominis sp. nov. for some group A-3 strains. J Clin Microbiol 33, 2091–2097.
     [Google Scholar]
  14. Hall, T. A. ( 1999; ). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95–98.
     [Google Scholar]
  15. Jones, B. E., Grant, W. D., Duckworth, A. W., Schumann, P., Weiss, N. & Stackebrandt, E. ( 2005; ). Cellulomonas bogoriensis sp. nov., an alkaliphilic cellulomonad. Int J Syst Evol Microbiol 55, 1711–1714.[CrossRef]
    [Google Scholar]
  16. Kim, M. K., Im, W.-T., Ohta, H., Lee, M. & Lee, S.-T. ( 2005; ). Sphingopyxis granuli sp. nov., a β-glucosidase producing bacterium in the family Sphingomonadaceae in α-4 subclass of the Proteobacteria. J Microbiol 43, 152–157.
     [Google Scholar]
  17. Kimura, M. ( 1983; ). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  18. Komagata, K. & Suzuki, K. ( 1987; ). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161–207.
     [Google Scholar]
  19. Kouker, G. & Jaeger, K. E. ( 1987; ). Specific and sensitive plate assay for bacterial lipases. Appl Environ Microbiol 53, 211–213.
     [Google Scholar]
  20. Kumar, S., Tamura, K. & Nei, M. ( 2004; ). mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef]
    [Google Scholar]
  21. 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]
  22. Minnikin, D. E., O'Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A. & Parlett, J. H. ( 1984; ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef]
    [Google Scholar]
  23. Oshima, H., Miyazaki, R., Ohe, Y., Hayashi, H., Kawamura, K. & Kikuyama, S. ( 2002; ). Isolation and sequence of a novel amphibian pancreatic chitinase. Comp Biochem Physiol B Biochem Mol Biol 132, 381–388.[CrossRef]
    [Google Scholar]
  24. Rivas, R., Trujillo, M. E., Mateos, P. F., Martínez-Molina, E. & Velázquez, E. ( 2004; ). Cellulomonas xylanilytica sp. nov., a cellulolytic and xylanolytic bacterium isolated from a decayed elm tree. Int J Syst Evol Microbiol 54, 533–536.[CrossRef]
    [Google Scholar]
  25. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
     [Google Scholar]
  26. Sasser, M. ( 1990; ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  27. Schleifer, K. H. & Kandler, O. ( 1972; ). Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36, 407–477.
     [Google Scholar]
  28. 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]
  29. Stackebrandt, E. & Kandler, O. ( 1979; ). Taxonomy of the genus Cellulomonas, based on phenotypic characters and deoxyribonucleic acid-deoxyribonucleic acid homology, and proposal of seven neotype strains. Int J Syst Bacteriol 29, 273–282.[CrossRef]
    [Google Scholar]
  30. Stackebrandt, E. & Keddie, R. M. ( 1986; ). Genus Cellulomonas. In Bergey's Manual of Systematic Bacteriology, vol. 2, pp. 1325–1329. Edited by P. H. A. Sneath, N. S. Mair, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
  31. Stackebrandt, E. & Schumann, P. ( 2000; ). Description of Bogoriellaceae fam. nov., Dermacoccaceae fam. nov., Rarobacteraceae fam. nov. and Sanguibacteraceae fam. nov. and emendation of some families of the suborder Micrococcineae. Int J Syst Evol Microbiol 50, 1279–1285.[CrossRef]
    [Google Scholar]
  32. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A. D., Kämpfer, P., Maiden, M. C., Nesme, X., Rosselló-Mora, R., Swings, J. & 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]
  33. Staneck, J. L. & Roberts, G. D. ( 1974; ). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28, 226–231.
     [Google Scholar]
  34. Ten, L. N., Im, W.-T., Kim, M.-K., Kang, M.-S. & Lee, S.-T. ( 2004; ). Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. J Microbiol Methods 56, 375–382.[CrossRef]
    [Google Scholar]
  35. Ten, L. N., Im, W.-T., Kim, M.-K. & Lee, S.-T. ( 2005; ). A plate assay for simultaneous screening of polysaccharide- and protein-degrading microorganisms. Lett Appl Microbiol 40, 92–98.[CrossRef]
    [Google Scholar]
  36. Terra, W. R. & Ferreira, C. ( 1994; ). Insect digestive enzymes: properties, compartmentalization and function. Comp Biochem Physiol B Biochem Mol Biol 109, 1–62.[CrossRef]
    [Google Scholar]
  37. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef]
    [Google Scholar]
  38. Tschech, A. & Pfennig, N. ( 1984; ). Growth yield increase linked to caffeate reduction in Acetobacterium woodii. Arch Microbiol 137, 163–167.[CrossRef]
    [Google Scholar]
  39. Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & 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]
  40. Widdel, F. & Bak, F. ( 1992; ). Gram-negative mesophilic sulfate-reducing bacteria. In The Prokaryotes, 2nd edn, pp. 3352–3378. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York: Springer.
  41. Widdel, F., Kohring, G. & Mayer, F. ( 1983; ). Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids. III. Characterization of the filamentous gliding Desulfonema limicola gen. nov. sp. nov., and Desulfonema magnum sp. nov. Arch Microbiol 134, 286–294.[CrossRef]
    [Google Scholar]
  42. Yi, H., Schumann, P. & Chun, J. ( 2007; ). Demequina aestuarii gen. nov., sp. nov., a novel actinomycete of the suborder Micrococcineae, and reclassification of Cellulomonas fermentans Bagnara et al. 1985 as Actinotalea fermentans gen. nov., comb. nov. Int J Syst Evol Microbiol 57, 151–156.[CrossRef]
    [Google Scholar]
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Cellulomonas chitinilytica sp. nov., a chitinolytic bacterium isolated from cattle-farm compost
Int J Syst Evol Microbiol 58, 1878 (2008); https://doi.org/10.1099/ijs.0.64768-0
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vol. , part 8, pp. 1878 - 1884

Comparison of selected characteristics (obtained using API 20NE and API 32GN galleries) of sp. nov. X.bu-b with those of the type strains of the two species to which it is most closely related.

Cellular fatty acid composition (%) of sp. nov. X.bu-b and related species.

Two-dimensional thin-layer chromatogram of the polar lipids of strain X.bu-b .

[PDF file of Supplementary Tables and Figure](110 KB)

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