1887

Abstract

A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium capable of growing at 15–42 °C (optimum 30 °C) and at pH 5–11 (optimum pH 7) was isolated from compost. Its taxonomic position was deduced using a polyphasic approach and the strain was designated RC2. 16S rRNA gene sequence analysis showed that the isolate belongs to the division , forming a clade within the cluster containing IFO 15715, and showed highest similarity to IFO 15715 (98.1 %). The cell wall contained -diaminopimelic acid as the diagnostic diamino acid. The major cellular fatty acids of the novel strain were iso-C (36.83 %), anteiso-C (49.19 %) and C (5.19 %). DNA–DNA hybridization between strain RC2 and DSM 1320 showed a level of relatedness of 54.5 %. The polar lipid profile of strain RC2 showed the presence of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The predominant isoprenoid quinone was MK-7 and the G+C content of strain RC2 was 37.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and the results of biochemical and physiological tests, strain RC2 was clearly distinguished from closely related members of the genus, and the strain is assigned to a novel species, for which the name sp. nov. is proposed. The type strain is RC2 ( = MTCC 9831 = MCC 2100 = KCTC 13724 = CCM 7754).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.048223-0
2013-12-01
2024-10-04
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/12/4735.html?itemId=/content/journal/ijsem/10.1099/ijs.0.048223-0&mimeType=html&fmt=ahah

