1887

Abstract

A new strain of the genus , CAP94, was isolated from the surface sterilized root of (Australian native pine tree). This strain was a Gram-stain-positive, aerobic actinobacterium with hyphae breaking up into fragments which were non-motile, rod-like, coccoid elements. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this isolate as a member of the family , and most closely to NBRC 14650 (99.4 %), DSM 19349 (99.2 %) and V54A (99.1 %). Chemotaxonomic data including cell-wall components, major menaquinone and major fatty acids confirmed the affiliation of strain CAP94 to the genus The results of the phylogenetic analysis, including physiological and biochemical studies in combination with DNA–DNA hybridization, allowed the genotypic and phenotypic differentiation of strain CAP94 and the closest species with validly published names. The name proposed for the new species is sp. nov. The type strain is CAP94 (=DSM 103339=TBRC 6025).

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2017-09-01
2020-01-22
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References

  1. Krasil’nikov NA, Kalakoutskii LV, Kirillova NF. A new genus of Actinomycetales, Promicromonospora gen. nov. Bull Acad Sci USSR Ser Biol 1961;1:107–112
    [Google Scholar]
  2. Zhi XY, Li WJ, Stackebrandt E. 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 2009;59:589–608 [CrossRef][PubMed]
    [Google Scholar]
  3. Schumann P, Stackebrandt E. Family XII.Promicromonosporaceae Rainey, Ward-Rainey and Stackebrandt 1997, 484VP emend. Zhi, Li and Stackebrandt 2009, 598 p. 995. In Whitman WB, Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME et al. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed.vol. 4 New York: Springer; 2012; pp.1750
    [Google Scholar]
  4. Takahashi Y, Tanaka Y, Iwai Y, Omura S. Promicromonospora sukumoe sp. nov., a new species of the Actinomycetales. J Gen Appl Microbiol 1987;33:507–519 [CrossRef]
    [Google Scholar]
  5. Alonso-Vega P, Santamaría RI, Martínez-Molina E, Trujillo ME. Promicromonospora kroppenstedtii sp. nov., isolated from sandy soil. Int J Syst Evol Microbiol 2008;58:1476–1481 [CrossRef][PubMed]
    [Google Scholar]
  6. Mohammadipanah F, Hamedi J, Spröer C, Montero-Calasanz MC, Schumann P et al. Promicromonospora iranensis sp. nov., an actinobacterium isolated from rhizospheric soil. Int J Syst Evol Microbiol 2014;64:3314–3319 [CrossRef][PubMed]
    [Google Scholar]
  7. Mohammadipanah F, Montero-Calasanz MD, Schumann P, Spröer C, Klenk HP et al. Promicromonospora kermanensis sp. nov., a new actinobacterium isolated from soil. Int J Syst Evol Microbiol 2016;67:262–267
    [Google Scholar]
  8. Thawai C, Kudo T. Promicromonospora thailandica sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2012;62:2140–2144 [CrossRef][PubMed]
    [Google Scholar]
  9. Busse HJ, Zlamala C, Buczolits S, Lubitz W, Kämpfer P et al. Promicromonospora vindobonensis sp. nov. and Promicromonospora aerolata sp. nov., isolated from the air in the medieval 'Virgilkapelle' in Vienna. Int J Syst Evol Microbiol 2003;53:1503–1507 [CrossRef][PubMed]
    [Google Scholar]
  10. Martin K, Schäfer J, Kämpfer P. Promicromonospora umidemergens sp. nov., isolated from moisture from indoor wall material. Int J Syst Evol Microbiol 2010;60:537–541 [CrossRef][PubMed]
    [Google Scholar]
  11. Guo LF, Liu CX, Zhao JW, Li C, Guo SY et al. Promicromonospora alba nov., an actinomycete isolated from the cuticle of Camponotus japonicas Mayr. Int J Syst Evol Microbiol 2016;66:1340–1345[CrossRef]
    [Google Scholar]
  12. Qin S, Jiang JH, Klenk HP, Zhu WY, Zhao GZ et al. Promicromonospora xylanilytica sp. nov., an endophytic actinomycete isolated from surface-sterilized leaves of the medicinal plant Maytenus austroyunnanensis. Int J Syst Evol Microbiol 2012;62:84–89 [CrossRef][PubMed]
    [Google Scholar]
  13. Kaewkla O, Franco CM. Promicromonospora endophytica sp. nov., an endophytic actinobacterium isolated from the root of an Australian native Grey Box tree. Int J Syst Evol Microbiol 2012;62:1687–1691 [CrossRef][PubMed]
