1887

Abstract

A novel endophytic actinobacterium, designated strain EUM 378, was isolated from the surface-sterilized root tissue of , a eucalyptus tree known as Grey Box. Phylogenetic evaluation based on 16S rRNA gene sequence analysis, including alignment with taxon-specific 16S rRNA gene signature nucleotides, placed this isolate as a member of the family . Strain EUM 378 showed >5.5 % 16S rRNA gene sequence divergence from other members of this family and was related most closely to YIM 48868 (94.2 %) and IM 7744 (94.4 %). This Gram-positive, aerobic actinobacterium has well-developed substrate mycelia that fragment into small rods. Chemotaxonomic data revealed that the cell wall contains -diaminopimelic acid, ribose, glucose and rhamnose. MK-10(H) is the predominant menaquinone. Chemotaxonomic and phylogenetic evidence confirmed that strain EUM 378 represents a novel species of a new genus, for which the name gen. nov., sp. nov. is proposed. The type strain is EUM 378 ( = DSM 45355 = ACM 5289).

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2011-09-01
2021-10-18
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References

  1. Altschul S. F., Madden T. L., Schäffer 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 [View Article][PubMed]
    [Google Scholar]
  2. Atlas R. M. 1993 Handbook of Microbiological Media Edited by Parks L. C. Boca Raton, FL: CRC Press;
    [Google Scholar]
  3. Bousfield I. J., Keddie R. M., Dando T. R., Shaw S. 1985; Simple rapid methods of cell wall analysis as an aid in the identification of aerobic coryneform bacteria. In Chemical Methods in Bacterial Systematics (Society for Applied Bacteriology Technical Series vol. 20) pp. 221–236 Edited by Goodfellow M., Minnikin D. E. London: Academic Press;
    [Google Scholar]
  4. Brouwers J. F., Vernooij E. A., Tielens A. G., van Golde L. M. 1999; Rapid separation and identification of phosphatidylethanolamine molecular species. J Lipid Res 40:164–169[PubMed]
    [Google Scholar]
  5. Cao Y. R., Jiang Y., Wu J. Y., Xu L. H., Jiang C. L. 2009; Actinopolymorpha alba sp. nov., isolated from a rhizosphere soil. Int J Syst Evol Microbiol 59:2200–2203 [View Article][PubMed]
    [Google Scholar]
  6. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. 1977; Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230[PubMed] [CrossRef]
    [Google Scholar]
  7. Collins M. D., Dorsch M., Stackebrandt E. 1989; Transfer of Pimelobacter tumescens to Terrabacter gen. nov. as Terrabacter tumescens comb. nov. and of Pimelobacter jensenii to Nocardioides as Nocardioides jensenii comb. nov.. Int J Syst Bacteriol 39:1–6 [View Article]
    [Google Scholar]
  8. Conn V. M., Franco C. M. M. 2004; Analysis of the endophytic actinobacterial population in the roots of wheat (Triticum aestivum L.) by terminal restriction fragment length polymorphism and sequencing of 16S rRNA clones. Appl Environ Microbiol 70:1787–1794 [View Article][PubMed]
    [Google Scholar]
  9. Coombs J. T., Franco C. M. M. 2003; Isolation and identification of actinobacteria from surface-sterilized wheat roots. Appl Environ Microbiol 69:5603–5608 [View Article][PubMed]
    [Google Scholar]
  10. Fang J., Barcelona M. J. 1998; Structural determination and quantitative analysis of bacterial phospholipids using liquid chromatography/electrospray ionization/mass spectrometry. J Microbiol Methods 33:23–35 [View Article]
    [Google Scholar]
  11. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  12. Gordon R. E., Barnett D. A., Handerhan J. E., Pang C. H. 1974; Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24:54–63 [View Article]
    [Google Scholar]
  13. Hasegawa T., Takisawa M., Tanida S. 1983; A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29:319–322 [View Article]
    [Google Scholar]
  14. Hudson J. A., Schofield K. M., Morgan H. W., Daniel R. M. 1989; Thermonema lapsum gen. nov., sp. nov., a thermophilic gliding bacterium. Int J Syst Bacteriol 39:485–487 [View Article]
    [Google Scholar]
  15. 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 [View Article][PubMed]
    [Google Scholar]
  16. Kluge A. G., Farris F. S. 1969; Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32 [View Article]
    [Google Scholar]
  17. Kornerup J., Wanscher H. 1978 Methuen Handbook of Colour, 3rd edn. Fakenham, UK: Cox & Wyman;
    [Google Scholar]
  18. Kurup P. V., Schmitt J. A. 1973; Numerical taxonomy of Nocardia . Can J Microbiol 19:1035–1048 [View Article][PubMed]
    [Google Scholar]
  19. Mazzella N., Molinet J., Syakti A. D., Dodi A., Doumenq P., Artaud J., Bertrand J. C. 2004; Bacterial phospholipid molecular species analysis by ion-pair reversed-phase HPLC/ESI/MS. J Lipid Res 45:1355–1363 [View Article][PubMed]