References

  1. Adani F., Genevini P. L., Gasperi F., Zorzi G. ( 1997 ). Organic matter evolution index (OMEI) as a measure of composting efficiency. . Compost Sci Util 5, 5362. [View Article]
    [Google Scholar]
  2. Ash C., Farrow J. A. E., Wallbanks S., Collins M. D. ( 1991 ). Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. . Lett Appl Microbiol 13, 202206. [View Article]
    [Google Scholar]
  3. Cayol J. L., Ollivier B., Lawson Anani Soh A. & other authors ( 1994 ). Haloincola saccharolytica subsp. senegalensis subsp. nov., isolated from the sediments of a hypersaline lake, and emended description of Haloincola saccharolytica . . Int J Syst Bacteriol 44, 805811. [View Article]
    [Google Scholar]
  4. Claus D., Berkeley C. W. ( 1986 ). Genus Bacillus Cohn 1872174AL . . In Bergey’s Manual of Systematic Bacteriology, vol. 2, pp. 11051139. Edited by Sneath P. H. A., Mair N. S., Sharpe M. E., Holt J. G. . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  5. Collins M. D., Jones D. ( 1981 ). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. . Microbiol Rev 45, 316354.[PubMed]
    [Google Scholar]
  6. Cowan S. T., Steel K. J. ( 1965 ). Manual for Identification of Medical Bacteria, , 3rd edn.. Edited by Barrow G. I., Feltham R. K. A. . London:: Cambridge University Press;.
    [Google Scholar]
  7. Doncean A., Şumălan R., Şumălan R. ( 2011 ). Comparative study of aerobic microorganisms in compost. . J Hortic Forest Biotechnol 15, 2934.
    [Google Scholar]
  8. Falcon M. A., Corominas E., Perez M. L., Perestelo F. ( 1987 ). Aerobic bacterial populations and environmental factors involved in the composting of agricultural and forest wastes of the Canary Islands. . Biol Wastes 20, 8999. [View Article]
    [Google Scholar]
  9. Farmer J. III ( 1999 ). Enterobacteriaceae: introduction and identification. . In Manual of Clinical Microbiology, , 7th edn., pp. 448452. Edited by Murray P. R., Baron E. J., Pfaller M. A., Tenover F. C., Yolken R. H. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  10. Felsenstein J. ( 1993 ). phylip (phylogeny inference package), version 3.5c. . Distributed by the author. Department of Genome Sciences, University of Washington;, Seattle, USA:.
    [Google Scholar]
  11. Fritze D. ( 2002 ). Bacillus identification – traditional approaches. . In Applications and Systematics of Bacillus and Relatives, pp. 100122. Edited by Berkeley R. C. W., Heyndrickx M., Logan N. A., De Vos P. . Oxford:: Blackwell Science;. [View Article]
    [Google Scholar]
  12. Gerhardt P., Murray R. G. E., Costilow R. N., Nester E. W., Wood W. A., Krieg N. R., Phillips G. B. (editors) ( 1981 ). Manual of Methods for General Bacteriology. Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  13. Gordon R. E., Haynes W. C., Pang C. H.-N. ( 1973 ). The Genus Bacillus. Agricultural Handbook no. 427. Washington, DC:: US Dept of Agriculture Agricultural Research Service;.
    [Google Scholar]
  14. Goris J., Suzuki K., De Vos P., Nakase T., Kersters K. ( 1998 ). Evaluation of a microplate DNA-DNA hybridization method compared with the initial renaturation method. . Can J Microbiol 44, 11481153. [View Article]
    [Google Scholar]
  15. Guindon S., Lethiec F., Duroux P., Gascuel O. ( 2005 ). PHYML Online–a web server for fast maximum likelihood-based phylogenetic inference. . Nucleic Acids Res 33, W557-W559. [View Article] [PubMed]
    [Google Scholar]
  16. Heyndrickx M., Vandemeulebroecke K., Scheldeman P., Kersters K., de Vos P., Logan N. A., Aziz A. M., Ali N., Berkeley R. C. W. ( 1996 ). A polyphasic reassessment of the genus Paenibacillus, reclassification of Bacillus lautus (Nakamura 1984) as Paenibacillus lautus comb. nov. and of Bacillus peoriae (Montefusco et al. 1993) as Paenibacillus peoriae comb. nov., and emended descriptions of P. lautus and of P. peoriae . . Int J Syst Bacteriol 46, 9881003. [View Article] [PubMed]
    [Google Scholar]
  17. Kim B. Y., Lee S. Y., Weon H. Y., Kwon S. W., Go S. J., Park Y. K., Schumann P., Fritze D. ( 2006 ). Ureibacillus suwonensis sp. nov., isolated from cotton waste composts. . Int J Syst Evol Microbiol 56, 663666. [View Article] [PubMed]
    [Google Scholar]
  18. Komagata K., Suzuki K. ( 1987 ). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19, 161207. [View Article]
    [Google Scholar]
  19. Laemmli U. K. ( 1970 ). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. . Nature 227, 680685. [View Article] [PubMed]
    [Google Scholar]
  20. Lechner S., Mayr R., Francis K. P., Prüss B. M., Kaplan T., Wiessner-Gunkel E., Stewart G. S., Scherer S. ( 1998 ). Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group. . Int J Syst Bacteriol 48, 13731382. [View Article] [PubMed]
    [Google Scholar]
  21. Logan N. A., De Vos P. ( 2009 ). Genus Bacillus Cohn 1872. . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 3, pp. 21128. Edited by De Vos P., Garrity G. M., Jones D., Krieg N. R., Ludwig W., Rainey F. A., Schleifer K. H., Whitman W. B. . New York:: Springer;.
    [Google Scholar]
  22. Logan N. A., Berge O., Bishop A. H., Busse H. J., De Vos P., Fritze D., Heyndrickx M., Kämpfer P., Rabinovitch L. & other authors ( 2009 ). Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. . Int J Syst Evol Microbiol 59, 21142121. [View Article] [PubMed]
    [Google Scholar]
  23. Marmur J. ( 1961 ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. . J Mol Biol 3, 208218. [View Article]
    [Google Scholar]
  24. Marmur J., Doty P. ( 1962 ). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. . J Mol Biol 5, 109118. [View Article] [PubMed]
    [Google Scholar]
  25. 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, 233241. [View Article]
    [Google Scholar]
  26. Morris J. A., Park R. W. A. ( 1973 ). A comparison using gel electrophoresis of cell proteins of campylobacters (vibrios) associated with infertility, abortion and swine dysentery. . J Gen Microbiol 78, 165178. [View Article] [PubMed]
    [Google Scholar]
  27. Nakamura L. K., Roberts M. S., Cohan F. M. ( 1999 ). Relationship of Bacillus subtilis clades associated with strains 168 and W23: a proposal for Bacillus subtilis subsp. subtilis subsp. nov. and Bacillus subtilis subsp. spizizenii subsp. nov.. Int J Syst Bacteriol 49, 12111215. [View Article] [PubMed]
    [Google Scholar]
  28. Nei M., Kumar S. ( 2000 ). Molecular Evolution and Phylogenetics. New York:: Oxford University Press;.
    [Google Scholar]
  29. Nielsen P., Rainey F. A., Outtrup H., Priest F. G., Fritze D. ( 1994 ). Comparative 16S rDNA sequence analysis of some alkaliphilic bacilli and the establishment of a sixth rRNA group within the genus Bacillus . . FEMS Microbiol Lett 117, 6166. [View Article]
    [Google Scholar]
  30. Nielsen P., Fritze D., Priest F. G. ( 1995 ). Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. . Microbiology 141, 17451761. [View Article]
    [Google Scholar]
  31. Palmisano M. M., Nakamura L. K., Duncan K. E., Istock C. A., Cohan F. M. ( 2001 ). Bacillus sonorensis sp. nov., a close relative of Bacillus licheniformis, isolated from soil in the Sonoran Desert, Arizona. . Int J Syst Evol Microbiol 51, 16711679. [View Article] [PubMed]
    [Google Scholar]
  32. Palys T., Nakamura L. K., Cohan F. M. ( 1997 ). Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. . Int J Syst Bacteriol 47, 11451156. [View Article] [PubMed]
    [Google Scholar]
  33. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  34. Schlaberg R., Simmon K. E., Fisher M. A. ( 2012 ). A systematic approach for discovering novel, clinically relevant bacteria. . Emerg Infect Dis 18, 422430. [View Article] [PubMed]
    [Google Scholar]
  35. Schleifer K. H., Kandler O. ( 1972 ). Peptidoglycan types of bacterial cell walls and their taxonomic implications. . Bacteriol Rev 36, 407477.[PubMed]
    [Google Scholar]
  36. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607655. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  37. 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, 846849. [View Article]
    [Google Scholar]
  38. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 27312739. [View Article] [PubMed]
    [Google Scholar]
  39. 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, 48764882. [View Article] [PubMed]
    [Google Scholar]
  40. Tourova T. P., Antonov A. S. ( 1987 ). Identification of microorganisms by rapid DNA-DNA hybridization. . Methods Microbiol 19, 333355. [View Article]
    [Google Scholar]
  41. 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, 569570.[PubMed]
    [Google Scholar]
  42. 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, 463464. [View Article]
    [Google Scholar]
  43. Weltzien H. C. ( 1991 ). Biocontrol of foliar fungal diseases with compost extracts. . In Microbial Ecology of Leaves, pp. 430450. Edited by Andrews J. H., Hirano S. S. . New York:: Springer;. [View Article]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijs.0.048223-0
Loading
/content/journal/ijsem/10.1099/ijs.0.048223-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error