    [Google Scholar]
  14. Kaewkla O, Franco CM. Rational approaches to improving the isolation of endophytic actinobacteria from Australian native trees. Microb Ecol 2013;65:384–393 [CrossRef][PubMed]
    [Google Scholar]
  15. Schoenborn L, Yates PS, Grinton BE, Hugenholtz P, Janssen PH. Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria. Appl Environ Microbiol 2004;70:4363–4366 [CrossRef][PubMed]
    [Google Scholar]
  16. Coombs JT, Franco CM. Isolation and identification of actinobacteria from surface-sterilized wheat roots. Appl Environ Microbiol 2003;69:5603–5608 [CrossRef][PubMed]
    [Google Scholar]
  17. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  18. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  19. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  20. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425[PubMed]
    [Google Scholar]
  21. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  22. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993;10:512–526[PubMed]
    [Google Scholar]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  24. Ezaki T, Hashimoto Y, Yabuuchi E. 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 1989;39:224–229 [CrossRef]
    [Google Scholar]
  25. Kusunoki S, Ezaki T, Tamesada M, Hatanaka Y, Asano K et al. Application of colorimetric microdilution plate hybridization for rapid genetic identification of 22 Mycobacterium species. J Clin Microbiol 1991;29:1596–1603[PubMed]
    [Google Scholar]
  26. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  27. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987;37:463–464 [CrossRef]
    [Google Scholar]
  28. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989;39:159–167 [CrossRef]
    [Google Scholar]
  29. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984;2:233–241 [CrossRef]
    [Google Scholar]
  30. Komagata K, Suzuki K. Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 1987;19:161–207[CrossRef]
    [Google Scholar]
  31. Lechevalier MP, de Bievre C, Lechevalier H. Chemotaxonomy of aerobic Actinomycetes: phospholipid composition. Biochem Syst Ecol 1977;5:249–260 [CrossRef]
    [Google Scholar]
  32. Kaewkla O, Franco CMM. Actinopolymorpha pittospori sp. nov., an endophytic actinobacterium isolated from surface-sterilized leaves of an Australian native apricot tree. Int J Syst Evol Microbiol 2011;62:2616–2620[CrossRef]
    [Google Scholar]
  33. Schleifer KH. Analysis of the chemical composition and primary structure of murein. Methods Microbiol 1985;18:123–156[CrossRef]
    [Google Scholar]
  34. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974;28:226–231[PubMed]
    [Google Scholar]
  35. Alaiz M, Navarro JL, Girón J, Vioque E. Amino acid analysis by high-performance liquid chromatography after derivatization with diethyl ethoxymethylenemalonate. J Chromatogr 1992;591:181–186 [CrossRef][PubMed]
    [Google Scholar]
  36. Schumann P, Kämpfer P, Busse HJ, Evtushenko LI. Subcommittee on the taxonomy of the suborder Micrococcineae of the International committee on systematics of prokaryotes proposed minimal standards for describing new genera and species of the suborder Micrococcineae. Int J Syst Evol Microbiol 2009;59:1823–1849[CrossRef]
    [Google Scholar]
  37. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983;29:319–322 [CrossRef]
    [Google Scholar]
  38. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. Technical Note# 2001;101:
    [Google Scholar]
  39. Atlas RM. editor Handbook of Microbiological Media, 4th ed. Boca Raton: CRC Press; 2010;[CrossRef]
    [Google Scholar]
  40. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16:313–340 [CrossRef]
    [Google Scholar]
  41. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin Strain. Int J Syst Bacteriol 1974;24:54–63 [CrossRef]
    [Google Scholar]
  42. Kurup PV, Schmitt JA. Numerical taxonomy of Nocardia. Can J Microbiol 1973;19:1035–1048 [CrossRef]
    [Google Scholar]
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