1887

Abstract

A Gram-stain-positive, aerobic organism was isolated as an endophyte from the stem tissue of healthy maize ( and investigated in detail for its taxonomic position. On the basis of the 16S rRNA gene sequence analysis, strain JM-601 was shown to be most closely related to (98.3 %), and (98.0 %). The 16S rRNA gene sequence similarity to all other species of the genus was ≤ 98.0 %. The diagnostic diamino acid of the peptidoglycan was -diaminopimelic acid. The major quinone of strain JM-601 was menaquinone MK-8(H). The polar lipid profile revealed the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylcholine and an unidentified phospholipid. The polyamine pattern contained predominantly spermine and moderate amounts of spermidine. In the fatty acid profile, iso-C, Cω8 and 10-methyl C were present in major amounts. All these data support the allocation of the strain to the genus . The results of physiological and biochemical characterization allow in addition a phenotypic differentiation of strain JM-601 from and . Strain JM-601 represents a novel species of the genus , for which we propose the name sp. nov., with JM-601 ( = CCM 8654 = CIP 110980) as the type strain.

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2016-04-01
2024-04-18
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References

  1. Altenburger P., Kämpfer P., Makristathis A., Lubitz W., Busse H.-J. 1996; Classification of bacteria isolated from a medieval wall painting. J Biotechnol 47:39–52 [View Article]
    [Google Scholar]
  2. Altenburger P., Kämpfer P., Akimov V. N., Lubitz W., Busse H.-J. 1997; Polyamine distribution in actinomycetes with group B peptidoglycan and species of the genera Brevibacterium . Corynebacterium and Tsukamurella. Int J Syst Bacteriol 47:270–277 [View Article]
    [Google Scholar]
  3. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. 1978; Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . Proc Natl Acad Sci U S A 75:4801–4805 [View Article][PubMed]
    [Google Scholar]
  4. Busse H.-J., Auling G. 1988; Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 11:1–8 [View Article]
    [Google Scholar]
  5. Busse H.-J., Schumann P. 1999; Polyamine profiles within genera of the class Actinobacteria with ll-diaminopimelic acid in the peptidoglycan. Int J Syst Bacteriol 49:179–184 [View Article][PubMed]
    [Google Scholar]
  6. Busse H.-J., Bunka S., Hensel A., Lubitz W. 1997; Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 47:698–708 [View Article]
    [Google Scholar]
  7. Collins M. D., Keddie R. M., Kroppenstedt R. M. 1983; Lipid composition of Arthrobacter simplex. Arthrobacter tumescens and possibly related taxa. Syst Appl Microbiol 4:18–26 [View Article][PubMed]
    [Google Scholar]
  8. Du H. J., Wei Y. Z., Su J., Liu H. Y., Ma B. P., Guo B. L., Zhang Y. Q., Yu L. Y. 2013; Nocardioides perillae sp. nov., isolated from surface-sterilized roots of Perilla frutescens . Int J Syst Evol Microbiol 63:1068–1072 [View Article][PubMed]
    [Google Scholar]
  9. Euzéby J. P. 1997; List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47:590–592 [View Article][PubMed]
    [Google Scholar]
  10. Felsenstein J. 1985; Confidence limits of phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  11. Felsenstein J. 2005; phylip (phylogeny inference package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington; Seattle, USA:
    [Google Scholar]
  12. Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. editors 1994 Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology;
    [Google Scholar]
  13. Glaeser S. P., McInroy J. A., Busse H. J., Kämpfer P. 2014; Nocardioides zeae sp. nov., isolated from the stem of Zea mays . Int J Syst Evol Microbiol 64:2491–2496 [View Article][PubMed]
    [Google Scholar]
  14. Han J. H., Kim T. S., Joung Y., Kim M. N., Shin K. S., Bae T., Kim S. B. 2013; Nocardioides endophyticus sp. nov. and Nocardioides conyzicola sp. nov., isolated from herbaceous plant roots. Int J Syst Evol Microbiol 63:4730–4734 [View Article][PubMed]
    [Google Scholar]