    [Google Scholar]
  20. 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 [View Article]
    [Google Scholar]
  21. Miller E. S., Woese C. R., Brenner S. 1991; Description of the erythromycin-producing bacterium Arthrobacter sp. strain NRRL B-3381 as Aeromicrobium erythreum gen. nov., sp. nov.. Int J Syst Bacteriol 41:363–368 [View Article][PubMed]
    [Google Scholar]
  22. Minnikin D. E., Alshamaony L., Goodfellow M. 1975; Differentiation of Mycobacterium, Nocardia, and related taxa by thin-layer chromatographic analysis of whole-organism methanolysates. J Gen Microbiol 88:200–204[PubMed] [CrossRef]
    [Google Scholar]
  23. Minnikin D. E., Hutchinson I. G., Caldicott A. B., Goodfellow M. 1980; Thin layer chromatography of methanolysates of mycolic acid containing bacteria. J Chromatogr A 188:221–233 [View Article]
    [Google Scholar]
  24. 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 [View Article]
    [Google Scholar]
  25. Nesterenko O. A., Kvasnikov E. I., Nogina T. M. 1985; Nocardioidaceae fam. nov., a new family of the order Actinomycetales Buchanan 1917. Mikrobiol Zh 47:3–12
    [Google Scholar]
  26. Park Y. H., Yoon J. H., Shin Y. K., Suzuki K., Kudo T., Seino A., Kim H. J., Lee J. S., Lee S. T. 1999; Classification of ‘Nocardioides fulvus’ IFO 14399 and Nocardioides sp. ATCC 39419 in Kribbella gen. nov., as Kribbella flavida sp. nov. and Kribbella sandramycini sp. nov.. Int J Syst Bacteriol 49:743–752 [View Article][PubMed]
    [Google Scholar]
  27. Prauser H. 1976; Nocardioides, a new genus of the order Actinomycetales . Int J Syst Bacteriol 26:58–65 [View Article]
    [Google Scholar]
  28. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
  29. Sasser M. 2001; Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.; http://www.microbialid.com/PDF/TechNote_101.pdf
  30. Schoenborn L., Yates P. S., Grinton B. E., Hugenholtz P., Janssen P. H. 2004; Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria. Appl Environ Microbiol 70:4363–4366 [View Article][PubMed]
    [Google Scholar]
  31. Shirling E. B., Gottlieb D. 1966; Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340 [View Article]
    [Google Scholar]
  32. Song L., Li W. J., Wang Q. L., Chen G. Z., Zhang Y. S., Xu L. H. 2005; Jiangella gansuensis gen. nov., sp. nov., a novel actinomycete from a desert soil in north-west China. Int J Syst Evol Microbiol 55:881–884 [View Article][PubMed]
    [Google Scholar]
  33. 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 [View Article]
    [Google Scholar]
  34. Suzuki S., Komagata K. 1983; Pimelobacter gen. nov., a new genus of coryneform bacteria with ll-diaminopimelic acid in the cell wall. J Gen Appl Microbiol 29:59–71 [View Article]
    [Google Scholar]
  35. Tamura K., Dudley J., Nei M., Kumar S. 2007; mega4: Molecular Evolutionary Genetics Analysis (mega) software version 4.0. Mol Biol Evol 24:1596–1599 [View Article][PubMed]
    [Google Scholar]
  36. 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 [View Article][PubMed]
    [Google Scholar]
  37. Uchida K., Seino A. 1997; Intra- and intergenic relationships of various actinomycete strains based on the acyl types of the muramyl residue in cell wall peptidoglycans examined in a glycolate test. Int J Syst Bacteriol 47:182–190 [View Article]
    [Google Scholar]
  38. Urzì C., Salamone P., Schumann P., Stackebrandt E. 2000; Marmoricola aurantiacus gen. nov., sp. nov., a coccoid member of the family Nocardioidaceae isolated from a marble statue. Int J Syst Evol Microbiol 50:529–536 [View Article][PubMed]
    [Google Scholar]
  39. Wang Y. M., Zhang Z. S., Xu X. L., Ruan J. S., Wang Y. 2001; Actinopolymorpha singaporensis gen. nov., sp. nov., a novel actinomycete from the tropical rainforest of Singapore. Int J Syst Evol Microbiol 51:467–473[PubMed] [CrossRef]
    [Google Scholar]
  40. Wang Y. X., Zhang Y. Q., Xu L. H., Li W. J. 2008; Actinopolymorpha rutila sp. nov., isolated from a forest soil. Int J Syst Evol Microbiol 58:2443–2446 [View Article][PubMed]
    [Google Scholar]
  41. Yuan L. J., Zhang Y. Q., Yu L. Y., Sun C. H., Wei Y. Z., Liu H. Y., Li W. J., Zhang Y. Q. 2010; Actinopolymorpha cephalotaxi sp. nov., a novel actinomycete isolated from rhizosphere soil of the plant Cephalotaxus fortunei . Int J Syst Evol Microbiol 60:51–54 [View Article][PubMed]
    [Google Scholar]
  42. Zhi X. Y., Li W. J., Stackebrandt E. 2009; An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 59:589–608 [View Article][PubMed]
    [Google Scholar]
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