  15. Kämpfer P. 1990; Evaluation of the Titertek-Enterobac-Automated System (TTE-AS) for identification of members of the family Enterobacteriaceae . Zentralbl Bakteriol 273:164–172 [View Article][PubMed]
    [Google Scholar]
  16. Kämpfer P., Kroppenstedt R. M. 1996; Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989–1005 [View Article]
    [Google Scholar]
  17. Kämpfer P., Steiof M., Dott W. 1991; Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 21:227–251 [View Article][PubMed]
    [Google Scholar]
  18. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H., other authors. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721 [View Article][PubMed]
    [Google Scholar]
  19. Kim M., Oh H.-S., Park S. C., Chun J. 2014; Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351 [View Article][PubMed]
    [Google Scholar]
  20. Lane D. J. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp 115–175Edited by Stackebrandt E., Goodfellow M. Chichester: Wiley;
    [Google Scholar]
  21. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S., other authors. 2004; arb: a software environment for sequence data. Nucleic Acids Res 32:1363–1371 [View Article][PubMed]
    [Google Scholar]
  22. Meier-Kolthoff J. P., Göker M., Spröer C., Klenk H.-P. 2013; When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 195:413–418 [View Article][PubMed]
    [Google Scholar]
  23. O'Donnell A. G., Goodfellow M., Minnikin D. E. et al. 1982; Lipids in the classification of Nocardioides: reclassification of Arthrobacter simplex (Jensen) Lochhead in the genus Nocardioides (Prauser) emend. O' Donnell et al. as Nocardioides simplex comb. nov. Arch Microbiol 133:323–329 [View Article][PubMed]
    [Google Scholar]
  24. Prauser H. 1976; Nocardioides, a new genus of the order Actinomycetales . Int J Syst Bacteriol 26:58–65 [View Article]
    [Google Scholar]
  25. Pruesse E., Quast C., Knittel K., Fuchs B. M., Ludwig W., Peplies J., Glöckner F. O. 2007; silva: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB . Nucleic Acids Res 35:7188–7196 [View Article][PubMed]
    [Google Scholar]
  26. Pruesse E., Peplies J., Glöckner F. O. 2012; sina: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823–1829 [View Article][PubMed]
    [Google Scholar]
  27. Qin S., Yuan B., Zhang Y. J., Bian G. K., Tamura T., Sun B. Z., Li W. J., Jiang J. H. 2012; Nocardioides panzhihuaensis sp. nov., a novel endophytic actinomycete isolated from medicinal plant Jatropha curcas L. Antonie van Leeuwenhoek 102:353–360 [View Article][PubMed]
    [Google Scholar]
  28. Schumann P. 2011; Peptidoglycan structure. Methods Microbiol 38:101–129 [CrossRef]
    [Google Scholar]
  29. Song G. C., Yasir M., Bibi F., Chung E. J., Jeon C. O., Chung Y. R. 2011; Nocardioides caricicola sp. nov., an endophytic bacterium isolated from a halophyte, Carex scabrifolia Steud . Int J Syst Evol Microbiol 61:105–109 [View Article][PubMed]
    [Google Scholar]
  30. Stamatakis A. 2006; RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690 [View Article][PubMed]
    [Google Scholar]
  31. Stolz A., Busse H.-J., Kämpfer P. 2007; Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 57:572–576 [View Article][PubMed]
    [Google Scholar]
  32. Tindall B. J. 1990a; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66:199–202 [View Article]
    [Google Scholar]
  33. Tindall B. J. 1990b; A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130 [View Article]
    [Google Scholar]
  34. Yarza P., Richter M., Peplies J., Euzeby J., Amann R., Schleifer K. H., Ludwig W., Glöckner F. O., Rosselló-Móra R. 2008; The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250 [View Article][PubMed]
    [Google Scholar]
  35. Yoon J.-H., Kim I.-G., Lee M.-H., Lee C.-H., Oh T. K. 2005; Nocardioides alkalitolerans sp. nov., isolated from an alkaline serpentinite soil in Korea. Int J Syst Evol Microbiol 55:809–814 [View Article][PubMed]
    [Google Scholar]
  36. Zhang D. C., Schumann P., Redzic M., Zhou Y. G., Liu H. C., Schinner F., Margesin R. 2012; Nocardioides alpinus sp. nov., a psychrophilic actinomycete isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 62:445–450 [View Article][PubMed]
    [Google Scholar]
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